# Copyright 2021 by Michiel de Hoon. All rights reserved. # # This code is part of the Biopython distribution and governed by its # license. Please see the LICENSE file that should have been included # as part of this package. """Tests for Bio.Align.tabular module.""" import os import unittest from Bio import Align from Bio import SeqIO from Bio.Seq import Seq try: import numpy as np except ImportError: from Bio import MissingPythonDependencyError raise MissingPythonDependencyError( "Install numpy if you want to use Bio.Align.emboss." ) from None class TestFastaProtein(unittest.TestCase): query = Seq( "MPMILGYWNVRGLTHPIRMLLEYTDSSYDEKRYTMGDAPDFDRSQWLNEKFKLGLDFPNLPYLIDGSHKITQSNAILRYLARKHHLDGETEEERIRADIVENQVMDTRMQLIMLCYNPDFEKQKPEFLKTIPEKMKLYSEFLGKRPWFAGDKVTYVDFLAYDILDQYRMFEPKCLDAFPNLRDFLARFEGLKKISAYMKSSRYIATPIFSKMAHWSNK" ) filename = os.path.join("Fasta", "protein_lib.fa") records = SeqIO.parse(filename, "fasta") targets = {record.id: record.seq.upper() for record in records} def test_m8CB(self): # Alignment file obtained by running # fasta36 -q -m 8CB seq/mgstm1.aa seq/prot_test.lseg # in the fasta36 source distribution path = "Fasta/protein_m8CB.txt" alignments = Align.parse(path, "tabular") self.check_m8CB(alignments) alignments = iter(alignments) self.check_m8CB(alignments) with Align.parse(path, "tabular") as alignments: self.check_m8CB(alignments) with self.assertRaises(AttributeError): alignments._stream with Align.parse(path, "tabular") as alignments: pass with self.assertRaises(AttributeError): alignments._stream def check_m8CB(self, alignments): self.assertEqual( alignments.metadata["Command line"], "fasta36 -q -m 8CB seq/mgstm1.aa seq/prot_test.lseg", ) self.assertEqual(alignments.metadata["Program"], "FASTA") self.assertEqual(alignments.metadata["Version"], "36.3.8h May, 2020") self.assertEqual(alignments.metadata["Database"], "seq/prot_test.lseg") # sp|P10649|GSTM1_MOUSE sp|P09488|GSTM1_HUMAN alignment = next(alignments) self.assertEqual(len(alignment), 2) self.assertAlmostEqual(alignment.annotations["% identity"], 77.98) self.assertEqual(alignment.annotations["gap opens"], 0) aligned = alignment.aligned self.assertEqual(sum(end - start for start, end in aligned[0]), 218) self.assertEqual(sum(end - start for start, end in aligned[1]), 218) self.assertEqual(alignment.shape, (2, 218 + 0)) self.assertEqual(alignment.sequences[0].id, "sp|P09488|GSTM1_HUMAN") self.assertEqual(alignment.sequences[1].id, "sp|P10649|GSTM1_MOUSE") self.assertEqual(alignment.annotations["mismatches"], 48) self.assertAlmostEqual(alignment.annotations["evalue"], 6.1e-78, places=79) self.assertAlmostEqual(alignment.annotations["bit score"], 275.6) self.assertEqual( str(alignment), """\ sp|P09488 0 ???????????????????????????????????????????????????????????? 0 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| sp|P10649 0 ???????????????????????????????????????????????????????????? sp|P09488 60 ???????????????????????????????????????????????????????????? 60 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| sp|P10649 60 ???????????????????????????????????????????????????????????? sp|P09488 120 ???????????????????????????????????????????????????????????? 120 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| sp|P10649 120 ???????????????????????????????????????????????????????????? sp|P09488 180 ?????????????????????????????????????? 218 180 |||||||||||||||||||||||||||||||||||||| 218 sp|P10649 180 ?????????????????????????????????????? 218 """, ) self.assertTrue( np.array_equal( alignment.coordinates, np.array([[0, 218], [0, 218]]), ) ) query = self.query target = self.targets[alignment.sequences[0].id] self.assertEqual(len(alignment.sequences[0].seq), 218) self.assertEqual(len(alignment.sequences[1].seq), len(query)) alignment.sequences[0].seq = target alignment.sequences[1].seq = query self.assertEqual( alignment[0], "MPMILGYWDIRGLAHAIRLLLEYTDSSYEEKKYTMGDAPDYDRSQWLNEKFKLGLDFPNLPYLIDGAHKITQSNAILCYIARKHNLCGETEEEKIRVDILENQTMDNHMQLGMICYNPEFEKLKPKYLEELPEKLKLYSEFLGKRPWFAGNKITFVDFLVYDVLDLHRIFEPKCLDAFPNLKDFISRFEGLEKISAYMKSSRFLPRPVFSKMAVWGNK", ) self.assertEqual( alignment[1], "MPMILGYWNVRGLTHPIRMLLEYTDSSYDEKRYTMGDAPDFDRSQWLNEKFKLGLDFPNLPYLIDGSHKITQSNAILRYLARKHHLDGETEEERIRADIVENQVMDTRMQLIMLCYNPDFEKQKPEFLKTIPEKMKLYSEFLGKRPWFAGDKVTYVDFLAYDILDQYRMFEPKCLDAFPNLRDFLARFEGLKKISAYMKSSRYIATPIFSKMAHWSNK", ) # sp|P10649|GSTM1_MOUSE sp|P00502|GSTA1_RAT self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['M', 'P', 'M', 'I', 'L', 'G', 'Y', 'W', 'D', 'I', 'R', 'G', 'L', 'A', 'H', 'A', 'I', 'R', 'L', 'L', 'L', 'E', 'Y', 'T', 'D', 'S', 'S', 'Y', 'E', 'E', 'K', 'K', 'Y', 'T', 'M', 'G', 'D', 'A', 'P', 'D', 'Y', 'D', 'R', 'S', 'Q', 'W', 'L', 'N', 'E', 'K', 'F', 'K', 'L', 'G', 'L', 'D', 'F', 'P', 'N', 'L', 'P', 'Y', 'L', 'I', 'D', 'G', 'A', 'H', 'K', 'I', 'T', 'Q', 'S', 'N', 'A', 'I', 'L', 'C', 'Y', 'I', 'A', 'R', 'K', 'H', 'N', 'L', 'C', 'G', 'E', 'T', 'E', 'E', 'E', 'K', 'I', 'R', 'V', 'D', 'I', 'L', 'E', 'N', 'Q', 'T', 'M', 'D', 'N', 'H', 'M', 'Q', 'L', 'G', 'M', 'I', 'C', 'Y', 'N', 'P', 'E', 'F', 'E', 'K', 'L', 'K', 'P', 'K', 'Y', 'L', 'E', 'E', 'L', 'P', 'E', 'K', 'L', 'K', 'L', 'Y', 'S', 'E', 'F', 'L', 'G', 'K', 'R', 'P', 'W', 'F', 'A', 'G', 'N', 'K', 'I', 'T', 'F', 'V', 'D', 'F', 'L', 'V', 'Y', 'D', 'V', 'L', 'D', 'L', 'H', 'R', 'I', 'F', 'E', 'P', 'K', 'C', 'L', 'D', 'A', 'F', 'P', 'N', 'L', 'K', 'D', 'F', 'I', 'S', 'R', 'F', 'E', 'G', 'L', 'E', 'K', 'I', 'S', 'A', 'Y', 'M', 'K', 'S', 'S', 'R', 'F', 'L', 'P', 'R', 'P', 'V', 'F', 'S', 'K', 'M', 'A', 'V', 'W', 'G', 'N', 'K'], ['M', 'P', 'M', 'I', 'L', 'G', 'Y', 'W', 'N', 'V', 'R', 'G', 'L', 'T', 'H', 'P', 'I', 'R', 'M', 'L', 'L', 'E', 'Y', 'T', 'D', 'S', 'S', 'Y', 'D', 'E', 'K', 'R', 'Y', 'T', 'M', 'G', 'D', 'A', 'P', 'D', 'F', 'D', 'R', 'S', 'Q', 'W', 'L', 'N', 'E', 'K', 'F', 'K', 'L', 'G', 'L', 'D', 'F', 'P', 'N', 'L', 'P', 'Y', 'L', 'I', 'D', 'G', 'S', 'H', 'K', 'I', 'T', 'Q', 'S', 'N', 'A', 'I', 'L', 'R', 'Y', 'L', 'A', 'R', 'K', 'H', 'H', 'L', 'D', 'G', 'E', 'T', 'E', 'E', 'E', 'R', 'I', 'R', 'A', 'D', 'I', 'V', 'E', 'N', 'Q', 'V', 'M', 'D', 'T', 'R', 'M', 'Q', 'L', 'I', 'M', 'L', 'C', 'Y', 'N', 'P', 'D', 'F', 'E', 'K', 'Q', 'K', 'P', 'E', 'F', 'L', 'K', 'T', 'I', 'P', 'E', 'K', 'M', 'K', 'L', 'Y', 'S', 'E', 'F', 'L', 'G', 'K', 'R', 'P', 'W', 'F', 'A', 'G', 'D', 'K', 'V', 'T', 'Y', 'V', 'D', 'F', 'L', 'A', 'Y', 'D', 'I', 'L', 'D', 'Q', 'Y', 'R', 'M', 'F', 'E', 'P', 'K', 'C', 'L', 'D', 'A', 'F', 'P', 'N', 'L', 'R', 'D', 'F', 'L', 'A', 'R', 'F', 'E', 'G', 'L', 'K', 'K', 'I', 'S', 'A', 'Y', 'M', 'K', 'S', 'S', 'R', 'Y', 'I', 'A', 'T', 'P', 'I', 'F', 'S', 'K', 'M', 'A', 'H', 'W', 'S', 'N', 'K']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertEqual(len(alignment), 2) self.assertAlmostEqual(alignment.annotations["% identity"], 29.76) self.assertEqual(alignment.annotations["gap opens"], 18) aligned = alignment.aligned self.assertEqual(sum(end - start for start, end in aligned[0]), 205) self.assertEqual(sum(end - start for start, end in aligned[1]), 205) self.assertEqual(alignment.shape, (2, 205 + 18)) self.assertEqual(alignment.sequences[0].id, "sp|P00502|GSTA1_RAT") self.assertEqual(alignment.sequences[1].id, "sp|P10649|GSTM1_MOUSE") self.assertEqual(alignment.annotations["mismatches"], 144) self.assertAlmostEqual(alignment.annotations["evalue"], 3.1e-13, places=14) self.assertAlmostEqual(alignment.annotations["bit score"], 60.7) self.assertEqual( str(alignment), """\ sp|P00502 5 ????????????????????????????---------??????????????????????? 0 ||||||||||||||||||||||||||||---------|||||||||||||--|||||||| sp|P10649 3 ??????????????????????????????????????????????????--???????? sp|P00502 56 ??????-????????????????????????????????????????????????????? 60 ||-|||-|||||||||||||||||||||||||||||||||||||||-||||||||||||| sp|P10649 61 ??-???????????????????????????????????????????-????????????? sp|P00502 115 ???????????????????????????????????????????????????????????? 120 ||||||||||--|||||||||||||||--||||||||||||||||||||||||||||||| sp|P10649 119 ??????????--???????????????--??????????????????????????????? sp|P00502 175 ??????????????????????????????????????????? 218 180 ||||||||||||||||||||||||||||||||||||||||||| 223 sp|P10649 175 ??????????????????????????????????????????? 218 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 5, 33, 33, 46, 48, 58, 59, 62, 62, 101, 102, 125, 127, 142, 144, 218], [ 3, 31, 40, 53, 53, 63, 63, 66, 67, 106, 106, 129, 129, 144, 144, 218]]) # fmt: on ) ) query = self.query target = self.targets[alignment.sequences[0].id] self.assertEqual(len(alignment.sequences[0].seq), 218) self.assertEqual(len(alignment.sequences[1].seq), len(query)) alignment.sequences[0].seq = target alignment.sequences[1].seq = query self.assertEqual( alignment[0], "VLHYFNARGRMECIRWLLAAAGVEFDEK---------FIQSPEDLEKLKKDGNLMFDQVPMVEIDG-MKLAQTRAILNYIATKYDLYGKDMKERALIDMYTEGILDLTEMIMQLVICPPDQKEAKTALAKDRTKNRYLPAFEKVLKSHGQDYLVGNRLTRVDIHLLELLLYVEEFDASLLTSFPLLKAFKSRISSLPNVKKFLQPGSQRKLPVDAKQIEEARK", ) self.assertEqual( alignment[1], "ILGYWNVRGLTHPIRMLLEYTDSSYDEKRYTMGDAPDFDRSQWLNEKFKL--GLDFPNLPYL-IDGSHKITQSNAILRYLARKHHLDGETEEERIRADIVENQVMD-TRMQLIMLCYNPDFEKQKPEFLK--TIPEKMKLYSEFLGK--RPWFAGDKVTYVDFLAYDILDQYRMFEPKCLDAFPNLRDFLARFEGLKKISAYMKSSRYIATPIFSKMAHWSNK", ) # sp|P10649|GSTM1_MOUSE sp|P69905|HBA_HUMAN self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['V', 'L', 'H', 'Y', 'F', 'N', 'A', 'R', 'G', 'R', 'M', 'E', 'C', 'I', 'R', 'W', 'L', 'L', 'A', 'A', 'A', 'G', 'V', 'E', 'F', 'D', 'E', 'K', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'F', 'I', 'Q', 'S', 'P', 'E', 'D', 'L', 'E', 'K', 'L', 'K', 'K', 'D', 'G', 'N', 'L', 'M', 'F', 'D', 'Q', 'V', 'P', 'M', 'V', 'E', 'I', 'D', 'G', '-', 'M', 'K', 'L', 'A', 'Q', 'T', 'R', 'A', 'I', 'L', 'N', 'Y', 'I', 'A', 'T', 'K', 'Y', 'D', 'L', 'Y', 'G', 'K', 'D', 'M', 'K', 'E', 'R', 'A', 'L', 'I', 'D', 'M', 'Y', 'T', 'E', 'G', 'I', 'L', 'D', 'L', 'T', 'E', 'M', 'I', 'M', 'Q', 'L', 'V', 'I', 'C', 'P', 'P', 'D', 'Q', 'K', 'E', 'A', 'K', 'T', 'A', 'L', 'A', 'K', 'D', 'R', 'T', 'K', 'N', 'R', 'Y', 'L', 'P', 'A', 'F', 'E', 'K', 'V', 'L', 'K', 'S', 'H', 'G', 'Q', 'D', 'Y', 'L', 'V', 'G', 'N', 'R', 'L', 'T', 'R', 'V', 'D', 'I', 'H', 'L', 'L', 'E', 'L', 'L', 'L', 'Y', 'V', 'E', 'E', 'F', 'D', 'A', 'S', 'L', 'L', 'T', 'S', 'F', 'P', 'L', 'L', 'K', 'A', 'F', 'K', 'S', 'R', 'I', 'S', 'S', 'L', 'P', 'N', 'V', 'K', 'K', 'F', 'L', 'Q', 'P', 'G', 'S', 'Q', 'R', 'K', 'L', 'P', 'V', 'D', 'A', 'K', 'Q', 'I', 'E', 'E', 'A', 'R', 'K'], ['I', 'L', 'G', 'Y', 'W', 'N', 'V', 'R', 'G', 'L', 'T', 'H', 'P', 'I', 'R', 'M', 'L', 'L', 'E', 'Y', 'T', 'D', 'S', 'S', 'Y', 'D', 'E', 'K', 'R', 'Y', 'T', 'M', 'G', 'D', 'A', 'P', 'D', 'F', 'D', 'R', 'S', 'Q', 'W', 'L', 'N', 'E', 'K', 'F', 'K', 'L', '-', '-', 'G', 'L', 'D', 'F', 'P', 'N', 'L', 'P', 'Y', 'L', '-', 'I', 'D', 'G', 'S', 'H', 'K', 'I', 'T', 'Q', 'S', 'N', 'A', 'I', 'L', 'R', 'Y', 'L', 'A', 'R', 'K', 'H', 'H', 'L', 'D', 'G', 'E', 'T', 'E', 'E', 'E', 'R', 'I', 'R', 'A', 'D', 'I', 'V', 'E', 'N', 'Q', 'V', 'M', 'D', '-', 'T', 'R', 'M', 'Q', 'L', 'I', 'M', 'L', 'C', 'Y', 'N', 'P', 'D', 'F', 'E', 'K', 'Q', 'K', 'P', 'E', 'F', 'L', 'K', '-', '-', 'T', 'I', 'P', 'E', 'K', 'M', 'K', 'L', 'Y', 'S', 'E', 'F', 'L', 'G', 'K', '-', '-', 'R', 'P', 'W', 'F', 'A', 'G', 'D', 'K', 'V', 'T', 'Y', 'V', 'D', 'F', 'L', 'A', 'Y', 'D', 'I', 'L', 'D', 'Q', 'Y', 'R', 'M', 'F', 'E', 'P', 'K', 'C', 'L', 'D', 'A', 'F', 'P', 'N', 'L', 'R', 'D', 'F', 'L', 'A', 'R', 'F', 'E', 'G', 'L', 'K', 'K', 'I', 'S', 'A', 'Y', 'M', 'K', 'S', 'S', 'R', 'Y', 'I', 'A', 'T', 'P', 'I', 'F', 'S', 'K', 'M', 'A', 'H', 'W', 'S', 'N', 'K']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertEqual(len(alignment), 2) self.assertAlmostEqual(alignment.annotations["% identity"], 27.03) self.assertEqual(alignment.annotations["gap opens"], 2) aligned = alignment.aligned self.assertEqual(sum(end - start for start, end in aligned[0]), 37) self.assertEqual(sum(end - start for start, end in aligned[1]), 37) self.assertEqual(alignment.shape, (2, 37 + 2)) self.assertEqual(alignment.sequences[0].id, "sp|P69905|HBA_HUMAN") self.assertEqual(alignment.sequences[1].id, "sp|P10649|GSTM1_MOUSE") self.assertEqual(alignment.annotations["mismatches"], 27) self.assertAlmostEqual(alignment.annotations["evalue"], 0.19) self.assertAlmostEqual(alignment.annotations["bit score"], 20.9) self.assertEqual( str(alignment), """\ sp|P69905 35 ?????????????-????????????????????????? 73 0 |||||||||||||-||||||||||-|||||||||||||| 39 sp|P10649 176 ????????????????????????-?????????????? 214 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 35, 48, 48, 58, 59, 73], [176, 189, 190, 200, 200, 214]]), # fmt: on ) ) query = self.query target = self.targets[alignment.sequences[0].id] self.assertEqual(len(alignment.sequences[0].seq), 73) self.assertEqual(len(alignment.sequences[1].seq), len(query)) alignment.sequences[0].seq = target alignment.sequences[1].seq = query self.assertEqual(alignment[0], "SFPTTKTYFPHFD-LSHGSAQVKGHGKKVADALTNAVAH") self.assertEqual(alignment[1], "AFPNLRDFLARFEGLKKISAYMKS-SRYIATPIFSKMAH") # sp|P10649|GSTM1_MOUSE sp|P00517|KAPCA_BOVIN self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['S', 'F', 'P', 'T', 'T', 'K', 'T', 'Y', 'F', 'P', 'H', 'F', 'D', '-', 'L', 'S', 'H', 'G', 'S', 'A', 'Q', 'V', 'K', 'G', 'H', 'G', 'K', 'K', 'V', 'A', 'D', 'A', 'L', 'T', 'N', 'A', 'V', 'A', 'H'], ['A', 'F', 'P', 'N', 'L', 'R', 'D', 'F', 'L', 'A', 'R', 'F', 'E', 'G', 'L', 'K', 'K', 'I', 'S', 'A', 'Y', 'M', 'K', 'S', '-', 'S', 'R', 'Y', 'I', 'A', 'T', 'P', 'I', 'F', 'S', 'K', 'M', 'A', 'H']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertEqual(len(alignment), 2) self.assertAlmostEqual(alignment.annotations["% identity"], 24.29) self.assertEqual(alignment.annotations["gap opens"], 2) aligned = alignment.aligned self.assertEqual(sum(end - start for start, end in aligned[0]), 70) self.assertEqual(sum(end - start for start, end in aligned[1]), 70) self.assertEqual(alignment.shape, (2, 70 + 2)) self.assertEqual(alignment.sequences[0].id, "sp|P00517|KAPCA_BOVIN") self.assertEqual(alignment.sequences[1].id, "sp|P10649|GSTM1_MOUSE") self.assertEqual(alignment.annotations["mismatches"], 53) self.assertAlmostEqual(alignment.annotations["evalue"], 1.4) self.assertAlmostEqual(alignment.annotations["bit score"], 19.2) self.assertEqual( str(alignment), """\ sp|P00517 228 ???????????????????????????????????????????????????????????? 0 ||||||||||||||||||||||||||||||||||||||||||||||--|||||||||||| sp|P10649 136 ??????????????????????????????????????????????--???????????? sp|P00517 288 ???????????? 300 60 |||||||||||| 72 sp|P10649 194 ???????????? 206 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[228, 274, 276, 300], [136, 182, 182, 206]]) # fmt: on ) ) query = self.query target = self.targets[alignment.sequences[0].id] self.assertEqual(len(alignment.sequences[0].seq), 300) self.assertEqual(len(alignment.sequences[1].seq), len(query)) alignment.sequences[0].seq = target alignment.sequences[1].seq = query self.assertEqual( alignment[0], "IYEMAAGYPPFFADQPIQIYEKIVSGKVRFPSHFSSDLKDLLRNLLQVDLTKRFGNLKNGVNDIKNHKWFAT", ) self.assertEqual( alignment[1], "LYSEFLGKRPWFAGDKVTYVDFLAYDILDQYRMFEPKCLDAFPNLR--DFLARFEGLKKISAYMKSSRYIAT", ) # sp|P10649|GSTM1_MOUSE sp|P14960|RBS_GUITH self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['I', 'Y', 'E', 'M', 'A', 'A', 'G', 'Y', 'P', 'P', 'F', 'F', 'A', 'D', 'Q', 'P', 'I', 'Q', 'I', 'Y', 'E', 'K', 'I', 'V', 'S', 'G', 'K', 'V', 'R', 'F', 'P', 'S', 'H', 'F', 'S', 'S', 'D', 'L', 'K', 'D', 'L', 'L', 'R', 'N', 'L', 'L', 'Q', 'V', 'D', 'L', 'T', 'K', 'R', 'F', 'G', 'N', 'L', 'K', 'N', 'G', 'V', 'N', 'D', 'I', 'K', 'N', 'H', 'K', 'W', 'F', 'A', 'T'], ['L', 'Y', 'S', 'E', 'F', 'L', 'G', 'K', 'R', 'P', 'W', 'F', 'A', 'G', 'D', 'K', 'V', 'T', 'Y', 'V', 'D', 'F', 'L', 'A', 'Y', 'D', 'I', 'L', 'D', 'Q', 'Y', 'R', 'M', 'F', 'E', 'P', 'K', 'C', 'L', 'D', 'A', 'F', 'P', 'N', 'L', 'R', '-', '-', 'D', 'F', 'L', 'A', 'R', 'F', 'E', 'G', 'L', 'K', 'K', 'I', 'S', 'A', 'Y', 'M', 'K', 'S', 'S', 'R', 'Y', 'I', 'A', 'T']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertEqual(len(alignment), 2) self.assertAlmostEqual(alignment.annotations["% identity"], 57.14) self.assertEqual(alignment.annotations["gap opens"], 0) aligned = alignment.aligned self.assertEqual(sum(end - start for start, end in aligned[0]), 7) self.assertEqual(sum(end - start for start, end in aligned[1]), 7) self.assertEqual(alignment.shape, (2, 7 + 0)) self.assertEqual(alignment.sequences[0].id, "sp|P14960|RBS_GUITH") self.assertEqual(alignment.sequences[1].id, "sp|P10649|GSTM1_MOUSE") self.assertEqual(alignment.annotations["mismatches"], 3) self.assertAlmostEqual(alignment.annotations["evalue"], 1.6) self.assertAlmostEqual(alignment.annotations["bit score"], 17.7) self.assertEqual( str(alignment), """\ sp|P14960 46 ??????? 53 0 ||||||| 7 sp|P10649 6 ??????? 13 """, ) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[46, 53], [6, 13]])) ) query = self.query target = self.targets[alignment.sequences[0].id] self.assertEqual(len(alignment.sequences[0].seq), 53) self.assertEqual(len(alignment.sequences[1].seq), len(query)) alignment.sequences[0].seq = target alignment.sequences[1].seq = query self.assertEqual(alignment[0], "YWDLWGL") self.assertEqual(alignment[1], "YWNVRGL") # sp|P10649|GSTM1_MOUSE sp|P01593|KV101_HUMAN self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['Y', 'W', 'D', 'L', 'W', 'G', 'L'], ['Y', 'W', 'N', 'V', 'R', 'G', 'L']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertEqual(len(alignment), 2) self.assertAlmostEqual(alignment.annotations["% identity"], 45.00) self.assertEqual(alignment.annotations["gap opens"], 10) aligned = alignment.aligned self.assertEqual(sum(end - start for start, end in aligned[0]), 40) self.assertEqual(sum(end - start for start, end in aligned[1]), 40) self.assertEqual(alignment.shape, (2, 40 + 10)) self.assertEqual(alignment.sequences[0].id, "sp|P01593|KV101_HUMAN") self.assertEqual(alignment.sequences[1].id, "sp|P10649|GSTM1_MOUSE") self.assertEqual(alignment.annotations["mismatches"], 22) self.assertAlmostEqual(alignment.annotations["evalue"], 2.5) self.assertAlmostEqual(alignment.annotations["bit score"], 16.6) self.assertEqual( str(alignment), """\ sp|P01593 15 ????????????????????????????????????-????????????? 64 0 ||||||||||||||---||||||||---||||--||-|||||||-||||| 50 sp|P10649 149 ??????????????---????????---????--??????????-????? 190 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 15, 29, 32, 40, 43, 47, 49, 51, 51, 58, 59, 64], [149, 163, 163, 171, 171, 175, 175, 177, 178, 185, 185, 190]]) # fmt: on ) ) query = self.query target = self.targets[alignment.sequences[0].id] self.assertEqual(len(alignment.sequences[0].seq), 64) self.assertEqual(len(alignment.sequences[1].seq), len(query)) alignment.sequences[0].seq = target alignment.sequences[1].seq = query self.assertEqual( alignment[0], "GDRVTITCQASQDINHYLNWYQQGPKKAPKILIYDA-SNLETGVPSRFSG" ) self.assertEqual( alignment[1], "GDKVTYVDFLAYDI---LDQYRMFE---PKCL--DAFPNLRDFL-ARFEG" ) # sp|P10649|GSTM1_MOUSE sp|P99998|CYC_PANTR self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['G', 'D', 'R', 'V', 'T', 'I', 'T', 'C', 'Q', 'A', 'S', 'Q', 'D', 'I', 'N', 'H', 'Y', 'L', 'N', 'W', 'Y', 'Q', 'Q', 'G', 'P', 'K', 'K', 'A', 'P', 'K', 'I', 'L', 'I', 'Y', 'D', 'A', '-', 'S', 'N', 'L', 'E', 'T', 'G', 'V', 'P', 'S', 'R', 'F', 'S', 'G'], ['G', 'D', 'K', 'V', 'T', 'Y', 'V', 'D', 'F', 'L', 'A', 'Y', 'D', 'I', '-', '-', '-', 'L', 'D', 'Q', 'Y', 'R', 'M', 'F', 'E', '-', '-', '-', 'P', 'K', 'C', 'L', '-', '-', 'D', 'A', 'F', 'P', 'N', 'L', 'R', 'D', 'F', 'L', '-', 'A', 'R', 'F', 'E', 'G']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertEqual(len(alignment), 2) self.assertAlmostEqual(alignment.annotations["% identity"], 31.03) self.assertEqual(alignment.annotations["gap opens"], 10) aligned = alignment.aligned self.assertEqual(sum(end - start for start, end in aligned[0]), 58) self.assertEqual(sum(end - start for start, end in aligned[1]), 58) self.assertEqual(alignment.shape, (2, 58 + 10)) self.assertEqual(alignment.sequences[0].id, "sp|P99998|CYC_PANTR") self.assertEqual(alignment.sequences[1].id, "sp|P10649|GSTM1_MOUSE") self.assertEqual(alignment.annotations["mismatches"], 40) self.assertAlmostEqual(alignment.annotations["evalue"], 2.7) self.assertAlmostEqual(alignment.annotations["bit score"], 16.4) self.assertEqual( str(alignment), """\ sp|P99998 27 ???????????????????????????????-??????????-?????--?????????- 0 ||||||||||||||||||||---||||||||-||||||||||-|||||--|||||||||- sp|P10649 128 ????????????????????---????????????????????????????????????? sp|P99998 82 --?????? 88 60 --|||||| 68 sp|P10649 185 ???????? 193 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 27, 47, 50, 58, 58, 68, 68, 73, 73, 82, 82, 88], [128, 148, 148, 156, 157, 167, 168, 173, 175, 184, 187, 193]]) # fmt: on ) ) query = self.query target = self.targets[alignment.sequences[0].id] self.assertEqual(len(alignment.sequences[0].seq), 88) self.assertEqual(len(alignment.sequences[1].seq), len(query)) alignment.sequences[0].seq = target alignment.sequences[1].seq = query self.assertEqual( alignment[0], "KTGPNLHGLFGRKTGQAPGYSYTAANKNKGI-IWGEDTLMEY-LENPK--KYIPGTKMI---FVGIKK", ) self.assertEqual( alignment[1], "KTIPEKMKLYSEFLGKRPWF---AGDKVTYVDFLAYDILDQYRMFEPKCLDAFPNLRDFLARFEGLKK", ) # sp|P10649|GSTM1_MOUSE sp|P02585|TNNC2_HUMAN self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['K', 'T', 'G', 'P', 'N', 'L', 'H', 'G', 'L', 'F', 'G', 'R', 'K', 'T', 'G', 'Q', 'A', 'P', 'G', 'Y', 'S', 'Y', 'T', 'A', 'A', 'N', 'K', 'N', 'K', 'G', 'I', '-', 'I', 'W', 'G', 'E', 'D', 'T', 'L', 'M', 'E', 'Y', '-', 'L', 'E', 'N', 'P', 'K', '-', '-', 'K', 'Y', 'I', 'P', 'G', 'T', 'K', 'M', 'I', '-', '-', '-', 'F', 'V', 'G', 'I', 'K', 'K'], ['K', 'T', 'I', 'P', 'E', 'K', 'M', 'K', 'L', 'Y', 'S', 'E', 'F', 'L', 'G', 'K', 'R', 'P', 'W', 'F', '-', '-', '-', 'A', 'G', 'D', 'K', 'V', 'T', 'Y', 'V', 'D', 'F', 'L', 'A', 'Y', 'D', 'I', 'L', 'D', 'Q', 'Y', 'R', 'M', 'F', 'E', 'P', 'K', 'C', 'L', 'D', 'A', 'F', 'P', 'N', 'L', 'R', 'D', 'F', 'L', 'A', 'R', 'F', 'E', 'G', 'L', 'K', 'K']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertEqual(len(alignment), 2) self.assertAlmostEqual(alignment.annotations["% identity"], 31.11) self.assertEqual(alignment.annotations["gap opens"], 9) aligned = alignment.aligned self.assertEqual(sum(end - start for start, end in aligned[0]), 45) self.assertEqual(sum(end - start for start, end in aligned[1]), 45) self.assertEqual(alignment.shape, (2, 45 + 9)) self.assertEqual(alignment.sequences[0].id, "sp|P02585|TNNC2_HUMAN") self.assertEqual(alignment.sequences[1].id, "sp|P10649|GSTM1_MOUSE") self.assertEqual(alignment.annotations["mismatches"], 31) self.assertAlmostEqual(alignment.annotations["evalue"], 3.9) self.assertAlmostEqual(alignment.annotations["bit score"], 16.4) self.assertEqual( str(alignment), """\ sp|P02585 12 ??????????????----???????????????????????????????????? 62 0 ||||||||||||||----||||||||||--|||||||||||---|||||||||| 54 sp|P10649 43 ????????????????????????????--???????????---?????????? 92 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array( [[12, 26, 26, 36, 38, 49, 52, 62], [43, 57, 61, 71, 71, 82, 82, 92]]) # fmt: on ) ) query = self.query target = self.targets[alignment.sequences[0].id] self.assertEqual(len(alignment.sequences[0].seq), 62) self.assertEqual(len(alignment.sequences[1].seq), len(query)) alignment.sequences[0].seq = target alignment.sequences[1].seq = query self.assertEqual( alignment[0], "SEEMIAEFKAAFDM----FDADGGGDISVKELGTVMRMLGQTPTKEELDAIIEE" ) self.assertEqual( alignment[1], "SQWLNEKFKLGLDFPNLPYLIDGSHKIT--QSNAILRYLAR---KHHLDGETEE" ) # sp|P10649|GSTM1_MOUSE sp|P60615|NXL1A_BUNMU self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['S', 'E', 'E', 'M', 'I', 'A', 'E', 'F', 'K', 'A', 'A', 'F', 'D', 'M', '-', '-', '-', '-', 'F', 'D', 'A', 'D', 'G', 'G', 'G', 'D', 'I', 'S', 'V', 'K', 'E', 'L', 'G', 'T', 'V', 'M', 'R', 'M', 'L', 'G', 'Q', 'T', 'P', 'T', 'K', 'E', 'E', 'L', 'D', 'A', 'I', 'I', 'E', 'E'], ['S', 'Q', 'W', 'L', 'N', 'E', 'K', 'F', 'K', 'L', 'G', 'L', 'D', 'F', 'P', 'N', 'L', 'P', 'Y', 'L', 'I', 'D', 'G', 'S', 'H', 'K', 'I', 'T', '-', '-', 'Q', 'S', 'N', 'A', 'I', 'L', 'R', 'Y', 'L', 'A', 'R', '-', '-', '-', 'K', 'H', 'H', 'L', 'D', 'G', 'E', 'T', 'E', 'E']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertEqual(len(alignment), 2) self.assertAlmostEqual(alignment.annotations["% identity"], 66.67) self.assertEqual(alignment.annotations["gap opens"], 2) aligned = alignment.aligned self.assertEqual(sum(end - start for start, end in aligned[0]), 9) self.assertEqual(sum(end - start for start, end in aligned[1]), 9) self.assertEqual(alignment.shape, (2, 9 + 2)) self.assertEqual(alignment.sequences[0].id, "sp|P60615|NXL1A_BUNMU") self.assertEqual(alignment.sequences[1].id, "sp|P10649|GSTM1_MOUSE") self.assertEqual(alignment.annotations["mismatches"], 3) self.assertAlmostEqual(alignment.annotations["evalue"], 4.2) self.assertAlmostEqual(alignment.annotations["bit score"], 15.6) self.assertEqual( str(alignment), """\ sp|P60615 85 ?-???-????? 94 0 |-|||-||||| 11 sp|P10649 114 ??????????? 125 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 85, 86, 86, 89, 89, 94], [114, 115, 116, 119, 120, 125]]) # fmt: on ) ) query = self.query target = self.targets[alignment.sequences[0].id] self.assertEqual(len(alignment.sequences[0].seq), 94) self.assertEqual(len(alignment.sequences[1].seq), len(query)) alignment.sequences[0].seq = target alignment.sequences[1].seq = query self.assertEqual(alignment[0], "C-NPH-PKQRP") self.assertEqual(alignment[1], "CYNPDFEKQKP") # sp|P10649|GSTM1_MOUSE sp|P00193|FER_PEPAS self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['C', '-', 'N', 'P', 'H', '-', 'P', 'K', 'Q', 'R', 'P'], ['C', 'Y', 'N', 'P', 'D', 'F', 'E', 'K', 'Q', 'K', 'P']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertEqual(len(alignment), 2) self.assertAlmostEqual(alignment.annotations["% identity"], 50.00) self.assertEqual(alignment.annotations["gap opens"], 0) aligned = alignment.aligned self.assertEqual(sum(end - start for start, end in aligned[0]), 4) self.assertEqual(sum(end - start for start, end in aligned[1]), 4) self.assertEqual(alignment.shape, (2, 4 + 0)) self.assertEqual(alignment.sequences[0].id, "sp|P00193|FER_PEPAS") self.assertEqual(alignment.sequences[1].id, "sp|P10649|GSTM1_MOUSE") self.assertEqual(alignment.annotations["mismatches"], 2) self.assertAlmostEqual(alignment.annotations["evalue"], 4.2) self.assertAlmostEqual(alignment.annotations["bit score"], 14.7) self.assertEqual( str(alignment), """\ sp|P00193 14 ???? 18 0 |||| 4 sp|P10649 170 ???? 174 """, ) self.assertTrue( np.array_equal( alignment.coordinates, np.array([[14, 18], [170, 174]]), ) ) query = self.query target = self.targets[alignment.sequences[0].id] self.assertEqual(len(alignment.sequences[0].seq), 18) self.assertEqual(len(alignment.sequences[1].seq), len(query)) alignment.sequences[0].seq = target alignment.sequences[1].seq = query self.assertEqual(alignment[0], "KPEC") self.assertEqual(alignment[1], "EPKC") # sp|P10649|GSTM1_MOUSE sp|P03435|HEMA_I75A3 self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['K', 'P', 'E', 'C'], ['E', 'P', 'K', 'C']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertEqual(len(alignment), 2) self.assertAlmostEqual(alignment.annotations["% identity"], 28.95) self.assertEqual(alignment.annotations["gap opens"], 1) aligned = alignment.aligned self.assertEqual(sum(end - start for start, end in aligned[0]), 38) self.assertEqual(sum(end - start for start, end in aligned[1]), 38) self.assertEqual(alignment.shape, (2, 38 + 1)) self.assertEqual(alignment.sequences[0].id, "sp|P03435|HEMA_I75A3") self.assertEqual(alignment.sequences[1].id, "sp|P10649|GSTM1_MOUSE") self.assertEqual(alignment.annotations["mismatches"], 27) self.assertAlmostEqual(alignment.annotations["evalue"], 4.7) self.assertAlmostEqual(alignment.annotations["bit score"], 17.9) self.assertEqual( str(alignment), """\ sp|P03435 398 ??????????????????????????????????????? 437 0 ||||||||||-|||||||||||||||||||||||||||| 39 sp|P10649 73 ??????????-???????????????????????????? 111 """, ) self.assertTrue( np.array_equal( alignment.coordinates, np.array([[398, 408, 409, 437], [73, 83, 83, 111]]), ) ) query = self.query target = self.targets[alignment.sequences[0].id] self.assertEqual(len(alignment.sequences[0].seq), 437) self.assertEqual(len(alignment.sequences[1].seq), len(query)) alignment.sequences[0].seq = target alignment.sequences[1].seq = query self.assertEqual(alignment[0], "NRVIEKTNEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDL") self.assertEqual(alignment[1], "NAILRYLARK-HHLDGETEEERIRADIVENQVMDTRMQL") # sp|P10649|GSTM1_MOUSE sp|P01834|IGKC_HUMAN self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['N', 'R', 'V', 'I', 'E', 'K', 'T', 'N', 'E', 'K', 'F', 'H', 'Q', 'I', 'E', 'K', 'E', 'F', 'S', 'E', 'V', 'E', 'G', 'R', 'I', 'Q', 'D', 'L', 'E', 'K', 'Y', 'V', 'E', 'D', 'T', 'K', 'I', 'D', 'L'], ['N', 'A', 'I', 'L', 'R', 'Y', 'L', 'A', 'R', 'K', '-', 'H', 'H', 'L', 'D', 'G', 'E', 'T', 'E', 'E', 'E', 'R', 'I', 'R', 'A', 'D', 'I', 'V', 'E', 'N', 'Q', 'V', 'M', 'D', 'T', 'R', 'M', 'Q', 'L']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertEqual(len(alignment), 2) self.assertAlmostEqual(alignment.annotations["% identity"], 19.40) self.assertEqual(alignment.annotations["gap opens"], 4) aligned = alignment.aligned self.assertEqual(sum(end - start for start, end in aligned[0]), 67) self.assertEqual(sum(end - start for start, end in aligned[1]), 67) self.assertEqual(alignment.shape, (2, 67 + 4)) self.assertEqual(alignment.sequences[0].id, "sp|P01834|IGKC_HUMAN") self.assertEqual(alignment.sequences[1].id, "sp|P10649|GSTM1_MOUSE") self.assertEqual(alignment.annotations["mismatches"], 54) self.assertAlmostEqual(alignment.annotations["evalue"], 6.3) self.assertAlmostEqual(alignment.annotations["bit score"], 14.9) self.assertEqual( str(alignment), """\ sp|P01834 11 ???????????????????????????????????????????????????????????? 0 ||||||||||||||--||||||||||||||||||||||||||||||||||||||||--|| sp|P10649 57 ??????????????--????????????????????????????????????????--?? sp|P01834 71 ??????????? 82 60 ||||||||||| 71 sp|P10649 113 ??????????? 124 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[11, 25, 27, 67, 69, 82], [57, 71, 71, 111, 111, 124]]) # fmt: on ) ) query = self.query target = self.targets[alignment.sequences[0].id] self.assertEqual(len(alignment.sequences[0].seq), 82) self.assertEqual(len(alignment.sequences[1].seq), len(query)) alignment.sequences[0].seq = target alignment.sequences[1].seq = query self.assertEqual( alignment[0], "PSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHK", ) self.assertEqual( alignment[1], "PNLPYLIDGSHKIT--QSNAILRYLARKHHLDGETEEERIRADIVENQVMDTRMQL--IMLCYNPDFEKQK", ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['P', 'S', 'D', 'E', 'Q', 'L', 'K', 'S', 'G', 'T', 'A', 'S', 'V', 'V', 'C', 'L', 'L', 'N', 'N', 'F', 'Y', 'P', 'R', 'E', 'A', 'K', 'V', 'Q', 'W', 'K', 'V', 'D', 'N', 'A', 'L', 'Q', 'S', 'G', 'N', 'S', 'Q', 'E', 'S', 'V', 'T', 'E', 'Q', 'D', 'S', 'K', 'D', 'S', 'T', 'Y', 'S', 'L', 'S', 'S', 'T', 'L', 'T', 'L', 'S', 'K', 'A', 'D', 'Y', 'E', 'K', 'H', 'K'], ['P', 'N', 'L', 'P', 'Y', 'L', 'I', 'D', 'G', 'S', 'H', 'K', 'I', 'T', '-', '-', 'Q', 'S', 'N', 'A', 'I', 'L', 'R', 'Y', 'L', 'A', 'R', 'K', 'H', 'H', 'L', 'D', 'G', 'E', 'T', 'E', 'E', 'E', 'R', 'I', 'R', 'A', 'D', 'I', 'V', 'E', 'N', 'Q', 'V', 'M', 'D', 'T', 'R', 'M', 'Q', 'L', '-', '-', 'I', 'M', 'L', 'C', 'Y', 'N', 'P', 'D', 'F', 'E', 'K', 'Q', 'K']], dtype='U') # fmt: on ) ) with self.assertRaises(StopIteration): next(alignments) def test_m8CC(self): # Alignment file obtained by running # fasta36 -q -m 8CB seq/mgstm1.aa seq/prot_test.lseg # in the fasta36 source distribution path = "Fasta/protein_m8CC.txt" alignments = Align.parse(path, "tabular") self.assertEqual( alignments.metadata["Command line"], "fasta36 -q -m 8CC seq/mgstm1.aa seq/prot_test.lseg", ) self.assertEqual(alignments.metadata["Program"], "FASTA") self.assertEqual(alignments.metadata["Version"], "36.3.8h May, 2020") self.assertEqual(alignments.metadata["Database"], "seq/prot_test.lseg") # sp|P10649|GSTM1_MOUSE sp|P09488|GSTM1_HUMAN alignment = next(alignments) self.assertEqual(len(alignment), 2) self.assertAlmostEqual(alignment.annotations["% identity"], 77.98) self.assertEqual(alignment.annotations["gap opens"], 0) aligned = alignment.aligned self.assertEqual(sum(end - start for start, end in aligned[0]), 218) self.assertEqual(sum(end - start for start, end in aligned[1]), 218) self.assertEqual(alignment.shape, (2, 218 + 0)) self.assertEqual(alignment.sequences[0].id, "sp|P09488|GSTM1_HUMAN") self.assertEqual(alignment.sequences[1].id, "sp|P10649|GSTM1_MOUSE") self.assertEqual(alignment.annotations["mismatches"], 48) self.assertAlmostEqual(alignment.annotations["evalue"], 7.6e-83, places=84) self.assertAlmostEqual(alignment.annotations["bit score"], 291.9) self.assertEqual( str(alignment), """\ sp|P09488 0 ???????????????????????????????????????????????????????????? 0 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| sp|P10649 0 ???????????????????????????????????????????????????????????? sp|P09488 60 ???????????????????????????????????????????????????????????? 60 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| sp|P10649 60 ???????????????????????????????????????????????????????????? sp|P09488 120 ???????????????????????????????????????????????????????????? 120 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| sp|P10649 120 ???????????????????????????????????????????????????????????? sp|P09488 180 ?????????????????????????????????????? 218 180 |||||||||||||||||||||||||||||||||||||| 218 sp|P10649 180 ?????????????????????????????????????? 218 """, ) self.assertTrue( np.array_equal( alignment.coordinates, np.array([[0, 218], [0, 218]]), ) ) query = self.query target = self.targets[alignment.sequences[0].id] self.assertEqual(len(alignment.sequences[0].seq), 218) self.assertEqual(len(alignment.sequences[1].seq), len(query)) alignment.sequences[0].seq = target alignment.sequences[1].seq = query self.assertEqual( alignment[0], "MPMILGYWDIRGLAHAIRLLLEYTDSSYEEKKYTMGDAPDYDRSQWLNEKFKLGLDFPNLPYLIDGAHKITQSNAILCYIARKHNLCGETEEEKIRVDILENQTMDNHMQLGMICYNPEFEKLKPKYLEELPEKLKLYSEFLGKRPWFAGNKITFVDFLVYDVLDLHRIFEPKCLDAFPNLKDFISRFEGLEKISAYMKSSRFLPRPVFSKMAVWGNK", ) self.assertEqual( alignment[1], "MPMILGYWNVRGLTHPIRMLLEYTDSSYDEKRYTMGDAPDFDRSQWLNEKFKLGLDFPNLPYLIDGSHKITQSNAILRYLARKHHLDGETEEERIRADIVENQVMDTRMQLIMLCYNPDFEKQKPEFLKTIPEKMKLYSEFLGKRPWFAGDKVTYVDFLAYDILDQYRMFEPKCLDAFPNLRDFLARFEGLKKISAYMKSSRYIATPIFSKMAHWSNK", ) # sp|P10649|GSTM1_MOUSE sp|P00502|GSTA1_RAT self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['M', 'P', 'M', 'I', 'L', 'G', 'Y', 'W', 'D', 'I', 'R', 'G', 'L', 'A', 'H', 'A', 'I', 'R', 'L', 'L', 'L', 'E', 'Y', 'T', 'D', 'S', 'S', 'Y', 'E', 'E', 'K', 'K', 'Y', 'T', 'M', 'G', 'D', 'A', 'P', 'D', 'Y', 'D', 'R', 'S', 'Q', 'W', 'L', 'N', 'E', 'K', 'F', 'K', 'L', 'G', 'L', 'D', 'F', 'P', 'N', 'L', 'P', 'Y', 'L', 'I', 'D', 'G', 'A', 'H', 'K', 'I', 'T', 'Q', 'S', 'N', 'A', 'I', 'L', 'C', 'Y', 'I', 'A', 'R', 'K', 'H', 'N', 'L', 'C', 'G', 'E', 'T', 'E', 'E', 'E', 'K', 'I', 'R', 'V', 'D', 'I', 'L', 'E', 'N', 'Q', 'T', 'M', 'D', 'N', 'H', 'M', 'Q', 'L', 'G', 'M', 'I', 'C', 'Y', 'N', 'P', 'E', 'F', 'E', 'K', 'L', 'K', 'P', 'K', 'Y', 'L', 'E', 'E', 'L', 'P', 'E', 'K', 'L', 'K', 'L', 'Y', 'S', 'E', 'F', 'L', 'G', 'K', 'R', 'P', 'W', 'F', 'A', 'G', 'N', 'K', 'I', 'T', 'F', 'V', 'D', 'F', 'L', 'V', 'Y', 'D', 'V', 'L', 'D', 'L', 'H', 'R', 'I', 'F', 'E', 'P', 'K', 'C', 'L', 'D', 'A', 'F', 'P', 'N', 'L', 'K', 'D', 'F', 'I', 'S', 'R', 'F', 'E', 'G', 'L', 'E', 'K', 'I', 'S', 'A', 'Y', 'M', 'K', 'S', 'S', 'R', 'F', 'L', 'P', 'R', 'P', 'V', 'F', 'S', 'K', 'M', 'A', 'V', 'W', 'G', 'N', 'K'], ['M', 'P', 'M', 'I', 'L', 'G', 'Y', 'W', 'N', 'V', 'R', 'G', 'L', 'T', 'H', 'P', 'I', 'R', 'M', 'L', 'L', 'E', 'Y', 'T', 'D', 'S', 'S', 'Y', 'D', 'E', 'K', 'R', 'Y', 'T', 'M', 'G', 'D', 'A', 'P', 'D', 'F', 'D', 'R', 'S', 'Q', 'W', 'L', 'N', 'E', 'K', 'F', 'K', 'L', 'G', 'L', 'D', 'F', 'P', 'N', 'L', 'P', 'Y', 'L', 'I', 'D', 'G', 'S', 'H', 'K', 'I', 'T', 'Q', 'S', 'N', 'A', 'I', 'L', 'R', 'Y', 'L', 'A', 'R', 'K', 'H', 'H', 'L', 'D', 'G', 'E', 'T', 'E', 'E', 'E', 'R', 'I', 'R', 'A', 'D', 'I', 'V', 'E', 'N', 'Q', 'V', 'M', 'D', 'T', 'R', 'M', 'Q', 'L', 'I', 'M', 'L', 'C', 'Y', 'N', 'P', 'D', 'F', 'E', 'K', 'Q', 'K', 'P', 'E', 'F', 'L', 'K', 'T', 'I', 'P', 'E', 'K', 'M', 'K', 'L', 'Y', 'S', 'E', 'F', 'L', 'G', 'K', 'R', 'P', 'W', 'F', 'A', 'G', 'D', 'K', 'V', 'T', 'Y', 'V', 'D', 'F', 'L', 'A', 'Y', 'D', 'I', 'L', 'D', 'Q', 'Y', 'R', 'M', 'F', 'E', 'P', 'K', 'C', 'L', 'D', 'A', 'F', 'P', 'N', 'L', 'R', 'D', 'F', 'L', 'A', 'R', 'F', 'E', 'G', 'L', 'K', 'K', 'I', 'S', 'A', 'Y', 'M', 'K', 'S', 'S', 'R', 'Y', 'I', 'A', 'T', 'P', 'I', 'F', 'S', 'K', 'M', 'A', 'H', 'W', 'S', 'N', 'K']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertEqual(len(alignment), 2) self.assertAlmostEqual(alignment.annotations["% identity"], 29.76) self.assertEqual(alignment.annotations["gap opens"], 18) aligned = alignment.aligned self.assertEqual(sum(end - start for start, end in aligned[0]), 205) self.assertEqual(sum(end - start for start, end in aligned[1]), 205) self.assertEqual(alignment.shape, (2, 205 + 18)) self.assertEqual(alignment.sequences[0].id, "sp|P00502|GSTA1_RAT") self.assertEqual(alignment.sequences[1].id, "sp|P10649|GSTM1_MOUSE") self.assertEqual(alignment.annotations["mismatches"], 144) self.assertAlmostEqual(alignment.annotations["evalue"], 4.4e-14, places=15) self.assertAlmostEqual(alignment.annotations["bit score"], 63.5) self.assertEqual( str(alignment), """\ sp|P00502 5 ????????????????????????????---------??????????????????????? 0 ||||||||||||||||||||||||||||---------|||||||||||||--|||||||| sp|P10649 3 ??????????????????????????????????????????????????--???????? sp|P00502 56 ??????-????????????????????????????????????????????????????? 60 ||-|||-|||||||||||||||||||||||||||||||||||||||-||||||||||||| sp|P10649 61 ??-???????????????????????????????????????????-????????????? sp|P00502 115 ???????????????????????????????????????????????????????????? 120 ||||||||||--|||||||||||||||--||||||||||||||||||||||||||||||| sp|P10649 119 ??????????--???????????????--??????????????????????????????? sp|P00502 175 ??????????????????????????????????????????? 218 180 ||||||||||||||||||||||||||||||||||||||||||| 223 sp|P10649 175 ??????????????????????????????????????????? 218 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 5, 33, 33, 46, 48, 58, 59, 62, 62, 101, 102, 125, 127, 142, 144, 218], [ 3, 31, 40, 53, 53, 63, 63, 66, 67, 106, 106, 129, 129, 144, 144, 218]]) # fmt: on ) ) query = self.query target = self.targets[alignment.sequences[0].id] self.assertEqual(len(alignment.sequences[0].seq), 218) self.assertEqual(len(alignment.sequences[1].seq), len(query)) alignment.sequences[0].seq = target alignment.sequences[1].seq = query self.assertEqual( alignment[0], "VLHYFNARGRMECIRWLLAAAGVEFDEK---------FIQSPEDLEKLKKDGNLMFDQVPMVEIDG-MKLAQTRAILNYIATKYDLYGKDMKERALIDMYTEGILDLTEMIMQLVICPPDQKEAKTALAKDRTKNRYLPAFEKVLKSHGQDYLVGNRLTRVDIHLLELLLYVEEFDASLLTSFPLLKAFKSRISSLPNVKKFLQPGSQRKLPVDAKQIEEARK", ) self.assertEqual( alignment[1], "ILGYWNVRGLTHPIRMLLEYTDSSYDEKRYTMGDAPDFDRSQWLNEKFKL--GLDFPNLPYL-IDGSHKITQSNAILRYLARKHHLDGETEEERIRADIVENQVMD-TRMQLIMLCYNPDFEKQKPEFLK--TIPEKMKLYSEFLGK--RPWFAGDKVTYVDFLAYDILDQYRMFEPKCLDAFPNLRDFLARFEGLKKISAYMKSSRYIATPIFSKMAHWSNK", ) # sp|P10649|GSTM1_MOUSE sp|P69905|HBA_HUMAN self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['V', 'L', 'H', 'Y', 'F', 'N', 'A', 'R', 'G', 'R', 'M', 'E', 'C', 'I', 'R', 'W', 'L', 'L', 'A', 'A', 'A', 'G', 'V', 'E', 'F', 'D', 'E', 'K', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'F', 'I', 'Q', 'S', 'P', 'E', 'D', 'L', 'E', 'K', 'L', 'K', 'K', 'D', 'G', 'N', 'L', 'M', 'F', 'D', 'Q', 'V', 'P', 'M', 'V', 'E', 'I', 'D', 'G', '-', 'M', 'K', 'L', 'A', 'Q', 'T', 'R', 'A', 'I', 'L', 'N', 'Y', 'I', 'A', 'T', 'K', 'Y', 'D', 'L', 'Y', 'G', 'K', 'D', 'M', 'K', 'E', 'R', 'A', 'L', 'I', 'D', 'M', 'Y', 'T', 'E', 'G', 'I', 'L', 'D', 'L', 'T', 'E', 'M', 'I', 'M', 'Q', 'L', 'V', 'I', 'C', 'P', 'P', 'D', 'Q', 'K', 'E', 'A', 'K', 'T', 'A', 'L', 'A', 'K', 'D', 'R', 'T', 'K', 'N', 'R', 'Y', 'L', 'P', 'A', 'F', 'E', 'K', 'V', 'L', 'K', 'S', 'H', 'G', 'Q', 'D', 'Y', 'L', 'V', 'G', 'N', 'R', 'L', 'T', 'R', 'V', 'D', 'I', 'H', 'L', 'L', 'E', 'L', 'L', 'L', 'Y', 'V', 'E', 'E', 'F', 'D', 'A', 'S', 'L', 'L', 'T', 'S', 'F', 'P', 'L', 'L', 'K', 'A', 'F', 'K', 'S', 'R', 'I', 'S', 'S', 'L', 'P', 'N', 'V', 'K', 'K', 'F', 'L', 'Q', 'P', 'G', 'S', 'Q', 'R', 'K', 'L', 'P', 'V', 'D', 'A', 'K', 'Q', 'I', 'E', 'E', 'A', 'R', 'K'], ['I', 'L', 'G', 'Y', 'W', 'N', 'V', 'R', 'G', 'L', 'T', 'H', 'P', 'I', 'R', 'M', 'L', 'L', 'E', 'Y', 'T', 'D', 'S', 'S', 'Y', 'D', 'E', 'K', 'R', 'Y', 'T', 'M', 'G', 'D', 'A', 'P', 'D', 'F', 'D', 'R', 'S', 'Q', 'W', 'L', 'N', 'E', 'K', 'F', 'K', 'L', '-', '-', 'G', 'L', 'D', 'F', 'P', 'N', 'L', 'P', 'Y', 'L', '-', 'I', 'D', 'G', 'S', 'H', 'K', 'I', 'T', 'Q', 'S', 'N', 'A', 'I', 'L', 'R', 'Y', 'L', 'A', 'R', 'K', 'H', 'H', 'L', 'D', 'G', 'E', 'T', 'E', 'E', 'E', 'R', 'I', 'R', 'A', 'D', 'I', 'V', 'E', 'N', 'Q', 'V', 'M', 'D', '-', 'T', 'R', 'M', 'Q', 'L', 'I', 'M', 'L', 'C', 'Y', 'N', 'P', 'D', 'F', 'E', 'K', 'Q', 'K', 'P', 'E', 'F', 'L', 'K', '-', '-', 'T', 'I', 'P', 'E', 'K', 'M', 'K', 'L', 'Y', 'S', 'E', 'F', 'L', 'G', 'K', '-', '-', 'R', 'P', 'W', 'F', 'A', 'G', 'D', 'K', 'V', 'T', 'Y', 'V', 'D', 'F', 'L', 'A', 'Y', 'D', 'I', 'L', 'D', 'Q', 'Y', 'R', 'M', 'F', 'E', 'P', 'K', 'C', 'L', 'D', 'A', 'F', 'P', 'N', 'L', 'R', 'D', 'F', 'L', 'A', 'R', 'F', 'E', 'G', 'L', 'K', 'K', 'I', 'S', 'A', 'Y', 'M', 'K', 'S', 'S', 'R', 'Y', 'I', 'A', 'T', 'P', 'I', 'F', 'S', 'K', 'M', 'A', 'H', 'W', 'S', 'N', 'K']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertEqual(len(alignment), 2) self.assertAlmostEqual(alignment.annotations["% identity"], 27.03) self.assertEqual(alignment.annotations["gap opens"], 2) aligned = alignment.aligned self.assertEqual(sum(end - start for start, end in aligned[0]), 37) self.assertEqual(sum(end - start for start, end in aligned[1]), 37) self.assertEqual(alignment.shape, (2, 37 + 2)) self.assertEqual(alignment.sequences[0].id, "sp|P69905|HBA_HUMAN") self.assertEqual(alignment.sequences[1].id, "sp|P10649|GSTM1_MOUSE") self.assertEqual(alignment.annotations["mismatches"], 27) self.assertAlmostEqual(alignment.annotations["evalue"], 0.15) self.assertAlmostEqual(alignment.annotations["bit score"], 21.2) self.assertEqual( str(alignment), """\ sp|P69905 35 ?????????????-????????????????????????? 73 0 |||||||||||||-||||||||||-|||||||||||||| 39 sp|P10649 176 ????????????????????????-?????????????? 214 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 35, 48, 48, 58, 59, 73], [176, 189, 190, 200, 200, 214]]) # fmt: on ) ) query = self.query target = self.targets[alignment.sequences[0].id] self.assertEqual(len(alignment.sequences[0].seq), 73) self.assertEqual(len(alignment.sequences[1].seq), len(query)) alignment.sequences[0].seq = target alignment.sequences[1].seq = query self.assertEqual(alignment[0], "SFPTTKTYFPHFD-LSHGSAQVKGHGKKVADALTNAVAH") self.assertEqual(alignment[1], "AFPNLRDFLARFEGLKKISAYMKS-SRYIATPIFSKMAH") # sp|P10649|GSTM1_MOUSE sp|P00517|KAPCA_BOVIN self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['S', 'F', 'P', 'T', 'T', 'K', 'T', 'Y', 'F', 'P', 'H', 'F', 'D', '-', 'L', 'S', 'H', 'G', 'S', 'A', 'Q', 'V', 'K', 'G', 'H', 'G', 'K', 'K', 'V', 'A', 'D', 'A', 'L', 'T', 'N', 'A', 'V', 'A', 'H'], ['A', 'F', 'P', 'N', 'L', 'R', 'D', 'F', 'L', 'A', 'R', 'F', 'E', 'G', 'L', 'K', 'K', 'I', 'S', 'A', 'Y', 'M', 'K', 'S', '-', 'S', 'R', 'Y', 'I', 'A', 'T', 'P', 'I', 'F', 'S', 'K', 'M', 'A', 'H']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertEqual(len(alignment), 2) self.assertAlmostEqual(alignment.annotations["% identity"], 24.29) self.assertEqual(alignment.annotations["gap opens"], 2) aligned = alignment.aligned self.assertEqual(sum(end - start for start, end in aligned[0]), 70) self.assertEqual(sum(end - start for start, end in aligned[1]), 70) self.assertEqual(alignment.shape, (2, 70 + 2)) self.assertEqual(alignment.sequences[0].id, "sp|P00517|KAPCA_BOVIN") self.assertEqual(alignment.sequences[1].id, "sp|P10649|GSTM1_MOUSE") self.assertEqual(alignment.annotations["mismatches"], 53) self.assertAlmostEqual(alignment.annotations["evalue"], 1.2) self.assertAlmostEqual(alignment.annotations["bit score"], 19.4) self.assertEqual( str(alignment), """\ sp|P00517 228 ???????????????????????????????????????????????????????????? 0 ||||||||||||||||||||||||||||||||||||||||||||||--|||||||||||| sp|P10649 136 ??????????????????????????????????????????????--???????????? sp|P00517 288 ???????????? 300 60 |||||||||||| 72 sp|P10649 194 ???????????? 206 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[228, 274, 276, 300], [136, 182, 182, 206]]), # fmt: on ) ) query = self.query target = self.targets[alignment.sequences[0].id] self.assertEqual(len(alignment.sequences[0].seq), 300) self.assertEqual(len(alignment.sequences[1].seq), len(query)) alignment.sequences[0].seq = target alignment.sequences[1].seq = query self.assertEqual( alignment[0], "IYEMAAGYPPFFADQPIQIYEKIVSGKVRFPSHFSSDLKDLLRNLLQVDLTKRFGNLKNGVNDIKNHKWFAT", ) self.assertEqual( alignment[1], "LYSEFLGKRPWFAGDKVTYVDFLAYDILDQYRMFEPKCLDAFPNLR--DFLARFEGLKKISAYMKSSRYIAT", ) # sp|P10649|GSTM1_MOUSE sp|P14960|RBS_GUITH self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['I', 'Y', 'E', 'M', 'A', 'A', 'G', 'Y', 'P', 'P', 'F', 'F', 'A', 'D', 'Q', 'P', 'I', 'Q', 'I', 'Y', 'E', 'K', 'I', 'V', 'S', 'G', 'K', 'V', 'R', 'F', 'P', 'S', 'H', 'F', 'S', 'S', 'D', 'L', 'K', 'D', 'L', 'L', 'R', 'N', 'L', 'L', 'Q', 'V', 'D', 'L', 'T', 'K', 'R', 'F', 'G', 'N', 'L', 'K', 'N', 'G', 'V', 'N', 'D', 'I', 'K', 'N', 'H', 'K', 'W', 'F', 'A', 'T'], ['L', 'Y', 'S', 'E', 'F', 'L', 'G', 'K', 'R', 'P', 'W', 'F', 'A', 'G', 'D', 'K', 'V', 'T', 'Y', 'V', 'D', 'F', 'L', 'A', 'Y', 'D', 'I', 'L', 'D', 'Q', 'Y', 'R', 'M', 'F', 'E', 'P', 'K', 'C', 'L', 'D', 'A', 'F', 'P', 'N', 'L', 'R', '-', '-', 'D', 'F', 'L', 'A', 'R', 'F', 'E', 'G', 'L', 'K', 'K', 'I', 'S', 'A', 'Y', 'M', 'K', 'S', 'S', 'R', 'Y', 'I', 'A', 'T']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertEqual(len(alignment), 2) self.assertAlmostEqual(alignment.annotations["% identity"], 57.14) self.assertEqual(alignment.annotations["gap opens"], 0) aligned = alignment.aligned self.assertEqual(sum(end - start for start, end in aligned[0]), 7) self.assertEqual(sum(end - start for start, end in aligned[1]), 7) self.assertEqual(alignment.shape, (2, 7 + 0)) self.assertEqual(alignment.sequences[0].id, "sp|P14960|RBS_GUITH") self.assertEqual(alignment.sequences[1].id, "sp|P10649|GSTM1_MOUSE") self.assertEqual(alignment.annotations["mismatches"], 3) self.assertAlmostEqual(alignment.annotations["evalue"], 1.5) self.assertAlmostEqual(alignment.annotations["bit score"], 17.8) self.assertEqual( str(alignment), """\ sp|P14960 46 ??????? 53 0 ||||||| 7 sp|P10649 6 ??????? 13 """, ) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[46, 53], [6, 13]])) ) query = self.query target = self.targets[alignment.sequences[0].id] self.assertEqual(len(alignment.sequences[0].seq), 53) self.assertEqual(len(alignment.sequences[1].seq), len(query)) alignment.sequences[0].seq = target alignment.sequences[1].seq = query self.assertEqual(alignment[0], "YWDLWGL") self.assertEqual(alignment[1], "YWNVRGL") # sp|P10649|GSTM1_MOUSE sp|P01593|KV101_HUMAN self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['Y', 'W', 'D', 'L', 'W', 'G', 'L'], ['Y', 'W', 'N', 'V', 'R', 'G', 'L']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertEqual(len(alignment), 2) self.assertAlmostEqual(alignment.annotations["% identity"], 45.00) self.assertEqual(alignment.annotations["gap opens"], 10) aligned = alignment.aligned self.assertEqual(sum(end - start for start, end in aligned[0]), 40) self.assertEqual(sum(end - start for start, end in aligned[1]), 40) self.assertEqual(alignment.shape, (2, 40 + 10)) self.assertEqual(alignment.sequences[0].id, "sp|P01593|KV101_HUMAN") self.assertEqual(alignment.sequences[1].id, "sp|P10649|GSTM1_MOUSE") self.assertEqual(alignment.annotations["mismatches"], 22) self.assertAlmostEqual(alignment.annotations["evalue"], 2.4) self.assertAlmostEqual(alignment.annotations["bit score"], 16.7) self.assertEqual( str(alignment), """\ sp|P01593 15 ????????????????????????????????????-????????????? 64 0 ||||||||||||||---||||||||---||||--||-|||||||-||||| 50 sp|P10649 149 ??????????????---????????---????--??????????-????? 190 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[15, 29, 32, 40, 43, 47, 49, 51, 51, 58, 59, 64], [149, 163, 163, 171, 171, 175, 175, 177, 178, 185, 185, 190]]) # fmt: on ) ) query = self.query target = self.targets[alignment.sequences[0].id] self.assertEqual(len(alignment.sequences[0].seq), 64) self.assertEqual(len(alignment.sequences[1].seq), len(query)) alignment.sequences[0].seq = target alignment.sequences[1].seq = query self.assertEqual( alignment[0], "GDRVTITCQASQDINHYLNWYQQGPKKAPKILIYDA-SNLETGVPSRFSG" ) self.assertEqual( alignment[1], "GDKVTYVDFLAYDI---LDQYRMFE---PKCL--DAFPNLRDFL-ARFEG" ) # sp|P10649|GSTM1_MOUSE sp|P99998|CYC_PANTR self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['G', 'D', 'R', 'V', 'T', 'I', 'T', 'C', 'Q', 'A', 'S', 'Q', 'D', 'I', 'N', 'H', 'Y', 'L', 'N', 'W', 'Y', 'Q', 'Q', 'G', 'P', 'K', 'K', 'A', 'P', 'K', 'I', 'L', 'I', 'Y', 'D', 'A', '-', 'S', 'N', 'L', 'E', 'T', 'G', 'V', 'P', 'S', 'R', 'F', 'S', 'G'], ['G', 'D', 'K', 'V', 'T', 'Y', 'V', 'D', 'F', 'L', 'A', 'Y', 'D', 'I', '-', '-', '-', 'L', 'D', 'Q', 'Y', 'R', 'M', 'F', 'E', '-', '-', '-', 'P', 'K', 'C', 'L', '-', '-', 'D', 'A', 'F', 'P', 'N', 'L', 'R', 'D', 'F', 'L', '-', 'A', 'R', 'F', 'E', 'G']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertEqual(len(alignment), 2) self.assertAlmostEqual(alignment.annotations["% identity"], 31.03) self.assertEqual(alignment.annotations["gap opens"], 10) aligned = alignment.aligned self.assertEqual(sum(end - start for start, end in aligned[0]), 58) self.assertEqual(sum(end - start for start, end in aligned[1]), 58) self.assertEqual(alignment.shape, (2, 58 + 10)) self.assertEqual(alignment.sequences[0].id, "sp|P99998|CYC_PANTR") self.assertEqual(alignment.sequences[1].id, "sp|P10649|GSTM1_MOUSE") self.assertEqual(alignment.annotations["mismatches"], 40) self.assertAlmostEqual(alignment.annotations["evalue"], 2.7) self.assertAlmostEqual(alignment.annotations["bit score"], 16.5) self.assertEqual( str(alignment), """\ sp|P99998 27 ???????????????????????????????-??????????-?????--?????????- 0 ||||||||||||||||||||---||||||||-||||||||||-|||||--|||||||||- sp|P10649 128 ????????????????????---????????????????????????????????????? sp|P99998 82 --?????? 88 60 --|||||| 68 sp|P10649 185 ???????? 193 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 27, 47, 50, 58, 58, 68, 68, 73, 73, 82, 82, 88], [128, 148, 148, 156, 157, 167, 168, 173, 175, 184, 187, 193]]) # fmt: on ) ) query = self.query target = self.targets[alignment.sequences[0].id] self.assertEqual(len(alignment.sequences[0].seq), 88) self.assertEqual(len(alignment.sequences[1].seq), len(query)) alignment.sequences[0].seq = target alignment.sequences[1].seq = query self.assertEqual( alignment[0], "KTGPNLHGLFGRKTGQAPGYSYTAANKNKGI-IWGEDTLMEY-LENPK--KYIPGTKMI---FVGIKK", ) self.assertEqual( alignment[1], "KTIPEKMKLYSEFLGKRPWF---AGDKVTYVDFLAYDILDQYRMFEPKCLDAFPNLRDFLARFEGLKK", ) # sp|P10649|GSTM1_MOUSE sp|P02585|TNNC2_HUMAN self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['K', 'T', 'G', 'P', 'N', 'L', 'H', 'G', 'L', 'F', 'G', 'R', 'K', 'T', 'G', 'Q', 'A', 'P', 'G', 'Y', 'S', 'Y', 'T', 'A', 'A', 'N', 'K', 'N', 'K', 'G', 'I', '-', 'I', 'W', 'G', 'E', 'D', 'T', 'L', 'M', 'E', 'Y', '-', 'L', 'E', 'N', 'P', 'K', '-', '-', 'K', 'Y', 'I', 'P', 'G', 'T', 'K', 'M', 'I', '-', '-', '-', 'F', 'V', 'G', 'I', 'K', 'K'], ['K', 'T', 'I', 'P', 'E', 'K', 'M', 'K', 'L', 'Y', 'S', 'E', 'F', 'L', 'G', 'K', 'R', 'P', 'W', 'F', '-', '-', '-', 'A', 'G', 'D', 'K', 'V', 'T', 'Y', 'V', 'D', 'F', 'L', 'A', 'Y', 'D', 'I', 'L', 'D', 'Q', 'Y', 'R', 'M', 'F', 'E', 'P', 'K', 'C', 'L', 'D', 'A', 'F', 'P', 'N', 'L', 'R', 'D', 'F', 'L', 'A', 'R', 'F', 'E', 'G', 'L', 'K', 'K']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertEqual(len(alignment), 2) self.assertAlmostEqual(alignment.annotations["% identity"], 31.11) self.assertEqual(alignment.annotations["gap opens"], 9) aligned = alignment.aligned self.assertEqual(sum(end - start for start, end in aligned[0]), 45) self.assertEqual(sum(end - start for start, end in aligned[1]), 45) self.assertEqual(alignment.shape, (2, 45 + 9)) self.assertEqual(alignment.sequences[0].id, "sp|P02585|TNNC2_HUMAN") self.assertEqual(alignment.sequences[1].id, "sp|P10649|GSTM1_MOUSE") self.assertEqual(alignment.annotations["mismatches"], 31) self.assertAlmostEqual(alignment.annotations["evalue"], 3.8) self.assertAlmostEqual(alignment.annotations["bit score"], 16.5) self.assertEqual( str(alignment), """\ sp|P02585 12 ??????????????----???????????????????????????????????? 62 0 ||||||||||||||----||||||||||--|||||||||||---|||||||||| 54 sp|P10649 43 ????????????????????????????--???????????---?????????? 92 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[12, 26, 26, 36, 38, 49, 52, 62], [43, 57, 61, 71, 71, 82, 82, 92]]) # fmt: on ) ) query = self.query target = self.targets[alignment.sequences[0].id] self.assertEqual(len(alignment.sequences[0].seq), 62) self.assertEqual(len(alignment.sequences[1].seq), len(query)) alignment.sequences[0].seq = target alignment.sequences[1].seq = query self.assertEqual( alignment[0], "SEEMIAEFKAAFDM----FDADGGGDISVKELGTVMRMLGQTPTKEELDAIIEE" ) self.assertEqual( alignment[1], "SQWLNEKFKLGLDFPNLPYLIDGSHKIT--QSNAILRYLAR---KHHLDGETEE" ) # sp|P10649|GSTM1_MOUSE sp|P60615|NXL1A_BUNMU self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['S', 'E', 'E', 'M', 'I', 'A', 'E', 'F', 'K', 'A', 'A', 'F', 'D', 'M', '-', '-', '-', '-', 'F', 'D', 'A', 'D', 'G', 'G', 'G', 'D', 'I', 'S', 'V', 'K', 'E', 'L', 'G', 'T', 'V', 'M', 'R', 'M', 'L', 'G', 'Q', 'T', 'P', 'T', 'K', 'E', 'E', 'L', 'D', 'A', 'I', 'I', 'E', 'E'], ['S', 'Q', 'W', 'L', 'N', 'E', 'K', 'F', 'K', 'L', 'G', 'L', 'D', 'F', 'P', 'N', 'L', 'P', 'Y', 'L', 'I', 'D', 'G', 'S', 'H', 'K', 'I', 'T', '-', '-', 'Q', 'S', 'N', 'A', 'I', 'L', 'R', 'Y', 'L', 'A', 'R', '-', '-', '-', 'K', 'H', 'H', 'L', 'D', 'G', 'E', 'T', 'E', 'E']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertEqual(len(alignment), 2) self.assertAlmostEqual(alignment.annotations["% identity"], 66.67) self.assertEqual(alignment.annotations["gap opens"], 2) aligned = alignment.aligned self.assertEqual(sum(end - start for start, end in aligned[0]), 9) self.assertEqual(sum(end - start for start, end in aligned[1]), 9) self.assertEqual(alignment.shape, (2, 9 + 2)) self.assertEqual(alignment.sequences[0].id, "sp|P60615|NXL1A_BUNMU") self.assertEqual(alignment.sequences[1].id, "sp|P10649|GSTM1_MOUSE") self.assertEqual(alignment.annotations["mismatches"], 3) self.assertAlmostEqual(alignment.annotations["evalue"], 4.2) self.assertAlmostEqual(alignment.annotations["bit score"], 15.6) self.assertEqual( str(alignment), """\ sp|P60615 85 ?-???-????? 94 0 |-|||-||||| 11 sp|P10649 114 ??????????? 125 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 85, 86, 86, 89, 89, 94], [114, 115, 116, 119, 120, 125]]), # fmt: on ) ) query = self.query target = self.targets[alignment.sequences[0].id] self.assertEqual(len(alignment.sequences[0].seq), 94) self.assertEqual(len(alignment.sequences[1].seq), len(query)) alignment.sequences[0].seq = target alignment.sequences[1].seq = query self.assertEqual(alignment[0], "C-NPH-PKQRP") self.assertEqual(alignment[1], "CYNPDFEKQKP") # sp|P10649|GSTM1_MOUSE sp|P03435|HEMA_I75A3 self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['C', '-', 'N', 'P', 'H', '-', 'P', 'K', 'Q', 'R', 'P'], ['C', 'Y', 'N', 'P', 'D', 'F', 'E', 'K', 'Q', 'K', 'P']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertEqual(len(alignment), 2) self.assertAlmostEqual(alignment.annotations["% identity"], 28.95) self.assertEqual(alignment.annotations["gap opens"], 1) aligned = alignment.aligned self.assertEqual(sum(end - start for start, end in aligned[0]), 38) self.assertEqual(sum(end - start for start, end in aligned[1]), 38) self.assertEqual(alignment.shape, (2, 38 + 1)) self.assertEqual(alignment.sequences[0].id, "sp|P03435|HEMA_I75A3") self.assertEqual(alignment.sequences[1].id, "sp|P10649|GSTM1_MOUSE") self.assertEqual(alignment.annotations["mismatches"], 27) self.assertAlmostEqual(alignment.annotations["evalue"], 4.4) self.assertAlmostEqual(alignment.annotations["bit score"], 18.1) self.assertEqual( str(alignment), """\ sp|P03435 398 ??????????????????????????????????????? 437 0 ||||||||||-|||||||||||||||||||||||||||| 39 sp|P10649 73 ??????????-???????????????????????????? 111 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[398, 408, 409, 437], [ 73, 83, 83, 111]]) # fmt: on ) ) query = self.query target = self.targets[alignment.sequences[0].id] self.assertEqual(len(alignment.sequences[0].seq), 437) self.assertEqual(len(alignment.sequences[1].seq), len(query)) alignment.sequences[0].seq = target alignment.sequences[1].seq = query self.assertEqual(alignment[0], "NRVIEKTNEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDL") self.assertEqual(alignment[1], "NAILRYLARK-HHLDGETEEERIRADIVENQVMDTRMQL") # sp|P10649|GSTM1_MOUSE sp|P00193|FER_PEPAS self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['N', 'R', 'V', 'I', 'E', 'K', 'T', 'N', 'E', 'K', 'F', 'H', 'Q', 'I', 'E', 'K', 'E', 'F', 'S', 'E', 'V', 'E', 'G', 'R', 'I', 'Q', 'D', 'L', 'E', 'K', 'Y', 'V', 'E', 'D', 'T', 'K', 'I', 'D', 'L'], ['N', 'A', 'I', 'L', 'R', 'Y', 'L', 'A', 'R', 'K', '-', 'H', 'H', 'L', 'D', 'G', 'E', 'T', 'E', 'E', 'E', 'R', 'I', 'R', 'A', 'D', 'I', 'V', 'E', 'N', 'Q', 'V', 'M', 'D', 'T', 'R', 'M', 'Q', 'L']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertEqual(len(alignment), 2) self.assertAlmostEqual(alignment.annotations["% identity"], 50.00) self.assertEqual(alignment.annotations["gap opens"], 0) aligned = alignment.aligned self.assertEqual(sum(end - start for start, end in aligned[0]), 4) self.assertEqual(sum(end - start for start, end in aligned[1]), 4) self.assertEqual(alignment.shape, (2, 4 + 0)) self.assertEqual(alignment.sequences[0].id, "sp|P00193|FER_PEPAS") self.assertEqual(alignment.sequences[1].id, "sp|P10649|GSTM1_MOUSE") self.assertEqual(alignment.annotations["mismatches"], 2) self.assertAlmostEqual(alignment.annotations["evalue"], 4.4) self.assertAlmostEqual(alignment.annotations["bit score"], 14.7) self.assertEqual( str(alignment), """\ sp|P00193 14 ???? 18 0 |||| 4 sp|P10649 170 ???? 174 """, ) self.assertTrue( np.array_equal( alignment.coordinates, np.array([[14, 18], [170, 174]]), ) ) query = self.query target = self.targets[alignment.sequences[0].id] self.assertEqual(len(alignment.sequences[0].seq), 18) self.assertEqual(len(alignment.sequences[1].seq), len(query)) alignment.sequences[0].seq = target alignment.sequences[1].seq = query self.assertEqual(alignment[0], "KPEC") self.assertEqual(alignment[1], "EPKC") # sp|P10649|GSTM1_MOUSE sp|P01834|IGKC_HUMAN self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['K', 'P', 'E', 'C'], ['E', 'P', 'K', 'C']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertEqual(len(alignment), 2) self.assertAlmostEqual(alignment.annotations["% identity"], 19.40) self.assertEqual(alignment.annotations["gap opens"], 4) aligned = alignment.aligned self.assertEqual(sum(end - start for start, end in aligned[0]), 67) self.assertEqual(sum(end - start for start, end in aligned[1]), 67) self.assertEqual(alignment.shape, (2, 67 + 4)) self.assertEqual(alignment.sequences[0].id, "sp|P01834|IGKC_HUMAN") self.assertEqual(alignment.sequences[1].id, "sp|P10649|GSTM1_MOUSE") self.assertEqual(alignment.annotations["mismatches"], 54) self.assertAlmostEqual(alignment.annotations["evalue"], 6.4) self.assertAlmostEqual(alignment.annotations["bit score"], 14.9) self.assertEqual( str(alignment), """\ sp|P01834 11 ???????????????????????????????????????????????????????????? 0 ||||||||||||||--||||||||||||||||||||||||||||||||||||||||--|| sp|P10649 57 ??????????????--????????????????????????????????????????--?? sp|P01834 71 ??????????? 82 60 ||||||||||| 71 sp|P10649 113 ??????????? 124 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[11, 25, 27, 67, 69, 82], [57, 71, 71, 111, 111, 124]]) # fmt: on ) ) query = self.query target = self.targets[alignment.sequences[0].id] self.assertEqual(len(alignment.sequences[0].seq), 82) self.assertEqual(len(alignment.sequences[1].seq), len(query)) alignment.sequences[0].seq = target alignment.sequences[1].seq = query self.assertEqual( alignment[0], "PSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHK", ) self.assertEqual( alignment[1], "PNLPYLIDGSHKIT--QSNAILRYLARKHHLDGETEEERIRADIVENQVMDTRMQL--IMLCYNPDFEKQK", ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['P', 'S', 'D', 'E', 'Q', 'L', 'K', 'S', 'G', 'T', 'A', 'S', 'V', 'V', 'C', 'L', 'L', 'N', 'N', 'F', 'Y', 'P', 'R', 'E', 'A', 'K', 'V', 'Q', 'W', 'K', 'V', 'D', 'N', 'A', 'L', 'Q', 'S', 'G', 'N', 'S', 'Q', 'E', 'S', 'V', 'T', 'E', 'Q', 'D', 'S', 'K', 'D', 'S', 'T', 'Y', 'S', 'L', 'S', 'S', 'T', 'L', 'T', 'L', 'S', 'K', 'A', 'D', 'Y', 'E', 'K', 'H', 'K'], ['P', 'N', 'L', 'P', 'Y', 'L', 'I', 'D', 'G', 'S', 'H', 'K', 'I', 'T', '-', '-', 'Q', 'S', 'N', 'A', 'I', 'L', 'R', 'Y', 'L', 'A', 'R', 'K', 'H', 'H', 'L', 'D', 'G', 'E', 'T', 'E', 'E', 'E', 'R', 'I', 'R', 'A', 'D', 'I', 'V', 'E', 'N', 'Q', 'V', 'M', 'D', 'T', 'R', 'M', 'Q', 'L', '-', '-', 'I', 'M', 'L', 'C', 'Y', 'N', 'P', 'D', 'F', 'E', 'K', 'Q', 'K']], dtype='U') # fmt: on ) ) with self.assertRaises(StopIteration): next(alignments) class TestFastaNucleotide(unittest.TestCase): query = Seq( "ATGCCTATGATACTGGGATACTGGAACGTCCGCGGACTGACACACCCGATCCGCATGCTCCTGGAATACACAGACTCAAGCTATGATGAGAAGAGATACACCATGGGTGACGCTCCCGACTTTGACAGAAGCCAGTGGCTGAATGAGAAGTTCAAGCTGGGCCTGGACTTTCCCAATCTGCCTTACTTGATCGATGGATCACACAAGATCACCCAGAGCAATGCCATCCTGCGCTACCTTGCCCGAAAGCACCACCTGGATGGAGAGACAGAGGAGGAGAGGATCCGTGCAGACATTGTGGAGAACCAGGTCATGGACACCCGCATGCAGCTCATCATGCTCTGTTACAACCCTGACTTTGAGAAGCAGAAGCCAGAGTTCTTGAAGACCATCCCTGAGAAAATGAAGCTCTACTCTGAGTTCCTGGGCAAGAGGCCATGGTTTGCAGGGGACAAGGTCACCTATGTGGATTTCCTTGCTTATGACATTCTTGACCAGTACCGTATGTTTGAGCCCAAGTGCCTGGACGCCTTCCCAAACCTGAGGGACTTCCTGGCCCGCTTCGAGGGCCTCAAGAAGATCTCTGCCTACATGAAGAGTAGCCGCTACATCGCAACACCTATATTTTCAAAGATGGCCCACTGGAGTAACAAGTAG" ) filename = os.path.join("Fasta", "nucleotide_lib.fa") records = SeqIO.parse(filename, "fasta") targets = {record.id: record.seq.upper() for record in records} def test_m8CB(self): # Alignment file obtained by running # fasta36 -m 8CB seq/mgstm1.nt seq/gst.nlib # in the fasta36 source distribution path = "Fasta/nucleotide_m8CB.txt" alignments = Align.parse(path, "tabular") self.assertEqual( alignments.metadata["Command line"], "fasta36 -m 8CB seq/mgstm1.nt seq/gst.nlib", ) self.assertEqual(alignments.metadata["Program"], "FASTA") self.assertEqual(alignments.metadata["Version"], "36.3.8h May, 2020") self.assertEqual(alignments.metadata["Database"], "seq/gst.nlib") # pGT875 pGT875 alignment = next(alignments) self.assertEqual(len(alignment), 2) self.assertAlmostEqual(alignment.annotations["% identity"], 100.00) self.assertEqual(alignment.annotations["gap opens"], 0) aligned = alignment.aligned self.assertEqual(sum(end - start for start, end in aligned[0]), 657) self.assertEqual(sum(end - start for start, end in aligned[1]), 657) self.assertEqual(alignment.shape, (2, 657 + 0)) self.assertEqual(alignment.sequences[0].id, "pGT875") self.assertEqual(alignment.sequences[1].id, "pGT875") self.assertEqual(alignment.annotations["mismatches"], 0) self.assertAlmostEqual(alignment.annotations["evalue"], 3.6e-194, places=195) self.assertAlmostEqual(alignment.annotations["bit score"], 666.0) self.assertEqual( str(alignment), """\ pGT875 37 ???????????????????????????????????????????????????????????? 0 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| pGT875 0 ???????????????????????????????????????????????????????????? pGT875 97 ???????????????????????????????????????????????????????????? 60 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| pGT875 60 ???????????????????????????????????????????????????????????? pGT875 157 ???????????????????????????????????????????????????????????? 120 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| pGT875 120 ???????????????????????????????????????????????????????????? pGT875 217 ???????????????????????????????????????????????????????????? 180 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| pGT875 180 ???????????????????????????????????????????????????????????? pGT875 277 ???????????????????????????????????????????????????????????? 240 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| pGT875 240 ???????????????????????????????????????????????????????????? pGT875 337 ???????????????????????????????????????????????????????????? 300 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| pGT875 300 ???????????????????????????????????????????????????????????? pGT875 397 ???????????????????????????????????????????????????????????? 360 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| pGT875 360 ???????????????????????????????????????????????????????????? pGT875 457 ???????????????????????????????????????????????????????????? 420 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| pGT875 420 ???????????????????????????????????????????????????????????? pGT875 517 ???????????????????????????????????????????????????????????? 480 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| pGT875 480 ???????????????????????????????????????????????????????????? pGT875 577 ???????????????????????????????????????????????????????????? 540 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| pGT875 540 ???????????????????????????????????????????????????????????? pGT875 637 ????????????????????????????????????????????????????????? 694 600 ||||||||||||||||||||||||||||||||||||||||||||||||||||||||| 657 pGT875 600 ????????????????????????????????????????????????????????? 657 """, ) self.assertTrue( np.array_equal( alignment.coordinates, np.array([[37, 694], [0, 657]]), ) ) query = self.query target = self.targets[alignment.sequences[0].id] self.assertEqual(len(alignment.sequences[0].seq), 694) self.assertEqual(len(alignment.sequences[1].seq), len(query)) alignment.sequences[0].seq = target alignment.sequences[1].seq = query self.assertEqual( alignment[0], "ATGCCTATGATACTGGGATACTGGAACGTCCGCGGACTGACACACCCGATCCGCATGCTCCTGGAATACACAGACTCAAGCTATGATGAGAAGAGATACACCATGGGTGACGCTCCCGACTTTGACAGAAGCCAGTGGCTGAATGAGAAGTTCAAGCTGGGCCTGGACTTTCCCAATCTGCCTTACTTGATCGATGGATCACACAAGATCACCCAGAGCAATGCCATCCTGCGCTACCTTGCCCGAAAGCACCACCTGGATGGAGAGACAGAGGAGGAGAGGATCCGTGCAGACATTGTGGAGAACCAGGTCATGGACACCCGCATGCAGCTCATCATGCTCTGTTACAACCCTGACTTTGAGAAGCAGAAGCCAGAGTTCTTGAAGACCATCCCTGAGAAAATGAAGCTCTACTCTGAGTTCCTGGGCAAGAGGCCATGGTTTGCAGGGGACAAGGTCACCTATGTGGATTTCCTTGCTTATGACATTCTTGACCAGTACCGTATGTTTGAGCCCAAGTGCCTGGACGCCTTCCCAAACCTGAGGGACTTCCTGGCCCGCTTCGAGGGCCTCAAGAAGATCTCTGCCTACATGAAGAGTAGCCGCTACATCGCAACACCTATATTTTCAAAGATGGCCCACTGGAGTAACAAGTAG", ) self.assertEqual( alignment[1], "ATGCCTATGATACTGGGATACTGGAACGTCCGCGGACTGACACACCCGATCCGCATGCTCCTGGAATACACAGACTCAAGCTATGATGAGAAGAGATACACCATGGGTGACGCTCCCGACTTTGACAGAAGCCAGTGGCTGAATGAGAAGTTCAAGCTGGGCCTGGACTTTCCCAATCTGCCTTACTTGATCGATGGATCACACAAGATCACCCAGAGCAATGCCATCCTGCGCTACCTTGCCCGAAAGCACCACCTGGATGGAGAGACAGAGGAGGAGAGGATCCGTGCAGACATTGTGGAGAACCAGGTCATGGACACCCGCATGCAGCTCATCATGCTCTGTTACAACCCTGACTTTGAGAAGCAGAAGCCAGAGTTCTTGAAGACCATCCCTGAGAAAATGAAGCTCTACTCTGAGTTCCTGGGCAAGAGGCCATGGTTTGCAGGGGACAAGGTCACCTATGTGGATTTCCTTGCTTATGACATTCTTGACCAGTACCGTATGTTTGAGCCCAAGTGCCTGGACGCCTTCCCAAACCTGAGGGACTTCCTGGCCCGCTTCGAGGGCCTCAAGAAGATCTCTGCCTACATGAAGAGTAGCCGCTACATCGCAACACCTATATTTTCAAAGATGGCCCACTGGAGTAACAAGTAG", ) # pGT875 RABGLTR alignment = next(alignments) self.assertEqual(len(alignment), 2) self.assertAlmostEqual(alignment.annotations["% identity"], 79.10) self.assertEqual(alignment.annotations["gap opens"], 0) aligned = alignment.aligned self.assertEqual(sum(end - start for start, end in aligned[0]), 646) self.assertEqual(sum(end - start for start, end in aligned[1]), 646) self.assertEqual(alignment.shape, (2, 646 + 0)) self.assertEqual(alignment.sequences[0].id, "RABGLTR") self.assertEqual(alignment.sequences[1].id, "pGT875") self.assertEqual(alignment.annotations["mismatches"], 135) self.assertAlmostEqual(alignment.annotations["evalue"], 1.9e-118, places=119) self.assertAlmostEqual(alignment.annotations["bit score"], 414.4) self.assertEqual( str(alignment), """\ RABGLTR 33 ???????????????????????????????????????????????????????????? 0 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| pGT875 0 ???????????????????????????????????????????????????????????? RABGLTR 93 ???????????????????????????????????????????????????????????? 60 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| pGT875 60 ???????????????????????????????????????????????????????????? RABGLTR 153 ???????????????????????????????????????????????????????????? 120 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| pGT875 120 ???????????????????????????????????????????????????????????? RABGLTR 213 ???????????????????????????????????????????????????????????? 180 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| pGT875 180 ???????????????????????????????????????????????????????????? RABGLTR 273 ???????????????????????????????????????????????????????????? 240 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| pGT875 240 ???????????????????????????????????????????????????????????? RABGLTR 333 ???????????????????????????????????????????????????????????? 300 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| pGT875 300 ???????????????????????????????????????????????????????????? RABGLTR 393 ???????????????????????????????????????????????????????????? 360 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| pGT875 360 ???????????????????????????????????????????????????????????? RABGLTR 453 ???????????????????????????????????????????????????????????? 420 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| pGT875 420 ???????????????????????????????????????????????????????????? RABGLTR 513 ???????????????????????????????????????????????????????????? 480 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| pGT875 480 ???????????????????????????????????????????????????????????? RABGLTR 573 ???????????????????????????????????????????????????????????? 540 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| pGT875 540 ???????????????????????????????????????????????????????????? RABGLTR 633 ?????????????????????????????????????????????? 679 600 |||||||||||||||||||||||||||||||||||||||||||||| 646 pGT875 600 ?????????????????????????????????????????????? 646 """, ) self.assertTrue( np.array_equal( alignment.coordinates, np.array([[33, 679], [0, 646]]), ) ) query = self.query target = self.targets[alignment.sequences[0].id] self.assertEqual(len(alignment.sequences[0].seq), 679) self.assertEqual(len(alignment.sequences[1].seq), len(query)) alignment.sequences[0].seq = target alignment.sequences[1].seq = query self.assertEqual( alignment[0], "ATGCCCATGACGCTGGGTTACTGGGACGTCCGTGGGCTGGCTCTGCCAATCCGCATGCTCCTGGAATACACGGACACCAGCTATGAGGAAAAGAAATACACCATGGGGGATGCTCCCAACTATGACCAAAGCAAGTGGCTGAGTGAGAAGTTCACCCTGGGCCTGGACTTTCCCAATCTGCCCTACCTAATTGATGGGACTCACAAGCTCACGCAGAGCAACGCCATCCTGCGCTACCTGGCCCGCAAGCACGGCCTGTGTGGGGAGACGGAAGAGGAGAGGATTCGCGTGGACATTCTGGAGAATCAGCTGATGGACAACCGCTTCCAACTTGTAAACGTCTGCTACAGTCCCGACTTTGAGAAGCTCAAGCCCGAGTACCTGAAGGGGCTCCCTGAGAAGCTGCAGCTGTACTCGCAGTTCCTGGGAAGCCTCCCCTGGTTCGCAGGGGACAAGATCACCTTCGCCGATTTCCTTGTCTACGACGTTCTTGACCAGAACCGGATATTTGTGCCTGGGTGCCTGGACGCGTTCCCAAACCTGAAGGACTTTCATGTCCGCTTTGAGGGCCTGCCGAAGATCTCTGCCTACATGAAGTCCAGCCGCTTTATCCGAGTCCCTGTGTTTTTAAAGAAGGCCACGTGGA", ) self.assertEqual( alignment[1], "ATGCCTATGATACTGGGATACTGGAACGTCCGCGGACTGACACACCCGATCCGCATGCTCCTGGAATACACAGACTCAAGCTATGATGAGAAGAGATACACCATGGGTGACGCTCCCGACTTTGACAGAAGCCAGTGGCTGAATGAGAAGTTCAAGCTGGGCCTGGACTTTCCCAATCTGCCTTACTTGATCGATGGATCACACAAGATCACCCAGAGCAATGCCATCCTGCGCTACCTTGCCCGAAAGCACCACCTGGATGGAGAGACAGAGGAGGAGAGGATCCGTGCAGACATTGTGGAGAACCAGGTCATGGACACCCGCATGCAGCTCATCATGCTCTGTTACAACCCTGACTTTGAGAAGCAGAAGCCAGAGTTCTTGAAGACCATCCCTGAGAAAATGAAGCTCTACTCTGAGTTCCTGGGCAAGAGGCCATGGTTTGCAGGGGACAAGGTCACCTATGTGGATTTCCTTGCTTATGACATTCTTGACCAGTACCGTATGTTTGAGCCCAAGTGCCTGGACGCCTTCCCAAACCTGAGGGACTTCCTGGCCCGCTTCGAGGGCCTCAAGAAGATCTCTGCCTACATGAAGAGTAGCCGCTACATCGCAACACCTATATTTTCAAAGATGGCCCACTGGA", ) # pGT875 BTGST alignment = next(alignments) self.assertEqual(len(alignment), 2) self.assertAlmostEqual(alignment.annotations["% identity"], 59.56) self.assertEqual(alignment.annotations["gap opens"], 21) aligned = alignment.aligned self.assertEqual(sum(end - start for start, end in aligned[0]), 413) self.assertEqual(sum(end - start for start, end in aligned[1]), 413) self.assertEqual(alignment.shape, (2, 413 + 21)) self.assertEqual(alignment.sequences[0].id, "BTGST") self.assertEqual(alignment.sequences[1].id, "pGT875") self.assertEqual(alignment.annotations["mismatches"], 167) self.assertAlmostEqual(alignment.annotations["evalue"], 1.2e-07, places=8) self.assertAlmostEqual(alignment.annotations["bit score"], 46.4) self.assertEqual( str(alignment), """\ BTGST 227 ???????????????????????????????????????????????????????????? 0 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| pGT875 175 ???????????????????????????????????????????????????????????? BTGST 287 ???????????????????????????????????????????????????????????? 60 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| pGT875 235 ???????????????????????????????????????????????????????????? BTGST 347 ?????????????????????????????-?????????????????????????---?? 120 |||||||||||||||||||||||||||||-|||||||-|||||||||||||||||---|| pGT875 295 ?????????????????????????????????????-?????????????????????? BTGST 403 ???????????????????????????????????????????????????????????? 180 ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||-- pGT875 354 ??????????????????????????????????????????????????????????-- BTGST 463 ???????????????????????????????????????????????????????????? 240 ---||||||-|||||||||||||--|||||||||||||----|||||||||||||||||| pGT875 412 ---??????-?????????????--?????????????----?????????????????? BTGST 523 ????????????????????--?????????????????????????????????????? 300 ||||||||||||--||||||--|||||||||||||||||||||||||||||||||||||| pGT875 462 ????????????--?????????????????????????????????????????????? BTGST 581 ???????????????????????????????????????????????????????????? 360 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| pGT875 520 ???????????????????????????????????????????????????????????? BTGST 641 ?????????????? 655 420 |||||||||||||| 434 pGT875 580 ?????????????? 594 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[227, 376, 376, 383, 384, 401, 401, 461, 466, 472, 473, 486, 488, 501, 505, 535, 537, 543, 543, 655], [175, 324, 325, 332, 332, 349, 352, 412, 412, 418, 418, 431, 431, 444, 444, 474, 474, 480, 482, 594]]) # fmt: on ) ) query = self.query target = self.targets[alignment.sequences[0].id] self.assertEqual(len(alignment.sequences[0].seq), 655) self.assertEqual(len(alignment.sequences[1].seq), len(query)) alignment.sequences[0].seq = target alignment.sequences[1].seq = query self.assertEqual( alignment[0], "AGCTCCCCAAGTTCCAGGACGGAGACCTCACGCTGTACCAGTCCAATGCCATCCTGCGGCACCTGGGCCGCACCCTCGGGCTGTATGGGAAGGACCAGCAGGAGGCGGCCCTGGTGGACATGGTGAATGACGGTGTAGAGGACCTTCGC-TGCAAATACGTCTCCCTCATTTACA---CCAACTACGAGGCGGGCAAGGAGGACTATGTGAAGGCGCTGCCCCAGCACCTGAAGCCTTTCGAGACCCTGCTGTCCCAGAACAAGGGTGGCCAGGCCTTCATCGTGGGCGACCAGATCTCCTTTGCGGACTACAACCTGCT--GGACCTGCTTCGGATTCACCAGGTCCTGGCCCCCAGCTGTCTGGACTCCTTCCCCCTGCTCTCAGCCTACGTGGCCCGTCTCAACTCCCGGCCCAAGCTCAAGGCCTTCCTG", ) self.assertEqual( alignment[1], "ATCTGCCTTACTTGATCGATGGATCACACAAGATCACCCAGAGCAATGCCATCCTGCGCTACCTTGCCCGAAAGCACCACCTGGATGGAGAGACAGAGGAGGAGAGGATCCGTGCAGACATTGTGGAGAACCAGGTCATGGACACCCGCATGCAGCT-CATCATGCTCTGTTACAACCCTGACTTTGAGAAGCAGAAGCCAGAGTTCTTGAAGACCATCCCTGAGAAAATGAAGCTCT-----ACTCTG-AGTTCCTGGGCAA--GAGGCCATGGTTT----GCAGGGGACAAGGTCACCTATGTGGATTTC--CTTGCTTATGACATTCTTGACCAGTACCGTATGTTTGAGCCCAAGTGCCTGGACGCCTTCCCAAACCTGAGGGACTTCCTGGCCCGCTTCGAGGGCCTCAAGAAGATCTCTGCCTACATG", ) # pGT875 RABGSTB self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['A', 'G', 'C', 'T', 'C', 'C', 'C', 'C', 'A', 'A', 'G', 'T', 'T', 'C', 'C', 'A', 'G', 'G', 'A', 'C', 'G', 'G', 'A', 'G', 'A', 'C', 'C', 'T', 'C', 'A', 'C', 'G', 'C', 'T', 'G', 'T', 'A', 'C', 'C', 'A', 'G', 'T', 'C', 'C', 'A', 'A', 'T', 'G', 'C', 'C', 'A', 'T', 'C', 'C', 'T', 'G', 'C', 'G', 'G', 'C', 'A', 'C', 'C', 'T', 'G', 'G', 'G', 'C', 'C', 'G', 'C', 'A', 'C', 'C', 'C', 'T', 'C', 'G', 'G', 'G', 'C', 'T', 'G', 'T', 'A', 'T', 'G', 'G', 'G', 'A', 'A', 'G', 'G', 'A', 'C', 'C', 'A', 'G', 'C', 'A', 'G', 'G', 'A', 'G', 'G', 'C', 'G', 'G', 'C', 'C', 'C', 'T', 'G', 'G', 'T', 'G', 'G', 'A', 'C', 'A', 'T', 'G', 'G', 'T', 'G', 'A', 'A', 'T', 'G', 'A', 'C', 'G', 'G', 'T', 'G', 'T', 'A', 'G', 'A', 'G', 'G', 'A', 'C', 'C', 'T', 'T', 'C', 'G', 'C', '-', 'T', 'G', 'C', 'A', 'A', 'A', 'T', 'A', 'C', 'G', 'T', 'C', 'T', 'C', 'C', 'C', 'T', 'C', 'A', 'T', 'T', 'T', 'A', 'C', 'A', '-', '-', '-', 'C', 'C', 'A', 'A', 'C', 'T', 'A', 'C', 'G', 'A', 'G', 'G', 'C', 'G', 'G', 'G', 'C', 'A', 'A', 'G', 'G', 'A', 'G', 'G', 'A', 'C', 'T', 'A', 'T', 'G', 'T', 'G', 'A', 'A', 'G', 'G', 'C', 'G', 'C', 'T', 'G', 'C', 'C', 'C', 'C', 'A', 'G', 'C', 'A', 'C', 'C', 'T', 'G', 'A', 'A', 'G', 'C', 'C', 'T', 'T', 'T', 'C', 'G', 'A', 'G', 'A', 'C', 'C', 'C', 'T', 'G', 'C', 'T', 'G', 'T', 'C', 'C', 'C', 'A', 'G', 'A', 'A', 'C', 'A', 'A', 'G', 'G', 'G', 'T', 'G', 'G', 'C', 'C', 'A', 'G', 'G', 'C', 'C', 'T', 'T', 'C', 'A', 'T', 'C', 'G', 'T', 'G', 'G', 'G', 'C', 'G', 'A', 'C', 'C', 'A', 'G', 'A', 'T', 'C', 'T', 'C', 'C', 'T', 'T', 'T', 'G', 'C', 'G', 'G', 'A', 'C', 'T', 'A', 'C', 'A', 'A', 'C', 'C', 'T', 'G', 'C', 'T', '-', '-', 'G', 'G', 'A', 'C', 'C', 'T', 'G', 'C', 'T', 'T', 'C', 'G', 'G', 'A', 'T', 'T', 'C', 'A', 'C', 'C', 'A', 'G', 'G', 'T', 'C', 'C', 'T', 'G', 'G', 'C', 'C', 'C', 'C', 'C', 'A', 'G', 'C', 'T', 'G', 'T', 'C', 'T', 'G', 'G', 'A', 'C', 'T', 'C', 'C', 'T', 'T', 'C', 'C', 'C', 'C', 'C', 'T', 'G', 'C', 'T', 'C', 'T', 'C', 'A', 'G', 'C', 'C', 'T', 'A', 'C', 'G', 'T', 'G', 'G', 'C', 'C', 'C', 'G', 'T', 'C', 'T', 'C', 'A', 'A', 'C', 'T', 'C', 'C', 'C', 'G', 'G', 'C', 'C', 'C', 'A', 'A', 'G', 'C', 'T', 'C', 'A', 'A', 'G', 'G', 'C', 'C', 'T', 'T', 'C', 'C', 'T', 'G'], ['A', 'T', 'C', 'T', 'G', 'C', 'C', 'T', 'T', 'A', 'C', 'T', 'T', 'G', 'A', 'T', 'C', 'G', 'A', 'T', 'G', 'G', 'A', 'T', 'C', 'A', 'C', 'A', 'C', 'A', 'A', 'G', 'A', 'T', 'C', 'A', 'C', 'C', 'C', 'A', 'G', 'A', 'G', 'C', 'A', 'A', 'T', 'G', 'C', 'C', 'A', 'T', 'C', 'C', 'T', 'G', 'C', 'G', 'C', 'T', 'A', 'C', 'C', 'T', 'T', 'G', 'C', 'C', 'C', 'G', 'A', 'A', 'A', 'G', 'C', 'A', 'C', 'C', 'A', 'C', 'C', 'T', 'G', 'G', 'A', 'T', 'G', 'G', 'A', 'G', 'A', 'G', 'A', 'C', 'A', 'G', 'A', 'G', 'G', 'A', 'G', 'G', 'A', 'G', 'A', 'G', 'G', 'A', 'T', 'C', 'C', 'G', 'T', 'G', 'C', 'A', 'G', 'A', 'C', 'A', 'T', 'T', 'G', 'T', 'G', 'G', 'A', 'G', 'A', 'A', 'C', 'C', 'A', 'G', 'G', 'T', 'C', 'A', 'T', 'G', 'G', 'A', 'C', 'A', 'C', 'C', 'C', 'G', 'C', 'A', 'T', 'G', 'C', 'A', 'G', 'C', 'T', '-', 'C', 'A', 'T', 'C', 'A', 'T', 'G', 'C', 'T', 'C', 'T', 'G', 'T', 'T', 'A', 'C', 'A', 'A', 'C', 'C', 'C', 'T', 'G', 'A', 'C', 'T', 'T', 'T', 'G', 'A', 'G', 'A', 'A', 'G', 'C', 'A', 'G', 'A', 'A', 'G', 'C', 'C', 'A', 'G', 'A', 'G', 'T', 'T', 'C', 'T', 'T', 'G', 'A', 'A', 'G', 'A', 'C', 'C', 'A', 'T', 'C', 'C', 'C', 'T', 'G', 'A', 'G', 'A', 'A', 'A', 'A', 'T', 'G', 'A', 'A', 'G', 'C', 'T', 'C', 'T', '-', '-', '-', '-', '-', 'A', 'C', 'T', 'C', 'T', 'G', '-', 'A', 'G', 'T', 'T', 'C', 'C', 'T', 'G', 'G', 'G', 'C', 'A', 'A', '-', '-', 'G', 'A', 'G', 'G', 'C', 'C', 'A', 'T', 'G', 'G', 'T', 'T', 'T', '-', '-', '-', '-', 'G', 'C', 'A', 'G', 'G', 'G', 'G', 'A', 'C', 'A', 'A', 'G', 'G', 'T', 'C', 'A', 'C', 'C', 'T', 'A', 'T', 'G', 'T', 'G', 'G', 'A', 'T', 'T', 'T', 'C', '-', '-', 'C', 'T', 'T', 'G', 'C', 'T', 'T', 'A', 'T', 'G', 'A', 'C', 'A', 'T', 'T', 'C', 'T', 'T', 'G', 'A', 'C', 'C', 'A', 'G', 'T', 'A', 'C', 'C', 'G', 'T', 'A', 'T', 'G', 'T', 'T', 'T', 'G', 'A', 'G', 'C', 'C', 'C', 'A', 'A', 'G', 'T', 'G', 'C', 'C', 'T', 'G', 'G', 'A', 'C', 'G', 'C', 'C', 'T', 'T', 'C', 'C', 'C', 'A', 'A', 'A', 'C', 'C', 'T', 'G', 'A', 'G', 'G', 'G', 'A', 'C', 'T', 'T', 'C', 'C', 'T', 'G', 'G', 'C', 'C', 'C', 'G', 'C', 'T', 'T', 'C', 'G', 'A', 'G', 'G', 'G', 'C', 'C', 'T', 'C', 'A', 'A', 'G', 'A', 'A', 'G', 'A', 'T', 'C', 'T', 'C', 'T', 'G', 'C', 'C', 'T', 'A', 'C', 'A', 'T', 'G']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertEqual(len(alignment), 2) self.assertAlmostEqual(alignment.annotations["% identity"], 66.93) self.assertEqual(alignment.annotations["gap opens"], 8) aligned = alignment.aligned self.assertEqual(sum(end - start for start, end in aligned[0]), 127) self.assertEqual(sum(end - start for start, end in aligned[1]), 127) self.assertEqual(alignment.shape, (2, 127 + 8)) self.assertEqual(alignment.sequences[0].id, "RABGSTB") self.assertEqual(alignment.sequences[1].id, "pGT875") self.assertEqual(alignment.annotations["mismatches"], 42) self.assertAlmostEqual(alignment.annotations["evalue"], 2.1e-07, places=8) self.assertAlmostEqual(alignment.annotations["bit score"], 45.6) self.assertEqual( str(alignment), """\ RABGSTB 156 ??????????????????????????????????--???????????????????????? 0 |||||||||||||||--|||||||||||||||||--|||||||||||-|||||||||||| pGT875 158 ???????????????--??????????????????????????????-???????????? RABGSTB 214 ??????????????????????????????????????????????????????????-? 60 ||||||||||||||||||||||||||||||||||||||||||||||-|||||||||||-| pGT875 215 ??????????????????????????????????????????????-????????????? RABGSTB 273 ??????-???????? 287 120 ||||||-|||||||| 135 pGT875 274 ??????????????? 289 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[156, 171, 173, 190, 190, 201, 202, 260, 261, 272, 272, 279, 279, 287], [158, 173, 173, 190, 192, 203, 203, 261, 261, 272, 273, 280, 281, 289]]) # fmt: on ) ) query = self.query target = self.targets[alignment.sequences[0].id] self.assertEqual(len(alignment.sequences[0].seq), 287) self.assertEqual(len(alignment.sequences[1].seq), len(query)) alignment.sequences[0].seq = target alignment.sequences[1].seq = query self.assertEqual( alignment[0], "GGGTATTGATGTTCCAGCAAGTGCCCATGGTTGA--GATTGATGGGATGAAGCTGGTGCAGACCAGAGCCATTTTCAACTACATTGCAGACAAGCACAACCTGTATGGGAAAGACATA-AAGGAGA-GAGCCCTG", ) self.assertEqual( alignment[1], "GGGCCTGGACTTTCC--CAATCTGCCTTACTTGATCGATGGATCACA-CAAGATCACCCAGAGCAATGCCATCCTGCGCTACCTTGCCCGAAAGCACCACCTGGAT-GGAGAGACAGAGGAGGAGAGGATCCGTG", ) # pGT875 OCDHPR self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['G', 'G', 'G', 'T', 'A', 'T', 'T', 'G', 'A', 'T', 'G', 'T', 'T', 'C', 'C', 'A', 'G', 'C', 'A', 'A', 'G', 'T', 'G', 'C', 'C', 'C', 'A', 'T', 'G', 'G', 'T', 'T', 'G', 'A', '-', '-', 'G', 'A', 'T', 'T', 'G', 'A', 'T', 'G', 'G', 'G', 'A', 'T', 'G', 'A', 'A', 'G', 'C', 'T', 'G', 'G', 'T', 'G', 'C', 'A', 'G', 'A', 'C', 'C', 'A', 'G', 'A', 'G', 'C', 'C', 'A', 'T', 'T', 'T', 'T', 'C', 'A', 'A', 'C', 'T', 'A', 'C', 'A', 'T', 'T', 'G', 'C', 'A', 'G', 'A', 'C', 'A', 'A', 'G', 'C', 'A', 'C', 'A', 'A', 'C', 'C', 'T', 'G', 'T', 'A', 'T', 'G', 'G', 'G', 'A', 'A', 'A', 'G', 'A', 'C', 'A', 'T', 'A', '-', 'A', 'A', 'G', 'G', 'A', 'G', 'A', '-', 'G', 'A', 'G', 'C', 'C', 'C', 'T', 'G'], ['G', 'G', 'G', 'C', 'C', 'T', 'G', 'G', 'A', 'C', 'T', 'T', 'T', 'C', 'C', '-', '-', 'C', 'A', 'A', 'T', 'C', 'T', 'G', 'C', 'C', 'T', 'T', 'A', 'C', 'T', 'T', 'G', 'A', 'T', 'C', 'G', 'A', 'T', 'G', 'G', 'A', 'T', 'C', 'A', 'C', 'A', '-', 'C', 'A', 'A', 'G', 'A', 'T', 'C', 'A', 'C', 'C', 'C', 'A', 'G', 'A', 'G', 'C', 'A', 'A', 'T', 'G', 'C', 'C', 'A', 'T', 'C', 'C', 'T', 'G', 'C', 'G', 'C', 'T', 'A', 'C', 'C', 'T', 'T', 'G', 'C', 'C', 'C', 'G', 'A', 'A', 'A', 'G', 'C', 'A', 'C', 'C', 'A', 'C', 'C', 'T', 'G', 'G', 'A', 'T', '-', 'G', 'G', 'A', 'G', 'A', 'G', 'A', 'C', 'A', 'G', 'A', 'G', 'G', 'A', 'G', 'G', 'A', 'G', 'A', 'G', 'G', 'A', 'T', 'C', 'C', 'G', 'T', 'G']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertEqual(len(alignment), 2) self.assertAlmostEqual(alignment.annotations["% identity"], 91.30) self.assertEqual(alignment.annotations["gap opens"], 1) aligned = alignment.aligned self.assertEqual(sum(end - start for start, end in aligned[0]), 23) self.assertEqual(sum(end - start for start, end in aligned[1]), 23) self.assertEqual(alignment.shape, (2, 23 + 1)) self.assertEqual(alignment.sequences[0].id, "OCDHPR") self.assertEqual(alignment.sequences[1].id, "pGT875") self.assertEqual(alignment.annotations["mismatches"], 2) self.assertAlmostEqual(alignment.annotations["evalue"], 0.0092) self.assertAlmostEqual(alignment.annotations["bit score"], 30.1) self.assertEqual( str(alignment), """\ OCDHPR 2302 ?????????????????-?????? 2325 0 |||||||||||||||||-|||||| 24 pGT875 265 ???????????????????????? 289 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[2302, 2319, 2319, 2325], [ 265, 282, 283, 289]]) # fmt: on ) ) query = self.query target = self.targets[alignment.sequences[0].id] self.assertEqual(len(alignment.sequences[0].seq), 2325) self.assertEqual(len(alignment.sequences[1].seq), len(query)) alignment.sequences[0].seq = target alignment.sequences[1].seq = query self.assertEqual(alignment[0], "AGACAGAGGAGGAGAAG-TCTGTG") self.assertEqual(alignment[1], "AGACAGAGGAGGAGAGGATCCGTG") # pGT875 RABALP1A self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['A', 'G', 'A', 'C', 'A', 'G', 'A', 'G', 'G', 'A', 'G', 'G', 'A', 'G', 'A', 'A', 'G', '-', 'T', 'C', 'T', 'G', 'T', 'G'], ['A', 'G', 'A', 'C', 'A', 'G', 'A', 'G', 'G', 'A', 'G', 'G', 'A', 'G', 'A', 'G', 'G', 'A', 'T', 'C', 'C', 'G', 'T', 'G']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertEqual(len(alignment), 2) self.assertAlmostEqual(alignment.annotations["% identity"], 76.19) self.assertEqual(alignment.annotations["gap opens"], 4) aligned = alignment.aligned self.assertEqual(sum(end - start for start, end in aligned[0]), 42) self.assertEqual(sum(end - start for start, end in aligned[1]), 42) self.assertEqual(alignment.shape, (2, 42 + 4)) self.assertEqual(alignment.sequences[0].id, "RABALP1A") self.assertEqual(alignment.sequences[1].id, "pGT875") self.assertEqual(alignment.annotations["mismatches"], 10) self.assertAlmostEqual(alignment.annotations["evalue"], 0.036) self.assertAlmostEqual(alignment.annotations["bit score"], 28.1) self.assertEqual( str(alignment), """\ RABALP1A 4973 ??????????????--???-?????????????????????????? 5016 0 ||||||||||||||--|||-||||||||||||-||||||||||||| 46 pGT875 240 ????????????????????????????????-????????????? 285 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[4973, 4987, 4987, 4990, 4990, 5002, 5003, 5016], [ 240, 254, 256, 259, 260, 272, 272, 285]]) # fmt: on ) ) query = self.query target = self.targets[alignment.sequences[0].id] self.assertEqual(len(alignment.sequences[0].seq), 5016) self.assertEqual(len(alignment.sequences[1].seq), len(query)) alignment.sequences[0].seq = target alignment.sequences[1].seq = query self.assertEqual(alignment[0], "GCTGGAGAGAGCCA--TGG-TGGAGGCTGCGATGGAGGAGAGGATC") self.assertEqual(alignment[1], "GCCCGAAAGCACCACCTGGATGGAGAGACAGA-GGAGGAGAGGATC") # pGT875 OCDHPR self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['G', 'C', 'T', 'G', 'G', 'A', 'G', 'A', 'G', 'A', 'G', 'C', 'C', 'A', '-', '-', 'T', 'G', 'G', '-', 'T', 'G', 'G', 'A', 'G', 'G', 'C', 'T', 'G', 'C', 'G', 'A', 'T', 'G', 'G', 'A', 'G', 'G', 'A', 'G', 'A', 'G', 'G', 'A', 'T', 'C'], ['G', 'C', 'C', 'C', 'G', 'A', 'A', 'A', 'G', 'C', 'A', 'C', 'C', 'A', 'C', 'C', 'T', 'G', 'G', 'A', 'T', 'G', 'G', 'A', 'G', 'A', 'G', 'A', 'C', 'A', 'G', 'A', '-', 'G', 'G', 'A', 'G', 'G', 'A', 'G', 'A', 'G', 'G', 'A', 'T', 'C']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertEqual(len(alignment), 2) self.assertAlmostEqual(alignment.annotations["% identity"], 100.00) self.assertEqual(alignment.annotations["gap opens"], 0) aligned = alignment.aligned self.assertEqual(sum(end - start for start, end in aligned[0]), 12) self.assertEqual(sum(start - end for start, end in aligned[1]), 12) self.assertEqual(alignment.shape, (2, 12 + 0)) self.assertEqual(alignment.sequences[0].id, "OCDHPR") self.assertEqual(alignment.sequences[1].id, "pGT875") self.assertEqual(alignment.annotations["mismatches"], 0) self.assertAlmostEqual(alignment.annotations["evalue"], 0.071) self.assertAlmostEqual(alignment.annotations["bit score"], 27.2) self.assertEqual( str(alignment), """\ OCDHPR 1499 ???????????? 1511 0 |||||||||||| 12 pGT875 316 ???????????? 304 """, ) self.assertTrue( np.array_equal( alignment.coordinates, np.array([[1499, 1511], [316, 304]]), ) ) query = self.query target = self.targets[alignment.sequences[0].id] self.assertEqual(len(alignment.sequences[0].seq), 1511) self.assertEqual(len(alignment.sequences[1].seq), len(query)) alignment.sequences[0].seq = target alignment.sequences[1].seq = query self.assertEqual(alignment[0], "CCATGACCTGGT") self.assertEqual(alignment[1], "CCATGACCTGGT") # pGT875 RABALP1A self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['C', 'C', 'A', 'T', 'G', 'A', 'C', 'C', 'T', 'G', 'G', 'T'], ['C', 'C', 'A', 'T', 'G', 'A', 'C', 'C', 'T', 'G', 'G', 'T']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertEqual(len(alignment), 2) self.assertAlmostEqual(alignment.annotations["% identity"], 100.00) self.assertEqual(alignment.annotations["gap opens"], 0) aligned = alignment.aligned self.assertEqual(sum(end - start for start, end in aligned[0]), 12) self.assertEqual(sum(start - end for start, end in aligned[1]), 12) self.assertEqual(alignment.shape, (2, 12 + 0)) self.assertEqual(alignment.sequences[0].id, "RABALP1A") self.assertEqual(alignment.sequences[1].id, "pGT875") self.assertEqual(alignment.annotations["mismatches"], 0) self.assertAlmostEqual(alignment.annotations["evalue"], 0.071) self.assertAlmostEqual(alignment.annotations["bit score"], 27.2) self.assertEqual( str(alignment), """\ RABALP1A 1499 ???????????? 1511 0 |||||||||||| 12 pGT875 316 ???????????? 304 """, ) self.assertTrue( np.array_equal( alignment.coordinates, np.array([[1499, 1511], [316, 304]]), ) ) query = self.query target = self.targets[alignment.sequences[0].id] self.assertEqual(len(alignment.sequences[0].seq), 1511) self.assertEqual(len(alignment.sequences[1].seq), len(query)) alignment.sequences[0].seq = target alignment.sequences[1].seq = query self.assertEqual(alignment[0], "CCATGACCTGGT") self.assertEqual(alignment[1], "CCATGACCTGGT") # pGT875 RABGSTB self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['C', 'C', 'A', 'T', 'G', 'A', 'C', 'C', 'T', 'G', 'G', 'T'], ['C', 'C', 'A', 'T', 'G', 'A', 'C', 'C', 'T', 'G', 'G', 'T']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertEqual(len(alignment), 2) self.assertAlmostEqual(alignment.annotations["% identity"], 87.50) self.assertEqual(alignment.annotations["gap opens"], 0) aligned = alignment.aligned self.assertEqual(sum(end - start for start, end in aligned[0]), 16) self.assertEqual(sum(start - end for start, end in aligned[1]), 16) self.assertEqual(alignment.shape, (2, 16 + 0)) self.assertEqual(alignment.sequences[0].id, "RABGSTB") self.assertEqual(alignment.sequences[1].id, "pGT875") self.assertEqual(alignment.annotations["mismatches"], 2) self.assertAlmostEqual(alignment.annotations["evalue"], 0.14) self.assertAlmostEqual(alignment.annotations["bit score"], 26.2) self.assertEqual( str(alignment), """\ RABGSTB 490 ???????????????? 506 0 |||||||||||||||| 16 pGT875 160 ???????????????? 144 """, ) self.assertTrue( np.array_equal( alignment.coordinates, np.array([[490, 506], [160, 144]]), ) ) query = self.query target = self.targets[alignment.sequences[0].id] self.assertEqual(len(alignment.sequences[0].seq), 506) self.assertEqual(len(alignment.sequences[1].seq), len(query)) alignment.sequences[0].seq = target alignment.sequences[1].seq = query self.assertEqual(alignment[0], "CCTGGTTGAACTTCTC") self.assertEqual(alignment[1], "CCAGCTTGAACTTCTC") # pGT875 RABGLTR self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['C', 'C', 'T', 'G', 'G', 'T', 'T', 'G', 'A', 'A', 'C', 'T', 'T', 'C', 'T', 'C'], ['C', 'C', 'A', 'G', 'C', 'T', 'T', 'G', 'A', 'A', 'C', 'T', 'T', 'C', 'T', 'C']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertEqual(len(alignment), 2) self.assertAlmostEqual(alignment.annotations["% identity"], 53.57) self.assertEqual(alignment.annotations["gap opens"], 0) aligned = alignment.aligned self.assertEqual(sum(end - start for start, end in aligned[0]), 84) self.assertEqual(sum(start - end for start, end in aligned[1]), 84) self.assertEqual(alignment.shape, (2, 84 + 0)) self.assertEqual(alignment.sequences[0].id, "RABGLTR") self.assertEqual(alignment.sequences[1].id, "pGT875") self.assertEqual(alignment.annotations["mismatches"], 39) self.assertAlmostEqual(alignment.annotations["evalue"], 0.28) self.assertAlmostEqual(alignment.annotations["bit score"], 25.2) self.assertEqual( str(alignment), """\ RABGLTR 1116 ???????????????????????????????????????????????????????????? 0 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| pGT875 242 ???????????????????????????????????????????????????????????? RABGLTR 1176 ???????????????????????? 1200 60 |||||||||||||||||||||||| 84 pGT875 182 ???????????????????????? 158 """, ) self.assertTrue( np.array_equal( alignment.coordinates, np.array([[1116, 1200], [242, 158]]), ) ) query = self.query target = self.targets[alignment.sequences[0].id] self.assertEqual(len(alignment.sequences[0].seq), 1200) self.assertEqual(len(alignment.sequences[1].seq), len(query)) alignment.sequences[0].seq = target alignment.sequences[1].seq = query self.assertEqual( alignment[0], "GCATGGCTGGGTGGGGCAGGATTAGTGTGGGGGGAGTTGGGTGCTCAGGCAGGGCTATGAGGGATCTTGTTCATTTCCGGGCCC", ) self.assertEqual( alignment[1], "GCAAGGTAGCGCAGGATGGCATTGCTCTGGGTGATCTTGTGTGATCCATCGATCAAGTAAGGCAGATTGGGAAAGTCCAGGCCC", ) # pGT875 pGT875 self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['G', 'C', 'A', 'T', 'G', 'G', 'C', 'T', 'G', 'G', 'G', 'T', 'G', 'G', 'G', 'G', 'C', 'A', 'G', 'G', 'A', 'T', 'T', 'A', 'G', 'T', 'G', 'T', 'G', 'G', 'G', 'G', 'G', 'G', 'A', 'G', 'T', 'T', 'G', 'G', 'G', 'T', 'G', 'C', 'T', 'C', 'A', 'G', 'G', 'C', 'A', 'G', 'G', 'G', 'C', 'T', 'A', 'T', 'G', 'A', 'G', 'G', 'G', 'A', 'T', 'C', 'T', 'T', 'G', 'T', 'T', 'C', 'A', 'T', 'T', 'T', 'C', 'C', 'G', 'G', 'G', 'C', 'C', 'C'], ['G', 'C', 'A', 'A', 'G', 'G', 'T', 'A', 'G', 'C', 'G', 'C', 'A', 'G', 'G', 'A', 'T', 'G', 'G', 'C', 'A', 'T', 'T', 'G', 'C', 'T', 'C', 'T', 'G', 'G', 'G', 'T', 'G', 'A', 'T', 'C', 'T', 'T', 'G', 'T', 'G', 'T', 'G', 'A', 'T', 'C', 'C', 'A', 'T', 'C', 'G', 'A', 'T', 'C', 'A', 'A', 'G', 'T', 'A', 'A', 'G', 'G', 'C', 'A', 'G', 'A', 'T', 'T', 'G', 'G', 'G', 'A', 'A', 'A', 'G', 'T', 'C', 'C', 'A', 'G', 'G', 'C', 'C', 'C']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertEqual(len(alignment), 2) self.assertAlmostEqual(alignment.annotations["% identity"], 100.00) self.assertEqual(alignment.annotations["gap opens"], 0) aligned = alignment.aligned self.assertEqual(sum(end - start for start, end in aligned[0]), 10) self.assertEqual(sum(start - end for start, end in aligned[1]), 10) self.assertEqual(alignment.shape, (2, 10 + 0)) self.assertEqual(alignment.sequences[0].id, "pGT875") self.assertEqual(alignment.sequences[1].id, "pGT875") self.assertEqual(alignment.annotations["mismatches"], 0) self.assertAlmostEqual(alignment.annotations["evalue"], 0.28) self.assertAlmostEqual(alignment.annotations["bit score"], 25.2) self.assertEqual( str(alignment), """\ pGT875 792 ?????????? 802 0 |||||||||| 10 pGT875 310 ?????????? 300 """, ) self.assertTrue( np.array_equal( alignment.coordinates, np.array([[792, 802], [310, 300]]), ) ) query = self.query target = self.targets[alignment.sequences[0].id] self.assertEqual(len(alignment.sequences[0].seq), 802) self.assertEqual(len(alignment.sequences[1].seq), len(query)) alignment.sequences[0].seq = target alignment.sequences[1].seq = query self.assertEqual(alignment[0], "CCTGGTTCTC") self.assertEqual(alignment[1], "CCTGGTTCTC") # pGT875 BTGST self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['C', 'C', 'T', 'G', 'G', 'T', 'T', 'C', 'T', 'C'], ['C', 'C', 'T', 'G', 'G', 'T', 'T', 'C', 'T', 'C']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertEqual(len(alignment), 2) self.assertAlmostEqual(alignment.annotations["% identity"], 59.15) self.assertEqual(alignment.annotations["gap opens"], 3) aligned = alignment.aligned self.assertEqual(sum(end - start for start, end in aligned[0]), 71) self.assertEqual(sum(start - end for start, end in aligned[1]), 71) self.assertEqual(alignment.shape, (2, 71 + 3)) self.assertEqual(alignment.sequences[0].id, "BTGST") self.assertEqual(alignment.sequences[1].id, "pGT875") self.assertEqual(alignment.annotations["mismatches"], 29) self.assertAlmostEqual(alignment.annotations["evalue"], 0.56) self.assertAlmostEqual(alignment.annotations["bit score"], 24.2) self.assertEqual( str(alignment), """\ BTGST 280 ????????????????????????-????????--????????????????????????? 0 ||||||||||||||||||||||||-||||||||--||||||||||||||||||||||||| pGT875 378 ???????????????????????????????????????????????????????????? BTGST 337 ?????????????? 351 60 |||||||||||||| 74 pGT875 318 ?????????????? 304 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[280, 304, 304, 312, 312, 351], [378, 354, 353, 345, 343, 304]]) # fmt: on ) ) query = self.query target = self.targets[alignment.sequences[0].id] self.assertEqual(len(alignment.sequences[0].seq), 351) self.assertEqual(len(alignment.sequences[1].seq), len(query)) alignment.sequences[0].seq = target alignment.sequences[1].seq = query self.assertEqual( alignment[0], "CTGCGGCACCTGGGCCGCACCCTC-GGGCTGTA--TGGGAAGGACCAGCAGGAGGCGGCCCTGGTGGACATGGT", ) self.assertEqual( alignment[1], "CTCTGGCTTCTGCTTCTCAAAGTCAGGGTTGTAACAGAGCATGATGAGCTGCATGCGGGTGTCCATGACCTGGT", ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['C', 'T', 'G', 'C', 'G', 'G', 'C', 'A', 'C', 'C', 'T', 'G', 'G', 'G', 'C', 'C', 'G', 'C', 'A', 'C', 'C', 'C', 'T', 'C', '-', 'G', 'G', 'G', 'C', 'T', 'G', 'T', 'A', '-', '-', 'T', 'G', 'G', 'G', 'A', 'A', 'G', 'G', 'A', 'C', 'C', 'A', 'G', 'C', 'A', 'G', 'G', 'A', 'G', 'G', 'C', 'G', 'G', 'C', 'C', 'C', 'T', 'G', 'G', 'T', 'G', 'G', 'A', 'C', 'A', 'T', 'G', 'G', 'T'], ['C', 'T', 'C', 'T', 'G', 'G', 'C', 'T', 'T', 'C', 'T', 'G', 'C', 'T', 'T', 'C', 'T', 'C', 'A', 'A', 'A', 'G', 'T', 'C', 'A', 'G', 'G', 'G', 'T', 'T', 'G', 'T', 'A', 'A', 'C', 'A', 'G', 'A', 'G', 'C', 'A', 'T', 'G', 'A', 'T', 'G', 'A', 'G', 'C', 'T', 'G', 'C', 'A', 'T', 'G', 'C', 'G', 'G', 'G', 'T', 'G', 'T', 'C', 'C', 'A', 'T', 'G', 'A', 'C', 'C', 'T', 'G', 'G', 'T']], dtype='U') # fmt: on ) ) with self.assertRaises(StopIteration): next(alignments) def test_m8CC(self): # Alignment file obtained by running # fasta36 -m 8CC seq/mgstm1.nt seq/gst.nlib # in the fasta36 source distribution path = "Fasta/nucleotide_m8CC.txt" alignments = Align.parse(path, "tabular") self.assertEqual( alignments.metadata["Command line"], "fasta36 -m 8CC seq/mgstm1.nt seq/gst.nlib", ) self.assertEqual(alignments.metadata["Program"], "FASTA") self.assertEqual(alignments.metadata["Version"], "36.3.8h May, 2020") self.assertEqual(alignments.metadata["Database"], "seq/gst.nlib") # pGT875 pGT875 alignment = next(alignments) self.assertEqual(len(alignment), 2) self.assertAlmostEqual(alignment.annotations["% identity"], 100.00) self.assertEqual(alignment.annotations["gap opens"], 0) aligned = alignment.aligned self.assertEqual(sum(end - start for start, end in aligned[0]), 657) self.assertEqual(sum(end - start for start, end in aligned[1]), 657) self.assertEqual(alignment.shape, (2, 657 + 0)) self.assertEqual(alignment.sequences[0].id, "pGT875") self.assertEqual(alignment.sequences[1].id, "pGT875") self.assertEqual(alignment.annotations["mismatches"], 0) self.assertAlmostEqual(alignment.annotations["evalue"], 4.6e-191, places=192) self.assertAlmostEqual(alignment.annotations["bit score"], 655.6) self.assertEqual( str(alignment), """\ pGT875 37 ???????????????????????????????????????????????????????????? 0 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| pGT875 0 ???????????????????????????????????????????????????????????? pGT875 97 ???????????????????????????????????????????????????????????? 60 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| pGT875 60 ???????????????????????????????????????????????????????????? pGT875 157 ???????????????????????????????????????????????????????????? 120 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| pGT875 120 ???????????????????????????????????????????????????????????? pGT875 217 ???????????????????????????????????????????????????????????? 180 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| pGT875 180 ???????????????????????????????????????????????????????????? pGT875 277 ???????????????????????????????????????????????????????????? 240 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| pGT875 240 ???????????????????????????????????????????????????????????? pGT875 337 ???????????????????????????????????????????????????????????? 300 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| pGT875 300 ???????????????????????????????????????????????????????????? pGT875 397 ???????????????????????????????????????????????????????????? 360 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| pGT875 360 ???????????????????????????????????????????????????????????? pGT875 457 ???????????????????????????????????????????????????????????? 420 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| pGT875 420 ???????????????????????????????????????????????????????????? pGT875 517 ???????????????????????????????????????????????????????????? 480 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| pGT875 480 ???????????????????????????????????????????????????????????? pGT875 577 ???????????????????????????????????????????????????????????? 540 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| pGT875 540 ???????????????????????????????????????????????????????????? pGT875 637 ????????????????????????????????????????????????????????? 694 600 ||||||||||||||||||||||||||||||||||||||||||||||||||||||||| 657 pGT875 600 ????????????????????????????????????????????????????????? 657 """, ) self.assertTrue( np.array_equal( alignment.coordinates, np.array([[37, 694], [0, 657]]), ) ) query = self.query target = self.targets[alignment.sequences[0].id] self.assertEqual(len(alignment.sequences[0].seq), 694) self.assertEqual(len(alignment.sequences[1].seq), len(query)) alignment.sequences[0].seq = target alignment.sequences[1].seq = query self.assertEqual( alignment[0], "ATGCCTATGATACTGGGATACTGGAACGTCCGCGGACTGACACACCCGATCCGCATGCTCCTGGAATACACAGACTCAAGCTATGATGAGAAGAGATACACCATGGGTGACGCTCCCGACTTTGACAGAAGCCAGTGGCTGAATGAGAAGTTCAAGCTGGGCCTGGACTTTCCCAATCTGCCTTACTTGATCGATGGATCACACAAGATCACCCAGAGCAATGCCATCCTGCGCTACCTTGCCCGAAAGCACCACCTGGATGGAGAGACAGAGGAGGAGAGGATCCGTGCAGACATTGTGGAGAACCAGGTCATGGACACCCGCATGCAGCTCATCATGCTCTGTTACAACCCTGACTTTGAGAAGCAGAAGCCAGAGTTCTTGAAGACCATCCCTGAGAAAATGAAGCTCTACTCTGAGTTCCTGGGCAAGAGGCCATGGTTTGCAGGGGACAAGGTCACCTATGTGGATTTCCTTGCTTATGACATTCTTGACCAGTACCGTATGTTTGAGCCCAAGTGCCTGGACGCCTTCCCAAACCTGAGGGACTTCCTGGCCCGCTTCGAGGGCCTCAAGAAGATCTCTGCCTACATGAAGAGTAGCCGCTACATCGCAACACCTATATTTTCAAAGATGGCCCACTGGAGTAACAAGTAG", ) self.assertEqual( alignment[1], "ATGCCTATGATACTGGGATACTGGAACGTCCGCGGACTGACACACCCGATCCGCATGCTCCTGGAATACACAGACTCAAGCTATGATGAGAAGAGATACACCATGGGTGACGCTCCCGACTTTGACAGAAGCCAGTGGCTGAATGAGAAGTTCAAGCTGGGCCTGGACTTTCCCAATCTGCCTTACTTGATCGATGGATCACACAAGATCACCCAGAGCAATGCCATCCTGCGCTACCTTGCCCGAAAGCACCACCTGGATGGAGAGACAGAGGAGGAGAGGATCCGTGCAGACATTGTGGAGAACCAGGTCATGGACACCCGCATGCAGCTCATCATGCTCTGTTACAACCCTGACTTTGAGAAGCAGAAGCCAGAGTTCTTGAAGACCATCCCTGAGAAAATGAAGCTCTACTCTGAGTTCCTGGGCAAGAGGCCATGGTTTGCAGGGGACAAGGTCACCTATGTGGATTTCCTTGCTTATGACATTCTTGACCAGTACCGTATGTTTGAGCCCAAGTGCCTGGACGCCTTCCCAAACCTGAGGGACTTCCTGGCCCGCTTCGAGGGCCTCAAGAAGATCTCTGCCTACATGAAGAGTAGCCGCTACATCGCAACACCTATATTTTCAAAGATGGCCCACTGGAGTAACAAGTAG", ) # pGT875 RABGLTR alignment = next(alignments) self.assertEqual(len(alignment), 2) self.assertAlmostEqual(alignment.annotations["% identity"], 79.10) self.assertEqual(alignment.annotations["gap opens"], 0) aligned = alignment.aligned self.assertEqual(sum(end - start for start, end in aligned[0]), 646) self.assertEqual(sum(end - start for start, end in aligned[1]), 646) self.assertEqual(alignment.shape, (2, 646 + 0)) self.assertEqual(alignment.sequences[0].id, "RABGLTR") self.assertEqual(alignment.sequences[1].id, "pGT875") self.assertEqual(alignment.annotations["mismatches"], 135) self.assertAlmostEqual(alignment.annotations["evalue"], 1.6e-116, places=117) self.assertAlmostEqual(alignment.annotations["bit score"], 408.0) self.assertEqual( str(alignment), """\ RABGLTR 33 ???????????????????????????????????????????????????????????? 0 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| pGT875 0 ???????????????????????????????????????????????????????????? RABGLTR 93 ???????????????????????????????????????????????????????????? 60 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| pGT875 60 ???????????????????????????????????????????????????????????? RABGLTR 153 ???????????????????????????????????????????????????????????? 120 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| pGT875 120 ???????????????????????????????????????????????????????????? RABGLTR 213 ???????????????????????????????????????????????????????????? 180 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| pGT875 180 ???????????????????????????????????????????????????????????? RABGLTR 273 ???????????????????????????????????????????????????????????? 240 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| pGT875 240 ???????????????????????????????????????????????????????????? RABGLTR 333 ???????????????????????????????????????????????????????????? 300 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| pGT875 300 ???????????????????????????????????????????????????????????? RABGLTR 393 ???????????????????????????????????????????????????????????? 360 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| pGT875 360 ???????????????????????????????????????????????????????????? RABGLTR 453 ???????????????????????????????????????????????????????????? 420 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| pGT875 420 ???????????????????????????????????????????????????????????? RABGLTR 513 ???????????????????????????????????????????????????????????? 480 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| pGT875 480 ???????????????????????????????????????????????????????????? RABGLTR 573 ???????????????????????????????????????????????????????????? 540 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| pGT875 540 ???????????????????????????????????????????????????????????? RABGLTR 633 ?????????????????????????????????????????????? 679 600 |||||||||||||||||||||||||||||||||||||||||||||| 646 pGT875 600 ?????????????????????????????????????????????? 646 """, ) self.assertTrue( np.array_equal( alignment.coordinates, np.array([[33, 679], [0, 646]]), ) ) query = self.query target = self.targets[alignment.sequences[0].id] self.assertEqual(len(alignment.sequences[0].seq), 679) self.assertEqual(len(alignment.sequences[1].seq), len(query)) alignment.sequences[0].seq = target alignment.sequences[1].seq = query self.assertEqual( alignment[0], "ATGCCCATGACGCTGGGTTACTGGGACGTCCGTGGGCTGGCTCTGCCAATCCGCATGCTCCTGGAATACACGGACACCAGCTATGAGGAAAAGAAATACACCATGGGGGATGCTCCCAACTATGACCAAAGCAAGTGGCTGAGTGAGAAGTTCACCCTGGGCCTGGACTTTCCCAATCTGCCCTACCTAATTGATGGGACTCACAAGCTCACGCAGAGCAACGCCATCCTGCGCTACCTGGCCCGCAAGCACGGCCTGTGTGGGGAGACGGAAGAGGAGAGGATTCGCGTGGACATTCTGGAGAATCAGCTGATGGACAACCGCTTCCAACTTGTAAACGTCTGCTACAGTCCCGACTTTGAGAAGCTCAAGCCCGAGTACCTGAAGGGGCTCCCTGAGAAGCTGCAGCTGTACTCGCAGTTCCTGGGAAGCCTCCCCTGGTTCGCAGGGGACAAGATCACCTTCGCCGATTTCCTTGTCTACGACGTTCTTGACCAGAACCGGATATTTGTGCCTGGGTGCCTGGACGCGTTCCCAAACCTGAAGGACTTTCATGTCCGCTTTGAGGGCCTGCCGAAGATCTCTGCCTACATGAAGTCCAGCCGCTTTATCCGAGTCCCTGTGTTTTTAAAGAAGGCCACGTGGA", ) self.assertEqual( alignment[1], "ATGCCTATGATACTGGGATACTGGAACGTCCGCGGACTGACACACCCGATCCGCATGCTCCTGGAATACACAGACTCAAGCTATGATGAGAAGAGATACACCATGGGTGACGCTCCCGACTTTGACAGAAGCCAGTGGCTGAATGAGAAGTTCAAGCTGGGCCTGGACTTTCCCAATCTGCCTTACTTGATCGATGGATCACACAAGATCACCCAGAGCAATGCCATCCTGCGCTACCTTGCCCGAAAGCACCACCTGGATGGAGAGACAGAGGAGGAGAGGATCCGTGCAGACATTGTGGAGAACCAGGTCATGGACACCCGCATGCAGCTCATCATGCTCTGTTACAACCCTGACTTTGAGAAGCAGAAGCCAGAGTTCTTGAAGACCATCCCTGAGAAAATGAAGCTCTACTCTGAGTTCCTGGGCAAGAGGCCATGGTTTGCAGGGGACAAGGTCACCTATGTGGATTTCCTTGCTTATGACATTCTTGACCAGTACCGTATGTTTGAGCCCAAGTGCCTGGACGCCTTCCCAAACCTGAGGGACTTCCTGGCCCGCTTCGAGGGCCTCAAGAAGATCTCTGCCTACATGAAGAGTAGCCGCTACATCGCAACACCTATATTTTCAAAGATGGCCCACTGGA", ) # pGT875 BTGST alignment = next(alignments) self.assertEqual(len(alignment), 2) self.assertAlmostEqual(alignment.annotations["% identity"], 59.56) self.assertEqual(alignment.annotations["gap opens"], 21) aligned = alignment.aligned self.assertEqual(sum(end - start for start, end in aligned[0]), 413) self.assertEqual(sum(end - start for start, end in aligned[1]), 413) self.assertEqual(alignment.shape, (2, 413 + 21)) self.assertEqual(alignment.sequences[0].id, "BTGST") self.assertEqual(alignment.sequences[1].id, "pGT875") self.assertEqual(alignment.annotations["mismatches"], 167) self.assertAlmostEqual(alignment.annotations["evalue"], 1.9e-07, places=8) self.assertAlmostEqual(alignment.annotations["bit score"], 45.7) self.assertEqual( str(alignment), """\ BTGST 227 ???????????????????????????????????????????????????????????? 0 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| pGT875 175 ???????????????????????????????????????????????????????????? BTGST 287 ???????????????????????????????????????????????????????????? 60 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| pGT875 235 ???????????????????????????????????????????????????????????? BTGST 347 ?????????????????????????????-?????????????????????????---?? 120 |||||||||||||||||||||||||||||-|||||||-|||||||||||||||||---|| pGT875 295 ?????????????????????????????????????-?????????????????????? BTGST 403 ???????????????????????????????????????????????????????????? 180 ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||-- pGT875 354 ??????????????????????????????????????????????????????????-- BTGST 463 ???????????????????????????????????????????????????????????? 240 ---||||||-|||||||||||||--|||||||||||||----|||||||||||||||||| pGT875 412 ---??????-?????????????--?????????????----?????????????????? BTGST 523 ????????????????????--?????????????????????????????????????? 300 ||||||||||||--||||||--|||||||||||||||||||||||||||||||||||||| pGT875 462 ????????????--?????????????????????????????????????????????? BTGST 581 ???????????????????????????????????????????????????????????? 360 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| pGT875 520 ???????????????????????????????????????????????????????????? BTGST 641 ?????????????? 655 420 |||||||||||||| 434 pGT875 580 ?????????????? 594 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[227, 376, 376, 383, 384, 401, 401, 461, 466, 472, 473, 486, 488, 501, 505, 535, 537, 543, 543, 655], [175, 324, 325, 332, 332, 349, 352, 412, 412, 418, 418, 431, 431, 444, 444, 474, 474, 480, 482, 594]]) # fmt: on ) ) query = self.query target = self.targets[alignment.sequences[0].id] self.assertEqual(len(alignment.sequences[0].seq), 655) self.assertEqual(len(alignment.sequences[1].seq), len(query)) alignment.sequences[0].seq = target alignment.sequences[1].seq = query self.assertEqual( alignment[0], "AGCTCCCCAAGTTCCAGGACGGAGACCTCACGCTGTACCAGTCCAATGCCATCCTGCGGCACCTGGGCCGCACCCTCGGGCTGTATGGGAAGGACCAGCAGGAGGCGGCCCTGGTGGACATGGTGAATGACGGTGTAGAGGACCTTCGC-TGCAAATACGTCTCCCTCATTTACA---CCAACTACGAGGCGGGCAAGGAGGACTATGTGAAGGCGCTGCCCCAGCACCTGAAGCCTTTCGAGACCCTGCTGTCCCAGAACAAGGGTGGCCAGGCCTTCATCGTGGGCGACCAGATCTCCTTTGCGGACTACAACCTGCT--GGACCTGCTTCGGATTCACCAGGTCCTGGCCCCCAGCTGTCTGGACTCCTTCCCCCTGCTCTCAGCCTACGTGGCCCGTCTCAACTCCCGGCCCAAGCTCAAGGCCTTCCTG", ) self.assertEqual( alignment[1], "ATCTGCCTTACTTGATCGATGGATCACACAAGATCACCCAGAGCAATGCCATCCTGCGCTACCTTGCCCGAAAGCACCACCTGGATGGAGAGACAGAGGAGGAGAGGATCCGTGCAGACATTGTGGAGAACCAGGTCATGGACACCCGCATGCAGCT-CATCATGCTCTGTTACAACCCTGACTTTGAGAAGCAGAAGCCAGAGTTCTTGAAGACCATCCCTGAGAAAATGAAGCTCT-----ACTCTG-AGTTCCTGGGCAA--GAGGCCATGGTTT----GCAGGGGACAAGGTCACCTATGTGGATTTC--CTTGCTTATGACATTCTTGACCAGTACCGTATGTTTGAGCCCAAGTGCCTGGACGCCTTCCCAAACCTGAGGGACTTCCTGGCCCGCTTCGAGGGCCTCAAGAAGATCTCTGCCTACATG", ) # pGT875 RABGSTB self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['A', 'G', 'C', 'T', 'C', 'C', 'C', 'C', 'A', 'A', 'G', 'T', 'T', 'C', 'C', 'A', 'G', 'G', 'A', 'C', 'G', 'G', 'A', 'G', 'A', 'C', 'C', 'T', 'C', 'A', 'C', 'G', 'C', 'T', 'G', 'T', 'A', 'C', 'C', 'A', 'G', 'T', 'C', 'C', 'A', 'A', 'T', 'G', 'C', 'C', 'A', 'T', 'C', 'C', 'T', 'G', 'C', 'G', 'G', 'C', 'A', 'C', 'C', 'T', 'G', 'G', 'G', 'C', 'C', 'G', 'C', 'A', 'C', 'C', 'C', 'T', 'C', 'G', 'G', 'G', 'C', 'T', 'G', 'T', 'A', 'T', 'G', 'G', 'G', 'A', 'A', 'G', 'G', 'A', 'C', 'C', 'A', 'G', 'C', 'A', 'G', 'G', 'A', 'G', 'G', 'C', 'G', 'G', 'C', 'C', 'C', 'T', 'G', 'G', 'T', 'G', 'G', 'A', 'C', 'A', 'T', 'G', 'G', 'T', 'G', 'A', 'A', 'T', 'G', 'A', 'C', 'G', 'G', 'T', 'G', 'T', 'A', 'G', 'A', 'G', 'G', 'A', 'C', 'C', 'T', 'T', 'C', 'G', 'C', '-', 'T', 'G', 'C', 'A', 'A', 'A', 'T', 'A', 'C', 'G', 'T', 'C', 'T', 'C', 'C', 'C', 'T', 'C', 'A', 'T', 'T', 'T', 'A', 'C', 'A', '-', '-', '-', 'C', 'C', 'A', 'A', 'C', 'T', 'A', 'C', 'G', 'A', 'G', 'G', 'C', 'G', 'G', 'G', 'C', 'A', 'A', 'G', 'G', 'A', 'G', 'G', 'A', 'C', 'T', 'A', 'T', 'G', 'T', 'G', 'A', 'A', 'G', 'G', 'C', 'G', 'C', 'T', 'G', 'C', 'C', 'C', 'C', 'A', 'G', 'C', 'A', 'C', 'C', 'T', 'G', 'A', 'A', 'G', 'C', 'C', 'T', 'T', 'T', 'C', 'G', 'A', 'G', 'A', 'C', 'C', 'C', 'T', 'G', 'C', 'T', 'G', 'T', 'C', 'C', 'C', 'A', 'G', 'A', 'A', 'C', 'A', 'A', 'G', 'G', 'G', 'T', 'G', 'G', 'C', 'C', 'A', 'G', 'G', 'C', 'C', 'T', 'T', 'C', 'A', 'T', 'C', 'G', 'T', 'G', 'G', 'G', 'C', 'G', 'A', 'C', 'C', 'A', 'G', 'A', 'T', 'C', 'T', 'C', 'C', 'T', 'T', 'T', 'G', 'C', 'G', 'G', 'A', 'C', 'T', 'A', 'C', 'A', 'A', 'C', 'C', 'T', 'G', 'C', 'T', '-', '-', 'G', 'G', 'A', 'C', 'C', 'T', 'G', 'C', 'T', 'T', 'C', 'G', 'G', 'A', 'T', 'T', 'C', 'A', 'C', 'C', 'A', 'G', 'G', 'T', 'C', 'C', 'T', 'G', 'G', 'C', 'C', 'C', 'C', 'C', 'A', 'G', 'C', 'T', 'G', 'T', 'C', 'T', 'G', 'G', 'A', 'C', 'T', 'C', 'C', 'T', 'T', 'C', 'C', 'C', 'C', 'C', 'T', 'G', 'C', 'T', 'C', 'T', 'C', 'A', 'G', 'C', 'C', 'T', 'A', 'C', 'G', 'T', 'G', 'G', 'C', 'C', 'C', 'G', 'T', 'C', 'T', 'C', 'A', 'A', 'C', 'T', 'C', 'C', 'C', 'G', 'G', 'C', 'C', 'C', 'A', 'A', 'G', 'C', 'T', 'C', 'A', 'A', 'G', 'G', 'C', 'C', 'T', 'T', 'C', 'C', 'T', 'G'], ['A', 'T', 'C', 'T', 'G', 'C', 'C', 'T', 'T', 'A', 'C', 'T', 'T', 'G', 'A', 'T', 'C', 'G', 'A', 'T', 'G', 'G', 'A', 'T', 'C', 'A', 'C', 'A', 'C', 'A', 'A', 'G', 'A', 'T', 'C', 'A', 'C', 'C', 'C', 'A', 'G', 'A', 'G', 'C', 'A', 'A', 'T', 'G', 'C', 'C', 'A', 'T', 'C', 'C', 'T', 'G', 'C', 'G', 'C', 'T', 'A', 'C', 'C', 'T', 'T', 'G', 'C', 'C', 'C', 'G', 'A', 'A', 'A', 'G', 'C', 'A', 'C', 'C', 'A', 'C', 'C', 'T', 'G', 'G', 'A', 'T', 'G', 'G', 'A', 'G', 'A', 'G', 'A', 'C', 'A', 'G', 'A', 'G', 'G', 'A', 'G', 'G', 'A', 'G', 'A', 'G', 'G', 'A', 'T', 'C', 'C', 'G', 'T', 'G', 'C', 'A', 'G', 'A', 'C', 'A', 'T', 'T', 'G', 'T', 'G', 'G', 'A', 'G', 'A', 'A', 'C', 'C', 'A', 'G', 'G', 'T', 'C', 'A', 'T', 'G', 'G', 'A', 'C', 'A', 'C', 'C', 'C', 'G', 'C', 'A', 'T', 'G', 'C', 'A', 'G', 'C', 'T', '-', 'C', 'A', 'T', 'C', 'A', 'T', 'G', 'C', 'T', 'C', 'T', 'G', 'T', 'T', 'A', 'C', 'A', 'A', 'C', 'C', 'C', 'T', 'G', 'A', 'C', 'T', 'T', 'T', 'G', 'A', 'G', 'A', 'A', 'G', 'C', 'A', 'G', 'A', 'A', 'G', 'C', 'C', 'A', 'G', 'A', 'G', 'T', 'T', 'C', 'T', 'T', 'G', 'A', 'A', 'G', 'A', 'C', 'C', 'A', 'T', 'C', 'C', 'C', 'T', 'G', 'A', 'G', 'A', 'A', 'A', 'A', 'T', 'G', 'A', 'A', 'G', 'C', 'T', 'C', 'T', '-', '-', '-', '-', '-', 'A', 'C', 'T', 'C', 'T', 'G', '-', 'A', 'G', 'T', 'T', 'C', 'C', 'T', 'G', 'G', 'G', 'C', 'A', 'A', '-', '-', 'G', 'A', 'G', 'G', 'C', 'C', 'A', 'T', 'G', 'G', 'T', 'T', 'T', '-', '-', '-', '-', 'G', 'C', 'A', 'G', 'G', 'G', 'G', 'A', 'C', 'A', 'A', 'G', 'G', 'T', 'C', 'A', 'C', 'C', 'T', 'A', 'T', 'G', 'T', 'G', 'G', 'A', 'T', 'T', 'T', 'C', '-', '-', 'C', 'T', 'T', 'G', 'C', 'T', 'T', 'A', 'T', 'G', 'A', 'C', 'A', 'T', 'T', 'C', 'T', 'T', 'G', 'A', 'C', 'C', 'A', 'G', 'T', 'A', 'C', 'C', 'G', 'T', 'A', 'T', 'G', 'T', 'T', 'T', 'G', 'A', 'G', 'C', 'C', 'C', 'A', 'A', 'G', 'T', 'G', 'C', 'C', 'T', 'G', 'G', 'A', 'C', 'G', 'C', 'C', 'T', 'T', 'C', 'C', 'C', 'A', 'A', 'A', 'C', 'C', 'T', 'G', 'A', 'G', 'G', 'G', 'A', 'C', 'T', 'T', 'C', 'C', 'T', 'G', 'G', 'C', 'C', 'C', 'G', 'C', 'T', 'T', 'C', 'G', 'A', 'G', 'G', 'G', 'C', 'C', 'T', 'C', 'A', 'A', 'G', 'A', 'A', 'G', 'A', 'T', 'C', 'T', 'C', 'T', 'G', 'C', 'C', 'T', 'A', 'C', 'A', 'T', 'G']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertEqual(len(alignment), 2) self.assertAlmostEqual(alignment.annotations["% identity"], 66.93) self.assertEqual(alignment.annotations["gap opens"], 8) aligned = alignment.aligned self.assertEqual(sum(end - start for start, end in aligned[0]), 127) self.assertEqual(sum(end - start for start, end in aligned[1]), 127) self.assertEqual(alignment.shape, (2, 127 + 8)) self.assertEqual(alignment.sequences[0].id, "RABGSTB") self.assertEqual(alignment.sequences[1].id, "pGT875") self.assertEqual(alignment.annotations["mismatches"], 42) self.assertAlmostEqual(alignment.annotations["evalue"], 3.2e-07, places=8) self.assertAlmostEqual(alignment.annotations["bit score"], 45.0) self.assertEqual( str(alignment), """\ RABGSTB 156 ??????????????????????????????????--???????????????????????? 0 |||||||||||||||--|||||||||||||||||--|||||||||||-|||||||||||| pGT875 158 ???????????????--??????????????????????????????-???????????? RABGSTB 214 ??????????????????????????????????????????????????????????-? 60 ||||||||||||||||||||||||||||||||||||||||||||||-|||||||||||-| pGT875 215 ??????????????????????????????????????????????-????????????? RABGSTB 273 ??????-???????? 287 120 ||||||-|||||||| 135 pGT875 274 ??????????????? 289 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[156, 171, 173, 190, 190, 201, 202, 260, 261, 272, 272, 279, 279, 287], [158, 173, 173, 190, 192, 203, 203, 261, 261, 272, 273, 280, 281, 289]]) # fmt: on ) ) query = self.query target = self.targets[alignment.sequences[0].id] self.assertEqual(len(alignment.sequences[0].seq), 287) self.assertEqual(len(alignment.sequences[1].seq), len(query)) alignment.sequences[0].seq = target alignment.sequences[1].seq = query self.assertEqual( alignment[0], "GGGTATTGATGTTCCAGCAAGTGCCCATGGTTGA--GATTGATGGGATGAAGCTGGTGCAGACCAGAGCCATTTTCAACTACATTGCAGACAAGCACAACCTGTATGGGAAAGACATA-AAGGAGA-GAGCCCTG", ) self.assertEqual( alignment[1], "GGGCCTGGACTTTCC--CAATCTGCCTTACTTGATCGATGGATCACA-CAAGATCACCCAGAGCAATGCCATCCTGCGCTACCTTGCCCGAAAGCACCACCTGGAT-GGAGAGACAGAGGAGGAGAGGATCCGTG", ) # pGT875 OCDHPR self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['G', 'G', 'G', 'T', 'A', 'T', 'T', 'G', 'A', 'T', 'G', 'T', 'T', 'C', 'C', 'A', 'G', 'C', 'A', 'A', 'G', 'T', 'G', 'C', 'C', 'C', 'A', 'T', 'G', 'G', 'T', 'T', 'G', 'A', '-', '-', 'G', 'A', 'T', 'T', 'G', 'A', 'T', 'G', 'G', 'G', 'A', 'T', 'G', 'A', 'A', 'G', 'C', 'T', 'G', 'G', 'T', 'G', 'C', 'A', 'G', 'A', 'C', 'C', 'A', 'G', 'A', 'G', 'C', 'C', 'A', 'T', 'T', 'T', 'T', 'C', 'A', 'A', 'C', 'T', 'A', 'C', 'A', 'T', 'T', 'G', 'C', 'A', 'G', 'A', 'C', 'A', 'A', 'G', 'C', 'A', 'C', 'A', 'A', 'C', 'C', 'T', 'G', 'T', 'A', 'T', 'G', 'G', 'G', 'A', 'A', 'A', 'G', 'A', 'C', 'A', 'T', 'A', '-', 'A', 'A', 'G', 'G', 'A', 'G', 'A', '-', 'G', 'A', 'G', 'C', 'C', 'C', 'T', 'G'], ['G', 'G', 'G', 'C', 'C', 'T', 'G', 'G', 'A', 'C', 'T', 'T', 'T', 'C', 'C', '-', '-', 'C', 'A', 'A', 'T', 'C', 'T', 'G', 'C', 'C', 'T', 'T', 'A', 'C', 'T', 'T', 'G', 'A', 'T', 'C', 'G', 'A', 'T', 'G', 'G', 'A', 'T', 'C', 'A', 'C', 'A', '-', 'C', 'A', 'A', 'G', 'A', 'T', 'C', 'A', 'C', 'C', 'C', 'A', 'G', 'A', 'G', 'C', 'A', 'A', 'T', 'G', 'C', 'C', 'A', 'T', 'C', 'C', 'T', 'G', 'C', 'G', 'C', 'T', 'A', 'C', 'C', 'T', 'T', 'G', 'C', 'C', 'C', 'G', 'A', 'A', 'A', 'G', 'C', 'A', 'C', 'C', 'A', 'C', 'C', 'T', 'G', 'G', 'A', 'T', '-', 'G', 'G', 'A', 'G', 'A', 'G', 'A', 'C', 'A', 'G', 'A', 'G', 'G', 'A', 'G', 'G', 'A', 'G', 'A', 'G', 'G', 'A', 'T', 'C', 'C', 'G', 'T', 'G']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertEqual(len(alignment), 2) self.assertAlmostEqual(alignment.annotations["% identity"], 91.30) self.assertEqual(alignment.annotations["gap opens"], 1) aligned = alignment.aligned self.assertEqual(sum(end - start for start, end in aligned[0]), 23) self.assertEqual(sum(end - start for start, end in aligned[1]), 23) self.assertEqual(alignment.shape, (2, 23 + 1)) self.assertEqual(alignment.sequences[0].id, "OCDHPR") self.assertEqual(alignment.sequences[1].id, "pGT875") self.assertEqual(alignment.annotations["mismatches"], 2) self.assertAlmostEqual(alignment.annotations["evalue"], 0.012) self.assertAlmostEqual(alignment.annotations["bit score"], 29.7) self.assertEqual( str(alignment), """\ OCDHPR 2302 ?????????????????-?????? 2325 0 |||||||||||||||||-|||||| 24 pGT875 265 ???????????????????????? 289 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[2302, 2319, 2319, 2325], [265, 282, 283, 289]]), # fmt: on ) ) query = self.query target = self.targets[alignment.sequences[0].id] self.assertEqual(len(alignment.sequences[0].seq), 2325) self.assertEqual(len(alignment.sequences[1].seq), len(query)) alignment.sequences[0].seq = target alignment.sequences[1].seq = query self.assertEqual(alignment[0], "AGACAGAGGAGGAGAAG-TCTGTG") self.assertEqual(alignment[1], "AGACAGAGGAGGAGAGGATCCGTG") # pGT875 RABALP1A self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['A', 'G', 'A', 'C', 'A', 'G', 'A', 'G', 'G', 'A', 'G', 'G', 'A', 'G', 'A', 'A', 'G', '-', 'T', 'C', 'T', 'G', 'T', 'G'], ['A', 'G', 'A', 'C', 'A', 'G', 'A', 'G', 'G', 'A', 'G', 'G', 'A', 'G', 'A', 'G', 'G', 'A', 'T', 'C', 'C', 'G', 'T', 'G']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertEqual(len(alignment), 2) self.assertAlmostEqual(alignment.annotations["% identity"], 76.19) self.assertEqual(alignment.annotations["gap opens"], 4) aligned = alignment.aligned self.assertEqual(sum(end - start for start, end in aligned[0]), 42) self.assertEqual(sum(end - start for start, end in aligned[1]), 42) self.assertEqual(alignment.shape, (2, 42 + 4)) self.assertEqual(alignment.sequences[0].id, "RABALP1A") self.assertEqual(alignment.sequences[1].id, "pGT875") self.assertEqual(alignment.annotations["mismatches"], 10) self.assertAlmostEqual(alignment.annotations["evalue"], 0.046) self.assertAlmostEqual(alignment.annotations["bit score"], 27.8) self.assertEqual( str(alignment), """\ RABALP1A 4973 ??????????????--???-?????????????????????????? 5016 0 ||||||||||||||--|||-||||||||||||-||||||||||||| 46 pGT875 240 ????????????????????????????????-????????????? 285 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[4973, 4987, 4987, 4990, 4990, 5002, 5003, 5016], [ 240, 254, 256, 259, 260, 272, 272, 285]]) # fmt: on ) ) query = self.query target = self.targets[alignment.sequences[0].id] self.assertEqual(len(alignment.sequences[0].seq), 5016) self.assertEqual(len(alignment.sequences[1].seq), len(query)) alignment.sequences[0].seq = target alignment.sequences[1].seq = query self.assertEqual(alignment[0], "GCTGGAGAGAGCCA--TGG-TGGAGGCTGCGATGGAGGAGAGGATC") self.assertEqual(alignment[1], "GCCCGAAAGCACCACCTGGATGGAGAGACAGA-GGAGGAGAGGATC") # pGT875 OCDHPR self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['G', 'C', 'T', 'G', 'G', 'A', 'G', 'A', 'G', 'A', 'G', 'C', 'C', 'A', '-', '-', 'T', 'G', 'G', '-', 'T', 'G', 'G', 'A', 'G', 'G', 'C', 'T', 'G', 'C', 'G', 'A', 'T', 'G', 'G', 'A', 'G', 'G', 'A', 'G', 'A', 'G', 'G', 'A', 'T', 'C'], ['G', 'C', 'C', 'C', 'G', 'A', 'A', 'A', 'G', 'C', 'A', 'C', 'C', 'A', 'C', 'C', 'T', 'G', 'G', 'A', 'T', 'G', 'G', 'A', 'G', 'A', 'G', 'A', 'C', 'A', 'G', 'A', '-', 'G', 'G', 'A', 'G', 'G', 'A', 'G', 'A', 'G', 'G', 'A', 'T', 'C']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertEqual(len(alignment), 2) self.assertAlmostEqual(alignment.annotations["% identity"], 100.00) self.assertEqual(alignment.annotations["gap opens"], 0) aligned = alignment.aligned self.assertEqual(sum(end - start for start, end in aligned[0]), 12) self.assertEqual(sum(start - end for start, end in aligned[1]), 12) self.assertEqual(alignment.shape, (2, 12 + 0)) self.assertEqual(alignment.sequences[0].id, "OCDHPR") self.assertEqual(alignment.sequences[1].id, "pGT875") self.assertEqual(alignment.annotations["mismatches"], 0) self.assertAlmostEqual(alignment.annotations["evalue"], 0.09) self.assertAlmostEqual(alignment.annotations["bit score"], 26.8) self.assertEqual( str(alignment), """\ OCDHPR 1499 ???????????? 1511 0 |||||||||||| 12 pGT875 316 ???????????? 304 """, ) self.assertTrue( np.array_equal( alignment.coordinates, np.array([[1499, 1511], [316, 304]]), ) ) query = self.query target = self.targets[alignment.sequences[0].id] self.assertEqual(len(alignment.sequences[0].seq), 1511) self.assertEqual(len(alignment.sequences[1].seq), len(query)) alignment.sequences[0].seq = target alignment.sequences[1].seq = query self.assertEqual(alignment[0], "CCATGACCTGGT") self.assertEqual(alignment[1], "CCATGACCTGGT") # pGT875 RABALP1A self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['C', 'C', 'A', 'T', 'G', 'A', 'C', 'C', 'T', 'G', 'G', 'T'], ['C', 'C', 'A', 'T', 'G', 'A', 'C', 'C', 'T', 'G', 'G', 'T']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertEqual(len(alignment), 2) self.assertAlmostEqual(alignment.annotations["% identity"], 100.00) self.assertEqual(alignment.annotations["gap opens"], 0) aligned = alignment.aligned self.assertEqual(sum(end - start for start, end in aligned[0]), 12) self.assertEqual(sum(start - end for start, end in aligned[1]), 12) self.assertEqual(alignment.shape, (2, 12 + 0)) self.assertEqual(alignment.sequences[0].id, "RABALP1A") self.assertEqual(alignment.sequences[1].id, "pGT875") self.assertEqual(alignment.annotations["mismatches"], 0) self.assertAlmostEqual(alignment.annotations["evalue"], 0.09) self.assertAlmostEqual(alignment.annotations["bit score"], 26.8) self.assertEqual( str(alignment), """\ RABALP1A 1499 ???????????? 1511 0 |||||||||||| 12 pGT875 316 ???????????? 304 """, ) self.assertTrue( np.array_equal( alignment.coordinates, np.array([[1499, 1511], [316, 304]]), ) ) query = self.query target = self.targets[alignment.sequences[0].id] self.assertEqual(len(alignment.sequences[0].seq), 1511) self.assertEqual(len(alignment.sequences[1].seq), len(query)) alignment.sequences[0].seq = target alignment.sequences[1].seq = query self.assertEqual(alignment[0], "CCATGACCTGGT") self.assertEqual(alignment[1], "CCATGACCTGGT") # pGT875 RABGSTB self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['C', 'C', 'A', 'T', 'G', 'A', 'C', 'C', 'T', 'G', 'G', 'T'], ['C', 'C', 'A', 'T', 'G', 'A', 'C', 'C', 'T', 'G', 'G', 'T']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertEqual(len(alignment), 2) self.assertAlmostEqual(alignment.annotations["% identity"], 87.50) self.assertEqual(alignment.annotations["gap opens"], 0) aligned = alignment.aligned self.assertEqual(sum(end - start for start, end in aligned[0]), 16) self.assertEqual(sum(start - end for start, end in aligned[1]), 16) self.assertEqual(alignment.shape, (2, 16 + 0)) self.assertEqual(alignment.sequences[0].id, "RABGSTB") self.assertEqual(alignment.sequences[1].id, "pGT875") self.assertEqual(alignment.annotations["mismatches"], 2) self.assertAlmostEqual(alignment.annotations["evalue"], 0.18) self.assertAlmostEqual(alignment.annotations["bit score"], 25.8) self.assertEqual( str(alignment), """\ RABGSTB 490 ???????????????? 506 0 |||||||||||||||| 16 pGT875 160 ???????????????? 144 """, ) self.assertTrue( np.array_equal( alignment.coordinates, np.array([[490, 506], [160, 144]]), ) ) query = self.query target = self.targets[alignment.sequences[0].id] self.assertEqual(len(alignment.sequences[0].seq), 506) self.assertEqual(len(alignment.sequences[1].seq), len(query)) alignment.sequences[0].seq = target alignment.sequences[1].seq = query self.assertEqual(alignment[0], "CCTGGTTGAACTTCTC") self.assertEqual(alignment[1], "CCAGCTTGAACTTCTC") # pGT875 RABGLTR self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['C', 'C', 'T', 'G', 'G', 'T', 'T', 'G', 'A', 'A', 'C', 'T', 'T', 'C', 'T', 'C'], ['C', 'C', 'A', 'G', 'C', 'T', 'T', 'G', 'A', 'A', 'C', 'T', 'T', 'C', 'T', 'C']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertEqual(len(alignment), 2) self.assertAlmostEqual(alignment.annotations["% identity"], 53.57) self.assertEqual(alignment.annotations["gap opens"], 0) aligned = alignment.aligned self.assertEqual(sum(end - start for start, end in aligned[0]), 84) self.assertEqual(sum(start - end for start, end in aligned[1]), 84) self.assertEqual(alignment.shape, (2, 84 + 0)) self.assertEqual(alignment.sequences[0].id, "RABGLTR") self.assertEqual(alignment.sequences[1].id, "pGT875") self.assertEqual(alignment.annotations["mismatches"], 39) self.assertAlmostEqual(alignment.annotations["evalue"], 0.35) self.assertAlmostEqual(alignment.annotations["bit score"], 24.9) self.assertEqual( str(alignment), """\ RABGLTR 1116 ???????????????????????????????????????????????????????????? 0 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| pGT875 242 ???????????????????????????????????????????????????????????? RABGLTR 1176 ???????????????????????? 1200 60 |||||||||||||||||||||||| 84 pGT875 182 ???????????????????????? 158 """, ) self.assertTrue( np.array_equal( alignment.coordinates, np.array([[1116, 1200], [242, 158]]), ) ) query = self.query target = self.targets[alignment.sequences[0].id] self.assertEqual(len(alignment.sequences[0].seq), 1200) self.assertEqual(len(alignment.sequences[1].seq), len(query)) alignment.sequences[0].seq = target alignment.sequences[1].seq = query self.assertEqual( alignment[0], "GCATGGCTGGGTGGGGCAGGATTAGTGTGGGGGGAGTTGGGTGCTCAGGCAGGGCTATGAGGGATCTTGTTCATTTCCGGGCCC", ) self.assertEqual( alignment[1], "GCAAGGTAGCGCAGGATGGCATTGCTCTGGGTGATCTTGTGTGATCCATCGATCAAGTAAGGCAGATTGGGAAAGTCCAGGCCC", ) # pGT875 pGT875 self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['G', 'C', 'A', 'T', 'G', 'G', 'C', 'T', 'G', 'G', 'G', 'T', 'G', 'G', 'G', 'G', 'C', 'A', 'G', 'G', 'A', 'T', 'T', 'A', 'G', 'T', 'G', 'T', 'G', 'G', 'G', 'G', 'G', 'G', 'A', 'G', 'T', 'T', 'G', 'G', 'G', 'T', 'G', 'C', 'T', 'C', 'A', 'G', 'G', 'C', 'A', 'G', 'G', 'G', 'C', 'T', 'A', 'T', 'G', 'A', 'G', 'G', 'G', 'A', 'T', 'C', 'T', 'T', 'G', 'T', 'T', 'C', 'A', 'T', 'T', 'T', 'C', 'C', 'G', 'G', 'G', 'C', 'C', 'C'], ['G', 'C', 'A', 'A', 'G', 'G', 'T', 'A', 'G', 'C', 'G', 'C', 'A', 'G', 'G', 'A', 'T', 'G', 'G', 'C', 'A', 'T', 'T', 'G', 'C', 'T', 'C', 'T', 'G', 'G', 'G', 'T', 'G', 'A', 'T', 'C', 'T', 'T', 'G', 'T', 'G', 'T', 'G', 'A', 'T', 'C', 'C', 'A', 'T', 'C', 'G', 'A', 'T', 'C', 'A', 'A', 'G', 'T', 'A', 'A', 'G', 'G', 'C', 'A', 'G', 'A', 'T', 'T', 'G', 'G', 'G', 'A', 'A', 'A', 'G', 'T', 'C', 'C', 'A', 'G', 'G', 'C', 'C', 'C']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertEqual(len(alignment), 2) self.assertAlmostEqual(alignment.annotations["% identity"], 100.00) self.assertEqual(alignment.annotations["gap opens"], 0) aligned = alignment.aligned self.assertEqual(sum(end - start for start, end in aligned[0]), 10) self.assertEqual(sum(start - end for start, end in aligned[1]), 10) self.assertEqual(alignment.shape, (2, 10 + 0)) self.assertEqual(alignment.sequences[0].id, "pGT875") self.assertEqual(alignment.sequences[1].id, "pGT875") self.assertEqual(alignment.annotations["mismatches"], 0) self.assertAlmostEqual(alignment.annotations["evalue"], 0.35) self.assertAlmostEqual(alignment.annotations["bit score"], 24.9) self.assertEqual( str(alignment), """\ pGT875 792 ?????????? 802 0 |||||||||| 10 pGT875 310 ?????????? 300 """, ) self.assertTrue( np.array_equal( alignment.coordinates, np.array([[792, 802], [310, 300]]), ) ) query = self.query target = self.targets[alignment.sequences[0].id] self.assertEqual(len(alignment.sequences[0].seq), 802) self.assertEqual(len(alignment.sequences[1].seq), len(query)) alignment.sequences[0].seq = target alignment.sequences[1].seq = query self.assertEqual(alignment[0], "CCTGGTTCTC") self.assertEqual(alignment[1], "CCTGGTTCTC") # pGT875 BTGST self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['C', 'C', 'T', 'G', 'G', 'T', 'T', 'C', 'T', 'C'], ['C', 'C', 'T', 'G', 'G', 'T', 'T', 'C', 'T', 'C']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertEqual(len(alignment), 2) self.assertAlmostEqual(alignment.annotations["% identity"], 59.15) self.assertEqual(alignment.annotations["gap opens"], 3) aligned = alignment.aligned self.assertEqual(sum(end - start for start, end in aligned[0]), 71) self.assertEqual(sum(start - end for start, end in aligned[1]), 71) self.assertEqual(alignment.shape, (2, 71 + 3)) self.assertEqual(alignment.sequences[0].id, "BTGST") self.assertEqual(alignment.sequences[1].id, "pGT875") self.assertEqual(alignment.annotations["mismatches"], 29) self.assertAlmostEqual(alignment.annotations["evalue"], 0.68) self.assertAlmostEqual(alignment.annotations["bit score"], 23.9) self.assertEqual( str(alignment), """\ BTGST 280 ????????????????????????-????????--????????????????????????? 0 ||||||||||||||||||||||||-||||||||--||||||||||||||||||||||||| pGT875 378 ???????????????????????????????????????????????????????????? BTGST 337 ?????????????? 351 60 |||||||||||||| 74 pGT875 318 ?????????????? 304 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[280, 304, 304, 312, 312, 351], [378, 354, 353, 345, 343, 304]]) # fmt: on ) ) query = self.query target = self.targets[alignment.sequences[0].id] self.assertEqual(len(alignment.sequences[0].seq), 351) self.assertEqual(len(alignment.sequences[1].seq), len(query)) alignment.sequences[0].seq = target alignment.sequences[1].seq = query self.assertEqual( alignment[0], "CTGCGGCACCTGGGCCGCACCCTC-GGGCTGTA--TGGGAAGGACCAGCAGGAGGCGGCCCTGGTGGACATGGT", ) self.assertEqual( alignment[1], "CTCTGGCTTCTGCTTCTCAAAGTCAGGGTTGTAACAGAGCATGATGAGCTGCATGCGGGTGTCCATGACCTGGT", ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['C', 'T', 'G', 'C', 'G', 'G', 'C', 'A', 'C', 'C', 'T', 'G', 'G', 'G', 'C', 'C', 'G', 'C', 'A', 'C', 'C', 'C', 'T', 'C', '-', 'G', 'G', 'G', 'C', 'T', 'G', 'T', 'A', '-', '-', 'T', 'G', 'G', 'G', 'A', 'A', 'G', 'G', 'A', 'C', 'C', 'A', 'G', 'C', 'A', 'G', 'G', 'A', 'G', 'G', 'C', 'G', 'G', 'C', 'C', 'C', 'T', 'G', 'G', 'T', 'G', 'G', 'A', 'C', 'A', 'T', 'G', 'G', 'T'], ['C', 'T', 'C', 'T', 'G', 'G', 'C', 'T', 'T', 'C', 'T', 'G', 'C', 'T', 'T', 'C', 'T', 'C', 'A', 'A', 'A', 'G', 'T', 'C', 'A', 'G', 'G', 'G', 'T', 'T', 'G', 'T', 'A', 'A', 'C', 'A', 'G', 'A', 'G', 'C', 'A', 'T', 'G', 'A', 'T', 'G', 'A', 'G', 'C', 'T', 'G', 'C', 'A', 'T', 'G', 'C', 'G', 'G', 'G', 'T', 'G', 'T', 'C', 'C', 'A', 'T', 'G', 'A', 'C', 'C', 'T', 'G', 'G', 'T']], dtype='U') # fmt: on ) ) with self.assertRaises(StopIteration): next(alignments) class TestFastaBasic(unittest.TestCase): def test_empty(self): import io stream = io.StringIO() with self.assertRaisesRegex(ValueError, "Empty file."): Align.parse(stream, "tabular") class TestBlast(unittest.TestCase): def test_2226_tblastn_001(self): path = "Blast/tab_2226_tblastn_001.txt" with open(path) as stream: with self.assertRaisesRegex(ValueError, "Missing header."): Align.parse(stream, "tabular") def test_2226_tblastn_002(self): path = "Blast/tab_2226_tblastn_002.txt" with open(path) as stream: with self.assertRaisesRegex(ValueError, "Empty file."): Align.parse(stream, "tabular") def test_2226_tblastn_003(self): path = "Blast/tab_2226_tblastn_003.txt" with open(path) as stream: with self.assertRaisesRegex(ValueError, "Missing header."): Align.parse(stream, "tabular") def test_2226_tblastn_004(self): path = "Blast/tab_2226_tblastn_004.txt" with open(path) as stream: with self.assertRaisesRegex(ValueError, "Missing header."): Align.parse(stream, "tabular") def test_2226_tblastn_005(self): path = "Blast/tab_2226_tblastn_005.txt" with open(path) as stream: alignments = Align.parse(stream, "tabular") self.assertEqual(alignments.metadata["Program"], "TBLASTN") self.assertEqual(alignments.metadata["Version"], "2.2.26+") self.assertEqual(alignments.metadata["Database"], "db/minirefseq_mrna") alignment = next(alignments) self.assertEqual(alignment.query.id, "gi|16080617|ref|NP_391444.1|") self.assertEqual(alignment.target.id, "gi|145479850|ref|XM_001425911.1|") self.assertEqual(alignment.query.annotations["start"], 30) self.assertEqual(alignment.query.annotations["end"], 73) self.assertEqual(alignment.target.annotations["start"], 1743) self.assertEqual(alignment.target.annotations["end"], 1872) self.assertAlmostEqual(alignment.annotations["evalue"], 1e-05) self.assertAlmostEqual(alignment.annotations["bit score"], 34.7) self.assertAlmostEqual(alignment.annotations["% identity"], 34.88) self.assertEqual(alignment.annotations["alignment length"], 43) self.assertEqual(alignment.annotations["mismatches"], 28) self.assertEqual(alignment.annotations["gap opens"], 0) alignment = next(alignments) self.assertEqual(alignment.query.id, "gi|16080617|ref|NP_391444.1|") self.assertEqual(alignment.target.id, "gi|72012412|ref|XM_777959.1|") self.assertEqual(alignment.query.annotations["start"], 43) self.assertEqual(alignment.query.annotations["end"], 94) self.assertEqual(alignment.target.annotations["start"], 1056) self.assertEqual(alignment.target.annotations["end"], 1233) self.assertAlmostEqual(alignment.annotations["evalue"], 1e-04) self.assertAlmostEqual(alignment.annotations["bit score"], 31.6) self.assertAlmostEqual(alignment.annotations["% identity"], 33.90) self.assertEqual(alignment.annotations["alignment length"], 59) self.assertEqual(alignment.annotations["mismatches"], 31) self.assertEqual(alignment.annotations["gap opens"], 1) alignment = next(alignments) self.assertEqual(alignment.query.id, "gi|16080617|ref|NP_391444.1|") self.assertEqual(alignment.target.id, "gi|115975252|ref|XM_001180111.1|") self.assertEqual(alignment.query.annotations["start"], 43) self.assertEqual(alignment.query.annotations["end"], 94) self.assertEqual(alignment.target.annotations["start"], 1056) self.assertEqual(alignment.target.annotations["end"], 1233) self.assertAlmostEqual(alignment.annotations["evalue"], 1e-04) self.assertAlmostEqual(alignment.annotations["bit score"], 31.6) self.assertAlmostEqual(alignment.annotations["% identity"], 33.90) self.assertEqual(alignment.annotations["alignment length"], 59) self.assertEqual(alignment.annotations["mismatches"], 31) self.assertEqual(alignment.annotations["gap opens"], 1) alignment = next(alignments) self.assertEqual(alignment.query.id, "gi|11464971:4-101") self.assertEqual(alignment.target.id, "gi|350596019|ref|XM_003360601.2|") self.assertEqual(alignment.query.description, "pleckstrin [Mus musculus]") self.assertEqual(alignment.query.annotations["start"], 0) self.assertEqual(alignment.query.annotations["end"], 98) self.assertEqual(alignment.target.annotations["start"], 94) self.assertEqual(alignment.target.annotations["end"], 388) self.assertAlmostEqual(alignment.annotations["evalue"], 2e-67, places=67) self.assertAlmostEqual(alignment.annotations["bit score"], 199) self.assertAlmostEqual(alignment.annotations["% identity"], 95.92) self.assertEqual(alignment.annotations["alignment length"], 98) self.assertEqual(alignment.annotations["mismatches"], 4) self.assertEqual(alignment.annotations["gap opens"], 0) alignment = next(alignments) self.assertEqual(alignment.query.id, "gi|11464971:4-101") self.assertEqual(alignment.target.id, "gi|350596019|ref|XM_003360601.2|") self.assertEqual(alignment.query.description, "pleckstrin [Mus musculus]") self.assertEqual(alignment.query.annotations["start"], 29) self.assertEqual(alignment.query.annotations["end"], 96) self.assertEqual(alignment.target.annotations["start"], 541) self.assertEqual(alignment.target.annotations["end"], 754) self.assertAlmostEqual(alignment.annotations["evalue"], 4e-05) self.assertAlmostEqual(alignment.annotations["bit score"], 32.7) self.assertAlmostEqual(alignment.annotations["% identity"], 29.58) self.assertEqual(alignment.annotations["alignment length"], 71) self.assertEqual(alignment.annotations["mismatches"], 46) self.assertEqual(alignment.annotations["gap opens"], 2) alignment = next(alignments) self.assertEqual(alignment.query.id, "gi|11464971:4-101") self.assertEqual(alignment.target.id, "gi|301779869|ref|XM_002925302.1|") self.assertEqual(alignment.query.description, "pleckstrin [Mus musculus]") self.assertEqual(alignment.query.annotations["start"], 0) self.assertEqual(alignment.query.annotations["end"], 98) self.assertEqual(alignment.target.annotations["start"], 77) self.assertEqual(alignment.target.annotations["end"], 371) self.assertAlmostEqual(alignment.annotations["evalue"], 2e-67, places=67) self.assertAlmostEqual(alignment.annotations["bit score"], 202) self.assertAlmostEqual(alignment.annotations["% identity"], 97.96) self.assertEqual(alignment.annotations["alignment length"], 98) self.assertEqual(alignment.annotations["mismatches"], 2) self.assertEqual(alignment.annotations["gap opens"], 0) alignment = next(alignments) self.assertEqual(alignment.query.id, "gi|11464971:4-101") self.assertEqual(alignment.target.id, "gi|301779869|ref|XM_002925302.1|") self.assertEqual(alignment.query.description, "pleckstrin [Mus musculus]") self.assertEqual(alignment.query.annotations["start"], 2) self.assertEqual(alignment.query.annotations["end"], 96) self.assertEqual(alignment.target.annotations["start"], 803) self.assertEqual(alignment.target.annotations["end"], 1103) self.assertAlmostEqual(alignment.annotations["evalue"], 3e-09, places=9) self.assertAlmostEqual(alignment.annotations["bit score"], 45.1) self.assertAlmostEqual(alignment.annotations["% identity"], 30.00) self.assertEqual(alignment.annotations["alignment length"], 100) self.assertEqual(alignment.annotations["mismatches"], 64) self.assertEqual(alignment.annotations["gap opens"], 2) alignment = next(alignments) self.assertEqual(alignment.query.id, "gi|11464971:4-101") self.assertEqual(alignment.target.id, "gi|296223671|ref|XM_002757683.1|") self.assertEqual(alignment.query.description, "pleckstrin [Mus musculus]") self.assertEqual(alignment.query.annotations["start"], 0) self.assertEqual(alignment.query.annotations["end"], 98) self.assertEqual(alignment.target.annotations["start"], 160) self.assertEqual(alignment.target.annotations["end"], 454) self.assertAlmostEqual(alignment.annotations["evalue"], 4e-67, places=67) self.assertAlmostEqual(alignment.annotations["bit score"], 202) self.assertAlmostEqual(alignment.annotations["% identity"], 97.96) self.assertEqual(alignment.annotations["alignment length"], 98) self.assertEqual(alignment.annotations["mismatches"], 2) self.assertEqual(alignment.annotations["gap opens"], 0) alignment = next(alignments) self.assertEqual(alignment.query.id, "gi|11464971:4-101") self.assertEqual(alignment.target.id, "gi|296223671|ref|XM_002757683.1|") self.assertEqual(alignment.query.description, "pleckstrin [Mus musculus]") self.assertEqual(alignment.query.annotations["start"], 2) self.assertEqual(alignment.query.annotations["end"], 96) self.assertEqual(alignment.target.annotations["start"], 865) self.assertEqual(alignment.target.annotations["end"], 1165) self.assertAlmostEqual(alignment.annotations["evalue"], 3e-09, places=9) self.assertAlmostEqual(alignment.annotations["bit score"], 45.1) self.assertAlmostEqual(alignment.annotations["% identity"], 30.00) self.assertEqual(alignment.annotations["alignment length"], 100) self.assertEqual(alignment.annotations["mismatches"], 64) self.assertEqual(alignment.annotations["gap opens"], 2) alignment = next(alignments) self.assertEqual(alignment.query.id, "gi|11464971:4-101") self.assertEqual(alignment.target.id, "gi|338714227|ref|XM_001492113.3|") self.assertEqual(alignment.query.description, "pleckstrin [Mus musculus]") self.assertEqual(alignment.query.annotations["start"], 0) self.assertEqual(alignment.query.annotations["end"], 98) self.assertEqual(alignment.target.annotations["start"], 172) self.assertEqual(alignment.target.annotations["end"], 466) self.assertAlmostEqual(alignment.annotations["evalue"], 2e-66, places=66) self.assertAlmostEqual(alignment.annotations["bit score"], 202) self.assertAlmostEqual(alignment.annotations["% identity"], 97.96) self.assertEqual(alignment.annotations["alignment length"], 98) self.assertEqual(alignment.annotations["mismatches"], 2) self.assertEqual(alignment.annotations["gap opens"], 0) alignment = next(alignments) self.assertEqual(alignment.query.id, "gi|11464971:4-101") self.assertEqual(alignment.target.id, "gi|338714227|ref|XM_001492113.3|") self.assertEqual(alignment.query.description, "pleckstrin [Mus musculus]") self.assertEqual(alignment.query.annotations["start"], 2) self.assertEqual(alignment.query.annotations["end"], 96) self.assertEqual(alignment.target.annotations["start"], 898) self.assertEqual(alignment.target.annotations["end"], 1198) self.assertAlmostEqual(alignment.annotations["evalue"], 1e-09, places=9) self.assertAlmostEqual(alignment.annotations["bit score"], 46.6) self.assertAlmostEqual(alignment.annotations["% identity"], 31.00) self.assertEqual(alignment.annotations["alignment length"], 100) self.assertEqual(alignment.annotations["mismatches"], 63) self.assertEqual(alignment.annotations["gap opens"], 2) alignment = next(alignments) self.assertEqual(alignment.query.id, "gi|11464971:4-101") self.assertEqual(alignment.target.id, "gi|365982352|ref|XM_003667962.1|") self.assertEqual(alignment.query.description, "pleckstrin [Mus musculus]") self.assertEqual(alignment.query.annotations["start"], 11) self.assertEqual(alignment.query.annotations["end"], 54) self.assertEqual(alignment.target.annotations["start"], 3180) self.assertEqual(alignment.target.annotations["end"], 3336) self.assertAlmostEqual(alignment.annotations["evalue"], 1.7) self.assertAlmostEqual(alignment.annotations["bit score"], 19.6) self.assertAlmostEqual(alignment.annotations["% identity"], 30.77) self.assertEqual(alignment.annotations["alignment length"], 52) self.assertEqual(alignment.annotations["mismatches"], 27) self.assertEqual(alignment.annotations["gap opens"], 1) with self.assertRaises(StopIteration): next(alignments) def test_2226_tblastn_007(self): path = "Blast/tab_2226_tblastn_007.txt" with open(path) as stream: alignments = Align.parse(stream, "tabular") self.assertEqual(alignments.metadata["Program"], "TBLASTN") self.assertEqual(alignments.metadata["Version"], "2.2.26+") self.assertEqual(alignments.metadata["Database"], "db/minirefseq_mrna") alignment = next(alignments) self.assertEqual(alignment.query.id, "gi|16080617|ref|NP_391444.1|") self.assertEqual(alignment.target.id, "gi|145479850|ref|XM_001425911.1|") self.assertEqual( alignment.query.description, "membrane bound lipoprotein [Bacillus subtilis subsp. subtilis str. 168]", ) self.assertEqual(alignment.query.annotations["start"], 30) self.assertEqual(alignment.query.annotations["end"], 73) self.assertEqual(alignment.target.annotations["start"], 1743) self.assertEqual(alignment.target.annotations["end"], 1872) self.assertAlmostEqual(alignment.annotations["evalue"], 1e-05) self.assertAlmostEqual(alignment.annotations["bit score"], 34.7) self.assertAlmostEqual(alignment.annotations["% identity"], 34.88) self.assertEqual(alignment.annotations["alignment length"], 43) self.assertEqual(alignment.annotations["mismatches"], 28) self.assertEqual(alignment.annotations["gap opens"], 0) alignment = next(alignments) self.assertEqual(alignment.query.id, "gi|16080617|ref|NP_391444.1|") self.assertEqual(alignment.target.id, "gi|72012412|ref|XM_777959.1|") self.assertEqual( alignment.query.description, "membrane bound lipoprotein [Bacillus subtilis subsp. subtilis str. 168]", ) self.assertEqual(alignment.query.annotations["start"], 43) self.assertEqual(alignment.query.annotations["end"], 94) self.assertEqual(alignment.target.annotations["start"], 1056) self.assertEqual(alignment.target.annotations["end"], 1233) self.assertAlmostEqual(alignment.annotations["evalue"], 1e-04) self.assertAlmostEqual(alignment.annotations["bit score"], 31.6) self.assertAlmostEqual(alignment.annotations["% identity"], 33.90) self.assertEqual(alignment.annotations["alignment length"], 59) self.assertEqual(alignment.annotations["mismatches"], 31) self.assertEqual(alignment.annotations["gap opens"], 1) alignment = next(alignments) self.assertEqual(alignment.query.id, "gi|16080617|ref|NP_391444.1|") self.assertEqual(alignment.target.id, "gi|115975252|ref|XM_001180111.1|") self.assertEqual( alignment.query.description, "membrane bound lipoprotein [Bacillus subtilis subsp. subtilis str. 168]", ) self.assertEqual(alignment.query.annotations["start"], 43) self.assertEqual(alignment.query.annotations["end"], 94) self.assertEqual(alignment.target.annotations["start"], 1056) self.assertEqual(alignment.target.annotations["end"], 1233) self.assertAlmostEqual(alignment.annotations["evalue"], 1e-04) self.assertAlmostEqual(alignment.annotations["bit score"], 31.6) self.assertAlmostEqual(alignment.annotations["% identity"], 33.90) self.assertEqual(alignment.annotations["alignment length"], 59) self.assertEqual(alignment.annotations["mismatches"], 31) self.assertEqual(alignment.annotations["gap opens"], 1) with self.assertRaises(StopIteration): next(alignments) def test_2226_tblastn_008(self): path = "Blast/tab_2226_tblastn_008.txt" with open(path) as stream: alignments = Align.parse(stream, "tabular") self.assertEqual(alignments.metadata["Program"], "TBLASTN") self.assertEqual(alignments.metadata["Version"], "2.2.26+") self.assertEqual(alignments.metadata["Database"], "db/minirefseq_mrna") alignment = next(alignments) self.assertEqual(alignment.query.id, "gi|11464971:4-101") self.assertEqual(alignment.target.id, "gi|350596019|ref|XM_003360601.2|") self.assertEqual(alignment.query.description, "pleckstrin [Mus musculus]") self.assertEqual(alignment.query.annotations["start"], 0) self.assertEqual(alignment.query.annotations["end"], 98) self.assertEqual(alignment.target.annotations["start"], 94) self.assertEqual(alignment.target.annotations["end"], 388) self.assertAlmostEqual(alignment.annotations["evalue"], 2e-67, places=67) self.assertAlmostEqual(alignment.annotations["bit score"], 199) self.assertAlmostEqual(alignment.annotations["% identity"], 95.92) self.assertEqual(alignment.annotations["alignment length"], 98) self.assertEqual(alignment.annotations["mismatches"], 4) self.assertEqual(alignment.annotations["gap opens"], 0) alignment = next(alignments) self.assertEqual(alignment.query.id, "gi|11464971:4-101") self.assertEqual(alignment.target.id, "gi|350596019|ref|XM_003360601.2|") self.assertEqual(alignment.query.description, "pleckstrin [Mus musculus]") self.assertEqual(alignment.query.annotations["start"], 29) self.assertEqual(alignment.query.annotations["end"], 96) self.assertEqual(alignment.target.annotations["start"], 541) self.assertEqual(alignment.target.annotations["end"], 754) self.assertAlmostEqual(alignment.annotations["evalue"], 4e-05) self.assertAlmostEqual(alignment.annotations["bit score"], 32.7) self.assertAlmostEqual(alignment.annotations["% identity"], 29.58) self.assertEqual(alignment.annotations["alignment length"], 71) self.assertEqual(alignment.annotations["mismatches"], 46) self.assertEqual(alignment.annotations["gap opens"], 2) alignment = next(alignments) self.assertEqual(alignment.query.id, "gi|11464971:4-101") self.assertEqual(alignment.target.id, "gi|301779869|ref|XM_002925302.1|") self.assertEqual(alignment.query.description, "pleckstrin [Mus musculus]") self.assertEqual(alignment.query.annotations["start"], 0) self.assertEqual(alignment.query.annotations["end"], 98) self.assertEqual(alignment.target.annotations["start"], 77) self.assertEqual(alignment.target.annotations["end"], 371) self.assertAlmostEqual(alignment.annotations["evalue"], 2e-67, places=67) self.assertAlmostEqual(alignment.annotations["bit score"], 202) self.assertAlmostEqual(alignment.annotations["% identity"], 97.96) self.assertEqual(alignment.annotations["alignment length"], 98) self.assertEqual(alignment.annotations["mismatches"], 2) self.assertEqual(alignment.annotations["gap opens"], 0) alignment = next(alignments) self.assertEqual(alignment.query.id, "gi|11464971:4-101") self.assertEqual(alignment.target.id, "gi|301779869|ref|XM_002925302.1|") self.assertEqual(alignment.query.description, "pleckstrin [Mus musculus]") self.assertEqual(alignment.query.annotations["start"], 2) self.assertEqual(alignment.query.annotations["end"], 96) self.assertEqual(alignment.target.annotations["start"], 803) self.assertEqual(alignment.target.annotations["end"], 1103) self.assertAlmostEqual(alignment.annotations["evalue"], 3e-09, places=9) self.assertAlmostEqual(alignment.annotations["bit score"], 45.1) self.assertAlmostEqual(alignment.annotations["% identity"], 30.00) self.assertEqual(alignment.annotations["alignment length"], 100) self.assertEqual(alignment.annotations["mismatches"], 64) self.assertEqual(alignment.annotations["gap opens"], 2) alignment = next(alignments) self.assertEqual(alignment.query.id, "gi|11464971:4-101") self.assertEqual(alignment.target.id, "gi|296223671|ref|XM_002757683.1|") self.assertEqual(alignment.query.description, "pleckstrin [Mus musculus]") self.assertEqual(alignment.query.annotations["start"], 0) self.assertEqual(alignment.query.annotations["end"], 98) self.assertEqual(alignment.target.annotations["start"], 160) self.assertEqual(alignment.target.annotations["end"], 454) self.assertAlmostEqual(alignment.annotations["evalue"], 4e-67, places=67) self.assertAlmostEqual(alignment.annotations["bit score"], 202) self.assertAlmostEqual(alignment.annotations["% identity"], 97.96) self.assertEqual(alignment.annotations["alignment length"], 98) self.assertEqual(alignment.annotations["mismatches"], 2) self.assertEqual(alignment.annotations["gap opens"], 0) alignment = next(alignments) self.assertEqual(alignment.query.id, "gi|11464971:4-101") self.assertEqual(alignment.target.id, "gi|296223671|ref|XM_002757683.1|") self.assertEqual(alignment.query.description, "pleckstrin [Mus musculus]") self.assertEqual(alignment.query.annotations["start"], 2) self.assertEqual(alignment.query.annotations["end"], 96) self.assertEqual(alignment.target.annotations["start"], 865) self.assertEqual(alignment.target.annotations["end"], 1165) self.assertAlmostEqual(alignment.annotations["evalue"], 3e-09, places=9) self.assertAlmostEqual(alignment.annotations["bit score"], 45.1) self.assertAlmostEqual(alignment.annotations["% identity"], 30.00) self.assertEqual(alignment.annotations["alignment length"], 100) self.assertEqual(alignment.annotations["mismatches"], 64) self.assertEqual(alignment.annotations["gap opens"], 2) alignment = next(alignments) self.assertEqual(alignment.query.id, "gi|11464971:4-101") self.assertEqual(alignment.target.id, "gi|338714227|ref|XM_001492113.3|") self.assertEqual(alignment.query.description, "pleckstrin [Mus musculus]") self.assertEqual(alignment.query.annotations["start"], 0) self.assertEqual(alignment.query.annotations["end"], 98) self.assertEqual(alignment.target.annotations["start"], 172) self.assertEqual(alignment.target.annotations["end"], 466) self.assertAlmostEqual(alignment.annotations["evalue"], 2e-66, places=66) self.assertAlmostEqual(alignment.annotations["bit score"], 202) self.assertAlmostEqual(alignment.annotations["% identity"], 97.96) self.assertEqual(alignment.annotations["alignment length"], 98) self.assertEqual(alignment.annotations["mismatches"], 2) self.assertEqual(alignment.annotations["gap opens"], 0) alignment = next(alignments) self.assertEqual(alignment.query.id, "gi|11464971:4-101") self.assertEqual(alignment.target.id, "gi|338714227|ref|XM_001492113.3|") self.assertEqual(alignment.query.description, "pleckstrin [Mus musculus]") self.assertEqual(alignment.query.annotations["start"], 2) self.assertEqual(alignment.query.annotations["end"], 96) self.assertEqual(alignment.target.annotations["start"], 898) self.assertEqual(alignment.target.annotations["end"], 1198) self.assertAlmostEqual(alignment.annotations["evalue"], 1e-09, places=9) self.assertAlmostEqual(alignment.annotations["bit score"], 46.6) self.assertAlmostEqual(alignment.annotations["% identity"], 31.00) self.assertEqual(alignment.annotations["alignment length"], 100) self.assertEqual(alignment.annotations["mismatches"], 63) self.assertEqual(alignment.annotations["gap opens"], 2) alignment = next(alignments) self.assertEqual(alignment.query.id, "gi|11464971:4-101") self.assertEqual(alignment.target.id, "gi|365982352|ref|XM_003667962.1|") self.assertEqual(alignment.query.description, "pleckstrin [Mus musculus]") self.assertEqual(alignment.query.annotations["start"], 11) self.assertEqual(alignment.query.annotations["end"], 54) self.assertEqual(alignment.target.annotations["start"], 3180) self.assertEqual(alignment.target.annotations["end"], 3336) self.assertAlmostEqual(alignment.annotations["evalue"], 1.7) self.assertAlmostEqual(alignment.annotations["bit score"], 19.6) self.assertAlmostEqual(alignment.annotations["% identity"], 30.77) self.assertEqual(alignment.annotations["alignment length"], 52) self.assertEqual(alignment.annotations["mismatches"], 27) self.assertEqual(alignment.annotations["gap opens"], 1) with self.assertRaises(StopIteration): next(alignments) def test_2226_tblastn_009(self): path = "Blast/tab_2226_tblastn_009.txt" with open(path) as stream: with self.assertRaisesRegex(ValueError, "Missing header."): Align.parse(stream, "tabular") def test_2226_tblastn_010(self): path = "Blast/tab_2226_tblastn_010.txt" with open(path) as stream: alignments = Align.parse(stream, "tabular") self.assertEqual(alignments.metadata["Program"], "TBLASTN") self.assertEqual(alignments.metadata["Version"], "2.2.26+") self.assertEqual(alignments.metadata["Database"], "db/minirefseq_mrna") alignment = next(alignments) self.assertEqual(alignment.query.id, "gi|16080617|ref|NP_391444.1|") self.assertEqual(alignment.target.id, "gi|145479850|ref|XM_001425911.1|") self.assertAlmostEqual(alignment.annotations["evalue"], 1e-05) self.assertAlmostEqual(alignment.annotations["bit score"], 34.7) alignment = next(alignments) self.assertEqual(alignment.query.id, "gi|16080617|ref|NP_391444.1|") self.assertEqual(alignment.target.id, "gi|72012412|ref|XM_777959.1|") self.assertAlmostEqual(alignment.annotations["evalue"], 1e-04) self.assertAlmostEqual(alignment.annotations["bit score"], 31.6) alignment = next(alignments) self.assertEqual(alignment.query.id, "gi|16080617|ref|NP_391444.1|") self.assertEqual(alignment.target.id, "gi|115975252|ref|XM_001180111.1|") self.assertAlmostEqual(alignment.annotations["evalue"], 1e-04) self.assertAlmostEqual(alignment.annotations["bit score"], 31.6) alignment = next(alignments) self.assertEqual(alignment.query.id, "gi|11464971:4-101") self.assertEqual(alignment.target.id, "gi|350596019|ref|XM_003360601.2|") self.assertAlmostEqual(alignment.annotations["evalue"], 2e-67, places=67) self.assertAlmostEqual(alignment.annotations["bit score"], 199) alignment = next(alignments) self.assertEqual(alignment.query.id, "gi|11464971:4-101") self.assertEqual(alignment.target.id, "gi|350596019|ref|XM_003360601.2|") self.assertAlmostEqual(alignment.annotations["evalue"], 4e-05) self.assertAlmostEqual(alignment.annotations["bit score"], 32.7) alignment = next(alignments) self.assertEqual(alignment.query.id, "gi|11464971:4-101") self.assertEqual(alignment.target.id, "gi|301779869|ref|XM_002925302.1|") self.assertAlmostEqual(alignment.annotations["evalue"], 2e-67, places=67) self.assertAlmostEqual(alignment.annotations["bit score"], 202) alignment = next(alignments) self.assertEqual(alignment.query.id, "gi|11464971:4-101") self.assertEqual(alignment.target.id, "gi|301779869|ref|XM_002925302.1|") self.assertAlmostEqual(alignment.annotations["evalue"], 3e-09, places=9) self.assertAlmostEqual(alignment.annotations["bit score"], 45.1) alignment = next(alignments) self.assertEqual(alignment.query.id, "gi|11464971:4-101") self.assertEqual(alignment.target.id, "gi|296223671|ref|XM_002757683.1|") self.assertAlmostEqual(alignment.annotations["evalue"], 4e-67, places=67) self.assertAlmostEqual(alignment.annotations["bit score"], 202) alignment = next(alignments) self.assertEqual(alignment.query.id, "gi|11464971:4-101") self.assertEqual(alignment.target.id, "gi|296223671|ref|XM_002757683.1|") self.assertAlmostEqual(alignment.annotations["evalue"], 3e-09, places=9) self.assertAlmostEqual(alignment.annotations["bit score"], 45.1) alignment = next(alignments) self.assertEqual(alignment.query.id, "gi|11464971:4-101") self.assertEqual(alignment.target.id, "gi|338714227|ref|XM_001492113.3|") self.assertAlmostEqual(alignment.annotations["evalue"], 2e-66, places=66) self.assertAlmostEqual(alignment.annotations["bit score"], 202) alignment = next(alignments) self.assertEqual(alignment.query.id, "gi|11464971:4-101") self.assertEqual(alignment.target.id, "gi|338714227|ref|XM_001492113.3|") self.assertAlmostEqual(alignment.annotations["evalue"], 1e-09, places=9) self.assertAlmostEqual(alignment.annotations["bit score"], 46.6) alignment = next(alignments) self.assertEqual(alignment.query.id, "gi|11464971:4-101") self.assertEqual(alignment.target.id, "gi|365982352|ref|XM_003667962.1|") self.assertAlmostEqual(alignment.annotations["evalue"], 1.7) self.assertAlmostEqual(alignment.annotations["bit score"], 19.6) with self.assertRaises(StopIteration): next(alignments) def test_2226_tblastn_011(self): path = "Blast/tab_2226_tblastn_011.txt" with open(path) as stream: alignments = Align.parse(stream, "tabular") self.assertEqual(alignments.metadata["Program"], "TBLASTN") self.assertEqual(alignments.metadata["Version"], "2.2.26+") self.assertEqual(alignments.metadata["Database"], "db/minirefseq_mrna") alignment = next(alignments) self.assertEqual(alignment.query.id, "gi|16080617|ref|NP_391444.1|") self.assertEqual( alignment.query.description, "membrane bound lipoprotein [Bacillus subtilis subsp. subtilis str. 168]", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual( alignment.query.annotations["acc."], "gi|16080617|ref|NP_391444.1|" ) self.assertEqual( alignment.query.annotations["acc.ver"], "gi|16080617|ref|NP_391444.1|" ) self.assertEqual(len(alignment.query.seq), 102) self.assertEqual(alignment.target.id, "gi|145479850|ref|XM_001425911.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|145479850|ref|XM_001425911.1|" ) self.assertEqual(alignment.target.annotations["gi"], "0") self.assertEqual(alignment.target.annotations["gis"], "0") self.assertEqual( alignment.target.annotations["acc."], "gi|145479850|ref|XM_001425911.1|" ) self.assertEqual( alignment.target.annotations["acc.ver"], "gi|145479850|ref|XM_001425911.1|", ) self.assertEqual(alignment.target.annotations["length"], 4632) self.assertEqual( str(alignment), """\ gi|145479 0 PKTATGTKKGTIIGLLSIHTILFILTSHALSLEVKEQT*KDID 43 0 |.....||.||..||...|||.........||...|....|.| 43 gi|160806 30 PDSNIETKEGTYVGLADTHTIEVTVDNEPVSLDITEESTSDLD 73 """, ) self.assertTrue( np.array_equal( alignment.coordinates, np.array([[0, 43], [30, 73]]), ) ) self.assertEqual(alignment.target.annotations["start"], 1743) self.assertEqual(alignment.target.annotations["end"], 1872) self.assertEqual( alignment.target.seq, "PKTATGTKKGTIIGLLSIHTILFILTSHALSLEVKEQT*KDID" ) self.assertEqual( alignment.query.seq[30:73], "PDSNIETKEGTYVGLADTHTIEVTVDNEPVSLDITEESTSDLD", ) self.assertAlmostEqual(alignment.annotations["evalue"], 1e-05) self.assertAlmostEqual(alignment.annotations["bit score"], 34.7) self.assertAlmostEqual(alignment.score, 78) self.assertEqual(alignment.shape, (2, 43)) self.assertAlmostEqual(alignment.annotations["% identity"], 34.88) self.assertEqual(alignment.annotations["identical"], 15) self.assertEqual(alignment.annotations["mismatches"], 28) self.assertEqual(alignment.annotations["positives"], 26) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 60.47) self.assertEqual(alignment.annotations["query/sbjct frames"], "0/1") self.assertEqual(alignment.query.annotations["frame"], "0") self.assertEqual(alignment.target.annotations["frame"], "1") alignment = next(alignments) self.assertEqual(alignment.query.id, "gi|16080617|ref|NP_391444.1|") self.assertEqual( alignment.query.description, "membrane bound lipoprotein [Bacillus subtilis subsp. subtilis str. 168]", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual( alignment.query.annotations["acc."], "gi|16080617|ref|NP_391444.1|" ) self.assertEqual( alignment.query.annotations["acc.ver"], "gi|16080617|ref|NP_391444.1|" ) self.assertEqual(len(alignment.query.seq), 102) self.assertEqual(alignment.target.id, "gi|72012412|ref|XM_777959.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|72012412|ref|XM_777959.1|" ) self.assertEqual(alignment.target.annotations["gi"], "0") self.assertEqual(alignment.target.annotations["gis"], "0") self.assertEqual( alignment.target.annotations["acc."], "gi|72012412|ref|XM_777959.1|" ) self.assertEqual( alignment.target.annotations["acc.ver"], "gi|72012412|ref|XM_777959.1|" ) self.assertEqual(alignment.target.annotations["length"], 1593) self.assertEqual( str(alignment), """\ gi|720124 0 GLVPDHTLILPVGHYQSMLDLTEEVQTELDQFKSALRKYYLSKGKTCVIYERNFRTQHL 0 ||...||....|......||.|||....||.|.|.--------.|....||.|...|.| gi|160806 43 GLADTHTIEVTVDNEPVSLDITEESTSDLDKFNSG--------DKVTITYEKNDEGQLL gi|720124 59 59 gi|160806 94 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 35, 43, 59], [43, 78, 78, 94]]) # fmt: on ) ) self.assertEqual(alignment.target.annotations["start"], 1056) self.assertEqual(alignment.target.annotations["end"], 1233) self.assertEqual( alignment.target.seq, "GLVPDHTLILPVGHYQSMLDLTEEVQTELDQFKSALRKYYLSKGKTCVIYERNFRTQHL", ) self.assertEqual( alignment.query.seq[43:94], "GLADTHTIEVTVDNEPVSLDITEESTSDLDKFNSGDKVTITYEKNDEGQLL", ) self.assertAlmostEqual(alignment.annotations["evalue"], 1e-04) self.assertAlmostEqual(alignment.annotations["bit score"], 31.6) self.assertAlmostEqual(alignment.score, 70) self.assertEqual(alignment.shape, (2, 59)) self.assertAlmostEqual(alignment.annotations["% identity"], 33.90) self.assertEqual(alignment.annotations["identical"], 20) self.assertEqual(alignment.annotations["mismatches"], 31) self.assertEqual(alignment.annotations["positives"], 29) self.assertEqual(alignment.annotations["gap opens"], 1) self.assertEqual(alignment.annotations["gaps"], 8) self.assertAlmostEqual(alignment.annotations["% positives"], 49.15) self.assertEqual(alignment.annotations["query/sbjct frames"], "0/1") self.assertEqual(alignment.query.annotations["frame"], "0") self.assertEqual(alignment.target.annotations["frame"], "1") alignment = next(alignments) self.assertEqual(alignment.query.id, "gi|16080617|ref|NP_391444.1|") self.assertEqual( alignment.query.description, "membrane bound lipoprotein [Bacillus subtilis subsp. subtilis str. 168]", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual( alignment.query.annotations["acc."], "gi|16080617|ref|NP_391444.1|" ) self.assertEqual( alignment.query.annotations["acc.ver"], "gi|16080617|ref|NP_391444.1|" ) self.assertEqual(len(alignment.query.seq), 102) self.assertEqual(alignment.target.id, "gi|115975252|ref|XM_001180111.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|115975252|ref|XM_001180111.1|" ) self.assertEqual(alignment.target.annotations["gi"], "0") self.assertEqual(alignment.target.annotations["gis"], "0") self.assertEqual( alignment.target.annotations["acc."], "gi|115975252|ref|XM_001180111.1|" ) self.assertEqual( alignment.target.annotations["acc.ver"], "gi|115975252|ref|XM_001180111.1|", ) self.assertEqual(alignment.target.annotations["length"], 1593) self.assertEqual( str(alignment), """\ gi|115975 0 GLVPDHTLILPVGHYQSMLDLTEEVQTELDQFKSALRKYYLSKGKTCVIYERNFRTQHL 0 ||...||....|......||.|||....||.|.|.--------.|....||.|...|.| gi|160806 43 GLADTHTIEVTVDNEPVSLDITEESTSDLDKFNSG--------DKVTITYEKNDEGQLL gi|115975 59 59 gi|160806 94 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 35, 43, 59], [43, 78, 78, 94]]) # fmt: on ) ) self.assertEqual(alignment.target.annotations["start"], 1056) self.assertEqual(alignment.target.annotations["end"], 1233) self.assertEqual( alignment.target.seq, "GLVPDHTLILPVGHYQSMLDLTEEVQTELDQFKSALRKYYLSKGKTCVIYERNFRTQHL", ) self.assertEqual( alignment.query.seq[43:94], "GLADTHTIEVTVDNEPVSLDITEESTSDLDKFNSGDKVTITYEKNDEGQLL", ) self.assertAlmostEqual(alignment.annotations["evalue"], 1e-04) self.assertAlmostEqual(alignment.annotations["bit score"], 31.6) self.assertAlmostEqual(alignment.score, 70) self.assertEqual(alignment.shape, (2, 59)) self.assertAlmostEqual(alignment.annotations["% identity"], 33.90) self.assertEqual(alignment.annotations["identical"], 20) self.assertEqual(alignment.annotations["mismatches"], 31) self.assertEqual(alignment.annotations["positives"], 29) self.assertEqual(alignment.annotations["gap opens"], 1) self.assertEqual(alignment.annotations["gaps"], 8) self.assertAlmostEqual(alignment.annotations["% positives"], 49.15) self.assertEqual(alignment.annotations["query/sbjct frames"], "0/1") self.assertEqual(alignment.query.annotations["frame"], "0") self.assertEqual(alignment.target.annotations["frame"], "1") alignment = next(alignments) self.assertEqual(alignment.query.id, "gi|11464971:4-101") self.assertEqual(alignment.query.description, "pleckstrin [Mus musculus]") self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|11464971:4-101") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|11464971:4-101" ) self.assertEqual(len(alignment.query.seq), 98) self.assertEqual(alignment.target.id, "gi|350596019|ref|XM_003360601.2|") self.assertEqual( alignment.target.annotations["ids"], "gi|350596019|ref|XM_003360601.2|" ) self.assertEqual(alignment.target.annotations["gi"], "0") self.assertEqual(alignment.target.annotations["gis"], "0") self.assertEqual( alignment.target.annotations["acc."], "gi|350596019|ref|XM_003360601.2|" ) self.assertEqual( alignment.target.annotations["acc.ver"], "gi|350596019|ref|XM_003360601.2|", ) self.assertEqual(alignment.target.annotations["length"], 772) self.assertEqual( str(alignment), """\ gi|350596 0 KRIREGYLVKKGSMFNTWKPMWVILLEDGIEFYKKKSDNSPKGMIPLKGSTLTSPCQDFG 0 |||||||||||||.|||||||||.|||||||||||||||||||||||||||||||||||| gi|114649 0 KRIREGYLVKKGSVFNTWKPMWVVLLEDGIEFYKKKSDNSPKGMIPLKGSTLTSPCQDFG gi|350596 60 KRMFVFKITTTKQQDHFFQAAFLEERDGWVRDIKKAIK 98 60 |||||.|||||||||||||||||||||.|||||||||| 98 gi|114649 60 KRMFVLKITTTKQQDHFFQAAFLEERDAWVRDIKKAIK 98 """, ) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[0, 98], [0, 98]])) ) self.assertEqual(alignment.target.annotations["start"], 94) self.assertEqual(alignment.target.annotations["end"], 388) self.assertEqual( alignment.target.seq, "KRIREGYLVKKGSMFNTWKPMWVILLEDGIEFYKKKSDNSPKGMIPLKGSTLTSPCQDFGKRMFVFKITTTKQQDHFFQAAFLEERDGWVRDIKKAIK", ) self.assertEqual( alignment.query.seq[0:98], "KRIREGYLVKKGSVFNTWKPMWVVLLEDGIEFYKKKSDNSPKGMIPLKGSTLTSPCQDFGKRMFVLKITTTKQQDHFFQAAFLEERDAWVRDIKKAIK", ) self.assertAlmostEqual(alignment.annotations["evalue"], 2e-67, places=67) self.assertAlmostEqual(alignment.annotations["bit score"], 199) self.assertAlmostEqual(alignment.score, 506) self.assertEqual(alignment.shape, (2, 98)) self.assertAlmostEqual(alignment.annotations["% identity"], 95.92) self.assertEqual(alignment.annotations["identical"], 94) self.assertEqual(alignment.annotations["mismatches"], 4) self.assertEqual(alignment.annotations["positives"], 96) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 97.96) self.assertEqual(alignment.annotations["query/sbjct frames"], "0/2") self.assertEqual(alignment.query.annotations["frame"], "0") self.assertEqual(alignment.target.annotations["frame"], "2") alignment = next(alignments) self.assertEqual(alignment.query.id, "gi|11464971:4-101") self.assertEqual(alignment.query.description, "pleckstrin [Mus musculus]") self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|11464971:4-101") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|11464971:4-101" ) self.assertEqual(len(alignment.query.seq), 98) self.assertEqual(alignment.target.id, "gi|350596019|ref|XM_003360601.2|") self.assertEqual( alignment.target.annotations["ids"], "gi|350596019|ref|XM_003360601.2|" ) self.assertEqual(alignment.target.annotations["gi"], "0") self.assertEqual(alignment.target.annotations["gis"], "0") self.assertEqual( alignment.target.annotations["acc."], "gi|350596019|ref|XM_003360601.2|" ) self.assertEqual( alignment.target.annotations["acc.ver"], "gi|350596019|ref|XM_003360601.2|", ) self.assertEqual(alignment.target.annotations["length"], 772) self.assertEqual( str(alignment), """\ gi|350596 0 LHYYDPAGGEDPLGAIHLRGCVVTSVESNTDGKNGFLWERAXXITADEVHYFLQAANPKE 0 ...|.......|.|.|.|.|...||-.....||..|...---..|......|.|||...| gi|114649 29 IEFYKKKSDNSPKGMIPLKGSTLTS-PCQDFGKRMFVLK---ITTTKQQDHFFQAAFLEE gi|350596 60 RTEWIKAIQVA 71 60 |..|...|..| 71 gi|114649 85 RDAWVRDIKKA 96 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 25, 26, 39, 42, 71], [29, 54, 54, 67, 67, 96]]) # fmt: on ) ) self.assertEqual(alignment.target.annotations["start"], 541) self.assertEqual(alignment.target.annotations["end"], 754) self.assertEqual( alignment.target.seq, "LHYYDPAGGEDPLGAIHLRGCVVTSVESNTDGKNGFLWERAXXITADEVHYFLQAANPKERTEWIKAIQVA", ) self.assertEqual( alignment.query.seq[29:96], "IEFYKKKSDNSPKGMIPLKGSTLTSPCQDFGKRMFVLKITTTKQQDHFFQAAFLEERDAWVRDIKKA", ) self.assertAlmostEqual(alignment.annotations["evalue"], 4e-05) self.assertAlmostEqual(alignment.annotations["bit score"], 32.7) self.assertAlmostEqual(alignment.score, 73) self.assertEqual(alignment.shape, (2, 71)) self.assertAlmostEqual(alignment.annotations["% identity"], 29.58) self.assertEqual(alignment.annotations["identical"], 21) self.assertEqual(alignment.annotations["mismatches"], 46) self.assertEqual(alignment.annotations["positives"], 33) self.assertEqual(alignment.annotations["gap opens"], 2) self.assertEqual(alignment.annotations["gaps"], 4) self.assertAlmostEqual(alignment.annotations["% positives"], 46.48) self.assertEqual(alignment.annotations["query/sbjct frames"], "0/2") self.assertEqual(alignment.query.annotations["frame"], "0") self.assertEqual(alignment.target.annotations["frame"], "2") alignment = next(alignments) self.assertEqual(alignment.query.id, "gi|11464971:4-101") self.assertEqual(alignment.query.description, "pleckstrin [Mus musculus]") self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|11464971:4-101") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|11464971:4-101" ) self.assertEqual(len(alignment.query.seq), 98) self.assertEqual(alignment.target.id, "gi|301779869|ref|XM_002925302.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|301779869|ref|XM_002925302.1|" ) self.assertEqual(alignment.target.annotations["gi"], "0") self.assertEqual(alignment.target.annotations["gis"], "0") self.assertEqual( alignment.target.annotations["acc."], "gi|301779869|ref|XM_002925302.1|" ) self.assertEqual( alignment.target.annotations["acc.ver"], "gi|301779869|ref|XM_002925302.1|", ) self.assertEqual(alignment.target.annotations["length"], 1144) self.assertEqual( str(alignment), """\ gi|301779 0 KRIREGYLVKRGSVFNTWKPMWVVLLEDGIEFYKKKSDNSPKGMIPLKGSTLTSPCQDFG 0 ||||||||||.||||||||||||||||||||||||||||||||||||||||||||||||| gi|114649 0 KRIREGYLVKKGSVFNTWKPMWVVLLEDGIEFYKKKSDNSPKGMIPLKGSTLTSPCQDFG gi|301779 60 KRMFVFKITTTKQQDHFFQAAFLEERDAWVRDIKKAIK 98 60 |||||.|||||||||||||||||||||||||||||||| 98 gi|114649 60 KRMFVLKITTTKQQDHFFQAAFLEERDAWVRDIKKAIK 98 """, ) self.assertTrue( np.array_equal( alignment.coordinates, np.array([[0, 98], [0, 98]]), ) ) self.assertEqual(alignment.target.annotations["start"], 77) self.assertEqual(alignment.target.annotations["end"], 371) self.assertEqual( alignment.target.seq, "KRIREGYLVKRGSVFNTWKPMWVVLLEDGIEFYKKKSDNSPKGMIPLKGSTLTSPCQDFGKRMFVFKITTTKQQDHFFQAAFLEERDAWVRDIKKAIK", ) self.assertEqual( alignment.query.seq[0:98], "KRIREGYLVKKGSVFNTWKPMWVVLLEDGIEFYKKKSDNSPKGMIPLKGSTLTSPCQDFGKRMFVLKITTTKQQDHFFQAAFLEERDAWVRDIKKAIK", ) self.assertAlmostEqual(alignment.annotations["evalue"], 2e-67, places=67) self.assertAlmostEqual(alignment.annotations["bit score"], 202) self.assertAlmostEqual(alignment.score, 515) self.assertEqual(alignment.shape, (2, 98)) self.assertAlmostEqual(alignment.annotations["% identity"], 97.96) self.assertEqual(alignment.annotations["identical"], 96) self.assertEqual(alignment.annotations["mismatches"], 2) self.assertEqual(alignment.annotations["positives"], 97) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 98.98) self.assertEqual(alignment.annotations["query/sbjct frames"], "0/3") self.assertEqual(alignment.query.annotations["frame"], "0") self.assertEqual(alignment.target.annotations["frame"], "3") alignment = next(alignments) self.assertEqual(alignment.query.id, "gi|11464971:4-101") self.assertEqual(alignment.query.description, "pleckstrin [Mus musculus]") self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|11464971:4-101") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|11464971:4-101" ) self.assertEqual(len(alignment.query.seq), 98) self.assertEqual(alignment.target.id, "gi|301779869|ref|XM_002925302.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|301779869|ref|XM_002925302.1|" ) self.assertEqual(alignment.target.annotations["gi"], "0") self.assertEqual(alignment.target.annotations["gis"], "0") self.assertEqual( alignment.target.annotations["acc."], "gi|301779869|ref|XM_002925302.1|" ) self.assertEqual( alignment.target.annotations["acc.ver"], "gi|301779869|ref|XM_002925302.1|", ) self.assertEqual(alignment.target.annotations["length"], 1144) self.assertEqual( str(alignment), """\ gi|301779 0 IKQGCLLKQGHRRKNWKVRKFILREDPAYLHYYDPAGGEDPLGAIHLRGCVVTSVESNPD 0 |..|.|.|.|.....||.....|.||.--...|.......|.|.|.|.|...||----|. gi|114649 2 IREGYLVKKGSVFNTWKPMWVVLLEDG--IEFYKKKSDNSPKGMIPLKGSTLTS----PC gi|301779 60 VRKSEEENLFEIITADEVHYFLQAATPKERTEWIKAIQVA 100 60 ...........|.|......|.|||...||..|...|..| 100 gi|114649 56 QDFGKRMFVLKITTTKQQDHFFQAAFLEERDAWVRDIKKA 96 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[0, 27, 29, 54, 58, 100], [2, 29, 29, 54, 54, 96]]) # fmt: on ) ) self.assertEqual(alignment.target.annotations["start"], 803) self.assertEqual(alignment.target.annotations["end"], 1103) self.assertEqual( alignment.target.seq, "IKQGCLLKQGHRRKNWKVRKFILREDPAYLHYYDPAGGEDPLGAIHLRGCVVTSVESNPDVRKSEEENLFEIITADEVHYFLQAATPKERTEWIKAIQVA", ) self.assertEqual( alignment.query.seq[2:96], "IREGYLVKKGSVFNTWKPMWVVLLEDGIEFYKKKSDNSPKGMIPLKGSTLTSPCQDFGKRMFVLKITTTKQQDHFFQAAFLEERDAWVRDIKKA", ) self.assertAlmostEqual(alignment.annotations["evalue"], 3e-09, places=9) self.assertAlmostEqual(alignment.annotations["bit score"], 45.1) self.assertAlmostEqual(alignment.score, 105) self.assertEqual(alignment.shape, (2, 100)) self.assertAlmostEqual(alignment.annotations["% identity"], 30.00) self.assertEqual(alignment.annotations["identical"], 30) self.assertEqual(alignment.annotations["mismatches"], 64) self.assertEqual(alignment.annotations["positives"], 48) self.assertEqual(alignment.annotations["gap opens"], 2) self.assertEqual(alignment.annotations["gaps"], 6) self.assertAlmostEqual(alignment.annotations["% positives"], 48.00) self.assertEqual(alignment.annotations["query/sbjct frames"], "0/3") self.assertEqual(alignment.query.annotations["frame"], "0") self.assertEqual(alignment.target.annotations["frame"], "3") alignment = next(alignments) self.assertEqual(alignment.query.id, "gi|11464971:4-101") self.assertEqual(alignment.query.description, "pleckstrin [Mus musculus]") self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|11464971:4-101") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|11464971:4-101" ) self.assertEqual(len(alignment.query.seq), 98) self.assertEqual(alignment.target.id, "gi|296223671|ref|XM_002757683.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|296223671|ref|XM_002757683.1|" ) self.assertEqual(alignment.target.annotations["gi"], "0") self.assertEqual(alignment.target.annotations["gis"], "0") self.assertEqual( alignment.target.annotations["acc."], "gi|296223671|ref|XM_002757683.1|" ) self.assertEqual( alignment.target.annotations["acc.ver"], "gi|296223671|ref|XM_002757683.1|", ) self.assertEqual(alignment.target.annotations["length"], 1183) self.assertEqual( str(alignment), """\ gi|296223 0 KRIREGYLVKKGSMFNTWKPMWVVLLEDGIEFYKKKSDNSPKGMIPLKGSTLTSPCQDFG 0 |||||||||||||.|||||||||||||||||||||||||||||||||||||||||||||| gi|114649 0 KRIREGYLVKKGSVFNTWKPMWVVLLEDGIEFYKKKSDNSPKGMIPLKGSTLTSPCQDFG gi|296223 60 KRMFVFKITTTKQQDHFFQAAFLEERDAWVRDIKKAIK 98 60 |||||.|||||||||||||||||||||||||||||||| 98 gi|114649 60 KRMFVLKITTTKQQDHFFQAAFLEERDAWVRDIKKAIK 98 """, ) self.assertTrue( np.array_equal( alignment.coordinates, np.array([[0, 98], [0, 98]]), ) ) self.assertEqual(alignment.target.annotations["start"], 160) self.assertEqual(alignment.target.annotations["end"], 454) self.assertEqual( alignment.target.seq, "KRIREGYLVKKGSMFNTWKPMWVVLLEDGIEFYKKKSDNSPKGMIPLKGSTLTSPCQDFGKRMFVFKITTTKQQDHFFQAAFLEERDAWVRDIKKAIK", ) self.assertEqual( alignment.query.seq[0:98], "KRIREGYLVKKGSVFNTWKPMWVVLLEDGIEFYKKKSDNSPKGMIPLKGSTLTSPCQDFGKRMFVLKITTTKQQDHFFQAAFLEERDAWVRDIKKAIK", ) self.assertAlmostEqual(alignment.annotations["evalue"], 4e-67, places=67) self.assertAlmostEqual(alignment.annotations["bit score"], 202) self.assertAlmostEqual(alignment.score, 515) self.assertEqual(alignment.shape, (2, 98)) self.assertAlmostEqual(alignment.annotations["% identity"], 97.96) self.assertEqual(alignment.annotations["identical"], 96) self.assertEqual(alignment.annotations["mismatches"], 2) self.assertEqual(alignment.annotations["positives"], 97) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 98.98) self.assertEqual(alignment.annotations["query/sbjct frames"], "0/2") self.assertEqual(alignment.query.annotations["frame"], "0") self.assertEqual(alignment.target.annotations["frame"], "2") alignment = next(alignments) self.assertEqual(alignment.query.id, "gi|11464971:4-101") self.assertEqual(alignment.query.description, "pleckstrin [Mus musculus]") self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|11464971:4-101") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|11464971:4-101" ) self.assertEqual(len(alignment.query.seq), 98) self.assertEqual(alignment.target.id, "gi|296223671|ref|XM_002757683.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|296223671|ref|XM_002757683.1|" ) self.assertEqual(alignment.target.annotations["gi"], "0") self.assertEqual(alignment.target.annotations["gis"], "0") self.assertEqual( alignment.target.annotations["acc."], "gi|296223671|ref|XM_002757683.1|" ) self.assertEqual( alignment.target.annotations["acc.ver"], "gi|296223671|ref|XM_002757683.1|", ) self.assertEqual(alignment.target.annotations["length"], 1183) self.assertEqual( str(alignment), """\ gi|296223 0 IKQGCLLKQGHRRKNWKVRKFILREDPAYLHYYDPAGGEDPLGAIHLRGCVVTSVESNSD 0 |..|.|.|.|.....||.....|.||.--...|.......|.|.|.|.|...||...... gi|114649 2 IREGYLVKKGSVFNTWKPMWVVLLEDG--IEFYKKKSDNSPKGMIPLKGSTLTSPCQDFG gi|296223 60 GRKSEEENLFEIITADEVHYFLQAATPKERTEWIKAIQVA 100 60 .|..----...|.|......|.|||...||..|...|..| 100 gi|114649 60 KRMF----VLKITTTKQQDHFFQAAFLEERDAWVRDIKKA 96 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[0, 27, 29, 64, 68, 100], [2, 29, 29, 64, 64, 96]]) # fmt: on ) ) self.assertEqual(alignment.target.annotations["start"], 865) self.assertEqual(alignment.target.annotations["end"], 1165) self.assertEqual( alignment.target.seq, "IKQGCLLKQGHRRKNWKVRKFILREDPAYLHYYDPAGGEDPLGAIHLRGCVVTSVESNSDGRKSEEENLFEIITADEVHYFLQAATPKERTEWIKAIQVA", ) self.assertEqual( alignment.query.seq[2:96], "IREGYLVKKGSVFNTWKPMWVVLLEDGIEFYKKKSDNSPKGMIPLKGSTLTSPCQDFGKRMFVLKITTTKQQDHFFQAAFLEERDAWVRDIKKA", ) self.assertAlmostEqual(alignment.annotations["evalue"], 3e-09, places=9) self.assertAlmostEqual(alignment.annotations["bit score"], 45.1) self.assertAlmostEqual(alignment.score, 105) self.assertEqual(alignment.shape, (2, 100)) self.assertAlmostEqual(alignment.annotations["% identity"], 30.00) self.assertEqual(alignment.annotations["identical"], 30) self.assertEqual(alignment.annotations["mismatches"], 64) self.assertEqual(alignment.annotations["positives"], 48) self.assertEqual(alignment.annotations["gap opens"], 2) self.assertEqual(alignment.annotations["gaps"], 6) self.assertAlmostEqual(alignment.annotations["% positives"], 48.00) self.assertEqual(alignment.annotations["query/sbjct frames"], "0/2") self.assertEqual(alignment.query.annotations["frame"], "0") self.assertEqual(alignment.target.annotations["frame"], "2") alignment = next(alignments) self.assertEqual(alignment.query.id, "gi|11464971:4-101") self.assertEqual(alignment.query.description, "pleckstrin [Mus musculus]") self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|11464971:4-101") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|11464971:4-101" ) self.assertEqual(len(alignment.query.seq), 98) self.assertEqual(alignment.target.id, "gi|338714227|ref|XM_001492113.3|") self.assertEqual( alignment.target.annotations["ids"], "gi|338714227|ref|XM_001492113.3|" ) self.assertEqual(alignment.target.annotations["gi"], "0") self.assertEqual(alignment.target.annotations["gis"], "0") self.assertEqual( alignment.target.annotations["acc."], "gi|338714227|ref|XM_001492113.3|" ) self.assertEqual( alignment.target.annotations["acc.ver"], "gi|338714227|ref|XM_001492113.3|", ) self.assertEqual(alignment.target.annotations["length"], 1390) self.assertEqual( str(alignment), """\ gi|338714 0 KRIREGYLVKRGSVFNTWKPMWVVLLEDGIEFYKKKSDNSPKGMIPLKGSTLTSPCQDFG 0 ||||||||||.||||||||||||||||||||||||||||||||||||||||||||||||| gi|114649 0 KRIREGYLVKKGSVFNTWKPMWVVLLEDGIEFYKKKSDNSPKGMIPLKGSTLTSPCQDFG gi|338714 60 KRMFVFKITTTKQQDHFFQAAFLEERDAWVRDIKKAIK 98 60 |||||.|||||||||||||||||||||||||||||||| 98 gi|114649 60 KRMFVLKITTTKQQDHFFQAAFLEERDAWVRDIKKAIK 98 """, ) self.assertTrue( np.array_equal( alignment.coordinates, np.array([[0, 98], [0, 98]]), ) ) self.assertEqual(alignment.target.annotations["start"], 172) self.assertEqual(alignment.target.annotations["end"], 466) self.assertEqual( alignment.target.seq, "KRIREGYLVKRGSVFNTWKPMWVVLLEDGIEFYKKKSDNSPKGMIPLKGSTLTSPCQDFGKRMFVFKITTTKQQDHFFQAAFLEERDAWVRDIKKAIK", ) self.assertEqual( alignment.query.seq[0:98], "KRIREGYLVKKGSVFNTWKPMWVVLLEDGIEFYKKKSDNSPKGMIPLKGSTLTSPCQDFGKRMFVLKITTTKQQDHFFQAAFLEERDAWVRDIKKAIK", ) self.assertAlmostEqual(alignment.annotations["evalue"], 2e-66, places=66) self.assertAlmostEqual(alignment.annotations["bit score"], 202) self.assertAlmostEqual(alignment.score, 515) self.assertEqual(alignment.shape, (2, 98)) self.assertAlmostEqual(alignment.annotations["% identity"], 97.96) self.assertEqual(alignment.annotations["identical"], 96) self.assertEqual(alignment.annotations["mismatches"], 2) self.assertEqual(alignment.annotations["positives"], 97) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 98.98) self.assertEqual(alignment.annotations["query/sbjct frames"], "0/2") self.assertEqual(alignment.query.annotations["frame"], "0") self.assertEqual(alignment.target.annotations["frame"], "2") alignment = next(alignments) self.assertEqual(alignment.query.id, "gi|11464971:4-101") self.assertEqual(alignment.query.description, "pleckstrin [Mus musculus]") self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|11464971:4-101") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|11464971:4-101" ) self.assertEqual(len(alignment.query.seq), 98) self.assertEqual(alignment.target.id, "gi|338714227|ref|XM_001492113.3|") self.assertEqual( alignment.target.annotations["ids"], "gi|338714227|ref|XM_001492113.3|" ) self.assertEqual(alignment.target.annotations["gi"], "0") self.assertEqual(alignment.target.annotations["gis"], "0") self.assertEqual( alignment.target.annotations["acc."], "gi|338714227|ref|XM_001492113.3|" ) self.assertEqual( alignment.target.annotations["acc.ver"], "gi|338714227|ref|XM_001492113.3|", ) self.assertEqual(alignment.target.annotations["length"], 1390) self.assertEqual( str(alignment), """\ gi|338714 0 IKQGCLLKQGHRRKNWKVRKFVLREDPAYVHYYDPAGGEEPLGAIHLRGCVVTSVEGNPD 0 |..|.|.|.|.....||....||.||.--...|.......|.|.|.|.|...||----|. gi|114649 2 IREGYLVKKGSVFNTWKPMWVVLLEDG--IEFYKKKSDNSPKGMIPLKGSTLTS----PC gi|338714 60 GKKSEEENLFEIITADEVHYFLQAATPKERTEWIKAIQVA 100 60 ...........|.|......|.|||...||..|...|..| 100 gi|114649 56 QDFGKRMFVLKITTTKQQDHFFQAAFLEERDAWVRDIKKA 96 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[0, 27, 29, 54, 58, 100], [2, 29, 29, 54, 54, 96]]) # fmt: on ) ) self.assertEqual(alignment.target.annotations["start"], 898) self.assertEqual(alignment.target.annotations["end"], 1198) self.assertEqual( alignment.target.seq, "IKQGCLLKQGHRRKNWKVRKFVLREDPAYVHYYDPAGGEEPLGAIHLRGCVVTSVEGNPDGKKSEEENLFEIITADEVHYFLQAATPKERTEWIKAIQVA", ) self.assertEqual( alignment.query.seq[2:96], "IREGYLVKKGSVFNTWKPMWVVLLEDGIEFYKKKSDNSPKGMIPLKGSTLTSPCQDFGKRMFVLKITTTKQQDHFFQAAFLEERDAWVRDIKKA", ) self.assertAlmostEqual(alignment.annotations["evalue"], 1e-09, places=9) self.assertAlmostEqual(alignment.annotations["bit score"], 46.6) self.assertAlmostEqual(alignment.score, 109) self.assertEqual(alignment.shape, (2, 100)) self.assertAlmostEqual(alignment.annotations["% identity"], 31.00) self.assertEqual(alignment.annotations["identical"], 31) self.assertEqual(alignment.annotations["mismatches"], 63) self.assertEqual(alignment.annotations["positives"], 48) self.assertEqual(alignment.annotations["gap opens"], 2) self.assertEqual(alignment.annotations["gaps"], 6) self.assertAlmostEqual(alignment.annotations["% positives"], 48.00) self.assertEqual(alignment.annotations["query/sbjct frames"], "0/2") self.assertEqual(alignment.query.annotations["frame"], "0") self.assertEqual(alignment.target.annotations["frame"], "2") alignment = next(alignments) self.assertEqual(alignment.query.id, "gi|11464971:4-101") self.assertEqual(alignment.query.description, "pleckstrin [Mus musculus]") self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|11464971:4-101") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|11464971:4-101" ) self.assertEqual(len(alignment.query.seq), 98) self.assertEqual(alignment.target.id, "gi|365982352|ref|XM_003667962.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|365982352|ref|XM_003667962.1|" ) self.assertEqual(alignment.target.annotations["gi"], "0") self.assertEqual(alignment.target.annotations["gis"], "0") self.assertEqual( alignment.target.annotations["acc."], "gi|365982352|ref|XM_003667962.1|" ) self.assertEqual( alignment.target.annotations["acc.ver"], "gi|365982352|ref|XM_003667962.1|", ) self.assertEqual(alignment.target.annotations["length"], 4932) self.assertEqual( str(alignment), """\ gi|365982 0 GSCFPTWDLIFIEVLNPFLKEKLWEADNEEISKFVDLTLKGLVDLYPSHFTS 52 0 ||.|.||.......|---------|...|...|..|...||...|..|..|| 52 gi|114649 11 GSVFNTWKPMWVVLL---------EDGIEFYKKKSDNSPKGMIPLKGSTLTS 54 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 15, 24, 52], [11, 26, 26, 54]]) # fmt: on ) ) self.assertEqual(alignment.target.annotations["start"], 3180) self.assertEqual(alignment.target.annotations["end"], 3336) self.assertEqual( alignment.target.seq, "GSCFPTWDLIFIEVLNPFLKEKLWEADNEEISKFVDLTLKGLVDLYPSHFTS", ) self.assertEqual( alignment.query.seq[11:54], "GSVFNTWKPMWVVLLEDGIEFYKKKSDNSPKGMIPLKGSTLTS", ) self.assertAlmostEqual(alignment.annotations["evalue"], 1.7) self.assertAlmostEqual(alignment.annotations["bit score"], 19.6) self.assertAlmostEqual(alignment.score, 39) self.assertEqual(alignment.shape, (2, 52)) self.assertAlmostEqual(alignment.annotations["% identity"], 30.77) self.assertEqual(alignment.annotations["identical"], 16) self.assertEqual(alignment.annotations["mismatches"], 27) self.assertEqual(alignment.annotations["positives"], 23) self.assertEqual(alignment.annotations["gap opens"], 1) self.assertEqual(alignment.annotations["gaps"], 9) self.assertAlmostEqual(alignment.annotations["% positives"], 44.23) self.assertEqual(alignment.annotations["query/sbjct frames"], "0/1") self.assertEqual(alignment.query.annotations["frame"], "0") self.assertEqual(alignment.target.annotations["frame"], "1") with self.assertRaises(StopIteration): next(alignments) def test_2226_tblastn_012(self): path = "Blast/tab_2226_tblastn_012.txt" with open(path) as stream: alignments = Align.parse(stream, "tabular") self.assertEqual(alignments.metadata["Program"], "TBLASTN") self.assertEqual(alignments.metadata["Version"], "2.2.26+") self.assertEqual(alignments.metadata["RID"], "X76FDCG9016") self.assertEqual(alignments.metadata["Database"], "refseq_rna") alignment = next(alignments) self.assertEqual(alignment.query.id, "gi|16080617|ref|NP_391444.1|") self.assertEqual(alignment.target.id, "gi|145479850|ref|XM_001425911.1|") self.assertEqual(alignment.query.annotations["start"], 30) self.assertEqual(alignment.query.annotations["end"], 73) self.assertEqual(alignment.target.annotations["start"], 1743) self.assertEqual(alignment.target.annotations["end"], 1872) self.assertAlmostEqual(alignment.annotations["evalue"], 0.76) self.assertAlmostEqual(alignment.annotations["bit score"], 34.7) self.assertAlmostEqual(alignment.annotations["% identity"], 34.88) self.assertEqual(alignment.annotations["alignment length"], 43) self.assertEqual(alignment.annotations["mismatches"], 28) self.assertEqual(alignment.annotations["gap opens"], 0) alignment = next(alignments) self.assertEqual(alignment.query.id, "gi|16080617|ref|NP_391444.1|") self.assertEqual(alignment.target.id, "gi|115975252|ref|XM_001180111.1|") self.assertEqual(alignment.query.annotations["start"], 43) self.assertEqual(alignment.query.annotations["end"], 94) self.assertEqual(alignment.target.annotations["start"], 1056) self.assertEqual(alignment.target.annotations["end"], 1233) self.assertAlmostEqual(alignment.annotations["evalue"], 7.2) self.assertAlmostEqual(alignment.annotations["bit score"], 31.6) self.assertAlmostEqual(alignment.annotations["% identity"], 33.90) self.assertEqual(alignment.annotations["alignment length"], 59) self.assertEqual(alignment.annotations["mismatches"], 31) self.assertEqual(alignment.annotations["gap opens"], 1) alignment = next(alignments) self.assertEqual(alignment.query.id, "gi|16080617|ref|NP_391444.1|") self.assertEqual(alignment.target.id, "gi|390342090|ref|XM_777959.2|") self.assertEqual(alignment.query.annotations["start"], 43) self.assertEqual(alignment.query.annotations["end"], 94) self.assertEqual(alignment.target.annotations["start"], 1266) self.assertEqual(alignment.target.annotations["end"], 1443) self.assertAlmostEqual(alignment.annotations["evalue"], 7.6) self.assertAlmostEqual(alignment.annotations["bit score"], 31.6) self.assertAlmostEqual(alignment.annotations["% identity"], 33.90) self.assertEqual(alignment.annotations["alignment length"], 59) self.assertEqual(alignment.annotations["mismatches"], 31) self.assertEqual(alignment.annotations["gap opens"], 1) alignment = next(alignments) self.assertEqual(alignment.query.id, "gi|11464971:4-101") self.assertEqual(alignment.target.id, "gi|354480463|ref|XM_003502378.1|") self.assertEqual(alignment.query.description, "pleckstrin [Mus musculus]") self.assertEqual(alignment.query.annotations["start"], 0) self.assertEqual(alignment.query.annotations["end"], 98) self.assertEqual(alignment.target.annotations["start"], 75) self.assertEqual(alignment.target.annotations["end"], 369) self.assertAlmostEqual(alignment.annotations["evalue"], 1e-63, places=63) self.assertAlmostEqual(alignment.annotations["bit score"], 205) self.assertAlmostEqual(alignment.annotations["% identity"], 100.00) self.assertEqual(alignment.annotations["alignment length"], 98) self.assertEqual(alignment.annotations["mismatches"], 0) self.assertEqual(alignment.annotations["gap opens"], 0) alignment = next(alignments) self.assertEqual(alignment.query.id, "gi|11464971:4-101") self.assertEqual(alignment.target.id, "gi|354480463|ref|XM_003502378.1|") self.assertEqual(alignment.query.description, "pleckstrin [Mus musculus]") self.assertEqual(alignment.query.annotations["start"], 2) self.assertEqual(alignment.query.annotations["end"], 96) self.assertEqual(alignment.target.annotations["start"], 801) self.assertEqual(alignment.target.annotations["end"], 1101) self.assertAlmostEqual(alignment.annotations["evalue"], 5e-04) self.assertAlmostEqual(alignment.annotations["bit score"], 43.9) self.assertAlmostEqual(alignment.annotations["% identity"], 30.00) self.assertEqual(alignment.annotations["alignment length"], 100) self.assertEqual(alignment.annotations["mismatches"], 64) self.assertEqual(alignment.annotations["gap opens"], 3) alignment = next(alignments) self.assertEqual(alignment.query.id, "gi|11464971:4-101") self.assertEqual(alignment.target.id, "gi|350596019|ref|XM_003360601.2|") self.assertEqual(alignment.query.description, "pleckstrin [Mus musculus]") self.assertEqual(alignment.query.annotations["start"], 0) self.assertEqual(alignment.query.annotations["end"], 98) self.assertEqual(alignment.target.annotations["start"], 94) self.assertEqual(alignment.target.annotations["end"], 388) self.assertAlmostEqual(alignment.annotations["evalue"], 1e-62, places=62) self.assertAlmostEqual(alignment.annotations["bit score"], 199) self.assertAlmostEqual(alignment.annotations["% identity"], 95.92) self.assertEqual(alignment.annotations["alignment length"], 98) self.assertEqual(alignment.annotations["mismatches"], 4) self.assertEqual(alignment.annotations["gap opens"], 0) alignment = next(alignments) self.assertEqual(alignment.query.id, "gi|11464971:4-101") self.assertEqual(alignment.target.id, "gi|350596019|ref|XM_003360601.2|") self.assertEqual(alignment.query.description, "pleckstrin [Mus musculus]") self.assertEqual(alignment.query.annotations["start"], 29) self.assertEqual(alignment.query.annotations["end"], 96) self.assertEqual(alignment.target.annotations["start"], 541) self.assertEqual(alignment.target.annotations["end"], 754) self.assertAlmostEqual(alignment.annotations["evalue"], 2.8) self.assertAlmostEqual(alignment.annotations["bit score"], 32.7) self.assertAlmostEqual(alignment.annotations["% identity"], 29.58) self.assertEqual(alignment.annotations["alignment length"], 71) self.assertEqual(alignment.annotations["mismatches"], 46) self.assertEqual(alignment.annotations["gap opens"], 2) alignment = next(alignments) self.assertEqual(alignment.query.id, "gi|11464971:4-101") self.assertEqual(alignment.target.id, "gi|301779869|ref|XM_002925302.1|") self.assertEqual(alignment.query.description, "pleckstrin [Mus musculus]") self.assertEqual(alignment.query.annotations["start"], 0) self.assertEqual(alignment.query.annotations["end"], 98) self.assertEqual(alignment.target.annotations["start"], 77) self.assertEqual(alignment.target.annotations["end"], 371) self.assertAlmostEqual(alignment.annotations["evalue"], 2e-62, places=62) self.assertAlmostEqual(alignment.annotations["bit score"], 202) self.assertAlmostEqual(alignment.annotations["% identity"], 97.96) self.assertEqual(alignment.annotations["alignment length"], 98) self.assertEqual(alignment.annotations["mismatches"], 2) self.assertEqual(alignment.annotations["gap opens"], 0) alignment = next(alignments) self.assertEqual(alignment.query.id, "gi|11464971:4-101") self.assertEqual(alignment.target.id, "gi|301779869|ref|XM_002925302.1|") self.assertEqual(alignment.query.description, "pleckstrin [Mus musculus]") self.assertEqual(alignment.query.annotations["start"], 2) self.assertEqual(alignment.query.annotations["end"], 96) self.assertEqual(alignment.target.annotations["start"], 803) self.assertEqual(alignment.target.annotations["end"], 1103) self.assertAlmostEqual(alignment.annotations["evalue"], 2e-04) self.assertAlmostEqual(alignment.annotations["bit score"], 45.1) self.assertAlmostEqual(alignment.annotations["% identity"], 30.00) self.assertEqual(alignment.annotations["alignment length"], 100) self.assertEqual(alignment.annotations["mismatches"], 64) self.assertEqual(alignment.annotations["gap opens"], 2) alignment = next(alignments) self.assertEqual(alignment.query.id, "gi|11464971:4-101") self.assertEqual(alignment.target.id, "gi|338714227|ref|XM_001492113.3|") self.assertEqual(alignment.query.description, "pleckstrin [Mus musculus]") self.assertEqual(alignment.query.annotations["start"], 0) self.assertEqual(alignment.query.annotations["end"], 98) self.assertEqual(alignment.target.annotations["start"], 172) self.assertEqual(alignment.target.annotations["end"], 466) self.assertAlmostEqual(alignment.annotations["evalue"], 1e-61, places=61) self.assertAlmostEqual(alignment.annotations["bit score"], 202) self.assertAlmostEqual(alignment.annotations["% identity"], 97.96) self.assertEqual(alignment.annotations["alignment length"], 98) self.assertEqual(alignment.annotations["mismatches"], 2) self.assertEqual(alignment.annotations["gap opens"], 0) alignment = next(alignments) self.assertEqual(alignment.query.id, "gi|11464971:4-101") self.assertEqual(alignment.target.id, "gi|338714227|ref|XM_001492113.3|") self.assertEqual(alignment.query.description, "pleckstrin [Mus musculus]") self.assertEqual(alignment.query.annotations["start"], 2) self.assertEqual(alignment.query.annotations["end"], 96) self.assertEqual(alignment.target.annotations["start"], 898) self.assertEqual(alignment.target.annotations["end"], 1198) self.assertAlmostEqual(alignment.annotations["evalue"], 9e-05) self.assertAlmostEqual(alignment.annotations["bit score"], 46.6) self.assertAlmostEqual(alignment.annotations["% identity"], 31.00) self.assertEqual(alignment.annotations["alignment length"], 100) self.assertEqual(alignment.annotations["mismatches"], 63) self.assertEqual(alignment.annotations["gap opens"], 2) alignment = next(alignments) self.assertEqual(alignment.query.id, "gi|11464971:4-101") self.assertEqual(alignment.target.id, "gi|390474391|ref|XM_002757683.2|") self.assertEqual(alignment.query.description, "pleckstrin [Mus musculus]") self.assertEqual(alignment.query.annotations["start"], 0) self.assertEqual(alignment.query.annotations["end"], 98) self.assertEqual(alignment.target.annotations["start"], 160) self.assertEqual(alignment.target.annotations["end"], 454) self.assertAlmostEqual(alignment.annotations["evalue"], 1e-61, places=61) self.assertAlmostEqual(alignment.annotations["bit score"], 202) self.assertAlmostEqual(alignment.annotations["% identity"], 97.96) self.assertEqual(alignment.annotations["alignment length"], 98) self.assertEqual(alignment.annotations["mismatches"], 2) self.assertEqual(alignment.annotations["gap opens"], 0) with self.assertRaises(StopIteration): next(alignments) def test_2228_tblastn_001(self): path = "Blast/tab_2228_tblastn_001.txt" with open(path) as stream: alignments = Align.parse(stream, "tabular") self.assertEqual(alignments.metadata["Program"], "TBLASTN") self.assertEqual(alignments.metadata["Version"], "2.2.28+") self.assertEqual(alignments.metadata["RID"], "M6BMVNA2015") self.assertEqual(alignments.metadata["Database"], "nr") alignment = next(alignments) self.assertEqual(alignment.query.id, "gi|148227874|ref|NP_001088636.1|") self.assertEqual(alignment.query.description, "sirtuin 2 [Xenopus laevis]") self.assertEqual( alignment.target.annotations["ids"], "gi|148227873|ref|NM_001095167.1|;gi|55250552|gb|BC086280.1|", ) self.assertAlmostEqual(alignment.annotations["evalue"], 0.0) alignment = next(alignments) self.assertEqual(alignment.query.id, "gi|148227874|ref|NP_001088636.1|") self.assertEqual(alignment.query.description, "sirtuin 2 [Xenopus laevis]") self.assertEqual( alignment.target.annotations["ids"], "gi|512812550|ref|XM_002935781.2|" ) self.assertAlmostEqual(alignment.annotations["evalue"], 0.0) alignment = next(alignments) self.assertEqual(alignment.query.id, "gi|148227874|ref|NP_001088636.1|") self.assertEqual(alignment.query.description, "sirtuin 2 [Xenopus laevis]") self.assertEqual( alignment.target.annotations["ids"], "gi|512812554|ref|XM_004910718.1|" ) self.assertAlmostEqual(alignment.annotations["evalue"], 0.0) alignment = next(alignments) self.assertEqual(alignment.query.id, "gi|148227874|ref|NP_001088636.1|") self.assertEqual(alignment.query.description, "sirtuin 2 [Xenopus laevis]") self.assertEqual( alignment.target.annotations["ids"], "gi|327289356|ref|XM_003229343.1|" ) self.assertAlmostEqual(alignment.annotations["evalue"], 0.0) alignment = next(alignments) self.assertEqual(alignment.query.id, "gi|148227874|ref|NP_001088636.1|") self.assertEqual(alignment.query.description, "sirtuin 2 [Xenopus laevis]") self.assertEqual( alignment.target.annotations["ids"], "gi|602661018|ref|XM_007436108.1|" ) self.assertAlmostEqual(alignment.annotations["evalue"], 0.0) alignment = next(alignments) self.assertEqual(alignment.query.id, "gi|148227874|ref|NP_001088636.1|") self.assertEqual(alignment.query.description, "sirtuin 2 [Xenopus laevis]") self.assertEqual( alignment.target.annotations["ids"], "gi|564242014|ref|XM_006277753.1|" ) self.assertAlmostEqual(alignment.annotations["evalue"], 0.0) alignment = next(alignments) self.assertEqual(alignment.query.id, "gi|148227874|ref|NP_001088636.1|") self.assertEqual(alignment.query.description, "sirtuin 2 [Xenopus laevis]") self.assertEqual( alignment.target.annotations["ids"], "gi|591387858|ref|XM_007068281.1|" ) self.assertAlmostEqual(alignment.annotations["evalue"], 2e-180, places=180) alignment = next(alignments) self.assertEqual(alignment.query.id, "gi|148227874|ref|NP_001088636.1|") self.assertEqual(alignment.query.description, "sirtuin 2 [Xenopus laevis]") self.assertEqual( alignment.target.annotations["ids"], "gi|558185265|ref|XM_006128143.1|" ) self.assertAlmostEqual(alignment.annotations["evalue"], 8e-180, places=180) alignment = next(alignments) self.assertEqual(alignment.query.id, "gi|148227874|ref|NP_001088636.1|") self.assertEqual(alignment.query.description, "sirtuin 2 [Xenopus laevis]") self.assertEqual( alignment.target.annotations["ids"], "gi|573878747|ref|XM_006627536.1|" ) self.assertAlmostEqual(alignment.annotations["evalue"], 5e-173, places=173) alignment = next(alignments) self.assertEqual(alignment.query.id, "gi|148227874|ref|NP_001088636.1|") self.assertEqual(alignment.query.description, "sirtuin 2 [Xenopus laevis]") self.assertEqual( alignment.target.annotations["ids"], "gi|410910671|ref|XM_003968765.1|" ) self.assertAlmostEqual(alignment.annotations["evalue"], 8e-173, places=173) with self.assertRaises(StopIteration): next(alignments) def test_2228_tblastx_001(self): path = "Blast/tab_2228_tblastx_001.txt" with open(path) as stream: alignments = Align.parse(stream, "tabular") self.assertEqual(alignments.metadata["Program"], "TBLASTX") self.assertEqual(alignments.metadata["Version"], "2.2.28+") self.assertEqual(alignments.metadata["RID"], "P06P5RN0015") self.assertEqual(alignments.metadata["Database"], "refseq_rna") alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|296147 0 WP*TLEGLTPCKGNLKQNCVLYLPNRKEEIQPFAMLVINPLRY*KEYIVLRS*KDIRISH 0 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| gi|296147 0 WP*TLEGLTPCKGNLKQNCVLYLPNRKEEIQPFAMLVINPLRY*KEYIVLRS*KDIRISH gi|296147 60 SLSCWLANQGMLK*RPWQCNAYRDCQPFHLFLEAGCLKFWMPSLRLLISRWRFN*K 116 60 |||||||||||||||||||||||||||||||||||||||||||||||||||||||| 116 gi|296147 60 SLSCWLANQGMLK*RPWQCNAYRDCQPFHLFLEAGCLKFWMPSLRLLISRWRFN*K 116 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 116], [ 0, 116]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|296147483|ref|NM_001183135.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|296147483|ref|NM_001183135.1|;gi|116616412|gb|EF059095.1|", ) self.assertEqual(alignment.target.annotations["gi"], "296147483") self.assertEqual(alignment.target.annotations["gis"], "296147483;116616412") self.assertEqual(alignment.target.annotations["acc."], "NM_001183135") self.assertEqual( alignment.target.annotations["accs."], "NM_001183135;EF059095" ) self.assertEqual(alignment.target.annotations["acc.ver"], "NM_001183135.1") self.assertEqual(alignment.target.annotations["length"], 4911) self.assertEqual(alignment.query.annotations["start"], 1) self.assertEqual(alignment.query.annotations["end"], 349) self.assertEqual(alignment.target.annotations["start"], 1) self.assertEqual(alignment.target.annotations["end"], 349) self.assertEqual( alignment.target.seq, "WP*TLEGLTPCKGNLKQNCVLYLPNRKEEIQPFAMLVINPLRY*KEYIVLRS*KDIRISHSLSCWLANQGMLK*RPWQCNAYRDCQPFHLFLEAGCLKFWMPSLRLLISRWRFN*K", ) self.assertEqual( alignment.query.seq, "WP*TLEGLTPCKGNLKQNCVLYLPNRKEEIQPFAMLVINPLRY*KEYIVLRS*KDIRISHSLSCWLANQGMLK*RPWQCNAYRDCQPFHLFLEAGCLKFWMPSLRLLISRWRFN*K", ) self.assertAlmostEqual(alignment.annotations["evalue"], 1e-76, places=76) self.assertAlmostEqual(alignment.annotations["bit score"], 289) self.assertAlmostEqual(alignment.score, 626) self.assertEqual(alignment.shape, (2, 116)) self.assertAlmostEqual(alignment.annotations["% identity"], 100.00) self.assertEqual(alignment.annotations["identical"], 116) self.assertEqual(alignment.annotations["mismatches"], 0) self.assertEqual(alignment.annotations["positives"], 116) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 100.00) self.assertEqual(alignment.annotations["query/sbjct frames"], "2/2") self.assertEqual(alignment.query.annotations["frame"], "2") self.assertEqual(alignment.target.annotations["frame"], "2") self.assertEqual(alignment.target.annotations["tax ids"], "32630;559292") self.assertEqual(alignment.target.annotations["sci names"], "N/A;N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A;N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Saccharomyces cerevisiae S288c Mon2p (MON2), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "Saccharomyces cerevisiae S288c Mon2p (MON2), mRNA<>Synthetic construct Saccharomyces cerevisiae clone FLH203015.01X MON2, complete sequence", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 100) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 99) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|296147 0 LLIESPSRDE*PQ*RHPKFQTAGFEE*MERLTVPVGIALPGSSF*HSLIGKPTRKGVRNP 0 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| gi|296147 0 LLIESPSRDE*PQ*RHPKFQTAGFEE*MERLTVPVGIALPGSSF*HSLIGKPTRKGVRNP gi|296147 60 DVFLAPQNYVLFSISQWIYH*HGEWLNFFFSIRKIKNAILLQVAFAWSQTLQCSWP 116 60 |||||||||||||||||||||||||||||||||||||||||||||||||||||||| 116 gi|296147 60 DVFLAPQNYVLFSISQWIYH*HGEWLNFFFSIRKIKNAILLQVAFAWSQTLQCSWP 116 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[0, 116], [0, 116]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|296147483|ref|NM_001183135.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|296147483|ref|NM_001183135.1|;gi|116616412|gb|EF059095.1|", ) self.assertEqual(alignment.target.annotations["gi"], "296147483") self.assertEqual(alignment.target.annotations["gis"], "296147483;116616412") self.assertEqual(alignment.target.annotations["acc."], "NM_001183135") self.assertEqual( alignment.target.annotations["accs."], "NM_001183135;EF059095" ) self.assertEqual(alignment.target.annotations["acc.ver"], "NM_001183135.1") self.assertEqual(alignment.target.annotations["length"], 4911) self.assertEqual(alignment.query.annotations["start"], 349) self.assertEqual(alignment.query.annotations["end"], 1) self.assertEqual(alignment.target.annotations["start"], 349) self.assertEqual(alignment.target.annotations["end"], 1) self.assertEqual( alignment.target.seq, "LLIESPSRDE*PQ*RHPKFQTAGFEE*MERLTVPVGIALPGSSF*HSLIGKPTRKGVRNPDVFLAPQNYVLFSISQWIYH*HGEWLNFFFSIRKIKNAILLQVAFAWSQTLQCSWP", ) self.assertEqual( alignment.query.seq, "LLIESPSRDE*PQ*RHPKFQTAGFEE*MERLTVPVGIALPGSSF*HSLIGKPTRKGVRNPDVFLAPQNYVLFSISQWIYH*HGEWLNFFFSIRKIKNAILLQVAFAWSQTLQCSWP", ) self.assertAlmostEqual(alignment.annotations["evalue"], 3e-73, places=73) self.assertAlmostEqual(alignment.annotations["bit score"], 278) self.assertAlmostEqual(alignment.score, 602) self.assertEqual(alignment.shape, (2, 116)) self.assertAlmostEqual(alignment.annotations["% identity"], 100.00) self.assertEqual(alignment.annotations["identical"], 116) self.assertEqual(alignment.annotations["mismatches"], 0) self.assertEqual(alignment.annotations["positives"], 116) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 100.00) self.assertEqual(alignment.annotations["query/sbjct frames"], "-2/-3") self.assertEqual(alignment.query.annotations["frame"], "-2") self.assertEqual(alignment.target.annotations["frame"], "-3") self.assertEqual(alignment.target.annotations["tax ids"], "32630;559292") self.assertEqual(alignment.target.annotations["sci names"], "N/A;N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A;N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Saccharomyces cerevisiae S288c Mon2p (MON2), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "Saccharomyces cerevisiae S288c Mon2p (MON2), mRNA<>Synthetic construct Saccharomyces cerevisiae clone FLH203015.01X MON2, complete sequence", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 100) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 99) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|296147 0 F*LNLHREMSSLNEGIQNFRQPASRNRWNG*QSL*ALHCQGRHFSIP*LASQHERECEIR 0 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| gi|296147 0 F*LNLHREMSSLNEGIQNFRQPASRNRWNG*QSL*ALHCQGRHFSIP*LASQHERECEIR gi|296147 60 MSF*LLKTMYSFQYLNGFITSMANG*ISSFRFGR*RTQFCFKLPLHGVKPSSVHGH 116 60 |||||||||||||||||||||||||||||||||||||||||||||||||||||||| 116 gi|296147 60 MSF*LLKTMYSFQYLNGFITSMANG*ISSFRFGR*RTQFCFKLPLHGVKPSSVHGH 116 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 116], [ 0, 116]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|296147483|ref|NM_001183135.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|296147483|ref|NM_001183135.1|;gi|116616412|gb|EF059095.1|", ) self.assertEqual(alignment.target.annotations["gi"], "296147483") self.assertEqual(alignment.target.annotations["gis"], "296147483;116616412") self.assertEqual(alignment.target.annotations["acc."], "NM_001183135") self.assertEqual( alignment.target.annotations["accs."], "NM_001183135;EF059095" ) self.assertEqual(alignment.target.annotations["acc.ver"], "NM_001183135.1") self.assertEqual(alignment.target.annotations["length"], 4911) self.assertEqual(alignment.query.annotations["start"], 348) self.assertEqual(alignment.query.annotations["end"], 0) self.assertEqual(alignment.target.annotations["start"], 348) self.assertEqual(alignment.target.annotations["end"], 0) self.assertEqual( alignment.target.seq, "F*LNLHREMSSLNEGIQNFRQPASRNRWNG*QSL*ALHCQGRHFSIP*LASQHERECEIRMSF*LLKTMYSFQYLNGFITSMANG*ISSFRFGR*RTQFCFKLPLHGVKPSSVHGH", ) self.assertEqual( alignment.query.seq, "F*LNLHREMSSLNEGIQNFRQPASRNRWNG*QSL*ALHCQGRHFSIP*LASQHERECEIRMSF*LLKTMYSFQYLNGFITSMANG*ISSFRFGR*RTQFCFKLPLHGVKPSSVHGH", ) self.assertAlmostEqual(alignment.annotations["evalue"], 5e-72, places=72) self.assertAlmostEqual(alignment.annotations["bit score"], 274) self.assertAlmostEqual(alignment.score, 593) self.assertEqual(alignment.shape, (2, 116)) self.assertAlmostEqual(alignment.annotations["% identity"], 100.00) self.assertEqual(alignment.annotations["identical"], 116) self.assertEqual(alignment.annotations["mismatches"], 0) self.assertEqual(alignment.annotations["positives"], 116) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 100.00) self.assertEqual(alignment.annotations["query/sbjct frames"], "-3/-1") self.assertEqual(alignment.query.annotations["frame"], "-3") self.assertEqual(alignment.target.annotations["frame"], "-1") self.assertEqual(alignment.target.annotations["tax ids"], "32630;559292") self.assertEqual(alignment.target.annotations["sci names"], "N/A;N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A;N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Saccharomyces cerevisiae S288c Mon2p (MON2), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "Saccharomyces cerevisiae S288c Mon2p (MON2), mRNA<>Synthetic construct Saccharomyces cerevisiae clone FLH203015.01X MON2, complete sequence", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 100) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 99) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|296147 0 GHEHWRV*LHAKAT*SRIAFFIFRIEKKKFNHSPC***IH*DIEKST*F*GARKTSGFRT 0 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| gi|296147 0 GHEHWRV*LHAKAT*SRIAFFIFRIEKKKFNHSPC***IH*DIEKST*F*GARKTSGFRT gi|296147 60 PFRVGLPIKEC*NDDPGNAMPTGTVNRSIYSSKPAV*NFGCLH*GYSSRDGDSIKS 116 60 |||||||||||||||||||||||||||||||||||||||||||||||||||||||| 116 gi|296147 60 PFRVGLPIKEC*NDDPGNAMPTGTVNRSIYSSKPAV*NFGCLH*GYSSRDGDSIKS 116 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 116], [ 0, 116]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|296147483|ref|NM_001183135.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|296147483|ref|NM_001183135.1|;gi|116616412|gb|EF059095.1|", ) self.assertEqual(alignment.target.annotations["gi"], "296147483") self.assertEqual(alignment.target.annotations["gis"], "296147483;116616412") self.assertEqual(alignment.target.annotations["acc."], "NM_001183135") self.assertEqual( alignment.target.annotations["accs."], "NM_001183135;EF059095" ) self.assertEqual(alignment.target.annotations["acc.ver"], "NM_001183135.1") self.assertEqual(alignment.target.annotations["length"], 4911) self.assertEqual(alignment.query.annotations["start"], 2) self.assertEqual(alignment.query.annotations["end"], 350) self.assertEqual(alignment.target.annotations["start"], 2) self.assertEqual(alignment.target.annotations["end"], 350) self.assertEqual( alignment.target.seq, "GHEHWRV*LHAKAT*SRIAFFIFRIEKKKFNHSPC***IH*DIEKST*F*GARKTSGFRTPFRVGLPIKEC*NDDPGNAMPTGTVNRSIYSSKPAV*NFGCLH*GYSSRDGDSIKS", ) self.assertEqual( alignment.query.seq, "GHEHWRV*LHAKAT*SRIAFFIFRIEKKKFNHSPC***IH*DIEKST*F*GARKTSGFRTPFRVGLPIKEC*NDDPGNAMPTGTVNRSIYSSKPAV*NFGCLH*GYSSRDGDSIKS", ) self.assertAlmostEqual(alignment.annotations["evalue"], 1e-70, places=70) self.assertAlmostEqual(alignment.annotations["bit score"], 270) self.assertAlmostEqual(alignment.score, 583) self.assertEqual(alignment.shape, (2, 116)) self.assertAlmostEqual(alignment.annotations["% identity"], 100.00) self.assertEqual(alignment.annotations["identical"], 116) self.assertEqual(alignment.annotations["mismatches"], 0) self.assertEqual(alignment.annotations["positives"], 116) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 100.00) self.assertEqual(alignment.annotations["query/sbjct frames"], "3/3") self.assertEqual(alignment.query.annotations["frame"], "3") self.assertEqual(alignment.target.annotations["frame"], "3") self.assertEqual(alignment.target.annotations["tax ids"], "32630;559292") self.assertEqual(alignment.target.annotations["sci names"], "N/A;N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A;N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Saccharomyces cerevisiae S288c Mon2p (MON2), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "Saccharomyces cerevisiae S288c Mon2p (MON2), mRNA<>Synthetic construct Saccharomyces cerevisiae clone FLH203015.01X MON2, complete sequence", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 100) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 99) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|296147 0 TFN*ISIAR*VASMKASKISDSRLRGIDGTVDSPCRHCIARVVILAFLDWQANTKGSAKS 0 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| gi|296147 0 TFN*ISIAR*VASMKASKISDSRLRGIDGTVDSPCRHCIARVVILAFLDWQANTKGSAKS gi|296147 60 GCLSSSSKLCTLFNISMDLSLAWRMVEFLLFDSEDKERNSASSCLCMESNPPVFMA 116 60 |||||||||||||||||||||||||||||||||||||||||||||||||||||||| 116 gi|296147 60 GCLSSSSKLCTLFNISMDLSLAWRMVEFLLFDSEDKERNSASSCLCMESNPPVFMA 116 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 116], [ 0, 116]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|296147483|ref|NM_001183135.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|296147483|ref|NM_001183135.1|;gi|116616412|gb|EF059095.1|", ) self.assertEqual(alignment.target.annotations["gi"], "296147483") self.assertEqual(alignment.target.annotations["gis"], "296147483;116616412") self.assertEqual(alignment.target.annotations["acc."], "NM_001183135") self.assertEqual( alignment.target.annotations["accs."], "NM_001183135;EF059095" ) self.assertEqual(alignment.target.annotations["acc.ver"], "NM_001183135.1") self.assertEqual(alignment.target.annotations["length"], 4911) self.assertEqual(alignment.query.annotations["start"], 350) self.assertEqual(alignment.query.annotations["end"], 2) self.assertEqual(alignment.target.annotations["start"], 350) self.assertEqual(alignment.target.annotations["end"], 2) self.assertEqual( alignment.target.seq, "TFN*ISIAR*VASMKASKISDSRLRGIDGTVDSPCRHCIARVVILAFLDWQANTKGSAKSGCLSSSSKLCTLFNISMDLSLAWRMVEFLLFDSEDKERNSASSCLCMESNPPVFMA", ) self.assertEqual( alignment.query.seq, "TFN*ISIAR*VASMKASKISDSRLRGIDGTVDSPCRHCIARVVILAFLDWQANTKGSAKSGCLSSSSKLCTLFNISMDLSLAWRMVEFLLFDSEDKERNSASSCLCMESNPPVFMA", ) self.assertAlmostEqual(alignment.annotations["evalue"], 2e-58, places=58) self.assertAlmostEqual(alignment.annotations["bit score"], 229) self.assertAlmostEqual(alignment.score, 495) self.assertEqual(alignment.shape, (2, 116)) self.assertAlmostEqual(alignment.annotations["% identity"], 100.00) self.assertEqual(alignment.annotations["identical"], 116) self.assertEqual(alignment.annotations["mismatches"], 0) self.assertEqual(alignment.annotations["positives"], 116) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 100.00) self.assertEqual(alignment.annotations["query/sbjct frames"], "-1/-2") self.assertEqual(alignment.query.annotations["frame"], "-1") self.assertEqual(alignment.target.annotations["frame"], "-2") self.assertEqual(alignment.target.annotations["tax ids"], "32630;559292") self.assertEqual(alignment.target.annotations["sci names"], "N/A;N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A;N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Saccharomyces cerevisiae S288c Mon2p (MON2), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "Saccharomyces cerevisiae S288c Mon2p (MON2), mRNA<>Synthetic construct Saccharomyces cerevisiae clone FLH203015.01X MON2, complete sequence", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 100) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 99) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|296147 0 TIRHASDKSIEILKRVHSFEELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSI 0 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| gi|296147 0 TIRHASDKSIEILKRVHSFEELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSI gi|296147 60 PRSRLSEILDAFIEATHLAMEIQLK 85 60 ||||||||||||||||||||||||| 85 gi|296147 60 PRSRLSEILDAFIEATHLAMEIQLK 85 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 85], [ 0, 85]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|296147483|ref|NM_001183135.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|296147483|ref|NM_001183135.1|;gi|116616412|gb|EF059095.1|", ) self.assertEqual(alignment.target.annotations["gi"], "296147483") self.assertEqual(alignment.target.annotations["gis"], "296147483;116616412") self.assertEqual(alignment.target.annotations["acc."], "NM_001183135") self.assertEqual( alignment.target.annotations["accs."], "NM_001183135;EF059095" ) self.assertEqual(alignment.target.annotations["acc.ver"], "NM_001183135.1") self.assertEqual(alignment.target.annotations["length"], 4911) self.assertEqual(alignment.query.annotations["start"], 93) self.assertEqual(alignment.query.annotations["end"], 348) self.assertEqual(alignment.target.annotations["start"], 93) self.assertEqual(alignment.target.annotations["end"], 348) self.assertEqual( alignment.target.seq, "TIRHASDKSIEILKRVHSFEELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAMEIQLK", ) self.assertEqual( alignment.query.seq, "TIRHASDKSIEILKRVHSFEELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAMEIQLK", ) self.assertAlmostEqual(alignment.annotations["evalue"], 1e-53, places=53) self.assertAlmostEqual(alignment.annotations["bit score"], 197) self.assertAlmostEqual(alignment.score, 425) self.assertEqual(alignment.shape, (2, 85)) self.assertAlmostEqual(alignment.annotations["% identity"], 100.00) self.assertEqual(alignment.annotations["identical"], 85) self.assertEqual(alignment.annotations["mismatches"], 0) self.assertEqual(alignment.annotations["positives"], 85) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 100.00) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "32630;559292") self.assertEqual(alignment.target.annotations["sci names"], "N/A;N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A;N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Saccharomyces cerevisiae S288c Mon2p (MON2), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "Saccharomyces cerevisiae S288c Mon2p (MON2), mRNA<>Synthetic construct Saccharomyces cerevisiae clone FLH203015.01X MON2, complete sequence", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 100) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 73) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|296147 0 MAMNTGGFDSMQRQ 14 0 |||||||||||||| 14 gi|296147 0 MAMNTGGFDSMQRQ 14 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 14], [ 0, 14]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|296147483|ref|NM_001183135.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|296147483|ref|NM_001183135.1|;gi|116616412|gb|EF059095.1|", ) self.assertEqual(alignment.target.annotations["gi"], "296147483") self.assertEqual(alignment.target.annotations["gis"], "296147483;116616412") self.assertEqual(alignment.target.annotations["acc."], "NM_001183135") self.assertEqual( alignment.target.annotations["accs."], "NM_001183135;EF059095" ) self.assertEqual(alignment.target.annotations["acc.ver"], "NM_001183135.1") self.assertEqual(alignment.target.annotations["length"], 4911) self.assertEqual(alignment.query.annotations["start"], 0) self.assertEqual(alignment.query.annotations["end"], 42) self.assertEqual(alignment.target.annotations["start"], 0) self.assertEqual(alignment.target.annotations["end"], 42) self.assertEqual(alignment.target.seq, "MAMNTGGFDSMQRQ") self.assertEqual(alignment.query.seq, "MAMNTGGFDSMQRQ") self.assertAlmostEqual(alignment.annotations["evalue"], 1e-53, places=53) self.assertAlmostEqual(alignment.annotations["bit score"], 36.3) self.assertAlmostEqual(alignment.score, 73) self.assertEqual(alignment.shape, (2, 14)) self.assertAlmostEqual(alignment.annotations["% identity"], 100.00) self.assertEqual(alignment.annotations["identical"], 14) self.assertEqual(alignment.annotations["mismatches"], 0) self.assertEqual(alignment.annotations["positives"], 14) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 100.00) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "32630;559292") self.assertEqual(alignment.target.annotations["sci names"], "N/A;N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A;N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Saccharomyces cerevisiae S288c Mon2p (MON2), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "Saccharomyces cerevisiae S288c Mon2p (MON2), mRNA<>Synthetic construct Saccharomyces cerevisiae clone FLH203015.01X MON2, complete sequence", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 100) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 12) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|365982 0 TIKHASDKSIDILKTIQNIEELVRHPDFVTPLVLACSSRNAKLTSIAMQCLQGLASVPSI 0 ||.|||||||.|||.....|||.|||||..|.||||.|||||.|..||||||||..|||| gi|296147 0 TIRHASDKSIEILKRVHSFEELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSI gi|365982 60 PESRIPEVLDGFIEATQLAMEIQLK 85 60 |.||..|.||.|||||.|||||||| 85 gi|296147 60 PRSRLSEILDAFIEATHLAMEIQLK 85 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 85], [ 0, 85]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|365982352|ref|XM_003667962.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|365982352|ref|XM_003667962.1|" ) self.assertEqual(alignment.target.annotations["gi"], "365982352") self.assertEqual(alignment.target.annotations["gis"], "365982352") self.assertEqual(alignment.target.annotations["acc."], "XM_003667962") self.assertEqual(alignment.target.annotations["accs."], "XM_003667962") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_003667962.1") self.assertEqual(alignment.target.annotations["length"], 4932) self.assertEqual(alignment.query.annotations["start"], 93) self.assertEqual(alignment.query.annotations["end"], 348) self.assertEqual(alignment.target.annotations["start"], 87) self.assertEqual(alignment.target.annotations["end"], 342) self.assertEqual( alignment.target.seq, "TIKHASDKSIDILKTIQNIEELVRHPDFVTPLVLACSSRNAKLTSIAMQCLQGLASVPSIPESRIPEVLDGFIEATQLAMEIQLK", ) self.assertEqual( alignment.query.seq, "TIRHASDKSIEILKRVHSFEELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAMEIQLK", ) self.assertAlmostEqual(alignment.annotations["evalue"], 3e-37, places=37) self.assertAlmostEqual(alignment.annotations["bit score"], 152) self.assertAlmostEqual(alignment.score, 327) self.assertEqual(alignment.shape, (2, 85)) self.assertAlmostEqual(alignment.annotations["% identity"], 72.94) self.assertEqual(alignment.annotations["identical"], 62) self.assertEqual(alignment.annotations["mismatches"], 23) self.assertEqual(alignment.annotations["positives"], 73) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 85.88) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "1071378") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Naumovozyma dairenensis CBS 421 hypothetical protein (NDAI0A06120), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "Naumovozyma dairenensis CBS 421 hypothetical protein (NDAI0A06120), mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 94) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 73) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|365982 0 FRI*KKKFNH*TC* 14 0 |||.||||||..|| 14 gi|296147 0 FRIEKKKFNHSPC* 14 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 14], [ 0, 14]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|365982352|ref|XM_003667962.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|365982352|ref|XM_003667962.1|" ) self.assertEqual(alignment.target.annotations["gi"], "365982352") self.assertEqual(alignment.target.annotations["gis"], "365982352") self.assertEqual(alignment.target.annotations["acc."], "XM_003667962") self.assertEqual(alignment.target.annotations["accs."], "XM_003667962") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_003667962.1") self.assertEqual(alignment.target.annotations["length"], 4932) self.assertEqual(alignment.query.annotations["start"], 68) self.assertEqual(alignment.query.annotations["end"], 110) self.assertEqual(alignment.target.annotations["start"], 62) self.assertEqual(alignment.target.annotations["end"], 104) self.assertEqual(alignment.target.seq, "FRI*KKKFNH*TC*") self.assertEqual(alignment.query.seq, "FRIEKKKFNHSPC*") self.assertAlmostEqual(alignment.annotations["evalue"], 3e-37, places=37) self.assertAlmostEqual(alignment.annotations["bit score"], 26.3) self.assertAlmostEqual(alignment.score, 51) self.assertEqual(alignment.shape, (2, 14)) self.assertAlmostEqual(alignment.annotations["% identity"], 78.57) self.assertEqual(alignment.annotations["identical"], 11) self.assertEqual(alignment.annotations["mismatches"], 3) self.assertEqual(alignment.annotations["positives"], 11) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 78.57) self.assertEqual(alignment.annotations["query/sbjct frames"], "3/3") self.assertEqual(alignment.query.annotations["frame"], "3") self.assertEqual(alignment.target.annotations["frame"], "3") self.assertEqual(alignment.target.annotations["tax ids"], "1071378") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Naumovozyma dairenensis CBS 421 hypothetical protein (NDAI0A06120), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "Naumovozyma dairenensis CBS 421 hypothetical protein (NDAI0A06120), mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 94) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 12) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|365982 0 TFNCISIAS*VASMNPSRTSGILDSGIEGTDANPCRHCMAIEVNLAFLDEQARTK 55 0 |||.||||.|||||..|..|.....||.||...|||||.|..|.|||||.||.|| 55 gi|296147 0 TFN*ISIAR*VASMKASKISDSRLRGIDGTVDSPCRHCIARVVILAFLDWQANTK 55 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 55], [ 0, 55]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|365982352|ref|XM_003667962.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|365982352|ref|XM_003667962.1|" ) self.assertEqual(alignment.target.annotations["gi"], "365982352") self.assertEqual(alignment.target.annotations["gis"], "365982352") self.assertEqual(alignment.target.annotations["acc."], "XM_003667962") self.assertEqual(alignment.target.annotations["accs."], "XM_003667962") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_003667962.1") self.assertEqual(alignment.target.annotations["length"], 4932) self.assertEqual(alignment.query.annotations["start"], 350) self.assertEqual(alignment.query.annotations["end"], 185) self.assertEqual(alignment.target.annotations["start"], 344) self.assertEqual(alignment.target.annotations["end"], 179) self.assertEqual( alignment.target.seq, "TFNCISIAS*VASMNPSRTSGILDSGIEGTDANPCRHCMAIEVNLAFLDEQARTK", ) self.assertEqual( alignment.query.seq, "TFN*ISIAR*VASMKASKISDSRLRGIDGTVDSPCRHCIARVVILAFLDWQANTK", ) self.assertAlmostEqual(alignment.annotations["evalue"], 6e-20, places=20) self.assertAlmostEqual(alignment.annotations["bit score"], 68.0) self.assertAlmostEqual(alignment.score, 142) self.assertEqual(alignment.shape, (2, 55)) self.assertAlmostEqual(alignment.annotations["% identity"], 61.82) self.assertEqual(alignment.annotations["identical"], 34) self.assertEqual(alignment.annotations["mismatches"], 21) self.assertEqual(alignment.annotations["positives"], 38) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 69.09) self.assertEqual(alignment.annotations["query/sbjct frames"], "-1/-2") self.assertEqual(alignment.query.annotations["frame"], "-1") self.assertEqual(alignment.target.annotations["frame"], "-2") self.assertEqual(alignment.target.annotations["tax ids"], "1071378") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Naumovozyma dairenensis CBS 421 hypothetical protein (NDAI0A06120), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "Naumovozyma dairenensis CBS 421 hypothetical protein (NDAI0A06120), mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 94) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 47) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|365982 0 VFRISIDLSLACLMVEFLLLDSEERECNSWSNCFRKEVN 39 0 .|.||.|||||..||||||.|||..|.||.|.|...|.| 39 gi|296147 0 LFNISMDLSLAWRMVEFLLFDSEDKERNSASSCLCMESN 39 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 39], [ 0, 39]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|365982352|ref|XM_003667962.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|365982352|ref|XM_003667962.1|" ) self.assertEqual(alignment.target.annotations["gi"], "365982352") self.assertEqual(alignment.target.annotations["gis"], "365982352") self.assertEqual(alignment.target.annotations["acc."], "XM_003667962") self.assertEqual(alignment.target.annotations["accs."], "XM_003667962") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_003667962.1") self.assertEqual(alignment.target.annotations["length"], 4932) self.assertEqual(alignment.query.annotations["start"], 137) self.assertEqual(alignment.query.annotations["end"], 20) self.assertEqual(alignment.target.annotations["start"], 131) self.assertEqual(alignment.target.annotations["end"], 14) self.assertEqual( alignment.target.seq, "VFRISIDLSLACLMVEFLLLDSEERECNSWSNCFRKEVN" ) self.assertEqual( alignment.query.seq, "LFNISMDLSLAWRMVEFLLFDSEDKERNSASSCLCMESN" ) self.assertAlmostEqual(alignment.annotations["evalue"], 6e-20, places=20) self.assertAlmostEqual(alignment.annotations["bit score"], 52.8) self.assertAlmostEqual(alignment.score, 109) self.assertEqual(alignment.shape, (2, 39)) self.assertAlmostEqual(alignment.annotations["% identity"], 61.54) self.assertEqual(alignment.annotations["identical"], 24) self.assertEqual(alignment.annotations["mismatches"], 15) self.assertEqual(alignment.annotations["positives"], 29) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 74.36) self.assertEqual(alignment.annotations["query/sbjct frames"], "-1/-2") self.assertEqual(alignment.query.annotations["frame"], "-1") self.assertEqual(alignment.target.annotations["frame"], "-2") self.assertEqual(alignment.target.annotations["tax ids"], "1071378") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Naumovozyma dairenensis CBS 421 hypothetical protein (NDAI0A06120), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "Naumovozyma dairenensis CBS 421 hypothetical protein (NDAI0A06120), mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 94) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 33) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|365982 0 NWTRNYTPFLQNLKEEIQPLNMLATNQSIF*RLFKI*KNL*GTLILLHLWSWPVHREMPN 0 |...|....|.|.||||||..||..|....|.............|...|..|.....|.. gi|296147 0 NLKQNCVLYLPNRKEEIQPFAMLVINPLRY*KEYIVLRS*KDIRISHSLSCWLANQGMLK gi|365982 60 *LQLPCNAYKDWRPYLQYQSQESQKF*TDSLKPLS*RWRYN*K 103 60 |....||||.|..|..........||...||..|..|||.||| 103 gi|296147 60 *RPWQCNAYRDCQPFHLFLEAGCLKFWMPSLRLLISRWRFN*K 103 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 103], [ 0, 103]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|365982352|ref|XM_003667962.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|365982352|ref|XM_003667962.1|" ) self.assertEqual(alignment.target.annotations["gi"], "365982352") self.assertEqual(alignment.target.annotations["gis"], "365982352") self.assertEqual(alignment.target.annotations["acc."], "XM_003667962") self.assertEqual(alignment.target.annotations["accs."], "XM_003667962") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_003667962.1") self.assertEqual(alignment.target.annotations["length"], 4932) self.assertEqual(alignment.query.annotations["start"], 40) self.assertEqual(alignment.query.annotations["end"], 349) self.assertEqual(alignment.target.annotations["start"], 34) self.assertEqual(alignment.target.annotations["end"], 343) self.assertEqual( alignment.target.seq, "NWTRNYTPFLQNLKEEIQPLNMLATNQSIF*RLFKI*KNL*GTLILLHLWSWPVHREMPN*LQLPCNAYKDWRPYLQYQSQESQKF*TDSLKPLS*RWRYN*K", ) self.assertEqual( alignment.query.seq, "NLKQNCVLYLPNRKEEIQPFAMLVINPLRY*KEYIVLRS*KDIRISHSLSCWLANQGMLK*RPWQCNAYRDCQPFHLFLEAGCLKFWMPSLRLLISRWRFN*K", ) self.assertAlmostEqual(alignment.annotations["evalue"], 9e-08, places=8) self.assertAlmostEqual(alignment.annotations["bit score"], 61.1) self.assertAlmostEqual(alignment.score, 127) self.assertEqual(alignment.shape, (2, 103)) self.assertAlmostEqual(alignment.annotations["% identity"], 34.95) self.assertEqual(alignment.annotations["identical"], 36) self.assertEqual(alignment.annotations["mismatches"], 67) self.assertEqual(alignment.annotations["positives"], 52) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 50.49) self.assertEqual(alignment.annotations["query/sbjct frames"], "2/2") self.assertEqual(alignment.query.annotations["frame"], "2") self.assertEqual(alignment.target.annotations["frame"], "2") self.assertEqual(alignment.target.annotations["tax ids"], "1071378") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Naumovozyma dairenensis CBS 421 hypothetical protein (NDAI0A06120), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "Naumovozyma dairenensis CBS 421 hypothetical protein (NDAI0A06120), mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 94) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 88) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|365982 0 GRQSL*ALHGN*S*FGISR*TGQDQRCNKIRVPYKFFYILNSL*NID*FVASMFNG*ISS 0 |.|||||||.....|.|.....|..|...||..........|......|..||.|||||| gi|296147 0 G*QSL*ALHCQGRHFSIP*LASQHERECEIRMSF*LLKTMYSFQYLNGFITSMANG*ISS gi|365982 60 FRF*R 65 60 |||.| 65 gi|296147 60 FRFGR 65 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 65], [ 0, 65]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|365982352|ref|XM_003667962.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|365982352|ref|XM_003667962.1|" ) self.assertEqual(alignment.target.annotations["gi"], "365982352") self.assertEqual(alignment.target.annotations["gis"], "365982352") self.assertEqual(alignment.target.annotations["acc."], "XM_003667962") self.assertEqual(alignment.target.annotations["accs."], "XM_003667962") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_003667962.1") self.assertEqual(alignment.target.annotations["length"], 4932) self.assertEqual(alignment.query.annotations["start"], 261) self.assertEqual(alignment.query.annotations["end"], 66) self.assertEqual(alignment.target.annotations["start"], 255) self.assertEqual(alignment.target.annotations["end"], 60) self.assertEqual( alignment.target.seq, "GRQSL*ALHGN*S*FGISR*TGQDQRCNKIRVPYKFFYILNSL*NID*FVASMFNG*ISSFRF*R", ) self.assertEqual( alignment.query.seq, "G*QSL*ALHCQGRHFSIP*LASQHERECEIRMSF*LLKTMYSFQYLNGFITSMANG*ISSFRFGR", ) self.assertAlmostEqual(alignment.annotations["evalue"], 0.029) self.assertAlmostEqual(alignment.annotations["bit score"], 42.8) self.assertAlmostEqual(alignment.score, 87) self.assertEqual(alignment.shape, (2, 65)) self.assertAlmostEqual(alignment.annotations["% identity"], 43.08) self.assertEqual(alignment.annotations["identical"], 28) self.assertEqual(alignment.annotations["mismatches"], 37) self.assertEqual(alignment.annotations["positives"], 36) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 55.38) self.assertEqual(alignment.annotations["query/sbjct frames"], "-3/-1") self.assertEqual(alignment.query.annotations["frame"], "-3") self.assertEqual(alignment.target.annotations["frame"], "-1") self.assertEqual(alignment.target.annotations["tax ids"], "1071378") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Naumovozyma dairenensis CBS 421 hypothetical protein (NDAI0A06120), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "Naumovozyma dairenensis CBS 421 hypothetical protein (NDAI0A06120), mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 94) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 56) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|366988 0 SIKHASDKSIEILKTIQNIEDLASHPDFVTPLVESCLSRNAKLTSIAMQCLQGLASAPSI 0 .|.|||||||||||.....|.|..||||..|.|..|.|||||.|..||||||||...||| gi|296147 0 TIRHASDKSIEILKRVHSFEELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSI gi|366988 60 PESRLSGVLDGFIEATHLAIEIQLK 85 60 |.||||..||.||||||||.||||| 85 gi|296147 60 PRSRLSEILDAFIEATHLAMEIQLK 85 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 85], [ 0, 85]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|366988334|ref|XM_003673886.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|366988334|ref|XM_003673886.1|" ) self.assertEqual(alignment.target.annotations["gi"], "366988334") self.assertEqual(alignment.target.annotations["gis"], "366988334") self.assertEqual(alignment.target.annotations["acc."], "XM_003673886") self.assertEqual(alignment.target.annotations["accs."], "XM_003673886") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_003673886.1") self.assertEqual(alignment.target.annotations["length"], 4938) self.assertEqual(alignment.query.annotations["start"], 93) self.assertEqual(alignment.query.annotations["end"], 348) self.assertEqual(alignment.target.annotations["start"], 93) self.assertEqual(alignment.target.annotations["end"], 348) self.assertEqual( alignment.target.seq, "SIKHASDKSIEILKTIQNIEDLASHPDFVTPLVESCLSRNAKLTSIAMQCLQGLASAPSIPESRLSGVLDGFIEATHLAIEIQLK", ) self.assertEqual( alignment.query.seq, "TIRHASDKSIEILKRVHSFEELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAMEIQLK", ) self.assertAlmostEqual(alignment.annotations["evalue"], 2e-32, places=32) self.assertAlmostEqual(alignment.annotations["bit score"], 143) self.assertAlmostEqual(alignment.score, 306) self.assertEqual(alignment.shape, (2, 85)) self.assertAlmostEqual(alignment.annotations["% identity"], 68.24) self.assertEqual(alignment.annotations["identical"], 58) self.assertEqual(alignment.annotations["mismatches"], 27) self.assertEqual(alignment.annotations["positives"], 71) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 83.53) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "1064592") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Naumovozyma castellii CBS 4309 hypothetical protein (NCAS0A09950) mRNA, complete cds", ) self.assertEqual( alignment.target.annotations["titles"], "Naumovozyma castellii CBS 4309 hypothetical protein (NCAS0A09950) mRNA, complete cds", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 100) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 73) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|366988 0 TFSCISIARCVASINPSRTPDSLLSGMDGADAKPCKHCIAIEVNLAFLDRHDST 54 0 ||..|||||.|||...|...||.|.|.||....||.||||..|.|||||....| 54 gi|296147 0 TFN*ISIAR*VASMKASKISDSRLRGIDGTVDSPCRHCIARVVILAFLDWQANT 54 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 54], [ 0, 54]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|366988334|ref|XM_003673886.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|366988334|ref|XM_003673886.1|" ) self.assertEqual(alignment.target.annotations["gi"], "366988334") self.assertEqual(alignment.target.annotations["gis"], "366988334") self.assertEqual(alignment.target.annotations["acc."], "XM_003673886") self.assertEqual(alignment.target.annotations["accs."], "XM_003673886") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_003673886.1") self.assertEqual(alignment.target.annotations["length"], 4938) self.assertEqual(alignment.query.annotations["start"], 350) self.assertEqual(alignment.query.annotations["end"], 188) self.assertEqual(alignment.target.annotations["start"], 350) self.assertEqual(alignment.target.annotations["end"], 188) self.assertEqual( alignment.target.seq, "TFSCISIARCVASINPSRTPDSLLSGMDGADAKPCKHCIAIEVNLAFLDRHDST", ) self.assertEqual( alignment.query.seq, "TFN*ISIAR*VASMKASKISDSRLRGIDGTVDSPCRHCIARVVILAFLDWQANT", ) self.assertAlmostEqual(alignment.annotations["evalue"], 7e-16, places=16) self.assertAlmostEqual(alignment.annotations["bit score"], 62.5) self.assertAlmostEqual(alignment.score, 130) self.assertEqual(alignment.shape, (2, 54)) self.assertAlmostEqual(alignment.annotations["% identity"], 55.56) self.assertEqual(alignment.annotations["identical"], 30) self.assertEqual(alignment.annotations["mismatches"], 24) self.assertEqual(alignment.annotations["positives"], 36) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 66.67) self.assertEqual(alignment.annotations["query/sbjct frames"], "-1/-2") self.assertEqual(alignment.query.annotations["frame"], "-1") self.assertEqual(alignment.target.annotations["frame"], "-2") self.assertEqual(alignment.target.annotations["tax ids"], "1064592") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Naumovozyma castellii CBS 4309 hypothetical protein (NCAS0A09950) mRNA, complete cds", ) self.assertEqual( alignment.target.annotations["titles"], "Naumovozyma castellii CBS 4309 hypothetical protein (NCAS0A09950) mRNA, complete cds", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 100) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 46) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|366988 0 VFKISIDLSLACLIEVFLLLDSEDNECNSRSNC 33 0 .|.||.|||||.....|||.||||.|.||.|.| 33 gi|296147 0 LFNISMDLSLAWRMVEFLLFDSEDKERNSASSC 33 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 33], [ 0, 33]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|366988334|ref|XM_003673886.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|366988334|ref|XM_003673886.1|" ) self.assertEqual(alignment.target.annotations["gi"], "366988334") self.assertEqual(alignment.target.annotations["gis"], "366988334") self.assertEqual(alignment.target.annotations["acc."], "XM_003673886") self.assertEqual(alignment.target.annotations["accs."], "XM_003673886") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_003673886.1") self.assertEqual(alignment.target.annotations["length"], 4938) self.assertEqual(alignment.query.annotations["start"], 137) self.assertEqual(alignment.query.annotations["end"], 38) self.assertEqual(alignment.target.annotations["start"], 137) self.assertEqual(alignment.target.annotations["end"], 38) self.assertEqual(alignment.target.seq, "VFKISIDLSLACLIEVFLLLDSEDNECNSRSNC") self.assertEqual(alignment.query.seq, "LFNISMDLSLAWRMVEFLLFDSEDKERNSASSC") self.assertAlmostEqual(alignment.annotations["evalue"], 7e-16, places=16) self.assertAlmostEqual(alignment.annotations["bit score"], 44.6) self.assertAlmostEqual(alignment.score, 91) self.assertEqual(alignment.shape, (2, 33)) self.assertAlmostEqual(alignment.annotations["% identity"], 60.61) self.assertEqual(alignment.annotations["identical"], 20) self.assertEqual(alignment.annotations["mismatches"], 13) self.assertEqual(alignment.annotations["positives"], 24) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 72.73) self.assertEqual(alignment.annotations["query/sbjct frames"], "-1/-2") self.assertEqual(alignment.query.annotations["frame"], "-1") self.assertEqual(alignment.target.annotations["frame"], "-2") self.assertEqual(alignment.target.annotations["tax ids"], "1064592") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Naumovozyma castellii CBS 4309 hypothetical protein (NCAS0A09950) mRNA, complete cds", ) self.assertEqual( alignment.target.annotations["titles"], "Naumovozyma castellii CBS 4309 hypothetical protein (NCAS0A09950) mRNA, complete cds", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 100) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 28) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|366988 0 *LYFNCKMCRFYKSIENSR*SAFRYGWCRC*AL*TLHSNRGQLSVP**T*FYQWSDKIRM 0 ||.....|......|.|.|..|.|..|.....||.||......|.||..........||| gi|296147 0 *LNLHREMSSLNEGIQNFRQPASRNRWNG*QSL*ALHCQGRHFSIP*LASQHERECEIRM gi|366988 60 ACQIFNVLDSF*DLDRLVTCMLDRSVPSFRFGRQ*MQF*VQLFLKGLKTCSLNSH 115 60 .........||..|....|.|......||||||...||...|.|.|.|..|...| 115 gi|296147 60 SF*LLKTMYSFQYLNGFITSMANG*ISSFRFGR*RTQFCFKLPLHGVKPSSVHGH 115 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 115], [ 0, 115]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|366988334|ref|XM_003673886.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|366988334|ref|XM_003673886.1|" ) self.assertEqual(alignment.target.annotations["gi"], "366988334") self.assertEqual(alignment.target.annotations["gis"], "366988334") self.assertEqual(alignment.target.annotations["acc."], "XM_003673886") self.assertEqual(alignment.target.annotations["accs."], "XM_003673886") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_003673886.1") self.assertEqual(alignment.target.annotations["length"], 4938) self.assertEqual(alignment.query.annotations["start"], 345) self.assertEqual(alignment.query.annotations["end"], 0) self.assertEqual(alignment.target.annotations["start"], 345) self.assertEqual(alignment.target.annotations["end"], 0) self.assertEqual( alignment.target.seq, "*LYFNCKMCRFYKSIENSR*SAFRYGWCRC*AL*TLHSNRGQLSVP**T*FYQWSDKIRMACQIFNVLDSF*DLDRLVTCMLDRSVPSFRFGRQ*MQF*VQLFLKGLKTCSLNSH", ) self.assertEqual( alignment.query.seq, "*LNLHREMSSLNEGIQNFRQPASRNRWNG*QSL*ALHCQGRHFSIP*LASQHERECEIRMSF*LLKTMYSFQYLNGFITSMANG*ISSFRFGR*RTQFCFKLPLHGVKPSSVHGH", ) self.assertAlmostEqual(alignment.annotations["evalue"], 1e-05) self.assertAlmostEqual(alignment.annotations["bit score"], 54.2) self.assertAlmostEqual(alignment.score, 112) self.assertEqual(alignment.shape, (2, 115)) self.assertAlmostEqual(alignment.annotations["% identity"], 33.04) self.assertEqual(alignment.annotations["identical"], 38) self.assertEqual(alignment.annotations["mismatches"], 77) self.assertEqual(alignment.annotations["positives"], 58) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 50.43) self.assertEqual(alignment.annotations["query/sbjct frames"], "-3/-1") self.assertEqual(alignment.query.annotations["frame"], "-3") self.assertEqual(alignment.target.annotations["frame"], "-1") self.assertEqual(alignment.target.annotations["tax ids"], "1064592") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Naumovozyma castellii CBS 4309 hypothetical protein (NCAS0A09950) mRNA, complete cds", ) self.assertEqual( alignment.target.annotations["titles"], "Naumovozyma castellii CBS 4309 hypothetical protein (NCAS0A09950) mRNA, complete cds", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 100) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 99) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|255710 0 VRHASDKSIEILKTVHEFEDLPRHPDFVTPFVLSCASKNAKLTSVSVQCLQKMSSVNCIP 0 .||||||||||||.||.||.|.|||||..||||.|.|.|||.|....||||..|.|..|| gi|296147 0 IRHASDKSIEILKRVHSFEELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIP gi|255710 60 EDRIEDVLDAFIDSTHLAAEIQLK 84 60 ..|....|||||..||||.||||| 84 gi|296147 60 RSRLSEILDAFIEATHLAMEIQLK 84 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 84], [ 0, 84]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|255710474|ref|XM_002551475.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|255710474|ref|XM_002551475.1|" ) self.assertEqual(alignment.target.annotations["gi"], "255710474") self.assertEqual(alignment.target.annotations["gis"], "255710474") self.assertEqual(alignment.target.annotations["acc."], "XM_002551475") self.assertEqual(alignment.target.annotations["accs."], "XM_002551475") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_002551475.1") self.assertEqual(alignment.target.annotations["length"], 4845) self.assertEqual(alignment.query.annotations["start"], 96) self.assertEqual(alignment.query.annotations["end"], 348) self.assertEqual(alignment.target.annotations["start"], 93) self.assertEqual(alignment.target.annotations["end"], 345) self.assertEqual( alignment.target.seq, "VRHASDKSIEILKTVHEFEDLPRHPDFVTPFVLSCASKNAKLTSVSVQCLQKMSSVNCIPEDRIEDVLDAFIDSTHLAAEIQLK", ) self.assertEqual( alignment.query.seq, "IRHASDKSIEILKRVHSFEELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAMEIQLK", ) self.assertAlmostEqual(alignment.annotations["evalue"], 5e-32, places=32) self.assertAlmostEqual(alignment.annotations["bit score"], 141) self.assertAlmostEqual(alignment.score, 303) self.assertEqual(alignment.shape, (2, 84)) self.assertAlmostEqual(alignment.annotations["% identity"], 65.48) self.assertEqual(alignment.annotations["identical"], 55) self.assertEqual(alignment.annotations["mismatches"], 29) self.assertEqual(alignment.annotations["positives"], 71) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 84.52) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "559295") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Lachancea thermotolerans CBS 6340 KLTH0A01342p (KLTH0A01342g) mRNA, complete cds", ) self.assertEqual( alignment.target.annotations["titles"], "Lachancea thermotolerans CBS 6340 KLTH0A01342p (KLTH0A01342g) mRNA, complete cds", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 73) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 72) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|255710 0 TLSCISAARWVESMNASSTSSILSSGMQLTDDIFCRHCTETLVSLAFLEAHERTK 55 0 |...||.||.|.||.||..|.....|...|.|..||||....|.||||.....|| 55 gi|296147 0 TFN*ISIAR*VASMKASKISDSRLRGIDGTVDSPCRHCIARVVILAFLDWQANTK 55 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 55], [ 0, 55]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|255710474|ref|XM_002551475.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|255710474|ref|XM_002551475.1|" ) self.assertEqual(alignment.target.annotations["gi"], "255710474") self.assertEqual(alignment.target.annotations["gis"], "255710474") self.assertEqual(alignment.target.annotations["acc."], "XM_002551475") self.assertEqual(alignment.target.annotations["accs."], "XM_002551475") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_002551475.1") self.assertEqual(alignment.target.annotations["length"], 4845) self.assertEqual(alignment.query.annotations["start"], 350) self.assertEqual(alignment.query.annotations["end"], 185) self.assertEqual(alignment.target.annotations["start"], 347) self.assertEqual(alignment.target.annotations["end"], 182) self.assertEqual( alignment.target.seq, "TLSCISAARWVESMNASSTSSILSSGMQLTDDIFCRHCTETLVSLAFLEAHERTK", ) self.assertEqual( alignment.query.seq, "TFN*ISIAR*VASMKASKISDSRLRGIDGTVDSPCRHCIARVVILAFLDWQANTK", ) self.assertAlmostEqual(alignment.annotations["evalue"], 0.006) self.assertAlmostEqual(alignment.annotations["bit score"], 45.1) self.assertAlmostEqual(alignment.score, 92) self.assertEqual(alignment.shape, (2, 55)) self.assertAlmostEqual(alignment.annotations["% identity"], 45.45) self.assertEqual(alignment.annotations["identical"], 25) self.assertEqual(alignment.annotations["mismatches"], 30) self.assertEqual(alignment.annotations["positives"], 29) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 52.73) self.assertEqual(alignment.annotations["query/sbjct frames"], "-1/-2") self.assertEqual(alignment.query.annotations["frame"], "-1") self.assertEqual(alignment.target.annotations["frame"], "-2") self.assertEqual(alignment.target.annotations["tax ids"], "559295") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Lachancea thermotolerans CBS 6340 KLTH0A01342p (KLTH0A01342g) mRNA, complete cds", ) self.assertEqual( alignment.target.annotations["titles"], "Lachancea thermotolerans CBS 6340 KLTH0A01342p (KLTH0A01342g) mRNA, complete cds", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 73) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 47) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|254579 0 IRNASDKSIEILKVVHSYEELSRHPDFIVPLVMSCASKNAKLTTISMQCFQKLATVPCIP 0 ||.||||||||||.|||.|||.|||||..|.|..|.|.|||.||..|||.|.|.|||.|| gi|296147 0 IRHASDKSIEILKRVHSFEELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIP gi|254579 60 VDKLSDVLDAFIEANQLAMDIKLK 84 60 ...||..|||||||..|||.|.|| 84 gi|296147 60 RSRLSEILDAFIEATHLAMEIQLK 84 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 84], [ 0, 84]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|254579534|ref|XM_002495708.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|254579534|ref|XM_002495708.1|" ) self.assertEqual(alignment.target.annotations["gi"], "254579534") self.assertEqual(alignment.target.annotations["gis"], "254579534") self.assertEqual(alignment.target.annotations["acc."], "XM_002495708") self.assertEqual(alignment.target.annotations["accs."], "XM_002495708") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_002495708.1") self.assertEqual(alignment.target.annotations["length"], 4866) self.assertEqual(alignment.query.annotations["start"], 96) self.assertEqual(alignment.query.annotations["end"], 348) self.assertEqual(alignment.target.annotations["start"], 96) self.assertEqual(alignment.target.annotations["end"], 348) self.assertEqual( alignment.target.seq, "IRNASDKSIEILKVVHSYEELSRHPDFIVPLVMSCASKNAKLTTISMQCFQKLATVPCIPVDKLSDVLDAFIEANQLAMDIKLK", ) self.assertEqual( alignment.query.seq, "IRHASDKSIEILKRVHSFEELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAMEIQLK", ) self.assertAlmostEqual(alignment.annotations["evalue"], 6e-32, places=32) self.assertAlmostEqual(alignment.annotations["bit score"], 141) self.assertAlmostEqual(alignment.score, 302) self.assertEqual(alignment.shape, (2, 84)) self.assertAlmostEqual(alignment.annotations["% identity"], 67.86) self.assertEqual(alignment.annotations["identical"], 57) self.assertEqual(alignment.annotations["mismatches"], 27) self.assertEqual(alignment.annotations["positives"], 72) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 85.71) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "559307") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Zygosaccharomyces rouxii hypothetical protein (ZYRO0C02266g) mRNA, complete cds", ) self.assertEqual( alignment.target.annotations["titles"], "Zygosaccharomyces rouxii hypothetical protein (ZYRO0C02266g) mRNA, complete cds", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 96) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 72) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|254579 0 TFSFISIASWLASINASSTSESLSTGIHGTVANFWKHCIDIVVNLAFLD 49 0 ||..||||...||..||..|.|...||.|||.....|||..||.||||| 49 gi|296147 0 TFN*ISIAR*VASMKASKISDSRLRGIDGTVDSPCRHCIARVVILAFLD 49 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 49], [ 0, 49]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|254579534|ref|XM_002495708.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|254579534|ref|XM_002495708.1|" ) self.assertEqual(alignment.target.annotations["gi"], "254579534") self.assertEqual(alignment.target.annotations["gis"], "254579534") self.assertEqual(alignment.target.annotations["acc."], "XM_002495708") self.assertEqual(alignment.target.annotations["accs."], "XM_002495708") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_002495708.1") self.assertEqual(alignment.target.annotations["length"], 4866) self.assertEqual(alignment.query.annotations["start"], 350) self.assertEqual(alignment.query.annotations["end"], 203) self.assertEqual(alignment.target.annotations["start"], 350) self.assertEqual(alignment.target.annotations["end"], 203) self.assertEqual( alignment.target.seq, "TFSFISIASWLASINASSTSESLSTGIHGTVANFWKHCIDIVVNLAFLD", ) self.assertEqual( alignment.query.seq, "TFN*ISIAR*VASMKASKISDSRLRGIDGTVDSPCRHCIARVVILAFLD" ) self.assertAlmostEqual(alignment.annotations["evalue"], 1e-11, places=11) self.assertAlmostEqual(alignment.annotations["bit score"], 51.0) self.assertAlmostEqual(alignment.score, 105) self.assertEqual(alignment.shape, (2, 49)) self.assertAlmostEqual(alignment.annotations["% identity"], 55.10) self.assertEqual(alignment.annotations["identical"], 27) self.assertEqual(alignment.annotations["mismatches"], 22) self.assertEqual(alignment.annotations["positives"], 33) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 67.35) self.assertEqual(alignment.annotations["query/sbjct frames"], "-1/-2") self.assertEqual(alignment.query.annotations["frame"], "-1") self.assertEqual(alignment.target.annotations["frame"], "-2") self.assertEqual(alignment.target.annotations["tax ids"], "559307") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Zygosaccharomyces rouxii hypothetical protein (ZYRO0C02266g) mRNA, complete cds", ) self.assertEqual( alignment.target.annotations["titles"], "Zygosaccharomyces rouxii hypothetical protein (ZYRO0C02266g) mRNA, complete cds", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 96) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 42) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|254579 0 TTFKISIDLSLAFLIAVFLFFDSDESECNSELSSFQKLPNSP 42 0 |.|.||.|||||.....||.|||...|.||..|......|.| 42 gi|296147 0 TLFNISMDLSLAWRMVEFLLFDSEDKERNSASSCLCMESNPP 42 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 42], [ 0, 42]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|254579534|ref|XM_002495708.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|254579534|ref|XM_002495708.1|" ) self.assertEqual(alignment.target.annotations["gi"], "254579534") self.assertEqual(alignment.target.annotations["gis"], "254579534") self.assertEqual(alignment.target.annotations["acc."], "XM_002495708") self.assertEqual(alignment.target.annotations["accs."], "XM_002495708") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_002495708.1") self.assertEqual(alignment.target.annotations["length"], 4866) self.assertEqual(alignment.query.annotations["start"], 140) self.assertEqual(alignment.query.annotations["end"], 14) self.assertEqual(alignment.target.annotations["start"], 140) self.assertEqual(alignment.target.annotations["end"], 14) self.assertEqual( alignment.target.seq, "TTFKISIDLSLAFLIAVFLFFDSDESECNSELSSFQKLPNSP" ) self.assertEqual( alignment.query.seq, "TLFNISMDLSLAWRMVEFLLFDSEDKERNSASSCLCMESNPP" ) self.assertAlmostEqual(alignment.annotations["evalue"], 1e-11, places=11) self.assertAlmostEqual(alignment.annotations["bit score"], 41.8) self.assertAlmostEqual(alignment.score, 85) self.assertEqual(alignment.shape, (2, 42)) self.assertAlmostEqual(alignment.annotations["% identity"], 47.62) self.assertEqual(alignment.annotations["identical"], 20) self.assertEqual(alignment.annotations["mismatches"], 22) self.assertEqual(alignment.annotations["positives"], 25) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 59.52) self.assertEqual(alignment.annotations["query/sbjct frames"], "-1/-2") self.assertEqual(alignment.query.annotations["frame"], "-1") self.assertEqual(alignment.target.annotations["frame"], "-2") self.assertEqual(alignment.target.annotations["tax ids"], "559307") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Zygosaccharomyces rouxii hypothetical protein (ZYRO0C02266g) mRNA, complete cds", ) self.assertEqual( alignment.target.annotations["titles"], "Zygosaccharomyces rouxii hypothetical protein (ZYRO0C02266g) mRNA, complete cds", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 96) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 36) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|254579 0 RVAFTFIRVEEKEYCY*EC*R*IN*NFESSSQL*GIIKTSRFYSTASDVMCIQECQIDYY 0 |.||...|.|.|......||.||.|..|.|...||..|||.|.........|.||..|.. gi|296147 0 RIAFFIFRIEKKKFNHSPC***IH*DIEKST*F*GARKTSGFRTPFRVGLPIKEC*NDDP gi|254579 60 INAMFPKIGHSAMYTGR*TLRRT*CVYRGQPAGNGYKTK 99 60 .|||.........|..........|...|.....|...| 99 gi|296147 60 GNAMPTGTVNRSIYSSKPAV*NFGCLH*GYSSRDGDSIK 99 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 99], [ 0, 99]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|254579534|ref|XM_002495708.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|254579534|ref|XM_002495708.1|" ) self.assertEqual(alignment.target.annotations["gi"], "254579534") self.assertEqual(alignment.target.annotations["gis"], "254579534") self.assertEqual(alignment.target.annotations["acc."], "XM_002495708") self.assertEqual(alignment.target.annotations["accs."], "XM_002495708") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_002495708.1") self.assertEqual(alignment.target.annotations["length"], 4866) self.assertEqual(alignment.query.annotations["start"], 50) self.assertEqual(alignment.query.annotations["end"], 347) self.assertEqual(alignment.target.annotations["start"], 50) self.assertEqual(alignment.target.annotations["end"], 347) self.assertEqual( alignment.target.seq, "RVAFTFIRVEEKEYCY*EC*R*IN*NFESSSQL*GIIKTSRFYSTASDVMCIQECQIDYYINAMFPKIGHSAMYTGR*TLRRT*CVYRGQPAGNGYKTK", ) self.assertEqual( alignment.query.seq, "RIAFFIFRIEKKKFNHSPC***IH*DIEKST*F*GARKTSGFRTPFRVGLPIKEC*NDDPGNAMPTGTVNRSIYSSKPAV*NFGCLH*GYSSRDGDSIK", ) self.assertAlmostEqual(alignment.annotations["evalue"], 0.006) self.assertAlmostEqual(alignment.annotations["bit score"], 45.1) self.assertAlmostEqual(alignment.score, 92) self.assertEqual(alignment.shape, (2, 99)) self.assertAlmostEqual(alignment.annotations["% identity"], 31.31) self.assertEqual(alignment.annotations["identical"], 31) self.assertEqual(alignment.annotations["mismatches"], 68) self.assertEqual(alignment.annotations["positives"], 53) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 53.54) self.assertEqual(alignment.annotations["query/sbjct frames"], "3/3") self.assertEqual(alignment.query.annotations["frame"], "3") self.assertEqual(alignment.target.annotations["frame"], "3") self.assertEqual(alignment.target.annotations["tax ids"], "559307") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Zygosaccharomyces rouxii hypothetical protein (ZYRO0C02266g) mRNA, complete cds", ) self.assertEqual( alignment.target.annotations["titles"], "Zygosaccharomyces rouxii hypothetical protein (ZYRO0C02266g) mRNA, complete cds", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 96) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 85) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|156843 0 VKHASDKSIEILKTVTNINDLTRHPDFVVPFILACSSGNAKLTSISMQCIQVISTVQCIP 0 ..|||||||||||.|.....|.|||||..||.|||.|.|||.|...|||.|..|||..|| gi|296147 0 IRHASDKSIEILKRVHSFEELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIP gi|156843 60 STRISEILDAFINATHLAVEIQLK 84 60 ..|.||||||||.|||||.||||| 84 gi|296147 60 RSRLSEILDAFIEATHLAMEIQLK 84 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 84], [ 0, 84]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|156843402|ref|XM_001644719.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|156843402|ref|XM_001644719.1|" ) self.assertEqual(alignment.target.annotations["gi"], "156843402") self.assertEqual(alignment.target.annotations["gis"], "156843402") self.assertEqual(alignment.target.annotations["acc."], "XM_001644719") self.assertEqual(alignment.target.annotations["accs."], "XM_001644719") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_001644719.1") self.assertEqual(alignment.target.annotations["length"], 4914) self.assertEqual(alignment.query.annotations["start"], 96) self.assertEqual(alignment.query.annotations["end"], 348) self.assertEqual(alignment.target.annotations["start"], 96) self.assertEqual(alignment.target.annotations["end"], 348) self.assertEqual( alignment.target.seq, "VKHASDKSIEILKTVTNINDLTRHPDFVVPFILACSSGNAKLTSISMQCIQVISTVQCIPSTRISEILDAFINATHLAVEIQLK", ) self.assertEqual( alignment.query.seq, "IRHASDKSIEILKRVHSFEELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAMEIQLK", ) self.assertAlmostEqual(alignment.annotations["evalue"], 2e-31, places=31) self.assertAlmostEqual(alignment.annotations["bit score"], 139) self.assertAlmostEqual(alignment.score, 299) self.assertEqual(alignment.shape, (2, 84)) self.assertAlmostEqual(alignment.annotations["% identity"], 66.67) self.assertEqual(alignment.annotations["identical"], 56) self.assertEqual(alignment.annotations["mismatches"], 28) self.assertEqual(alignment.annotations["positives"], 71) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 84.52) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "436907") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Vanderwaltozyma polyspora DSM 70294 hypothetical protein (Kpol_1020p19) partial mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "Vanderwaltozyma polyspora DSM 70294 hypothetical protein (Kpol_1020p19) partial mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 100) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 72) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|156843 0 WQLNLLILQPLKSN*LQTYNLYLLNRKEKVQMLNTLVINLLKF*KL*LI*MI*QDIQIS* 0 |...|..|.|.|.|..|...|||.||||..|....||||.|..||.......|.||.||. gi|296147 0 WP*TLEGLTPCKGNLKQNCVLYLPNRKEEIQPFAMLVINPLRY*KEYIVLRS*KDIRISH gi|156843 60 YHSFWHVLQEMQS*LQFLCNAFKLYQLYNVYQVLEFLKF*MLLLMLLI*RWKYN*K 116 60 ..|.|...|.|..|....|||....|..........|||.|..|.|||.||..||| 116 gi|296147 60 SLSCWLANQGMLK*RPWQCNAYRDCQPFHLFLEAGCLKFWMPSLRLLISRWRFN*K 116 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 116], [ 0, 116]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|156843402|ref|XM_001644719.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|156843402|ref|XM_001644719.1|" ) self.assertEqual(alignment.target.annotations["gi"], "156843402") self.assertEqual(alignment.target.annotations["gis"], "156843402") self.assertEqual(alignment.target.annotations["acc."], "XM_001644719") self.assertEqual(alignment.target.annotations["accs."], "XM_001644719") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_001644719.1") self.assertEqual(alignment.target.annotations["length"], 4914) self.assertEqual(alignment.query.annotations["start"], 1) self.assertEqual(alignment.query.annotations["end"], 349) self.assertEqual(alignment.target.annotations["start"], 1) self.assertEqual(alignment.target.annotations["end"], 349) self.assertEqual( alignment.target.seq, "WQLNLLILQPLKSN*LQTYNLYLLNRKEKVQMLNTLVINLLKF*KL*LI*MI*QDIQIS*YHSFWHVLQEMQS*LQFLCNAFKLYQLYNVYQVLEFLKF*MLLLMLLI*RWKYN*K", ) self.assertEqual( alignment.query.seq, "WP*TLEGLTPCKGNLKQNCVLYLPNRKEEIQPFAMLVINPLRY*KEYIVLRS*KDIRISHSLSCWLANQGMLK*RPWQCNAYRDCQPFHLFLEAGCLKFWMPSLRLLISRWRFN*K", ) self.assertAlmostEqual(alignment.annotations["evalue"], 7e-14, places=14) self.assertAlmostEqual(alignment.annotations["bit score"], 81.3) self.assertAlmostEqual(alignment.score, 171) self.assertEqual(alignment.shape, (2, 116)) self.assertAlmostEqual(alignment.annotations["% identity"], 42.24) self.assertEqual(alignment.annotations["identical"], 49) self.assertEqual(alignment.annotations["mismatches"], 67) self.assertEqual(alignment.annotations["positives"], 66) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 56.90) self.assertEqual(alignment.annotations["query/sbjct frames"], "2/2") self.assertEqual(alignment.query.annotations["frame"], "2") self.assertEqual(alignment.target.annotations["frame"], "2") self.assertEqual(alignment.target.annotations["tax ids"], "436907") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Vanderwaltozyma polyspora DSM 70294 hypothetical protein (Kpol_1020p19) partial mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "Vanderwaltozyma polyspora DSM 70294 hypothetical protein (Kpol_1020p19) partial mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 100) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 99) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|156843 0 F*LYFHR*MSSINKSI*NFRNSSTWYTLYS*YNLNALHRN*S*LCIS*RTCQNEWYYEIW 0 |||..||.|||.|..|.|||..........|..|.|||.......|.|...|.|...||. gi|296147 0 F*LNLHREMSSLNEGIQNFRQPASRNRWNG*QSL*ALHCQGRHFSIP*LASQHERECEIR gi|156843 60 MSC*IIYISYSFQNFNRFITSVFNICTFSFRFRR*RL*VCSQLLFKGCKIKRFNCH 116 60 ||.|.....||||..|.||||..|....||||.|||...|..|...|.|......| 116 gi|296147 60 MSF*LLKTMYSFQYLNGFITSMANG*ISSFRFGR*RTQFCFKLPLHGVKPSSVHGH 116 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 116], [ 0, 116]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|156843402|ref|XM_001644719.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|156843402|ref|XM_001644719.1|" ) self.assertEqual(alignment.target.annotations["gi"], "156843402") self.assertEqual(alignment.target.annotations["gis"], "156843402") self.assertEqual(alignment.target.annotations["acc."], "XM_001644719") self.assertEqual(alignment.target.annotations["accs."], "XM_001644719") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_001644719.1") self.assertEqual(alignment.target.annotations["length"], 4914) self.assertEqual(alignment.query.annotations["start"], 348) self.assertEqual(alignment.query.annotations["end"], 0) self.assertEqual(alignment.target.annotations["start"], 348) self.assertEqual(alignment.target.annotations["end"], 0) self.assertEqual( alignment.target.seq, "F*LYFHR*MSSINKSI*NFRNSSTWYTLYS*YNLNALHRN*S*LCIS*RTCQNEWYYEIWMSC*IIYISYSFQNFNRFITSVFNICTFSFRFRR*RL*VCSQLLFKGCKIKRFNCH", ) self.assertEqual( alignment.query.seq, "F*LNLHREMSSLNEGIQNFRQPASRNRWNG*QSL*ALHCQGRHFSIP*LASQHERECEIRMSF*LLKTMYSFQYLNGFITSMANG*ISSFRFGR*RTQFCFKLPLHGVKPSSVHGH", ) self.assertAlmostEqual(alignment.annotations["evalue"], 4e-11, places=11) self.assertAlmostEqual(alignment.annotations["bit score"], 72.1) self.assertAlmostEqual(alignment.score, 151) self.assertEqual(alignment.shape, (2, 116)) self.assertAlmostEqual(alignment.annotations["% identity"], 42.24) self.assertEqual(alignment.annotations["identical"], 49) self.assertEqual(alignment.annotations["mismatches"], 67) self.assertEqual(alignment.annotations["positives"], 60) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 51.72) self.assertEqual(alignment.annotations["query/sbjct frames"], "-3/-1") self.assertEqual(alignment.query.annotations["frame"], "-3") self.assertEqual(alignment.target.annotations["frame"], "-1") self.assertEqual(alignment.target.annotations["tax ids"], "436907") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Vanderwaltozyma polyspora DSM 70294 hypothetical protein (Kpol_1020p19) partial mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "Vanderwaltozyma polyspora DSM 70294 hypothetical protein (Kpol_1020p19) partial mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 100) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 99) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|156843 0 TFNCISTAK*VALIKASKISEILVLGIHCTVDIT*MHCIEIEVSFAF 47 0 |||.||.|.|||..||||||.....||..|||....|||...|..|| 47 gi|296147 0 TFN*ISIAR*VASMKASKISDSRLRGIDGTVDSPCRHCIARVVILAF 47 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 47], [ 0, 47]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|156843402|ref|XM_001644719.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|156843402|ref|XM_001644719.1|" ) self.assertEqual(alignment.target.annotations["gi"], "156843402") self.assertEqual(alignment.target.annotations["gis"], "156843402") self.assertEqual(alignment.target.annotations["acc."], "XM_001644719") self.assertEqual(alignment.target.annotations["accs."], "XM_001644719") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_001644719.1") self.assertEqual(alignment.target.annotations["length"], 4914) self.assertEqual(alignment.query.annotations["start"], 350) self.assertEqual(alignment.query.annotations["end"], 209) self.assertEqual(alignment.target.annotations["start"], 350) self.assertEqual(alignment.target.annotations["end"], 209) self.assertEqual( alignment.target.seq, "TFNCISTAK*VALIKASKISEILVLGIHCTVDIT*MHCIEIEVSFAF" ) self.assertEqual( alignment.query.seq, "TFN*ISIAR*VASMKASKISDSRLRGIDGTVDSPCRHCIARVVILAF" ) self.assertAlmostEqual(alignment.annotations["evalue"], 3e-10, places=10) self.assertAlmostEqual(alignment.annotations["bit score"], 47.3) self.assertAlmostEqual(alignment.score, 97) self.assertEqual(alignment.shape, (2, 47)) self.assertAlmostEqual(alignment.annotations["% identity"], 55.32) self.assertEqual(alignment.annotations["identical"], 26) self.assertEqual(alignment.annotations["mismatches"], 21) self.assertEqual(alignment.annotations["positives"], 30) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 63.83) self.assertEqual(alignment.annotations["query/sbjct frames"], "-1/-2") self.assertEqual(alignment.query.annotations["frame"], "-1") self.assertEqual(alignment.target.annotations["frame"], "-2") self.assertEqual(alignment.target.annotations["tax ids"], "436907") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Vanderwaltozyma polyspora DSM 70294 hypothetical protein (Kpol_1020p19) partial mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "Vanderwaltozyma polyspora DSM 70294 hypothetical protein (Kpol_1020p19) partial mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 100) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 40) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|156843 0 HFLKNMPK*MVLRNLDVLLNHLY*LQFSKFQ*IYH*RV*HLYFFFSIQKIKIVSL*SIAF 0 |.|...|.....||.||.|.......||..|.||||....|.|||||.|||...|...|| gi|296147 0 HSLIGKPTRKGVRNPDVFLAPQNYVLFSISQWIYH*HGEWLNFFFSIRKIKNAILLQVAF gi|156843 60 60 gi|296147 60 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 60], [ 0, 60]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|156843402|ref|XM_001644719.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|156843402|ref|XM_001644719.1|" ) self.assertEqual(alignment.target.annotations["gi"], "156843402") self.assertEqual(alignment.target.annotations["gis"], "156843402") self.assertEqual(alignment.target.annotations["acc."], "XM_001644719") self.assertEqual(alignment.target.annotations["accs."], "XM_001644719") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_001644719.1") self.assertEqual(alignment.target.annotations["length"], 4914) self.assertEqual(alignment.query.annotations["start"], 214) self.assertEqual(alignment.query.annotations["end"], 34) self.assertEqual(alignment.target.annotations["start"], 214) self.assertEqual(alignment.target.annotations["end"], 34) self.assertEqual( alignment.target.seq, "HFLKNMPK*MVLRNLDVLLNHLY*LQFSKFQ*IYH*RV*HLYFFFSIQKIKIVSL*SIAF", ) self.assertEqual( alignment.query.seq, "HSLIGKPTRKGVRNPDVFLAPQNYVLFSISQWIYH*HGEWLNFFFSIRKIKNAILLQVAF", ) self.assertAlmostEqual(alignment.annotations["evalue"], 3e-10, places=10) self.assertAlmostEqual(alignment.annotations["bit score"], 40.5) self.assertAlmostEqual(alignment.score, 82) self.assertEqual(alignment.shape, (2, 60)) self.assertAlmostEqual(alignment.annotations["% identity"], 45.00) self.assertEqual(alignment.annotations["identical"], 27) self.assertEqual(alignment.annotations["mismatches"], 33) self.assertEqual(alignment.annotations["positives"], 31) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 51.67) self.assertEqual(alignment.annotations["query/sbjct frames"], "-2/-3") self.assertEqual(alignment.query.annotations["frame"], "-2") self.assertEqual(alignment.target.annotations["frame"], "-3") self.assertEqual(alignment.target.annotations["tax ids"], "436907") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Vanderwaltozyma polyspora DSM 70294 hypothetical protein (Kpol_1020p19) partial mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "Vanderwaltozyma polyspora DSM 70294 hypothetical protein (Kpol_1020p19) partial mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 100) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 51) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|156843 0 KAIDYRLTIFIF*IEKKKYRC*TR***IY*NFENCN*YK*FNKTSRFRSTIHFGMFFRKC 0 ||...|...|||.|||||......||||.|..|...|.....|||.||.....|.....| gi|296147 0 KAT*SRIAFFIFRIEKKKFNHSPC***IH*DIEKST*F*GARKTSGFRTPFRVGLPIKEC gi|156843 60 KANFNFYAMHSSYINCTMYTKY*NF*NFRCFY*CYSFSGGNTIKS 105 60 .......||.....|...|......|||.|..|.||...|..||| 105 gi|296147 60 *NDDPGNAMPTGTVNRSIYSSKPAV*NFGCLH*GYSSRDGDSIKS 105 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 105], [ 0, 105]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|156843402|ref|XM_001644719.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|156843402|ref|XM_001644719.1|" ) self.assertEqual(alignment.target.annotations["gi"], "156843402") self.assertEqual(alignment.target.annotations["gis"], "156843402") self.assertEqual(alignment.target.annotations["acc."], "XM_001644719") self.assertEqual(alignment.target.annotations["accs."], "XM_001644719") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_001644719.1") self.assertEqual(alignment.target.annotations["length"], 4914) self.assertEqual(alignment.query.annotations["start"], 35) self.assertEqual(alignment.query.annotations["end"], 350) self.assertEqual(alignment.target.annotations["start"], 35) self.assertEqual(alignment.target.annotations["end"], 350) self.assertEqual( alignment.target.seq, "KAIDYRLTIFIF*IEKKKYRC*TR***IY*NFENCN*YK*FNKTSRFRSTIHFGMFFRKCKANFNFYAMHSSYINCTMYTKY*NF*NFRCFY*CYSFSGGNTIKS", ) self.assertEqual( alignment.query.seq, "KAT*SRIAFFIFRIEKKKFNHSPC***IH*DIEKST*F*GARKTSGFRTPFRVGLPIKEC*NDDPGNAMPTGTVNRSIYSSKPAV*NFGCLH*GYSSRDGDSIKS", ) self.assertAlmostEqual(alignment.annotations["evalue"], 3e-08, places=8) self.assertAlmostEqual(alignment.annotations["bit score"], 62.5) self.assertAlmostEqual(alignment.score, 130) self.assertEqual(alignment.shape, (2, 105)) self.assertAlmostEqual(alignment.annotations["% identity"], 38.10) self.assertEqual(alignment.annotations["identical"], 40) self.assertEqual(alignment.annotations["mismatches"], 65) self.assertEqual(alignment.annotations["positives"], 58) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 55.24) self.assertEqual(alignment.annotations["query/sbjct frames"], "3/3") self.assertEqual(alignment.query.annotations["frame"], "3") self.assertEqual(alignment.target.annotations["frame"], "3") self.assertEqual(alignment.target.annotations["tax ids"], "436907") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Vanderwaltozyma polyspora DSM 70294 hypothetical protein (Kpol_1020p19) partial mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "Vanderwaltozyma polyspora DSM 70294 hypothetical protein (Kpol_1020p19) partial mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 100) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 90) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|156843 0 TVFKISIDLSLACLTSVLFLFDSEDKDCKSVVNC 34 0 |.|.||.|||||.......|||||||...|...| 34 gi|296147 0 TLFNISMDLSLAWRMVEFLLFDSEDKERNSASSC 34 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 34], [ 0, 34]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|156843402|ref|XM_001644719.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|156843402|ref|XM_001644719.1|" ) self.assertEqual(alignment.target.annotations["gi"], "156843402") self.assertEqual(alignment.target.annotations["gis"], "156843402") self.assertEqual(alignment.target.annotations["acc."], "XM_001644719") self.assertEqual(alignment.target.annotations["accs."], "XM_001644719") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_001644719.1") self.assertEqual(alignment.target.annotations["length"], 4914) self.assertEqual(alignment.query.annotations["start"], 140) self.assertEqual(alignment.query.annotations["end"], 38) self.assertEqual(alignment.target.annotations["start"], 140) self.assertEqual(alignment.target.annotations["end"], 38) self.assertEqual(alignment.target.seq, "TVFKISIDLSLACLTSVLFLFDSEDKDCKSVVNC") self.assertEqual(alignment.query.seq, "TLFNISMDLSLAWRMVEFLLFDSEDKERNSASSC") self.assertAlmostEqual(alignment.annotations["evalue"], 0.19) self.assertAlmostEqual(alignment.annotations["bit score"], 40.0) self.assertAlmostEqual(alignment.score, 81) self.assertEqual(alignment.shape, (2, 34)) self.assertAlmostEqual(alignment.annotations["% identity"], 52.94) self.assertEqual(alignment.annotations["identical"], 18) self.assertEqual(alignment.annotations["mismatches"], 16) self.assertEqual(alignment.annotations["positives"], 22) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 64.71) self.assertEqual(alignment.annotations["query/sbjct frames"], "-1/-2") self.assertEqual(alignment.query.annotations["frame"], "-1") self.assertEqual(alignment.target.annotations["frame"], "-2") self.assertEqual(alignment.target.annotations["tax ids"], "436907") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Vanderwaltozyma polyspora DSM 70294 hypothetical protein (Kpol_1020p19) partial mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "Vanderwaltozyma polyspora DSM 70294 hypothetical protein (Kpol_1020p19) partial mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 100) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 29) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|410075 0 VKHASEKSLKILKTVHDSGDFLRHPDFVVPFVLACSSRSAKLTTIGLQGLQNLSSTNCIP 0 ..|||.||..|||.||......|||||..||||||.||.||.||...|.||.||....|| gi|296147 0 IRHASDKSIEILKRVHSFEELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIP gi|410075 60 KDRLIEVLDGFIDATHLAMEIQLK 84 60 ..||.|.||.||.||||||||||| 84 gi|296147 60 RSRLSEILDAFIEATHLAMEIQLK 84 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 84], [ 0, 84]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|410075642|ref|XM_003955355.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|410075642|ref|XM_003955355.1|" ) self.assertEqual(alignment.target.annotations["gi"], "410075642") self.assertEqual(alignment.target.annotations["gis"], "410075642") self.assertEqual(alignment.target.annotations["acc."], "XM_003955355") self.assertEqual(alignment.target.annotations["accs."], "XM_003955355") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_003955355.1") self.assertEqual(alignment.target.annotations["length"], 4881) self.assertEqual(alignment.query.annotations["start"], 96) self.assertEqual(alignment.query.annotations["end"], 348) self.assertEqual(alignment.target.annotations["start"], 96) self.assertEqual(alignment.target.annotations["end"], 348) self.assertEqual( alignment.target.seq, "VKHASEKSLKILKTVHDSGDFLRHPDFVVPFVLACSSRSAKLTTIGLQGLQNLSSTNCIPKDRLIEVLDGFIDATHLAMEIQLK", ) self.assertEqual( alignment.query.seq, "IRHASDKSIEILKRVHSFEELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAMEIQLK", ) self.assertAlmostEqual(alignment.annotations["evalue"], 2e-28, places=28) self.assertAlmostEqual(alignment.annotations["bit score"], 129) self.assertAlmostEqual(alignment.score, 276) self.assertEqual(alignment.shape, (2, 84)) self.assertAlmostEqual(alignment.annotations["% identity"], 61.90) self.assertEqual(alignment.annotations["identical"], 52) self.assertEqual(alignment.annotations["mismatches"], 32) self.assertEqual(alignment.annotations["positives"], 67) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 79.76) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "1071382") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Kazachstania africana CBS 2517 hypothetical protein (KAFR0A08350), partial mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "Kazachstania africana CBS 2517 hypothetical protein (KAFR0A08350), partial mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 90) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 72) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|410075 0 TFS*ISIAKCVASINPSNTSINRSLGIQLVDDKFCKP*RPIVVNLALRDEQAKTNGTTKS 0 ||.|||||..|||...|..|..|..||....|..|......||.||..|.||.|.|..|| gi|296147 0 TFN*ISIAR*VASMKASKISDSRLRGIDGTVDSPCRHCIARVVILAFLDWQANTKGSAKS gi|410075 60 GCLRKSPLSCTVFKILRDFSLACLTSEFLLLASDDKE*SPVSSCL 105 60 |||..|...||.|.|..|.|||....||||..|.|||....|||| 105 gi|296147 60 GCLSSSSKLCTLFNISMDLSLAWRMVEFLLFDSEDKERNSASSCL 105 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 105], [ 0, 105]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|410075642|ref|XM_003955355.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|410075642|ref|XM_003955355.1|" ) self.assertEqual(alignment.target.annotations["gi"], "410075642") self.assertEqual(alignment.target.annotations["gis"], "410075642") self.assertEqual(alignment.target.annotations["acc."], "XM_003955355") self.assertEqual(alignment.target.annotations["accs."], "XM_003955355") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_003955355.1") self.assertEqual(alignment.target.annotations["length"], 4881) self.assertEqual(alignment.query.annotations["start"], 350) self.assertEqual(alignment.query.annotations["end"], 35) self.assertEqual(alignment.target.annotations["start"], 350) self.assertEqual(alignment.target.annotations["end"], 35) self.assertEqual( alignment.target.seq, "TFS*ISIAKCVASINPSNTSINRSLGIQLVDDKFCKP*RPIVVNLALRDEQAKTNGTTKSGCLRKSPLSCTVFKILRDFSLACLTSEFLLLASDDKE*SPVSSCL", ) self.assertEqual( alignment.query.seq, "TFN*ISIAR*VASMKASKISDSRLRGIDGTVDSPCRHCIARVVILAFLDWQANTKGSAKSGCLSSSSKLCTLFNISMDLSLAWRMVEFLLFDSEDKERNSASSCL", ) self.assertAlmostEqual(alignment.annotations["evalue"], 1e-09, places=9) self.assertAlmostEqual(alignment.annotations["bit score"], 67.5) self.assertAlmostEqual(alignment.score, 141) self.assertEqual(alignment.shape, (2, 105)) self.assertAlmostEqual(alignment.annotations["% identity"], 49.52) self.assertEqual(alignment.annotations["identical"], 52) self.assertEqual(alignment.annotations["mismatches"], 53) self.assertEqual(alignment.annotations["positives"], 61) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 58.10) self.assertEqual(alignment.annotations["query/sbjct frames"], "-1/-2") self.assertEqual(alignment.query.annotations["frame"], "-1") self.assertEqual(alignment.target.annotations["frame"], "-2") self.assertEqual(alignment.target.annotations["tax ids"], "1071382") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Kazachstania africana CBS 2517 hypothetical protein (KAFR0A08350), partial mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "Kazachstania africana CBS 2517 hypothetical protein (KAFR0A08350), partial mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 90) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 90) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|470736 0 VKHASDRSLQILRIVHSFEELERHPDFILPFVLSCKSGNAKFTSLSMQSLQRLAIHQSIP 0 ..||||.|..||..|||||||||||||.|||||.|.|.|||.|.|.||.||.|....||| gi|296147 0 IRHASDKSIEILKRVHSFEELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIP gi|470736 60 REQIEHVLEALIDSTQLAVEIQLK 84 60 |......|.|.|..|.||.||||| 84 gi|296147 60 RSRLSEILDAFIEATHLAMEIQLK 84 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 84], [ 0, 84]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|47073627|ref|NM_210010.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|47073627|ref|NM_210010.1|" ) self.assertEqual(alignment.target.annotations["gi"], "47073627") self.assertEqual(alignment.target.annotations["gis"], "47073627") self.assertEqual(alignment.target.annotations["acc."], "NM_210010") self.assertEqual(alignment.target.annotations["accs."], "NM_210010") self.assertEqual(alignment.target.annotations["acc.ver"], "NM_210010.1") self.assertEqual(alignment.target.annotations["length"], 4776) self.assertEqual(alignment.query.annotations["start"], 96) self.assertEqual(alignment.query.annotations["end"], 348) self.assertEqual(alignment.target.annotations["start"], 93) self.assertEqual(alignment.target.annotations["end"], 345) self.assertEqual( alignment.target.seq, "VKHASDRSLQILRIVHSFEELERHPDFILPFVLSCKSGNAKFTSLSMQSLQRLAIHQSIPREQIEHVLEALIDSTQLAVEIQLK", ) self.assertEqual( alignment.query.seq, "IRHASDKSIEILKRVHSFEELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAMEIQLK", ) self.assertAlmostEqual(alignment.annotations["evalue"], 2e-28, places=28) self.assertAlmostEqual(alignment.annotations["bit score"], 129) self.assertAlmostEqual(alignment.score, 276) self.assertEqual(alignment.shape, (2, 84)) self.assertAlmostEqual(alignment.annotations["% identity"], 61.90) self.assertEqual(alignment.annotations["identical"], 52) self.assertEqual(alignment.annotations["mismatches"], 32) self.assertEqual(alignment.annotations["positives"], 70) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 83.33) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "284811") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Ashbya gossypii ATCC 10895 AEL204Cp (AGOS_AEL204C) mRNA, complete cds", ) self.assertEqual( alignment.target.annotations["titles"], "Ashbya gossypii ATCC 10895 AEL204Cp (AGOS_AEL204C) mRNA, complete cds", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 94) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 72) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|470736 0 TFS*ISTASCVESISASSTCSICSRGIDWWIARRCRLCIDSEVNFAFPDLHERTNGRIKS 0 ||.|||.|..|.|..||.......||||......||.||...|..||.|....|.|..|| gi|296147 0 TFN*ISIAR*VASMKASKISDSRLRGIDGTVDSPCRHCIARVVILAFLDWQANTKGSAKS gi|470736 60 GCRSSSSKLWTIRNICNERSLACFTSELRRLDSEARACRSCVSCLTVLVN 110 60 ||.||||||.|..||....|||....|....|||.....|..|||....| 110 gi|296147 60 GCLSSSSKLCTLFNISMDLSLAWRMVEFLLFDSEDKERNSASSCLCMESN 110 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 110], [ 0, 110]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|47073627|ref|NM_210010.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|47073627|ref|NM_210010.1|" ) self.assertEqual(alignment.target.annotations["gi"], "47073627") self.assertEqual(alignment.target.annotations["gis"], "47073627") self.assertEqual(alignment.target.annotations["acc."], "NM_210010") self.assertEqual(alignment.target.annotations["accs."], "NM_210010") self.assertEqual(alignment.target.annotations["acc.ver"], "NM_210010.1") self.assertEqual(alignment.target.annotations["length"], 4776) self.assertEqual(alignment.query.annotations["start"], 350) self.assertEqual(alignment.query.annotations["end"], 20) self.assertEqual(alignment.target.annotations["start"], 347) self.assertEqual(alignment.target.annotations["end"], 17) self.assertEqual( alignment.target.seq, "TFS*ISTASCVESISASSTCSICSRGIDWWIARRCRLCIDSEVNFAFPDLHERTNGRIKSGCRSSSSKLWTIRNICNERSLACFTSELRRLDSEARACRSCVSCLTVLVN", ) self.assertEqual( alignment.query.seq, "TFN*ISIAR*VASMKASKISDSRLRGIDGTVDSPCRHCIARVVILAFLDWQANTKGSAKSGCLSSSSKLCTLFNISMDLSLAWRMVEFLLFDSEDKERNSASSCLCMESN", ) self.assertAlmostEqual(alignment.annotations["evalue"], 4e-05) self.assertAlmostEqual(alignment.annotations["bit score"], 52.4) self.assertAlmostEqual(alignment.score, 108) self.assertEqual(alignment.shape, (2, 110)) self.assertAlmostEqual(alignment.annotations["% identity"], 44.55) self.assertEqual(alignment.annotations["identical"], 49) self.assertEqual(alignment.annotations["mismatches"], 61) self.assertEqual(alignment.annotations["positives"], 56) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 50.91) self.assertEqual(alignment.annotations["query/sbjct frames"], "-1/-2") self.assertEqual(alignment.query.annotations["frame"], "-1") self.assertEqual(alignment.target.annotations["frame"], "-2") self.assertEqual(alignment.target.annotations["tax ids"], "284811") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Ashbya gossypii ATCC 10895 AEL204Cp (AGOS_AEL204C) mRNA, complete cds", ) self.assertEqual( alignment.target.annotations["titles"], "Ashbya gossypii ATCC 10895 AEL204Cp (AGOS_AEL204C) mRNA, complete cds", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 94) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 94) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|470736 0 F*LNLNGQLCGINQCFEYMFYLLPWNRLVDSQTLQTLH*QRSKLRIS*LT*EDERKNKVW 0 |||||.......|............||....|.|..||.|.....|.||....||..... gi|296147 0 F*LNLHREMSSLNEGIQNFRQPASRNRWNG*QSL*ALHCQGRHFSIP*LASQHERECEIR gi|470736 60 VSF*FFKTMDYPQYL*RAIACMFHFRITSLRFRS*GVQILCQLP 104 60 .|||..|||...|||...|..|....|.|.||..|..|....|| 104 gi|296147 60 MSF*LLKTMYSFQYLNGFITSMANG*ISSFRFGR*RTQFCFKLP 104 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 104], [ 0, 104]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|47073627|ref|NM_210010.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|47073627|ref|NM_210010.1|" ) self.assertEqual(alignment.target.annotations["gi"], "47073627") self.assertEqual(alignment.target.annotations["gis"], "47073627") self.assertEqual(alignment.target.annotations["acc."], "NM_210010") self.assertEqual(alignment.target.annotations["accs."], "NM_210010") self.assertEqual(alignment.target.annotations["acc.ver"], "NM_210010.1") self.assertEqual(alignment.target.annotations["length"], 4776) self.assertEqual(alignment.query.annotations["start"], 348) self.assertEqual(alignment.query.annotations["end"], 36) self.assertEqual(alignment.target.annotations["start"], 345) self.assertEqual(alignment.target.annotations["end"], 33) self.assertEqual( alignment.target.seq, "F*LNLNGQLCGINQCFEYMFYLLPWNRLVDSQTLQTLH*QRSKLRIS*LT*EDERKNKVWVSF*FFKTMDYPQYL*RAIACMFHFRITSLRFRS*GVQILCQLP", ) self.assertEqual( alignment.query.seq, "F*LNLHREMSSLNEGIQNFRQPASRNRWNG*QSL*ALHCQGRHFSIP*LASQHERECEIRMSF*LLKTMYSFQYLNGFITSMANG*ISSFRFGR*RTQFCFKLP", ) self.assertAlmostEqual(alignment.annotations["evalue"], 2e-04) self.assertAlmostEqual(alignment.annotations["bit score"], 50.1) self.assertAlmostEqual(alignment.score, 103) self.assertEqual(alignment.shape, (2, 104)) self.assertAlmostEqual(alignment.annotations["% identity"], 35.58) self.assertEqual(alignment.annotations["identical"], 37) self.assertEqual(alignment.annotations["mismatches"], 67) self.assertEqual(alignment.annotations["positives"], 52) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 50.00) self.assertEqual(alignment.annotations["query/sbjct frames"], "-3/-1") self.assertEqual(alignment.query.annotations["frame"], "-3") self.assertEqual(alignment.target.annotations["frame"], "-1") self.assertEqual(alignment.target.annotations["tax ids"], "284811") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Ashbya gossypii ATCC 10895 AEL204Cp (AGOS_AEL204C) mRNA, complete cds", ) self.assertEqual( alignment.target.annotations["titles"], "Ashbya gossypii ATCC 10895 AEL204Cp (AGOS_AEL204C) mRNA, complete cds", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 94) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 89) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|502941 0 VKEASHKSIEILKTIKTINDLENHPDFVVPFALACKTKNAKMTTIAMQCLQNMASTRCIP 0 ...||.|||||||.......||.||||..||.|||...||||||.||||||.......|| gi|296147 0 IRHASDKSIEILKRVHSFEELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIP gi|502941 60 EKRMDMILDAFIEATQLAMDIQLK 84 60 ..|...|||||||||.|||.|||| 84 gi|296147 60 RSRLSEILDAFIEATHLAMEIQLK 84 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 84], [ 0, 84]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|50294190|ref|XM_449507.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|50294190|ref|XM_449507.1|" ) self.assertEqual(alignment.target.annotations["gi"], "50294190") self.assertEqual(alignment.target.annotations["gis"], "50294190") self.assertEqual(alignment.target.annotations["acc."], "XM_449507") self.assertEqual(alignment.target.annotations["accs."], "XM_449507") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_449507.1") self.assertEqual(alignment.target.annotations["length"], 4980) self.assertEqual(alignment.query.annotations["start"], 96) self.assertEqual(alignment.query.annotations["end"], 348) self.assertEqual(alignment.target.annotations["start"], 183) self.assertEqual(alignment.target.annotations["end"], 435) self.assertEqual( alignment.target.seq, "VKEASHKSIEILKTIKTINDLENHPDFVVPFALACKTKNAKMTTIAMQCLQNMASTRCIPEKRMDMILDAFIEATQLAMDIQLK", ) self.assertEqual( alignment.query.seq, "IRHASDKSIEILKRVHSFEELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAMEIQLK", ) self.assertAlmostEqual(alignment.annotations["evalue"], 5e-28, places=28) self.assertAlmostEqual(alignment.annotations["bit score"], 128) self.assertAlmostEqual(alignment.score, 274) self.assertEqual(alignment.shape, (2, 84)) self.assertAlmostEqual(alignment.annotations["% identity"], 60.71) self.assertEqual(alignment.annotations["identical"], 51) self.assertEqual(alignment.annotations["mismatches"], 33) self.assertEqual(alignment.annotations["positives"], 66) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 78.57) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "284593") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Candida glabrata CBS 138 hypothetical protein partial mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "Candida glabrata CBS 138 hypothetical protein partial mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 90) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 72) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|502941 0 TFNCISMASCVASINASNIISILFSGIHLVEAMFCRHCIAIVVILAFL 48 0 |||.||.|..|||..||.|......||.......||||||.||||||| 48 gi|296147 0 TFN*ISIAR*VASMKASKISDSRLRGIDGTVDSPCRHCIARVVILAFL 48 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 48], [ 0, 48]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|50294190|ref|XM_449507.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|50294190|ref|XM_449507.1|" ) self.assertEqual(alignment.target.annotations["gi"], "50294190") self.assertEqual(alignment.target.annotations["gis"], "50294190") self.assertEqual(alignment.target.annotations["acc."], "XM_449507") self.assertEqual(alignment.target.annotations["accs."], "XM_449507") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_449507.1") self.assertEqual(alignment.target.annotations["length"], 4980) self.assertEqual(alignment.query.annotations["start"], 350) self.assertEqual(alignment.query.annotations["end"], 206) self.assertEqual(alignment.target.annotations["start"], 437) self.assertEqual(alignment.target.annotations["end"], 293) self.assertEqual( alignment.target.seq, "TFNCISMASCVASINASNIISILFSGIHLVEAMFCRHCIAIVVILAFL" ) self.assertEqual( alignment.query.seq, "TFN*ISIAR*VASMKASKISDSRLRGIDGTVDSPCRHCIARVVILAFL" ) self.assertAlmostEqual(alignment.annotations["evalue"], 5e-07) self.assertAlmostEqual(alignment.annotations["bit score"], 49.2) self.assertAlmostEqual(alignment.score, 101) self.assertEqual(alignment.shape, (2, 48)) self.assertAlmostEqual(alignment.annotations["% identity"], 56.25) self.assertEqual(alignment.annotations["identical"], 27) self.assertEqual(alignment.annotations["mismatches"], 21) self.assertEqual(alignment.annotations["positives"], 29) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 60.42) self.assertEqual(alignment.annotations["query/sbjct frames"], "-1/-2") self.assertEqual(alignment.query.annotations["frame"], "-1") self.assertEqual(alignment.target.annotations["frame"], "-2") self.assertEqual(alignment.target.annotations["tax ids"], "284593") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Candida glabrata CBS 138 hypothetical protein partial mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "Candida glabrata CBS 138 hypothetical protein partial mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 90) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 41) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|502941 0 VFNISIDLWLASLTSELRLRASATSA*RSASNCL 34 0 .||||.||.||....|..|..|......|||.|| 34 gi|296147 0 LFNISMDLSLAWRMVEFLLFDSEDKERNSASSCL 34 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 34], [ 0, 34]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|50294190|ref|XM_449507.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|50294190|ref|XM_449507.1|" ) self.assertEqual(alignment.target.annotations["gi"], "50294190") self.assertEqual(alignment.target.annotations["gis"], "50294190") self.assertEqual(alignment.target.annotations["acc."], "XM_449507") self.assertEqual(alignment.target.annotations["accs."], "XM_449507") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_449507.1") self.assertEqual(alignment.target.annotations["length"], 4980) self.assertEqual(alignment.query.annotations["start"], 137) self.assertEqual(alignment.query.annotations["end"], 35) self.assertEqual(alignment.target.annotations["start"], 224) self.assertEqual(alignment.target.annotations["end"], 122) self.assertEqual(alignment.target.seq, "VFNISIDLWLASLTSELRLRASATSA*RSASNCL") self.assertEqual(alignment.query.seq, "LFNISMDLSLAWRMVEFLLFDSEDKERNSASSCL") self.assertAlmostEqual(alignment.annotations["evalue"], 5e-07) self.assertAlmostEqual(alignment.annotations["bit score"], 27.6) self.assertAlmostEqual(alignment.score, 54) self.assertEqual(alignment.shape, (2, 34)) self.assertAlmostEqual(alignment.annotations["% identity"], 47.06) self.assertEqual(alignment.annotations["identical"], 16) self.assertEqual(alignment.annotations["mismatches"], 18) self.assertEqual(alignment.annotations["positives"], 19) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 55.88) self.assertEqual(alignment.annotations["query/sbjct frames"], "-1/-2") self.assertEqual(alignment.query.annotations["frame"], "-1") self.assertEqual(alignment.target.annotations["frame"], "-2") self.assertEqual(alignment.target.annotations["tax ids"], "284593") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Candida glabrata CBS 138 hypothetical protein partial mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "Candida glabrata CBS 138 hypothetical protein partial mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 90) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 29) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|444314 0 VKHTSDKALEILKTCHSNLDLKRHPDFIIPLIKACSSKSAKLTTIAMQCLQRMSSVDCIP 0 ..|.|||..||||..||...|.|||||..|...||.|..||.||.||||||..|.|..|| gi|296147 0 IRHASDKSIEILKRVHSFEELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIP gi|444314 60 DSRISQVLDSFIEATLLASDIQLK 84 60 .||.|..||.|||||.||..|||| 84 gi|296147 60 RSRLSEILDAFIEATHLAMEIQLK 84 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 84], [ 0, 84]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|444314872|ref|XM_004178046.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|444314872|ref|XM_004178046.1|" ) self.assertEqual(alignment.target.annotations["gi"], "444314872") self.assertEqual(alignment.target.annotations["gis"], "444314872") self.assertEqual(alignment.target.annotations["acc."], "XM_004178046") self.assertEqual(alignment.target.annotations["accs."], "XM_004178046") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_004178046.1") self.assertEqual(alignment.target.annotations["length"], 5190) self.assertEqual(alignment.query.annotations["start"], 96) self.assertEqual(alignment.query.annotations["end"], 348) self.assertEqual(alignment.target.annotations["start"], 99) self.assertEqual(alignment.target.annotations["end"], 351) self.assertEqual( alignment.target.seq, "VKHTSDKALEILKTCHSNLDLKRHPDFIIPLIKACSSKSAKLTTIAMQCLQRMSSVDCIPDSRISQVLDSFIEATLLASDIQLK", ) self.assertEqual( alignment.query.seq, "IRHASDKSIEILKRVHSFEELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAMEIQLK", ) self.assertAlmostEqual(alignment.annotations["evalue"], 1e-27, places=27) self.assertAlmostEqual(alignment.annotations["bit score"], 127) self.assertAlmostEqual(alignment.score, 271) self.assertEqual(alignment.shape, (2, 84)) self.assertAlmostEqual(alignment.annotations["% identity"], 59.52) self.assertEqual(alignment.annotations["identical"], 50) self.assertEqual(alignment.annotations["mismatches"], 34) self.assertEqual(alignment.annotations["positives"], 69) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 82.14) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "1071380") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Tetrapisispora blattae CBS 6284 hypothetical protein (TBLA0A07860) mRNA, complete cds", ) self.assertEqual( alignment.target.annotations["titles"], "Tetrapisispora blattae CBS 6284 hypothetical protein (TBLA0A07860) mRNA, complete cds", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 82) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 72) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|444314 0 TFS*ISEANRVASMKESNT*DILESGIQSTDDILCKHCIAIVVNLALFELHAFIK 55 0 ||.|||.|..|||||.|...|....||..|.|..|.||||.||.||.....|..| 55 gi|296147 0 TFN*ISIAR*VASMKASKISDSRLRGIDGTVDSPCRHCIARVVILAFLDWQANTK 55 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 55], [ 0, 55]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|444314872|ref|XM_004178046.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|444314872|ref|XM_004178046.1|" ) self.assertEqual(alignment.target.annotations["gi"], "444314872") self.assertEqual(alignment.target.annotations["gis"], "444314872") self.assertEqual(alignment.target.annotations["acc."], "XM_004178046") self.assertEqual(alignment.target.annotations["accs."], "XM_004178046") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_004178046.1") self.assertEqual(alignment.target.annotations["length"], 5190) self.assertEqual(alignment.query.annotations["start"], 350) self.assertEqual(alignment.query.annotations["end"], 185) self.assertEqual(alignment.target.annotations["start"], 353) self.assertEqual(alignment.target.annotations["end"], 188) self.assertEqual( alignment.target.seq, "TFS*ISEANRVASMKESNT*DILESGIQSTDDILCKHCIAIVVNLALFELHAFIK", ) self.assertEqual( alignment.query.seq, "TFN*ISIAR*VASMKASKISDSRLRGIDGTVDSPCRHCIARVVILAFLDWQANTK", ) self.assertAlmostEqual(alignment.annotations["evalue"], 1e-05) self.assertAlmostEqual(alignment.annotations["bit score"], 48.7) self.assertAlmostEqual(alignment.score, 100) self.assertEqual(alignment.shape, (2, 55)) self.assertAlmostEqual(alignment.annotations["% identity"], 50.91) self.assertEqual(alignment.annotations["identical"], 28) self.assertEqual(alignment.annotations["mismatches"], 27) self.assertEqual(alignment.annotations["positives"], 31) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 56.36) self.assertEqual(alignment.annotations["query/sbjct frames"], "-1/-2") self.assertEqual(alignment.query.annotations["frame"], "-1") self.assertEqual(alignment.target.annotations["frame"], "-2") self.assertEqual(alignment.target.annotations["tax ids"], "1071380") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Tetrapisispora blattae CBS 6284 hypothetical protein (TBLA0A07860) mRNA, complete cds", ) self.assertEqual( alignment.target.annotations["titles"], "Tetrapisispora blattae CBS 6284 hypothetical protein (TBLA0A07860) mRNA, complete cds", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 82) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 47) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|444314 0 VLRISKALSLVCLTSEFFLLDSETK 25 0 ...||..|||.....||.|.|||.| 25 gi|296147 0 LFNISMDLSLAWRMVEFLLFDSEDK 25 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 25], [ 0, 25]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|444314872|ref|XM_004178046.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|444314872|ref|XM_004178046.1|" ) self.assertEqual(alignment.target.annotations["gi"], "444314872") self.assertEqual(alignment.target.annotations["gis"], "444314872") self.assertEqual(alignment.target.annotations["acc."], "XM_004178046") self.assertEqual(alignment.target.annotations["accs."], "XM_004178046") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_004178046.1") self.assertEqual(alignment.target.annotations["length"], 5190) self.assertEqual(alignment.query.annotations["start"], 137) self.assertEqual(alignment.query.annotations["end"], 62) self.assertEqual(alignment.target.annotations["start"], 140) self.assertEqual(alignment.target.annotations["end"], 65) self.assertEqual(alignment.target.seq, "VLRISKALSLVCLTSEFFLLDSETK") self.assertEqual(alignment.query.seq, "LFNISMDLSLAWRMVEFLLFDSEDK") self.assertAlmostEqual(alignment.annotations["evalue"], 1e-05) self.assertAlmostEqual(alignment.annotations["bit score"], 23.5) self.assertAlmostEqual(alignment.score, 45) self.assertEqual(alignment.shape, (2, 25)) self.assertAlmostEqual(alignment.annotations["% identity"], 48.00) self.assertEqual(alignment.annotations["identical"], 12) self.assertEqual(alignment.annotations["mismatches"], 13) self.assertEqual(alignment.annotations["positives"], 13) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 52.00) self.assertEqual(alignment.annotations["query/sbjct frames"], "-1/-2") self.assertEqual(alignment.query.annotations["frame"], "-1") self.assertEqual(alignment.target.annotations["frame"], "-2") self.assertEqual(alignment.target.annotations["tax ids"], "1071380") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Tetrapisispora blattae CBS 6284 hypothetical protein (TBLA0A07860) mRNA, complete cds", ) self.assertEqual( alignment.target.annotations["titles"], "Tetrapisispora blattae CBS 6284 hypothetical protein (TBLA0A07860) mRNA, complete cds", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 82) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 21) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|444314 0 SL*ALHCDSSQFGTLRTTCFYQRYYEIRVTF*IQIAMACLKDLQSFITCMFNF*IFSSGF 0 |||||||....|..........|..|||..||....|.....|..|||.|.|.||.|..| gi|296147 0 SL*ALHCQGRHFSIP*LASQHERECEIRMSF*LLKTMYSFQYLNGFITSMANG*ISSFRF gi|444314 60 60 gi|296147 60 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 60], [ 0, 60]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|444314872|ref|XM_004178046.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|444314872|ref|XM_004178046.1|" ) self.assertEqual(alignment.target.annotations["gi"], "444314872") self.assertEqual(alignment.target.annotations["gis"], "444314872") self.assertEqual(alignment.target.annotations["acc."], "XM_004178046") self.assertEqual(alignment.target.annotations["accs."], "XM_004178046") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_004178046.1") self.assertEqual(alignment.target.annotations["length"], 5190) self.assertEqual(alignment.query.annotations["start"], 252) self.assertEqual(alignment.query.annotations["end"], 72) self.assertEqual(alignment.target.annotations["start"], 255) self.assertEqual(alignment.target.annotations["end"], 75) self.assertEqual( alignment.target.seq, "SL*ALHCDSSQFGTLRTTCFYQRYYEIRVTF*IQIAMACLKDLQSFITCMFNF*IFSSGF", ) self.assertEqual( alignment.query.seq, "SL*ALHCQGRHFSIP*LASQHERECEIRMSF*LLKTMYSFQYLNGFITSMANG*ISSFRF", ) self.assertAlmostEqual(alignment.annotations["evalue"], 0.075) self.assertAlmostEqual(alignment.annotations["bit score"], 41.4) self.assertAlmostEqual(alignment.score, 84) self.assertEqual(alignment.shape, (2, 60)) self.assertAlmostEqual(alignment.annotations["% identity"], 41.67) self.assertEqual(alignment.annotations["identical"], 25) self.assertEqual(alignment.annotations["mismatches"], 35) self.assertEqual(alignment.annotations["positives"], 31) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 51.67) self.assertEqual(alignment.annotations["query/sbjct frames"], "-3/-1") self.assertEqual(alignment.query.annotations["frame"], "-3") self.assertEqual(alignment.target.annotations["frame"], "-1") self.assertEqual(alignment.target.annotations["tax ids"], "1071380") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Tetrapisispora blattae CBS 6284 hypothetical protein (TBLA0A07860) mRNA, complete cds", ) self.assertEqual( alignment.target.annotations["titles"], "Tetrapisispora blattae CBS 6284 hypothetical protein (TBLA0A07860) mRNA, complete cds", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 82) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 51) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|363751 0 VKHASDKSLQILRIVHSFQELERHPDFVHPFVLSCKSGNAKFTTLSMQCLQRLAIHRSIS 0 ..||||||..||..||||.||||||||..||||.|.|.|||.|||.|||||.|....||. gi|296147 0 IRHASDKSIEILKRVHSFEELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIP gi|363751 60 KEQIEPVLEALIDSTQLAVEIQLK 84 60 .......|.|.|..|.||.||||| 84 gi|296147 60 RSRLSEILDAFIEATHLAMEIQLK 84 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 84], [ 0, 84]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|363751207|ref|XM_003645773.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|363751207|ref|XM_003645773.1|" ) self.assertEqual(alignment.target.annotations["gi"], "363751207") self.assertEqual(alignment.target.annotations["gis"], "363751207") self.assertEqual(alignment.target.annotations["acc."], "XM_003645773") self.assertEqual(alignment.target.annotations["accs."], "XM_003645773") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_003645773.1") self.assertEqual(alignment.target.annotations["length"], 4794) self.assertEqual(alignment.query.annotations["start"], 96) self.assertEqual(alignment.query.annotations["end"], 348) self.assertEqual(alignment.target.annotations["start"], 93) self.assertEqual(alignment.target.annotations["end"], 345) self.assertEqual( alignment.target.seq, "VKHASDKSLQILRIVHSFQELERHPDFVHPFVLSCKSGNAKFTTLSMQCLQRLAIHRSISKEQIEPVLEALIDSTQLAVEIQLK", ) self.assertEqual( alignment.query.seq, "IRHASDKSIEILKRVHSFEELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAMEIQLK", ) self.assertAlmostEqual(alignment.annotations["evalue"], 1e-27, places=27) self.assertAlmostEqual(alignment.annotations["bit score"], 127) self.assertAlmostEqual(alignment.score, 271) self.assertEqual(alignment.shape, (2, 84)) self.assertAlmostEqual(alignment.annotations["% identity"], 60.71) self.assertEqual(alignment.annotations["identical"], 51) self.assertEqual(alignment.annotations["mismatches"], 33) self.assertEqual(alignment.annotations["positives"], 69) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 82.14) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "931890") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Eremothecium cymbalariae DBVPG#7215 hypothetical protein (Ecym_3526) mRNA, complete cds", ) self.assertEqual( alignment.target.annotations["titles"], "Eremothecium cymbalariae DBVPG#7215 hypothetical protein (Ecym_3526) mRNA, complete cds", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 89) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 72) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|363751 0 TFNWISTAN*VESINASKTGSICSLEIDLWIANRCKHCIERVVNLAFPDLHDNTK 55 0 |||.||.|.||.|..|||........||......|.|||.|||.|||.|...||| 55 gi|296147 0 TFN*ISIAR*VASMKASKISDSRLRGIDGTVDSPCRHCIARVVILAFLDWQANTK 55 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 55], [ 0, 55]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|363751207|ref|XM_003645773.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|363751207|ref|XM_003645773.1|" ) self.assertEqual(alignment.target.annotations["gi"], "363751207") self.assertEqual(alignment.target.annotations["gis"], "363751207") self.assertEqual(alignment.target.annotations["acc."], "XM_003645773") self.assertEqual(alignment.target.annotations["accs."], "XM_003645773") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_003645773.1") self.assertEqual(alignment.target.annotations["length"], 4794) self.assertEqual(alignment.query.annotations["start"], 350) self.assertEqual(alignment.query.annotations["end"], 185) self.assertEqual(alignment.target.annotations["start"], 347) self.assertEqual(alignment.target.annotations["end"], 182) self.assertEqual( alignment.target.seq, "TFNWISTAN*VESINASKTGSICSLEIDLWIANRCKHCIERVVNLAFPDLHDNTK", ) self.assertEqual( alignment.query.seq, "TFN*ISIAR*VASMKASKISDSRLRGIDGTVDSPCRHCIARVVILAFLDWQANTK", ) self.assertAlmostEqual(alignment.annotations["evalue"], 8e-08, places=8) self.assertAlmostEqual(alignment.annotations["bit score"], 52.4) self.assertAlmostEqual(alignment.score, 108) self.assertEqual(alignment.shape, (2, 55)) self.assertAlmostEqual(alignment.annotations["% identity"], 50.91) self.assertEqual(alignment.annotations["identical"], 28) self.assertEqual(alignment.annotations["mismatches"], 27) self.assertEqual(alignment.annotations["positives"], 32) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 58.18) self.assertEqual(alignment.annotations["query/sbjct frames"], "-1/-2") self.assertEqual(alignment.query.annotations["frame"], "-1") self.assertEqual(alignment.target.annotations["frame"], "-2") self.assertEqual(alignment.target.annotations["tax ids"], "931890") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Eremothecium cymbalariae DBVPG#7215 hypothetical protein (Ecym_3526) mRNA, complete cds", ) self.assertEqual( alignment.target.annotations["titles"], "Eremothecium cymbalariae DBVPG#7215 hypothetical protein (Ecym_3526) mRNA, complete cds", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 89) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 47) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|363751 0 TILKI*SDLSDACLTSEFLLLDSED 25 0 |...|..|||.|....||||.|||| 25 gi|296147 0 TLFNISMDLSLAWRMVEFLLFDSED 25 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 25], [ 0, 25]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|363751207|ref|XM_003645773.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|363751207|ref|XM_003645773.1|" ) self.assertEqual(alignment.target.annotations["gi"], "363751207") self.assertEqual(alignment.target.annotations["gis"], "363751207") self.assertEqual(alignment.target.annotations["acc."], "XM_003645773") self.assertEqual(alignment.target.annotations["accs."], "XM_003645773") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_003645773.1") self.assertEqual(alignment.target.annotations["length"], 4794) self.assertEqual(alignment.query.annotations["start"], 140) self.assertEqual(alignment.query.annotations["end"], 65) self.assertEqual(alignment.target.annotations["start"], 137) self.assertEqual(alignment.target.annotations["end"], 62) self.assertEqual(alignment.target.seq, "TILKI*SDLSDACLTSEFLLLDSED") self.assertEqual(alignment.query.seq, "TLFNISMDLSLAWRMVEFLLFDSED") self.assertAlmostEqual(alignment.annotations["evalue"], 8e-08, places=8) self.assertAlmostEqual(alignment.annotations["bit score"], 27.2) self.assertAlmostEqual(alignment.score, 53) self.assertEqual(alignment.shape, (2, 25)) self.assertAlmostEqual(alignment.annotations["% identity"], 56.00) self.assertEqual(alignment.annotations["identical"], 14) self.assertEqual(alignment.annotations["mismatches"], 11) self.assertEqual(alignment.annotations["positives"], 15) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 60.00) self.assertEqual(alignment.annotations["query/sbjct frames"], "-1/-2") self.assertEqual(alignment.query.annotations["frame"], "-1") self.assertEqual(alignment.target.annotations["frame"], "-2") self.assertEqual(alignment.target.annotations["tax ids"], "931890") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Eremothecium cymbalariae DBVPG#7215 hypothetical protein (Ecym_3526) mRNA, complete cds", ) self.assertEqual( alignment.target.annotations["titles"], "Eremothecium cymbalariae DBVPG#7215 hypothetical protein (Ecym_3526) mRNA, complete cds", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 89) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 21) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|363751 0 QSLQTLHRKSSKFSIS*FT**YKRVYKIGMSFQFLKTMNYS*DLKRFIRCMFNLRISSFG 0 |||..||.....|||.|......|...|.|||..||||.....|..||..|.|..||||. gi|296147 0 QSL*ALHCQGRHFSIP*LASQHERECEIRMSF*LLKTMYSFQYLNGFITSMANG*ISSFR gi|363751 60 FRRQRIQILIQL 72 60 |.|.|.|....| 72 gi|296147 60 FGR*RTQFCFKL 72 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 72], [ 0, 72]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|363751207|ref|XM_003645773.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|363751207|ref|XM_003645773.1|" ) self.assertEqual(alignment.target.annotations["gi"], "363751207") self.assertEqual(alignment.target.annotations["gis"], "363751207") self.assertEqual(alignment.target.annotations["acc."], "XM_003645773") self.assertEqual(alignment.target.annotations["accs."], "XM_003645773") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_003645773.1") self.assertEqual(alignment.target.annotations["length"], 4794) self.assertEqual(alignment.query.annotations["start"], 255) self.assertEqual(alignment.query.annotations["end"], 39) self.assertEqual(alignment.target.annotations["start"], 252) self.assertEqual(alignment.target.annotations["end"], 36) self.assertEqual( alignment.target.seq, "QSLQTLHRKSSKFSIS*FT**YKRVYKIGMSFQFLKTMNYS*DLKRFIRCMFNLRISSFGFRRQRIQILIQL", ) self.assertEqual( alignment.query.seq, "QSL*ALHCQGRHFSIP*LASQHERECEIRMSF*LLKTMYSFQYLNGFITSMANG*ISSFRFGR*RTQFCFKL", ) self.assertAlmostEqual(alignment.annotations["evalue"], 0.006) self.assertAlmostEqual(alignment.annotations["bit score"], 45.1) self.assertAlmostEqual(alignment.score, 92) self.assertEqual(alignment.shape, (2, 72)) self.assertAlmostEqual(alignment.annotations["% identity"], 44.44) self.assertEqual(alignment.annotations["identical"], 32) self.assertEqual(alignment.annotations["mismatches"], 40) self.assertEqual(alignment.annotations["positives"], 37) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 51.39) self.assertEqual(alignment.annotations["query/sbjct frames"], "-3/-1") self.assertEqual(alignment.query.annotations["frame"], "-3") self.assertEqual(alignment.target.annotations["frame"], "-1") self.assertEqual(alignment.target.annotations["tax ids"], "931890") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Eremothecium cymbalariae DBVPG#7215 hypothetical protein (Ecym_3526) mRNA, complete cds", ) self.assertEqual( alignment.target.annotations["titles"], "Eremothecium cymbalariae DBVPG#7215 hypothetical protein (Ecym_3526) mRNA, complete cds", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 89) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 62) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|363751 0 *HFLIYMIIQKGVQNRDVVPIPENYELFLRFEAIYQMHV*PQNFFFWIQK 50 0 ||.||.....|||.|.||...|.||.||.....||..|....||||.|.| 50 gi|296147 0 *HSLIGKPTRKGVRNPDVFLAPQNYVLFSISQWIYH*HGEWLNFFFSIRK 50 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 50], [ 0, 50]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|363751207|ref|XM_003645773.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|363751207|ref|XM_003645773.1|" ) self.assertEqual(alignment.target.annotations["gi"], "363751207") self.assertEqual(alignment.target.annotations["gis"], "363751207") self.assertEqual(alignment.target.annotations["acc."], "XM_003645773") self.assertEqual(alignment.target.annotations["accs."], "XM_003645773") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_003645773.1") self.assertEqual(alignment.target.annotations["length"], 4794) self.assertEqual(alignment.query.annotations["start"], 217) self.assertEqual(alignment.query.annotations["end"], 67) self.assertEqual(alignment.target.annotations["start"], 214) self.assertEqual(alignment.target.annotations["end"], 64) self.assertEqual( alignment.target.seq, "*HFLIYMIIQKGVQNRDVVPIPENYELFLRFEAIYQMHV*PQNFFFWIQK", ) self.assertEqual( alignment.query.seq, "*HSLIGKPTRKGVRNPDVFLAPQNYVLFSISQWIYH*HGEWLNFFFSIRK", ) self.assertAlmostEqual(alignment.annotations["evalue"], 0.021) self.assertAlmostEqual(alignment.annotations["bit score"], 43.2) self.assertAlmostEqual(alignment.score, 88) self.assertEqual(alignment.shape, (2, 50)) self.assertAlmostEqual(alignment.annotations["% identity"], 48.00) self.assertEqual(alignment.annotations["identical"], 24) self.assertEqual(alignment.annotations["mismatches"], 26) self.assertEqual(alignment.annotations["positives"], 29) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 58.00) self.assertEqual(alignment.annotations["query/sbjct frames"], "-2/-3") self.assertEqual(alignment.query.annotations["frame"], "-2") self.assertEqual(alignment.target.annotations["frame"], "-3") self.assertEqual(alignment.target.annotations["tax ids"], "931890") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Eremothecium cymbalariae DBVPG#7215 hypothetical protein (Ecym_3526) mRNA, complete cds", ) self.assertEqual( alignment.target.annotations["titles"], "Eremothecium cymbalariae DBVPG#7215 hypothetical protein (Ecym_3526) mRNA, complete cds", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 89) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 43) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|363751 0 VF*IQKKKF*G*TCI**IASNLKNSS*FSGIGTTSRFCTPFCIIM*IRKC*IYYSFYAMF 0 .|.|.||||....|.|||......|.||.|...||.|.|||.....|..||......||. gi|296147 0 IFRIEKKKFNHSPC***IH*DIEKST*F*GARKTSGFRTPFRVGLPIKEC*NDDPGNAMP gi|363751 60 AAIGNPQIY 69 60 ....|..|| 69 gi|296147 60 TGTVNRSIY 69 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 69], [ 0, 69]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|363751207|ref|XM_003645773.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|363751207|ref|XM_003645773.1|" ) self.assertEqual(alignment.target.annotations["gi"], "363751207") self.assertEqual(alignment.target.annotations["gis"], "363751207") self.assertEqual(alignment.target.annotations["acc."], "XM_003645773") self.assertEqual(alignment.target.annotations["accs."], "XM_003645773") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_003645773.1") self.assertEqual(alignment.target.annotations["length"], 4794) self.assertEqual(alignment.query.annotations["start"], 65) self.assertEqual(alignment.query.annotations["end"], 272) self.assertEqual(alignment.target.annotations["start"], 62) self.assertEqual(alignment.target.annotations["end"], 269) self.assertEqual( alignment.target.seq, "VF*IQKKKF*G*TCI**IASNLKNSS*FSGIGTTSRFCTPFCIIM*IRKC*IYYSFYAMFAAIGNPQIY", ) self.assertEqual( alignment.query.seq, "IFRIEKKKFNHSPC***IH*DIEKST*F*GARKTSGFRTPFRVGLPIKEC*NDDPGNAMPTGTVNRSIY", ) self.assertAlmostEqual(alignment.annotations["evalue"], 0.27) self.assertAlmostEqual(alignment.annotations["bit score"], 39.6) self.assertAlmostEqual(alignment.score, 80) self.assertEqual(alignment.shape, (2, 69)) self.assertAlmostEqual(alignment.annotations["% identity"], 40.58) self.assertEqual(alignment.annotations["identical"], 28) self.assertEqual(alignment.annotations["mismatches"], 41) self.assertEqual(alignment.annotations["positives"], 38) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 55.07) self.assertEqual(alignment.annotations["query/sbjct frames"], "3/3") self.assertEqual(alignment.query.annotations["frame"], "3") self.assertEqual(alignment.target.annotations["frame"], "3") self.assertEqual(alignment.target.annotations["tax ids"], "931890") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Eremothecium cymbalariae DBVPG#7215 hypothetical protein (Ecym_3526) mRNA, complete cds", ) self.assertEqual( alignment.target.annotations["titles"], "Eremothecium cymbalariae DBVPG#7215 hypothetical protein (Ecym_3526) mRNA, complete cds", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 89) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 59) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|366997 0 IHQASDKSIEILKTVKSIDELRRHPDFILPFIIATSSGNAKLTSIALQCIQRFLTVEYIP 0 |..||||||||||.|.|..||.|||||.|||..|..|.|||.|..|.||.|...||..|| gi|296147 0 IRHASDKSIEILKRVHSFEELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIP gi|366997 60 KSQLGALLDSFISATHLADEIKLK 84 60 .|.|...||.||.|||||.||.|| 84 gi|296147 60 RSRLSEILDAFIEATHLAMEIQLK 84 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 84], [ 0, 84]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|366997674|ref|XM_003683526.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|366997674|ref|XM_003683526.1|" ) self.assertEqual(alignment.target.annotations["gi"], "366997674") self.assertEqual(alignment.target.annotations["gis"], "366997674") self.assertEqual(alignment.target.annotations["acc."], "XM_003683526") self.assertEqual(alignment.target.annotations["accs."], "XM_003683526") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_003683526.1") self.assertEqual(alignment.target.annotations["length"], 4890) self.assertEqual(alignment.query.annotations["start"], 96) self.assertEqual(alignment.query.annotations["end"], 348) self.assertEqual(alignment.target.annotations["start"], 99) self.assertEqual(alignment.target.annotations["end"], 351) self.assertEqual( alignment.target.seq, "IHQASDKSIEILKTVKSIDELRRHPDFILPFIIATSSGNAKLTSIALQCIQRFLTVEYIPKSQLGALLDSFISATHLADEIKLK", ) self.assertEqual( alignment.query.seq, "IRHASDKSIEILKRVHSFEELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAMEIQLK", ) self.assertAlmostEqual(alignment.annotations["evalue"], 2e-26, places=26) self.assertAlmostEqual(alignment.annotations["bit score"], 123) self.assertAlmostEqual(alignment.score, 263) self.assertEqual(alignment.shape, (2, 84)) self.assertAlmostEqual(alignment.annotations["% identity"], 61.90) self.assertEqual(alignment.annotations["identical"], 52) self.assertEqual(alignment.annotations["mismatches"], 32) self.assertEqual(alignment.annotations["positives"], 65) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 77.38) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "1071381") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Tetrapisispora phaffii CBS 4417 hypothetical protein (TPHA0A00550) mRNA, complete cds", ) self.assertEqual( alignment.target.annotations["titles"], "Tetrapisispora phaffii CBS 4417 hypothetical protein (TPHA0A00550) mRNA, complete cds", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 96) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 72) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|366997 0 NQDVFSIHQLT*LFSKFQWTYH*LDESHCLFFLIRLIKDPSLIIVIF*KPRRLQ 54 0 |.|||...|...|||..||.|||..|....||.||.||...|..|.|.....|| 54 gi|296147 0 NPDVFLAPQNYVLFSISQWIYH*HGEWLNFFFSIRKIKNAILLQVAFAWSQTLQ 54 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 54], [ 0, 54]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|366997674|ref|XM_003683526.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|366997674|ref|XM_003683526.1|" ) self.assertEqual(alignment.target.annotations["gi"], "366997674") self.assertEqual(alignment.target.annotations["gis"], "366997674") self.assertEqual(alignment.target.annotations["acc."], "XM_003683526") self.assertEqual(alignment.target.annotations["accs."], "XM_003683526") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_003683526.1") self.assertEqual(alignment.target.annotations["length"], 4890) self.assertEqual(alignment.query.annotations["start"], 175) self.assertEqual(alignment.query.annotations["end"], 13) self.assertEqual(alignment.target.annotations["start"], 178) self.assertEqual(alignment.target.annotations["end"], 16) self.assertEqual( alignment.target.seq, "NQDVFSIHQLT*LFSKFQWTYH*LDESHCLFFLIRLIKDPSLIIVIF*KPRRLQ", ) self.assertEqual( alignment.query.seq, "NPDVFLAPQNYVLFSISQWIYH*HGEWLNFFFSIRKIKNAILLQVAFAWSQTLQ", ) self.assertAlmostEqual(alignment.annotations["evalue"], 5e-07) self.assertAlmostEqual(alignment.annotations["bit score"], 40.0) self.assertAlmostEqual(alignment.score, 81) self.assertEqual(alignment.shape, (2, 54)) self.assertAlmostEqual(alignment.annotations["% identity"], 46.30) self.assertEqual(alignment.annotations["identical"], 25) self.assertEqual(alignment.annotations["mismatches"], 29) self.assertEqual(alignment.annotations["positives"], 28) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 51.85) self.assertEqual(alignment.annotations["query/sbjct frames"], "-2/-3") self.assertEqual(alignment.query.annotations["frame"], "-2") self.assertEqual(alignment.target.annotations["frame"], "-3") self.assertEqual(alignment.target.annotations["tax ids"], "1071381") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Tetrapisispora phaffii CBS 4417 hypothetical protein (TPHA0A00550) mRNA, complete cds", ) self.assertEqual( alignment.target.annotations["titles"], "Tetrapisispora phaffii CBS 4417 hypothetical protein (TPHA0A00550) mRNA, complete cds", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 96) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 46) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|366997 0 TFNFISSAKWVAEIKESSKAPN*LLGIYSTVKNLCIHCKAILVNFA 46 0 |||.||.|..||..|.|......|.||..||...|.||.|..|..| 46 gi|296147 0 TFN*ISIAR*VASMKASKISDSRLRGIDGTVDSPCRHCIARVVILA 46 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 46], [ 0, 46]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|366997674|ref|XM_003683526.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|366997674|ref|XM_003683526.1|" ) self.assertEqual(alignment.target.annotations["gi"], "366997674") self.assertEqual(alignment.target.annotations["gis"], "366997674") self.assertEqual(alignment.target.annotations["acc."], "XM_003683526") self.assertEqual(alignment.target.annotations["accs."], "XM_003683526") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_003683526.1") self.assertEqual(alignment.target.annotations["length"], 4890) self.assertEqual(alignment.query.annotations["start"], 350) self.assertEqual(alignment.query.annotations["end"], 212) self.assertEqual(alignment.target.annotations["start"], 353) self.assertEqual(alignment.target.annotations["end"], 215) self.assertEqual( alignment.target.seq, "TFNFISSAKWVAEIKESSKAPN*LLGIYSTVKNLCIHCKAILVNFA" ) self.assertEqual( alignment.query.seq, "TFN*ISIAR*VASMKASKISDSRLRGIDGTVDSPCRHCIARVVILA" ) self.assertAlmostEqual(alignment.annotations["evalue"], 5e-07) self.assertAlmostEqual(alignment.annotations["bit score"], 36.8) self.assertAlmostEqual(alignment.score, 74) self.assertEqual(alignment.shape, (2, 46)) self.assertAlmostEqual(alignment.annotations["% identity"], 45.65) self.assertEqual(alignment.annotations["identical"], 21) self.assertEqual(alignment.annotations["mismatches"], 25) self.assertEqual(alignment.annotations["positives"], 27) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 58.70) self.assertEqual(alignment.annotations["query/sbjct frames"], "-1/-2") self.assertEqual(alignment.query.annotations["frame"], "-1") self.assertEqual(alignment.target.annotations["frame"], "-2") self.assertEqual(alignment.target.annotations["tax ids"], "1071381") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Tetrapisispora phaffii CBS 4417 hypothetical protein (TPHA0A00550) mRNA, complete cds", ) self.assertEqual( alignment.target.annotations["titles"], "Tetrapisispora phaffii CBS 4417 hypothetical protein (TPHA0A00550) mRNA, complete cds", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 96) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 39) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|366997 0 QMGS*NKRV*QSAQLTLRNIFNS*KSLYTLQSNTC*FCITRRGSNYKWQYKIRMSSQFIN 0 .|.|.|.......|...||..|.|.||..|......|.|....|.......||||..... gi|296147 0 EMSSLNEGIQNFRQPASRNRWNG*QSL*ALHCQGRHFSIP*LASQHERECEIRMSF*LLK gi|366997 60 *LNCFQNFNGLITSLMNLIVSSF*FV**KTQ 91 60 ....||..||.|||..|...|||.|..|.|| 91 gi|296147 60 TMYSFQYLNGFITSMANG*ISSFRFGR*RTQ 91 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 91], [ 0, 91]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|366997674|ref|XM_003683526.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|366997674|ref|XM_003683526.1|" ) self.assertEqual(alignment.target.annotations["gi"], "366997674") self.assertEqual(alignment.target.annotations["gis"], "366997674") self.assertEqual(alignment.target.annotations["acc."], "XM_003683526") self.assertEqual(alignment.target.annotations["accs."], "XM_003683526") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_003683526.1") self.assertEqual(alignment.target.annotations["length"], 4890) self.assertEqual(alignment.query.annotations["start"], 327) self.assertEqual(alignment.query.annotations["end"], 54) self.assertEqual(alignment.target.annotations["start"], 330) self.assertEqual(alignment.target.annotations["end"], 57) self.assertEqual( alignment.target.seq, "QMGS*NKRV*QSAQLTLRNIFNS*KSLYTLQSNTC*FCITRRGSNYKWQYKIRMSSQFIN*LNCFQNFNGLITSLMNLIVSSF*FV**KTQ", ) self.assertEqual( alignment.query.seq, "EMSSLNEGIQNFRQPASRNRWNG*QSL*ALHCQGRHFSIP*LASQHERECEIRMSF*LLKTMYSFQYLNGFITSMANG*ISSFRFGR*RTQ", ) self.assertAlmostEqual(alignment.annotations["evalue"], 0.001) self.assertAlmostEqual(alignment.annotations["bit score"], 47.3) self.assertAlmostEqual(alignment.score, 97) self.assertEqual(alignment.shape, (2, 91)) self.assertAlmostEqual(alignment.annotations["% identity"], 36.26) self.assertEqual(alignment.annotations["identical"], 33) self.assertEqual(alignment.annotations["mismatches"], 58) self.assertEqual(alignment.annotations["positives"], 47) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 51.65) self.assertEqual(alignment.annotations["query/sbjct frames"], "-3/-1") self.assertEqual(alignment.query.annotations["frame"], "-3") self.assertEqual(alignment.target.annotations["frame"], "-1") self.assertEqual(alignment.target.annotations["tax ids"], "1071381") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Tetrapisispora phaffii CBS 4417 hypothetical protein (TPHA0A00550) mRNA, complete cds", ) self.assertEqual( alignment.target.annotations["titles"], "Tetrapisispora phaffii CBS 4417 hypothetical protein (TPHA0A00550) mRNA, complete cds", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 96) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 78) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|366997 0 QTWVFYQTNQKEETMRFIKLVISPLKF*KQLSQLMN*EDILI 42 0 |..|.|..|.|||...|..|||.||..||....|..|.||.| 42 gi|296147 0 QNCVLYLPNRKEEIQPFAMLVINPLRY*KEYIVLRS*KDIRI 42 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 42], [ 0, 42]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|366997674|ref|XM_003683526.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|366997674|ref|XM_003683526.1|" ) self.assertEqual(alignment.target.annotations["gi"], "366997674") self.assertEqual(alignment.target.annotations["gis"], "366997674") self.assertEqual(alignment.target.annotations["acc."], "XM_003683526") self.assertEqual(alignment.target.annotations["accs."], "XM_003683526") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_003683526.1") self.assertEqual(alignment.target.annotations["length"], 4890) self.assertEqual(alignment.query.annotations["start"], 49) self.assertEqual(alignment.query.annotations["end"], 175) self.assertEqual(alignment.target.annotations["start"], 52) self.assertEqual(alignment.target.annotations["end"], 178) self.assertEqual( alignment.target.seq, "QTWVFYQTNQKEETMRFIKLVISPLKF*KQLSQLMN*EDILI" ) self.assertEqual( alignment.query.seq, "QNCVLYLPNRKEEIQPFAMLVINPLRY*KEYIVLRS*KDIRI" ) self.assertAlmostEqual(alignment.annotations["evalue"], 0.075) self.assertAlmostEqual(alignment.annotations["bit score"], 41.4) self.assertAlmostEqual(alignment.score, 84) self.assertEqual(alignment.shape, (2, 42)) self.assertAlmostEqual(alignment.annotations["% identity"], 47.62) self.assertEqual(alignment.annotations["identical"], 20) self.assertEqual(alignment.annotations["mismatches"], 22) self.assertEqual(alignment.annotations["positives"], 27) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 64.29) self.assertEqual(alignment.annotations["query/sbjct frames"], "2/2") self.assertEqual(alignment.query.annotations["frame"], "2") self.assertEqual(alignment.target.annotations["frame"], "2") self.assertEqual(alignment.target.annotations["tax ids"], "1071381") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Tetrapisispora phaffii CBS 4417 hypothetical protein (TPHA0A00550) mRNA, complete cds", ) self.assertEqual( alignment.target.annotations["titles"], "Tetrapisispora phaffii CBS 4417 hypothetical protein (TPHA0A00550) mRNA, complete cds", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 96) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 36) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|367014 0 IKQASDKSIEILRTVRNYEELSNRSEFLAPFLMSCSSKNAKLTSISMQCLQRLSSTPSLS 0 |..|||||||||..|...|||.....|..||...|.|.|||.|...|||||.||..||.. gi|296147 0 IRHASDKSIEILKRVHSFEELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIP gi|367014 60 KDKLSDVLEAFIVATQLALDMKLK 84 60 ...||..|.|||.||.||....|| 84 gi|296147 60 RSRLSEILDAFIEATHLAMEIQLK 84 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 84], [ 0, 84]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|367014048|ref|XM_003681476.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|367014048|ref|XM_003681476.1|" ) self.assertEqual(alignment.target.annotations["gi"], "367014048") self.assertEqual(alignment.target.annotations["gis"], "367014048") self.assertEqual(alignment.target.annotations["acc."], "XM_003681476") self.assertEqual(alignment.target.annotations["accs."], "XM_003681476") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_003681476.1") self.assertEqual(alignment.target.annotations["length"], 4902) self.assertEqual(alignment.query.annotations["start"], 96) self.assertEqual(alignment.query.annotations["end"], 348) self.assertEqual(alignment.target.annotations["start"], 96) self.assertEqual(alignment.target.annotations["end"], 348) self.assertEqual( alignment.target.seq, "IKQASDKSIEILRTVRNYEELSNRSEFLAPFLMSCSSKNAKLTSISMQCLQRLSSTPSLSKDKLSDVLEAFIVATQLALDMKLK", ) self.assertEqual( alignment.query.seq, "IRHASDKSIEILKRVHSFEELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAMEIQLK", ) self.assertAlmostEqual(alignment.annotations["evalue"], 3e-24, places=24) self.assertAlmostEqual(alignment.annotations["bit score"], 115) self.assertAlmostEqual(alignment.score, 246) self.assertEqual(alignment.shape, (2, 84)) self.assertAlmostEqual(alignment.annotations["% identity"], 52.38) self.assertEqual(alignment.annotations["identical"], 44) self.assertEqual(alignment.annotations["mismatches"], 40) self.assertEqual(alignment.annotations["positives"], 68) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 80.95) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "4950") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Torulaspora delbrueckii hypothetical protein (TDEL0E00700) mRNA, complete cds", ) self.assertEqual( alignment.target.annotations["titles"], "Torulaspora delbrueckii hypothetical protein (TDEL0E00700) mRNA, complete cds", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 90) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 72) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|367014 0 TFNFMSRAN*VATMNASRTSDNLSFDRDGVDDNLCKHCIDIDVNLAFFEEQ 51 0 |||..|.|.|||.|.||..||......||..|..|.|||...|.|||...| 51 gi|296147 0 TFN*ISIAR*VASMKASKISDSRLRGIDGTVDSPCRHCIARVVILAFLDWQ 51 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 51], [ 0, 51]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|367014048|ref|XM_003681476.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|367014048|ref|XM_003681476.1|" ) self.assertEqual(alignment.target.annotations["gi"], "367014048") self.assertEqual(alignment.target.annotations["gis"], "367014048") self.assertEqual(alignment.target.annotations["acc."], "XM_003681476") self.assertEqual(alignment.target.annotations["accs."], "XM_003681476") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_003681476.1") self.assertEqual(alignment.target.annotations["length"], 4902) self.assertEqual(alignment.query.annotations["start"], 350) self.assertEqual(alignment.query.annotations["end"], 197) self.assertEqual(alignment.target.annotations["start"], 350) self.assertEqual(alignment.target.annotations["end"], 197) self.assertEqual( alignment.target.seq, "TFNFMSRAN*VATMNASRTSDNLSFDRDGVDDNLCKHCIDIDVNLAFFEEQ", ) self.assertEqual( alignment.query.seq, "TFN*ISIAR*VASMKASKISDSRLRGIDGTVDSPCRHCIARVVILAFLDWQ", ) self.assertAlmostEqual(alignment.annotations["evalue"], 2e-11, places=11) self.assertAlmostEqual(alignment.annotations["bit score"], 48.3) self.assertAlmostEqual(alignment.score, 99) self.assertEqual(alignment.shape, (2, 51)) self.assertAlmostEqual(alignment.annotations["% identity"], 49.02) self.assertEqual(alignment.annotations["identical"], 25) self.assertEqual(alignment.annotations["mismatches"], 26) self.assertEqual(alignment.annotations["positives"], 32) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 62.75) self.assertEqual(alignment.annotations["query/sbjct frames"], "-1/-2") self.assertEqual(alignment.query.annotations["frame"], "-1") self.assertEqual(alignment.target.annotations["frame"], "-2") self.assertEqual(alignment.target.annotations["tax ids"], "4950") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Torulaspora delbrueckii hypothetical protein (TDEL0E00700) mRNA, complete cds", ) self.assertEqual( alignment.target.annotations["titles"], "Torulaspora delbrueckii hypothetical protein (TDEL0E00700) mRNA, complete cds", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 90) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 44) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|367014 0 TVLRISIDLSLACLMAELLFFASEDKSCNSEFNCL 35 0 |...||.|||||..|.|.|.|.||||..||...|| 35 gi|296147 0 TLFNISMDLSLAWRMVEFLLFDSEDKERNSASSCL 35 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 35], [ 0, 35]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|367014048|ref|XM_003681476.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|367014048|ref|XM_003681476.1|" ) self.assertEqual(alignment.target.annotations["gi"], "367014048") self.assertEqual(alignment.target.annotations["gis"], "367014048") self.assertEqual(alignment.target.annotations["acc."], "XM_003681476") self.assertEqual(alignment.target.annotations["accs."], "XM_003681476") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_003681476.1") self.assertEqual(alignment.target.annotations["length"], 4902) self.assertEqual(alignment.query.annotations["start"], 140) self.assertEqual(alignment.query.annotations["end"], 35) self.assertEqual(alignment.target.annotations["start"], 140) self.assertEqual(alignment.target.annotations["end"], 35) self.assertEqual( alignment.target.seq, "TVLRISIDLSLACLMAELLFFASEDKSCNSEFNCL" ) self.assertEqual(alignment.query.seq, "TLFNISMDLSLAWRMVEFLLFDSEDKERNSASSCL") self.assertAlmostEqual(alignment.annotations["evalue"], 2e-11, places=11) self.assertAlmostEqual(alignment.annotations["bit score"], 43.7) self.assertAlmostEqual(alignment.score, 89) self.assertEqual(alignment.shape, (2, 35)) self.assertAlmostEqual(alignment.annotations["% identity"], 57.14) self.assertEqual(alignment.annotations["identical"], 20) self.assertEqual(alignment.annotations["mismatches"], 15) self.assertEqual(alignment.annotations["positives"], 23) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 65.71) self.assertEqual(alignment.annotations["query/sbjct frames"], "-1/-2") self.assertEqual(alignment.query.annotations["frame"], "-1") self.assertEqual(alignment.target.annotations["frame"], "-2") self.assertEqual(alignment.target.annotations["tax ids"], "4950") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Torulaspora delbrueckii hypothetical protein (TDEL0E00700) mRNA, complete cds", ) self.assertEqual( alignment.target.annotations["titles"], "Torulaspora delbrueckii hypothetical protein (TDEL0E00700) mRNA, complete cds", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 90) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 30) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|503027 0 IKQACEKSIEILQRSHSEEELVRHPDFVDPFITACLSGNAKLTSISMQSMQRISGIRCIC 0 |..|..||||||.|.||.|||.|||||..||..||.|.|||.|...||..|..|....|. gi|296147 0 IRHASDKSIEILKRVHSFEELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIP gi|503027 60 TSKMESLLNALLKSTELAIDIQLK 84 60 .|.....|.|....|.||..|||| 84 gi|296147 60 RSRLSEILDAFIEATHLAMEIQLK 84 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 84], [ 0, 84]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|50302786|ref|XM_451330.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|50302786|ref|XM_451330.1|" ) self.assertEqual(alignment.target.annotations["gi"], "50302786") self.assertEqual(alignment.target.annotations["gis"], "50302786") self.assertEqual(alignment.target.annotations["acc."], "XM_451330") self.assertEqual(alignment.target.annotations["accs."], "XM_451330") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_451330.1") self.assertEqual(alignment.target.annotations["length"], 4809) self.assertEqual(alignment.query.annotations["start"], 96) self.assertEqual(alignment.query.annotations["end"], 348) self.assertEqual(alignment.target.annotations["start"], 93) self.assertEqual(alignment.target.annotations["end"], 345) self.assertEqual( alignment.target.seq, "IKQACEKSIEILQRSHSEEELVRHPDFVDPFITACLSGNAKLTSISMQSMQRISGIRCICTSKMESLLNALLKSTELAIDIQLK", ) self.assertEqual( alignment.query.seq, "IRHASDKSIEILKRVHSFEELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAMEIQLK", ) self.assertAlmostEqual(alignment.annotations["evalue"], 2e-20, places=20) self.assertAlmostEqual(alignment.annotations["bit score"], 103) self.assertAlmostEqual(alignment.score, 219) self.assertEqual(alignment.shape, (2, 84)) self.assertAlmostEqual(alignment.annotations["% identity"], 51.19) self.assertEqual(alignment.annotations["identical"], 43) self.assertEqual(alignment.annotations["mismatches"], 41) self.assertEqual(alignment.annotations["positives"], 63) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 75.00) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "284590") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Kluyveromyces lactis NRRL Y-1140 hypothetical protein partial mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "Kluyveromyces lactis NRRL Y-1140 hypothetical protein partial mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 72) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 72) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|367029 0 KNLRASTEVQASEELAQRPNFVNPFIIACGTKNVKFTGIAIVCLQRLIVSRALPRARLSQ 0 |.......|...|||...|.|..||..||...|.|.|..|..|||.|......||.|||. gi|296147 0 KSIEILKRVHSFEELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSE gi|367029 60 VLEALQQATSAGLDVQLK 78 60 .|.|...||......||| 78 gi|296147 60 ILDAFIEATHLAMEIQLK 78 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 78], [ 0, 78]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|367029360|ref|XM_003663916.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|367029360|ref|XM_003663916.1|" ) self.assertEqual(alignment.target.annotations["gi"], "367029360") self.assertEqual(alignment.target.annotations["gis"], "367029360") self.assertEqual(alignment.target.annotations["acc."], "XM_003663916") self.assertEqual(alignment.target.annotations["accs."], "XM_003663916") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_003663916.1") self.assertEqual(alignment.target.annotations["length"], 5145) self.assertEqual(alignment.query.annotations["start"], 114) self.assertEqual(alignment.query.annotations["end"], 348) self.assertEqual(alignment.target.annotations["start"], 105) self.assertEqual(alignment.target.annotations["end"], 339) self.assertEqual( alignment.target.seq, "KNLRASTEVQASEELAQRPNFVNPFIIACGTKNVKFTGIAIVCLQRLIVSRALPRARLSQVLEALQQATSAGLDVQLK", ) self.assertEqual( alignment.query.seq, "KSIEILKRVHSFEELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAMEIQLK", ) self.assertAlmostEqual(alignment.annotations["evalue"], 2e-13, places=13) self.assertAlmostEqual(alignment.annotations["bit score"], 79.9) self.assertAlmostEqual(alignment.score, 168) self.assertEqual(alignment.shape, (2, 78)) self.assertAlmostEqual(alignment.annotations["% identity"], 39.74) self.assertEqual(alignment.annotations["identical"], 31) self.assertEqual(alignment.annotations["mismatches"], 47) self.assertEqual(alignment.annotations["positives"], 52) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 66.67) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "573729") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Myceliophthora thermophila ATCC 42464 hypothetical protein (MYCTH_2139484) mRNA, complete cds", ) self.assertEqual( alignment.target.annotations["titles"], "Myceliophthora thermophila ATCC 42464 hypothetical protein (MYCTH_2139484) mRNA, complete cds", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 67) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 67) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|367039 0 KSLRASSEPQFADELAQRPNFVNPFIIACGTKNSKFTGIAIVCLQRLIIARAFPRSKLSQ 0 ||...........||...|.|..||..||...|.|.|..|..|||.|......|||.||. gi|296147 0 KSIEILKRVHSFEELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSE gi|367039 60 ILDALQQATSAGLDVQLK 78 60 ||||...||......||| 78 gi|296147 60 ILDAFIEATHLAMEIQLK 78 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 78], [ 0, 78]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|367039842|ref|XM_003650254.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|367039842|ref|XM_003650254.1|" ) self.assertEqual(alignment.target.annotations["gi"], "367039842") self.assertEqual(alignment.target.annotations["gis"], "367039842") self.assertEqual(alignment.target.annotations["acc."], "XM_003650254") self.assertEqual(alignment.target.annotations["accs."], "XM_003650254") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_003650254.1") self.assertEqual(alignment.target.annotations["length"], 5163) self.assertEqual(alignment.query.annotations["start"], 114) self.assertEqual(alignment.query.annotations["end"], 348) self.assertEqual(alignment.target.annotations["start"], 105) self.assertEqual(alignment.target.annotations["end"], 339) self.assertEqual( alignment.target.seq, "KSLRASSEPQFADELAQRPNFVNPFIIACGTKNSKFTGIAIVCLQRLIIARAFPRSKLSQILDALQQATSAGLDVQLK", ) self.assertEqual( alignment.query.seq, "KSIEILKRVHSFEELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAMEIQLK", ) self.assertAlmostEqual(alignment.annotations["evalue"], 5e-13, places=13) self.assertAlmostEqual(alignment.annotations["bit score"], 78.5) self.assertAlmostEqual(alignment.score, 165) self.assertEqual(alignment.shape, (2, 78)) self.assertAlmostEqual(alignment.annotations["% identity"], 41.03) self.assertEqual(alignment.annotations["identical"], 32) self.assertEqual(alignment.annotations["mismatches"], 46) self.assertEqual(alignment.annotations["positives"], 50) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 64.10) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "578455") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Thielavia terrestris NRRL 8126 hypothetical protein (THITE_2039383) mRNA, complete cds", ) self.assertEqual( alignment.target.annotations["titles"], "Thielavia terrestris NRRL 8126 hypothetical protein (THITE_2039383) mRNA, complete cds", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 67) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 67) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|302895 0 EELSQKVNFVNPFIIACGTKNAKFTAIAIVCLQRLIVAQALPRSKLNQVLEALMQATSAG 0 |||.....|..||..||...|||.|..|..|||.|......|||.|...|.|...||... gi|296147 0 EELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLA gi|302895 60 LDVQLK 66 60 ...||| 66 gi|296147 60 MEIQLK 66 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 66], [ 0, 66]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|302895812|ref|XM_003046741.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|302895812|ref|XM_003046741.1|" ) self.assertEqual(alignment.target.annotations["gi"], "302895812") self.assertEqual(alignment.target.annotations["gis"], "302895812") self.assertEqual(alignment.target.annotations["acc."], "XM_003046741") self.assertEqual(alignment.target.annotations["accs."], "XM_003046741") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_003046741.1") self.assertEqual(alignment.target.annotations["length"], 4878) self.assertEqual(alignment.query.annotations["start"], 150) self.assertEqual(alignment.query.annotations["end"], 348) self.assertEqual(alignment.target.annotations["start"], 141) self.assertEqual(alignment.target.annotations["end"], 339) self.assertEqual( alignment.target.seq, "EELSQKVNFVNPFIIACGTKNAKFTAIAIVCLQRLIVAQALPRSKLNQVLEALMQATSAGLDVQLK", ) self.assertEqual( alignment.query.seq, "EELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAMEIQLK", ) self.assertAlmostEqual(alignment.annotations["evalue"], 1e-12, places=12) self.assertAlmostEqual(alignment.annotations["bit score"], 77.1) self.assertAlmostEqual(alignment.score, 162) self.assertEqual(alignment.shape, (2, 66)) self.assertAlmostEqual(alignment.annotations["% identity"], 42.42) self.assertEqual(alignment.annotations["identical"], 28) self.assertEqual(alignment.annotations["mismatches"], 38) self.assertEqual(alignment.annotations["positives"], 48) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 72.73) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "660122") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Nectria haematococca mpVI 77-13-4 hypothetical protein, mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "Nectria haematococca mpVI 77-13-4 hypothetical protein, mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 57) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 57) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|302403 0 ELTQRPNFVNPFVIACGTKNTKFTAIAIVCLQRLILVRALPRGKLSHVLEALREATSAGL 0 ||...|.|..|||.||...|.|.|..|..|||.|..|...||..||..|.|..|||.... gi|296147 0 ELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAM gi|302403 60 DVQLK 65 60 ..||| 65 gi|296147 60 EIQLK 65 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 65], [ 0, 65]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|302403860|ref|XM_002999723.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|302403860|ref|XM_002999723.1|" ) self.assertEqual(alignment.target.annotations["gi"], "302403860") self.assertEqual(alignment.target.annotations["gis"], "302403860") self.assertEqual(alignment.target.annotations["acc."], "XM_002999723") self.assertEqual(alignment.target.annotations["accs."], "XM_002999723") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_002999723.1") self.assertEqual(alignment.target.annotations["length"], 5097) self.assertEqual(alignment.query.annotations["start"], 153) self.assertEqual(alignment.query.annotations["end"], 348) self.assertEqual(alignment.target.annotations["start"], 150) self.assertEqual(alignment.target.annotations["end"], 345) self.assertEqual( alignment.target.seq, "ELTQRPNFVNPFVIACGTKNTKFTAIAIVCLQRLILVRALPRGKLSHVLEALREATSAGLDVQLK", ) self.assertEqual( alignment.query.seq, "ELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAMEIQLK", ) self.assertAlmostEqual(alignment.annotations["evalue"], 2e-12, places=12) self.assertAlmostEqual(alignment.annotations["bit score"], 76.7) self.assertAlmostEqual(alignment.score, 161) self.assertEqual(alignment.shape, (2, 65)) self.assertAlmostEqual(alignment.annotations["% identity"], 46.15) self.assertEqual(alignment.annotations["identical"], 30) self.assertEqual(alignment.annotations["mismatches"], 35) self.assertEqual(alignment.annotations["positives"], 45) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 69.23) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "526221") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Verticillium albo-atrum VaMs.102 conserved hypothetical protein, mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "Verticillium albo-atrum VaMs.102 conserved hypothetical protein, mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 56) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 56) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|154323 0 DLTQRPNFVTPFLIACGTRNVKFTGIAVVCLQRLVVSRALPKSRLKEVLEALREATSAGL 0 .|...|.|..||..||..||.|.|..|..|||.|......|.|||.|.|.|..|||.... gi|296147 0 ELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAM gi|154323 60 DVQLK 65 60 ..||| 65 gi|296147 60 EIQLK 65 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 65], [ 0, 65]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|154323271|ref|XM_001560900.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|154323271|ref|XM_001560900.1|" ) self.assertEqual(alignment.target.annotations["gi"], "154323271") self.assertEqual(alignment.target.annotations["gis"], "154323271") self.assertEqual(alignment.target.annotations["acc."], "XM_001560900") self.assertEqual(alignment.target.annotations["accs."], "XM_001560900") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_001560900.1") self.assertEqual(alignment.target.annotations["length"], 3186) self.assertEqual(alignment.query.annotations["start"], 153) self.assertEqual(alignment.query.annotations["end"], 348) self.assertEqual(alignment.target.annotations["start"], 141) self.assertEqual(alignment.target.annotations["end"], 336) self.assertEqual( alignment.target.seq, "DLTQRPNFVTPFLIACGTRNVKFTGIAVVCLQRLVVSRALPKSRLKEVLEALREATSAGLDVQLK", ) self.assertEqual( alignment.query.seq, "ELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAMEIQLK", ) self.assertAlmostEqual(alignment.annotations["evalue"], 5e-12, places=12) self.assertAlmostEqual(alignment.annotations["bit score"], 75.3) self.assertAlmostEqual(alignment.score, 158) self.assertEqual(alignment.shape, (2, 65)) self.assertAlmostEqual(alignment.annotations["% identity"], 44.62) self.assertEqual(alignment.annotations["identical"], 29) self.assertEqual(alignment.annotations["mismatches"], 36) self.assertEqual(alignment.annotations["positives"], 45) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 69.23) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "332648") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Botryotinia fuckeliana B05.10 hypothetical protein (BC1G_00035) partial mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "Botryotinia fuckeliana B05.10 hypothetical protein (BC1G_00035) partial mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 56) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 56) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|389631 0 KSLNISSEAQLGPELTQKTNFANPFIIACGTKNAKFTGIAIVCLQRLIVSKALPRPRLNQ 0 ||..|........||.....||.||..||...|||.|..|..|||.|......||.||.. gi|296147 0 KSIEILKRVHSFEELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSE gi|389631 60 VLEALQGATSAGLDVQLK 78 60 .|.|...||......||| 78 gi|296147 60 ILDAFIEATHLAMEIQLK 78 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 78], [ 0, 78]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|389631003|ref|XM_003713107.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|389631003|ref|XM_003713107.1|" ) self.assertEqual(alignment.target.annotations["gi"], "389631003") self.assertEqual(alignment.target.annotations["gis"], "389631003") self.assertEqual(alignment.target.annotations["acc."], "XM_003713107") self.assertEqual(alignment.target.annotations["accs."], "XM_003713107") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_003713107.1") self.assertEqual(alignment.target.annotations["length"], 5566) self.assertEqual(alignment.query.annotations["start"], 114) self.assertEqual(alignment.query.annotations["end"], 348) self.assertEqual(alignment.target.annotations["start"], 293) self.assertEqual(alignment.target.annotations["end"], 527) self.assertEqual( alignment.target.seq, "KSLNISSEAQLGPELTQKTNFANPFIIACGTKNAKFTGIAIVCLQRLIVSKALPRPRLNQVLEALQGATSAGLDVQLK", ) self.assertEqual( alignment.query.seq, "KSIEILKRVHSFEELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAMEIQLK", ) self.assertAlmostEqual(alignment.annotations["evalue"], 2e-11, places=11) self.assertAlmostEqual(alignment.annotations["bit score"], 73.5) self.assertAlmostEqual(alignment.score, 154) self.assertEqual(alignment.shape, (2, 78)) self.assertAlmostEqual(alignment.annotations["% identity"], 39.74) self.assertEqual(alignment.annotations["identical"], 31) self.assertEqual(alignment.annotations["mismatches"], 47) self.assertEqual(alignment.annotations["positives"], 49) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 62.82) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/3") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "3") self.assertEqual(alignment.target.annotations["tax ids"], "242507") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Magnaporthe oryzae 70-15 hypothetical protein (MGG_07913) mRNA, complete cds", ) self.assertEqual( alignment.target.annotations["titles"], "Magnaporthe oryzae 70-15 hypothetical protein (MGG_07913) mRNA, complete cds", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 67) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 67) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|336276 0 KSLKVTSEAQISAELSQRSNFVNPFIIACGTKNVKFTGIAIVCLQRLIASRALPRFKLSQ 0 ||...........||.....|..||..||...|.|.|..|..|||.|......||..||. gi|296147 0 KSIEILKRVHSFEELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSE gi|336276 60 VLEALQQATSAGLDVQLK 78 60 .|.|...||......||| 78 gi|296147 60 ILDAFIEATHLAMEIQLK 78 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 78], [ 0, 78]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|336276565|ref|XM_003352988.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|336276565|ref|XM_003352988.1|" ) self.assertEqual(alignment.target.annotations["gi"], "336276565") self.assertEqual(alignment.target.annotations["gis"], "336276565") self.assertEqual(alignment.target.annotations["acc."], "XM_003352988") self.assertEqual(alignment.target.annotations["accs."], "XM_003352988") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_003352988.1") self.assertEqual(alignment.target.annotations["length"], 5166) self.assertEqual(alignment.query.annotations["start"], 114) self.assertEqual(alignment.query.annotations["end"], 348) self.assertEqual(alignment.target.annotations["start"], 105) self.assertEqual(alignment.target.annotations["end"], 339) self.assertEqual( alignment.target.seq, "KSLKVTSEAQISAELSQRSNFVNPFIIACGTKNVKFTGIAIVCLQRLIASRALPRFKLSQVLEALQQATSAGLDVQLK", ) self.assertEqual( alignment.query.seq, "KSIEILKRVHSFEELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAMEIQLK", ) self.assertAlmostEqual(alignment.annotations["evalue"], 3e-11, places=11) self.assertAlmostEqual(alignment.annotations["bit score"], 72.5) self.assertAlmostEqual(alignment.score, 152) self.assertEqual(alignment.shape, (2, 78)) self.assertAlmostEqual(alignment.annotations["% identity"], 35.90) self.assertEqual(alignment.annotations["identical"], 28) self.assertEqual(alignment.annotations["mismatches"], 50) self.assertEqual(alignment.annotations["positives"], 49) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 62.82) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "771870") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Sordaria macrospora k-hell hypothetical protein (SMAC_03354), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "Sordaria macrospora k-hell hypothetical protein (SMAC_03354), mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 67) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 67) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|164425 0 KSLKVTSEAQISAELSQRSNFVNPFIIACGTKNVKFTGIAIVCLQRLIASRALPRFKLSQ 0 ||...........||.....|..||..||...|.|.|..|..|||.|......||..||. gi|296147 0 KSIEILKRVHSFEELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSE gi|164425 60 VLEALQQATSAGLDVQLK 78 60 .|.|...||......||| 78 gi|296147 60 ILDAFIEATHLAMEIQLK 78 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 78], [ 0, 78]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|164425502|ref|XM_955020.2|") self.assertEqual( alignment.target.annotations["ids"], "gi|164425502|ref|XM_955020.2|" ) self.assertEqual(alignment.target.annotations["gi"], "164425502") self.assertEqual(alignment.target.annotations["gis"], "164425502") self.assertEqual(alignment.target.annotations["acc."], "XM_955020") self.assertEqual(alignment.target.annotations["accs."], "XM_955020") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_955020.2") self.assertEqual(alignment.target.annotations["length"], 5253) self.assertEqual(alignment.query.annotations["start"], 114) self.assertEqual(alignment.query.annotations["end"], 348) self.assertEqual(alignment.target.annotations["start"], 105) self.assertEqual(alignment.target.annotations["end"], 339) self.assertEqual( alignment.target.seq, "KSLKVTSEAQISAELSQRSNFVNPFIIACGTKNVKFTGIAIVCLQRLIASRALPRFKLSQVLEALQQATSAGLDVQLK", ) self.assertEqual( alignment.query.seq, "KSIEILKRVHSFEELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAMEIQLK", ) self.assertAlmostEqual(alignment.annotations["evalue"], 3e-11, places=11) self.assertAlmostEqual(alignment.annotations["bit score"], 72.5) self.assertAlmostEqual(alignment.score, 152) self.assertEqual(alignment.shape, (2, 78)) self.assertAlmostEqual(alignment.annotations["% identity"], 35.90) self.assertEqual(alignment.annotations["identical"], 28) self.assertEqual(alignment.annotations["mismatches"], 50) self.assertEqual(alignment.annotations["positives"], 49) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 62.82) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "367110") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Neurospora crassa OR74A hypothetical protein partial mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "Neurospora crassa OR74A hypothetical protein partial mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 67) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 67) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|296807 0 DLARKPQFARPFVLACQTRHTRLAAIGVANLQRLVTIGALPQERLKDVLQGLHETANLSL 0 .|.|.|.||.|||||||.|...........||.|.|....|..||...|....|...|.. gi|296147 0 ELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAM gi|296807 60 EIQLK 65 60 ||||| 65 gi|296147 60 EIQLK 65 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 65], [ 0, 65]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|296807956|ref|XM_002844271.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|296807956|ref|XM_002844271.1|" ) self.assertEqual(alignment.target.annotations["gi"], "296807956") self.assertEqual(alignment.target.annotations["gis"], "296807956") self.assertEqual(alignment.target.annotations["acc."], "XM_002844271") self.assertEqual(alignment.target.annotations["accs."], "XM_002844271") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_002844271.1") self.assertEqual(alignment.target.annotations["length"], 5127) self.assertEqual(alignment.query.annotations["start"], 153) self.assertEqual(alignment.query.annotations["end"], 348) self.assertEqual(alignment.target.annotations["start"], 144) self.assertEqual(alignment.target.annotations["end"], 339) self.assertEqual( alignment.target.seq, "DLARKPQFARPFVLACQTRHTRLAAIGVANLQRLVTIGALPQERLKDVLQGLHETANLSLEIQLK", ) self.assertEqual( alignment.query.seq, "ELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAMEIQLK", ) self.assertAlmostEqual(alignment.annotations["evalue"], 6e-11, places=11) self.assertAlmostEqual(alignment.annotations["bit score"], 71.6) self.assertAlmostEqual(alignment.score, 150) self.assertEqual(alignment.shape, (2, 65)) self.assertAlmostEqual(alignment.annotations["% identity"], 43.08) self.assertEqual(alignment.annotations["identical"], 28) self.assertEqual(alignment.annotations["mismatches"], 37) self.assertEqual(alignment.annotations["positives"], 44) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 67.69) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "554155") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Arthroderma otae CBS 113480 conserved hypothetical protein, mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "Arthroderma otae CBS 113480 conserved hypothetical protein, mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 56) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 56) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|327295 0 DLARKPQFARPFVLACQTRHTRLAAIGVTNLQRLVTIGALPHERLKDVLQGLHETANLSL 0 .|.|.|.||.|||||||.|...........||.|.|....|..||...|....|...|.. gi|296147 0 ELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAM gi|327295 60 EIQLK 65 60 ||||| 65 gi|296147 60 EIQLK 65 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 65], [ 0, 65]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|327295565|ref|XM_003232430.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|327295565|ref|XM_003232430.1|" ) self.assertEqual(alignment.target.annotations["gi"], "327295565") self.assertEqual(alignment.target.annotations["gis"], "327295565") self.assertEqual(alignment.target.annotations["acc."], "XM_003232430") self.assertEqual(alignment.target.annotations["accs."], "XM_003232430") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_003232430.1") self.assertEqual(alignment.target.annotations["length"], 5157) self.assertEqual(alignment.query.annotations["start"], 153) self.assertEqual(alignment.query.annotations["end"], 348) self.assertEqual(alignment.target.annotations["start"], 144) self.assertEqual(alignment.target.annotations["end"], 339) self.assertEqual( alignment.target.seq, "DLARKPQFARPFVLACQTRHTRLAAIGVTNLQRLVTIGALPHERLKDVLQGLHETANLSLEIQLK", ) self.assertEqual( alignment.query.seq, "ELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAMEIQLK", ) self.assertAlmostEqual(alignment.annotations["evalue"], 8e-11, places=11) self.assertAlmostEqual(alignment.annotations["bit score"], 71.2) self.assertAlmostEqual(alignment.score, 149) self.assertEqual(alignment.shape, (2, 65)) self.assertAlmostEqual(alignment.annotations["% identity"], 43.08) self.assertEqual(alignment.annotations["identical"], 28) self.assertEqual(alignment.annotations["mismatches"], 37) self.assertEqual(alignment.annotations["positives"], 43) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 66.15) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "559305") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Trichophyton rubrum CBS 118892 hypothetical protein (TERG_07323) mRNA, complete cds", ) self.assertEqual( alignment.target.annotations["titles"], "Trichophyton rubrum CBS 118892 hypothetical protein (TERG_07323) mRNA, complete cds", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 56) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 56) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|317026 0 DLVRKPKFANPFILACHSRHAKLAGIGVVCLQRLVASRSLPSERLKDVLAGLKETTNMSL 0 .|.|.|.||.||.|||.||.||.......|||.|....|.|..||...|....|.|.... gi|296147 0 ELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAM gi|317026 60 DIQLK 65 60 .|||| 65 gi|296147 60 EIQLK 65 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 65], [ 0, 65]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|317026200|ref|XM_001389120.2|") self.assertEqual( alignment.target.annotations["ids"], "gi|317026200|ref|XM_001389120.2|" ) self.assertEqual(alignment.target.annotations["gi"], "317026200") self.assertEqual(alignment.target.annotations["gis"], "317026200") self.assertEqual(alignment.target.annotations["acc."], "XM_001389120") self.assertEqual(alignment.target.annotations["accs."], "XM_001389120") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_001389120.2") self.assertEqual(alignment.target.annotations["length"], 5229) self.assertEqual(alignment.query.annotations["start"], 153) self.assertEqual(alignment.query.annotations["end"], 348) self.assertEqual(alignment.target.annotations["start"], 144) self.assertEqual(alignment.target.annotations["end"], 339) self.assertEqual( alignment.target.seq, "DLVRKPKFANPFILACHSRHAKLAGIGVVCLQRLVASRSLPSERLKDVLAGLKETTNMSLDIQLK", ) self.assertEqual( alignment.query.seq, "ELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAMEIQLK", ) self.assertAlmostEqual(alignment.annotations["evalue"], 8e-11, places=11) self.assertAlmostEqual(alignment.annotations["bit score"], 71.2) self.assertAlmostEqual(alignment.score, 149) self.assertEqual(alignment.shape, (2, 65)) self.assertAlmostEqual(alignment.annotations["% identity"], 44.62) self.assertEqual(alignment.annotations["identical"], 29) self.assertEqual(alignment.annotations["mismatches"], 36) self.assertEqual(alignment.annotations["positives"], 43) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 66.15) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "425011") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Aspergillus niger CBS 513.88 endosomal peripheral membrane protein (Mon2), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "Aspergillus niger CBS 513.88 endosomal peripheral membrane protein (Mon2), mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 56) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 56) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|156058 0 DLTQRANFVTPFLIACGTKNVKFTGIAVVCLQRLVVSRALPRSRLREVLEALREATSAGL 0 .|.....|..||..||...|.|.|..|..|||.|......|||||.|.|.|..|||.... gi|296147 0 ELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAM gi|156058 60 DVQLK 65 60 ..||| 65 gi|296147 60 EIQLK 65 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 65], [ 0, 65]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|156058004|ref|XM_001594876.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|156058004|ref|XM_001594876.1|" ) self.assertEqual(alignment.target.annotations["gi"], "156058004") self.assertEqual(alignment.target.annotations["gis"], "156058004") self.assertEqual(alignment.target.annotations["acc."], "XM_001594876") self.assertEqual(alignment.target.annotations["accs."], "XM_001594876") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_001594876.1") self.assertEqual(alignment.target.annotations["length"], 4755) self.assertEqual(alignment.query.annotations["start"], 153) self.assertEqual(alignment.query.annotations["end"], 348) self.assertEqual(alignment.target.annotations["start"], 144) self.assertEqual(alignment.target.annotations["end"], 339) self.assertEqual( alignment.target.seq, "DLTQRANFVTPFLIACGTKNVKFTGIAVVCLQRLVVSRALPRSRLREVLEALREATSAGLDVQLK", ) self.assertEqual( alignment.query.seq, "ELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAMEIQLK", ) self.assertAlmostEqual(alignment.annotations["evalue"], 8e-11, places=11) self.assertAlmostEqual(alignment.annotations["bit score"], 71.2) self.assertAlmostEqual(alignment.score, 149) self.assertEqual(alignment.shape, (2, 65)) self.assertAlmostEqual(alignment.annotations["% identity"], 43.08) self.assertEqual(alignment.annotations["identical"], 28) self.assertEqual(alignment.annotations["mismatches"], 37) self.assertEqual(alignment.annotations["positives"], 44) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 67.69) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "665079") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Sclerotinia sclerotiorum 1980 hypothetical protein (SS1G_04734) partial mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "Sclerotinia sclerotiorum 1980 hypothetical protein (SS1G_04734) partial mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 56) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 56) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|315042 0 DLARKPQFSRPFVLACQTRHARLAAIGVANLQRLVTIGALPHERLKDVVQGLHETANLSL 0 .|.|.|.|..|||||||.|.|.........||.|.|....|..||........|...|.. gi|296147 0 ELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAM gi|315042 60 EIQLK 65 60 ||||| 65 gi|296147 60 EIQLK 65 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 65], [ 0, 65]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|315042717|ref|XM_003170687.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|315042717|ref|XM_003170687.1|" ) self.assertEqual(alignment.target.annotations["gi"], "315042717") self.assertEqual(alignment.target.annotations["gis"], "315042717") self.assertEqual(alignment.target.annotations["acc."], "XM_003170687") self.assertEqual(alignment.target.annotations["accs."], "XM_003170687") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_003170687.1") self.assertEqual(alignment.target.annotations["length"], 5178) self.assertEqual(alignment.query.annotations["start"], 153) self.assertEqual(alignment.query.annotations["end"], 348) self.assertEqual(alignment.target.annotations["start"], 144) self.assertEqual(alignment.target.annotations["end"], 339) self.assertEqual( alignment.target.seq, "DLARKPQFSRPFVLACQTRHARLAAIGVANLQRLVTIGALPHERLKDVVQGLHETANLSLEIQLK", ) self.assertEqual( alignment.query.seq, "ELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAMEIQLK", ) self.assertAlmostEqual(alignment.annotations["evalue"], 2e-10, places=10) self.assertAlmostEqual(alignment.annotations["bit score"], 70.3) self.assertAlmostEqual(alignment.score, 147) self.assertEqual(alignment.shape, (2, 65)) self.assertAlmostEqual(alignment.annotations["% identity"], 41.54) self.assertEqual(alignment.annotations["identical"], 27) self.assertEqual(alignment.annotations["mismatches"], 38) self.assertEqual(alignment.annotations["positives"], 44) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 67.69) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "535722") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Arthroderma gypseum CBS 118893 hypothetical protein (MGYG_06723) mRNA, complete cds", ) self.assertEqual( alignment.target.annotations["titles"], "Arthroderma gypseum CBS 118893 hypothetical protein (MGYG_06723) mRNA, complete cds", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 56) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 56) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|255947 0 DLVRKPNFVEPFIIACHTRHAKLAGIGVICLQRLIASRSLPSSRLKDVLGGLKETTSLSL 0 .|.|.|.|..||..||..|.||.......|||.|....|.|.|||...|....|.|.|.. gi|296147 0 ELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAM gi|255947 60 DIQLK 65 60 .|||| 65 gi|296147 60 EIQLK 65 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 65], [ 0, 65]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|255947577|ref|XM_002564510.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|255947577|ref|XM_002564510.1|" ) self.assertEqual(alignment.target.annotations["gi"], "255947577") self.assertEqual(alignment.target.annotations["gis"], "255947577") self.assertEqual(alignment.target.annotations["acc."], "XM_002564510") self.assertEqual(alignment.target.annotations["accs."], "XM_002564510") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_002564510.1") self.assertEqual(alignment.target.annotations["length"], 5004) self.assertEqual(alignment.query.annotations["start"], 153) self.assertEqual(alignment.query.annotations["end"], 348) self.assertEqual(alignment.target.annotations["start"], 144) self.assertEqual(alignment.target.annotations["end"], 339) self.assertEqual( alignment.target.seq, "DLVRKPNFVEPFIIACHTRHAKLAGIGVICLQRLIASRSLPSSRLKDVLGGLKETTSLSLDIQLK", ) self.assertEqual( alignment.query.seq, "ELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAMEIQLK", ) self.assertAlmostEqual(alignment.annotations["evalue"], 2e-10, places=10) self.assertAlmostEqual(alignment.annotations["bit score"], 69.8) self.assertAlmostEqual(alignment.score, 146) self.assertEqual(alignment.shape, (2, 65)) self.assertAlmostEqual(alignment.annotations["% identity"], 43.08) self.assertEqual(alignment.annotations["identical"], 28) self.assertEqual(alignment.annotations["mismatches"], 37) self.assertEqual(alignment.annotations["positives"], 43) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 66.15) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "500485") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Penicillium chrysogenum Wisconsin 54-1255 hypothetical protein (Pc22g05210) mRNA, complete cds", ) self.assertEqual( alignment.target.annotations["titles"], "Penicillium chrysogenum Wisconsin 54-1255 hypothetical protein (Pc22g05210) mRNA, complete cds", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 56) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 56) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|121708 0 DLVRKPKFVDPFILACHSRHAKLSGIGVVCLQRLVASRSLPSSRLKDVLGGLRETTSLNL 0 .|.|.|.|..||.|||.||.||.......|||.|....|.|.|||...|....|.|.|.. gi|296147 0 ELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAM gi|121708 60 DVQLK 65 60 ..||| 65 gi|296147 60 EIQLK 65 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 65], [ 0, 65]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|121708212|ref|XM_001272061.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|121708212|ref|XM_001272061.1|" ) self.assertEqual(alignment.target.annotations["gi"], "121708212") self.assertEqual(alignment.target.annotations["gis"], "121708212") self.assertEqual(alignment.target.annotations["acc."], "XM_001272061") self.assertEqual(alignment.target.annotations["accs."], "XM_001272061") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_001272061.1") self.assertEqual(alignment.target.annotations["length"], 5226) self.assertEqual(alignment.query.annotations["start"], 153) self.assertEqual(alignment.query.annotations["end"], 348) self.assertEqual(alignment.target.annotations["start"], 150) self.assertEqual(alignment.target.annotations["end"], 345) self.assertEqual( alignment.target.seq, "DLVRKPKFVDPFILACHSRHAKLSGIGVVCLQRLVASRSLPSSRLKDVLGGLRETTSLNLDVQLK", ) self.assertEqual( alignment.query.seq, "ELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAMEIQLK", ) self.assertAlmostEqual(alignment.annotations["evalue"], 2e-10, places=10) self.assertAlmostEqual(alignment.annotations["bit score"], 69.8) self.assertAlmostEqual(alignment.score, 146) self.assertEqual(alignment.shape, (2, 65)) self.assertAlmostEqual(alignment.annotations["% identity"], 44.62) self.assertEqual(alignment.annotations["identical"], 29) self.assertEqual(alignment.annotations["mismatches"], 36) self.assertEqual(alignment.annotations["positives"], 42) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 64.62) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "344612") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Aspergillus clavatus NRRL 1 conserved hypothetical protein (ACLA_051080), partial mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "Aspergillus clavatus NRRL 1 conserved hypothetical protein (ACLA_051080), partial mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 56) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 56) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|303311 0 KAVPSTSEVQLAADLVRRPQFANPFILACHTRHAKLAAVGVGCIHRLVASGALPSEQLKD 0 |.......|.....|.|.|.||.||.|||..|.||.......|...|......|...|.. gi|296147 0 KSIEILKRVHSFEELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSE gi|303311 60 VVDGLHETTNLSLDVQLK 78 60 ..|...|.|.|....||| 78 gi|296147 60 ILDAFIEATHLAMEIQLK 78 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 78], [ 0, 78]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|303311206|ref|XM_003065569.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|303311206|ref|XM_003065569.1|" ) self.assertEqual(alignment.target.annotations["gi"], "303311206") self.assertEqual(alignment.target.annotations["gis"], "303311206") self.assertEqual(alignment.target.annotations["acc."], "XM_003065569") self.assertEqual(alignment.target.annotations["accs."], "XM_003065569") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_003065569.1") self.assertEqual(alignment.target.annotations["length"], 5588) self.assertEqual(alignment.query.annotations["start"], 114) self.assertEqual(alignment.query.annotations["end"], 348) self.assertEqual(alignment.target.annotations["start"], 289) self.assertEqual(alignment.target.annotations["end"], 523) self.assertEqual( alignment.target.seq, "KAVPSTSEVQLAADLVRRPQFANPFILACHTRHAKLAAVGVGCIHRLVASGALPSEQLKDVVDGLHETTNLSLDVQLK", ) self.assertEqual( alignment.query.seq, "KSIEILKRVHSFEELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAMEIQLK", ) self.assertAlmostEqual(alignment.annotations["evalue"], 3e-10, places=10) self.assertAlmostEqual(alignment.annotations["bit score"], 69.3) self.assertAlmostEqual(alignment.score, 145) self.assertEqual(alignment.shape, (2, 78)) self.assertAlmostEqual(alignment.annotations["% identity"], 33.33) self.assertEqual(alignment.annotations["identical"], 26) self.assertEqual(alignment.annotations["mismatches"], 52) self.assertEqual(alignment.annotations["positives"], 47) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 60.26) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/2") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "2") self.assertEqual(alignment.target.annotations["tax ids"], "222929") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Coccidioides posadasii C735 delta SOWgp HEAT repeat containing protein, mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "Coccidioides posadasii C735 delta SOWgp HEAT repeat containing protein, mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 67) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 67) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|709935 0 DLVRKPKFVDPFILACHSRHAKLAGIGVVCLQRLVASRSLPSERLKDVLGGLKETTSLSL 0 .|.|.|.|..||.|||.||.||.......|||.|....|.|..||...|....|.|.|.. gi|296147 0 ELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAM gi|709935 60 DIQLK 65 60 .|||| 65 gi|296147 60 EIQLK 65 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 65], [ 0, 65]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|70993553|ref|XM_746531.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|70993553|ref|XM_746531.1|" ) self.assertEqual(alignment.target.annotations["gi"], "70993553") self.assertEqual(alignment.target.annotations["gis"], "70993553") self.assertEqual(alignment.target.annotations["acc."], "XM_746531") self.assertEqual(alignment.target.annotations["accs."], "XM_746531") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_746531.1") self.assertEqual(alignment.target.annotations["length"], 5067) self.assertEqual(alignment.query.annotations["start"], 153) self.assertEqual(alignment.query.annotations["end"], 348) self.assertEqual(alignment.target.annotations["start"], 45) self.assertEqual(alignment.target.annotations["end"], 240) self.assertEqual( alignment.target.seq, "DLVRKPKFVDPFILACHSRHAKLAGIGVVCLQRLVASRSLPSERLKDVLGGLKETTSLSLDIQLK", ) self.assertEqual( alignment.query.seq, "ELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAMEIQLK", ) self.assertAlmostEqual(alignment.annotations["evalue"], 3e-10, places=10) self.assertAlmostEqual(alignment.annotations["bit score"], 69.3) self.assertAlmostEqual(alignment.score, 145) self.assertEqual(alignment.shape, (2, 65)) self.assertAlmostEqual(alignment.annotations["% identity"], 44.62) self.assertEqual(alignment.annotations["identical"], 29) self.assertEqual(alignment.annotations["mismatches"], 36) self.assertEqual(alignment.annotations["positives"], 41) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 63.08) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "330879") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Aspergillus fumigatus Af293 endosomal peripheral membrane protein (Mon2) (AFUA_4G12070), partial mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "Aspergillus fumigatus Af293 endosomal peripheral membrane protein (Mon2) (AFUA_4G12070), partial mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 56) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 56) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|212542 0 DLIRRPHFVTPFILACQTRQSKLASIGVVCLQRLATSHAISPSRLNDTLSALGDITGLSQ 0 .|.|.|.|..||.||||.|..|.......|||.|.|...|..|||...|.|....|.|.. gi|296147 0 ELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAM gi|212542 60 DVQLK 65 60 ..||| 65 gi|296147 60 EIQLK 65 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 65], [ 0, 65]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|212542406|ref|XM_002151322.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|212542406|ref|XM_002151322.1|" ) self.assertEqual(alignment.target.annotations["gi"], "212542406") self.assertEqual(alignment.target.annotations["gis"], "212542406") self.assertEqual(alignment.target.annotations["acc."], "XM_002151322") self.assertEqual(alignment.target.annotations["accs."], "XM_002151322") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_002151322.1") self.assertEqual(alignment.target.annotations["length"], 5214) self.assertEqual(alignment.query.annotations["start"], 153) self.assertEqual(alignment.query.annotations["end"], 348) self.assertEqual(alignment.target.annotations["start"], 144) self.assertEqual(alignment.target.annotations["end"], 339) self.assertEqual( alignment.target.seq, "DLIRRPHFVTPFILACQTRQSKLASIGVVCLQRLATSHAISPSRLNDTLSALGDITGLSQDVQLK", ) self.assertEqual( alignment.query.seq, "ELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAMEIQLK", ) self.assertAlmostEqual(alignment.annotations["evalue"], 4e-10, places=10) self.assertAlmostEqual(alignment.annotations["bit score"], 68.9) self.assertAlmostEqual(alignment.score, 144) self.assertEqual(alignment.shape, (2, 65)) self.assertAlmostEqual(alignment.annotations["% identity"], 43.08) self.assertEqual(alignment.annotations["identical"], 28) self.assertEqual(alignment.annotations["mismatches"], 37) self.assertEqual(alignment.annotations["positives"], 44) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 67.69) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "441960") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Penicillium marneffei ATCC 18224 endosomal peripheral membrane protein (Mon2), putative, mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "Penicillium marneffei ATCC 18224 endosomal peripheral membrane protein (Mon2), putative, mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 56) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 56) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|119500 0 DLVRKPRFVDPFILACHSRHAKLAGIGVVCLQRLVASRSLPSERLKDVLGGLKETTSLSL 0 .|.|.|.|..||.|||.||.||.......|||.|....|.|..||...|....|.|.|.. gi|296147 0 ELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAM gi|119500 60 DIQLK 65 60 .|||| 65 gi|296147 60 EIQLK 65 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 65], [ 0, 65]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|119500139|ref|XM_001266826.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|119500139|ref|XM_001266826.1|" ) self.assertEqual(alignment.target.annotations["gi"], "119500139") self.assertEqual(alignment.target.annotations["gis"], "119500139") self.assertEqual(alignment.target.annotations["acc."], "XM_001266826") self.assertEqual(alignment.target.annotations["accs."], "XM_001266826") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_001266826.1") self.assertEqual(alignment.target.annotations["length"], 4884) self.assertEqual(alignment.query.annotations["start"], 153) self.assertEqual(alignment.query.annotations["end"], 348) self.assertEqual(alignment.target.annotations["start"], 45) self.assertEqual(alignment.target.annotations["end"], 240) self.assertEqual( alignment.target.seq, "DLVRKPRFVDPFILACHSRHAKLAGIGVVCLQRLVASRSLPSERLKDVLGGLKETTSLSLDIQLK", ) self.assertEqual( alignment.query.seq, "ELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAMEIQLK", ) self.assertAlmostEqual(alignment.annotations["evalue"], 4e-10, places=10) self.assertAlmostEqual(alignment.annotations["bit score"], 68.9) self.assertAlmostEqual(alignment.score, 144) self.assertEqual(alignment.shape, (2, 65)) self.assertAlmostEqual(alignment.annotations["% identity"], 44.62) self.assertEqual(alignment.annotations["identical"], 29) self.assertEqual(alignment.annotations["mismatches"], 36) self.assertEqual(alignment.annotations["positives"], 41) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 63.08) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "331117") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Neosartorya fischeri NRRL 181 conserved hypothetical protein (NFIA_104180) partial mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "Neosartorya fischeri NRRL 181 conserved hypothetical protein (NFIA_104180) partial mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 56) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 56) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|119194 0 KALPSTSEVQLAADLVRRPQFANPFILACHTRHAKLAAVGVGCIHRLVASGALPSEQLKD 0 |.......|.....|.|.|.||.||.|||..|.||.......|...|......|...|.. gi|296147 0 KSIEILKRVHSFEELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSE gi|119194 60 VVDGLHETTNLSLDVQLK 78 60 ..|...|.|.|....||| 78 gi|296147 60 ILDAFIEATHLAMEIQLK 78 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 78], [ 0, 78]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|119194522|ref|XM_001247864.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|119194522|ref|XM_001247864.1|" ) self.assertEqual(alignment.target.annotations["gi"], "119194522") self.assertEqual(alignment.target.annotations["gis"], "119194522") self.assertEqual(alignment.target.annotations["acc."], "XM_001247864") self.assertEqual(alignment.target.annotations["accs."], "XM_001247864") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_001247864.1") self.assertEqual(alignment.target.annotations["length"], 5163) self.assertEqual(alignment.query.annotations["start"], 114) self.assertEqual(alignment.query.annotations["end"], 348) self.assertEqual(alignment.target.annotations["start"], 105) self.assertEqual(alignment.target.annotations["end"], 339) self.assertEqual( alignment.target.seq, "KALPSTSEVQLAADLVRRPQFANPFILACHTRHAKLAAVGVGCIHRLVASGALPSEQLKDVVDGLHETTNLSLDVQLK", ) self.assertEqual( alignment.query.seq, "KSIEILKRVHSFEELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAMEIQLK", ) self.assertAlmostEqual(alignment.annotations["evalue"], 4e-10, places=10) self.assertAlmostEqual(alignment.annotations["bit score"], 68.9) self.assertAlmostEqual(alignment.score, 144) self.assertEqual(alignment.shape, (2, 78)) self.assertAlmostEqual(alignment.annotations["% identity"], 33.33) self.assertEqual(alignment.annotations["identical"], 26) self.assertEqual(alignment.annotations["mismatches"], 52) self.assertEqual(alignment.annotations["positives"], 47) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 60.26) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "246410") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Coccidioides immitis RS hypothetical protein (CIMG_01636) partial mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "Coccidioides immitis RS hypothetical protein (CIMG_01636) partial mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 67) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 67) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|238486 0 DLVRKPKFVDPFILACHTRHAKLAGIGVVCLQRLVASRALPSERLKDVLSGLKETTNLSL 0 .|.|.|.|..||.|||..|.||.......|||.|......|..||...|....|.|.|.. gi|296147 0 ELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAM gi|238486 60 DIQLK 65 60 .|||| 65 gi|296147 60 EIQLK 65 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 65], [ 0, 65]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|238486173|ref|XM_002374284.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|238486173|ref|XM_002374284.1|" ) self.assertEqual(alignment.target.annotations["gi"], "238486173") self.assertEqual(alignment.target.annotations["gis"], "238486173") self.assertEqual(alignment.target.annotations["acc."], "XM_002374284") self.assertEqual(alignment.target.annotations["accs."], "XM_002374284") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_002374284.1") self.assertEqual(alignment.target.annotations["length"], 5160) self.assertEqual(alignment.query.annotations["start"], 153) self.assertEqual(alignment.query.annotations["end"], 348) self.assertEqual(alignment.target.annotations["start"], 144) self.assertEqual(alignment.target.annotations["end"], 339) self.assertEqual( alignment.target.seq, "DLVRKPKFVDPFILACHTRHAKLAGIGVVCLQRLVASRALPSERLKDVLSGLKETTNLSLDIQLK", ) self.assertEqual( alignment.query.seq, "ELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAMEIQLK", ) self.assertAlmostEqual(alignment.annotations["evalue"], 7e-10, places=10) self.assertAlmostEqual(alignment.annotations["bit score"], 68.0) self.assertAlmostEqual(alignment.score, 142) self.assertEqual(alignment.shape, (2, 65)) self.assertAlmostEqual(alignment.annotations["% identity"], 41.54) self.assertEqual(alignment.annotations["identical"], 27) self.assertEqual(alignment.annotations["mismatches"], 38) self.assertEqual(alignment.annotations["positives"], 42) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 64.62) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "332952") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Aspergillus flavus NRRL3357 endosomal peripheral membrane protein (Mon2), putative, mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "Aspergillus flavus NRRL3357 endosomal peripheral membrane protein (Mon2), putative, mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 56) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 56) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|505475 0 QDLKKDEKIAQPLVLACSSRNAKLTAIAVPLIQRLLAISALSDKSIPSVLGALEEATHLG 0 ..|......|.|.||||.|||||.|..|....|.|..............|.|..|||||. gi|296147 0 EELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLA gi|505475 60 VEIQLK 66 60 .||||| 66 gi|296147 60 MEIQLK 66 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 66], [ 0, 66]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|50547540|ref|XM_501240.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|50547540|ref|XM_501240.1|" ) self.assertEqual(alignment.target.annotations["gi"], "50547540") self.assertEqual(alignment.target.annotations["gis"], "50547540") self.assertEqual(alignment.target.annotations["acc."], "XM_501240") self.assertEqual(alignment.target.annotations["accs."], "XM_501240") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_501240.1") self.assertEqual(alignment.target.annotations["length"], 3855) self.assertEqual(alignment.query.annotations["start"], 150) self.assertEqual(alignment.query.annotations["end"], 348) self.assertEqual(alignment.target.annotations["start"], 117) self.assertEqual(alignment.target.annotations["end"], 315) self.assertEqual( alignment.target.seq, "QDLKKDEKIAQPLVLACSSRNAKLTAIAVPLIQRLLAISALSDKSIPSVLGALEEATHLGVEIQLK", ) self.assertEqual( alignment.query.seq, "EELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAMEIQLK", ) self.assertAlmostEqual(alignment.annotations["evalue"], 1e-09, places=9) self.assertAlmostEqual(alignment.annotations["bit score"], 67.0) self.assertAlmostEqual(alignment.score, 140) self.assertEqual(alignment.shape, (2, 66)) self.assertAlmostEqual(alignment.annotations["% identity"], 42.42) self.assertEqual(alignment.annotations["identical"], 28) self.assertEqual(alignment.annotations["mismatches"], 38) self.assertEqual(alignment.annotations["positives"], 42) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 63.64) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "284591") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Yarrowia lipolytica YALI0B22858p (YALI0B22858g) mRNA, complete cds", ) self.assertEqual( alignment.target.annotations["titles"], "Yarrowia lipolytica YALI0B22858p (YALI0B22858g) mRNA, complete cds", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 57) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 57) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|242768 0 DLIRRPHFVTPFILACQTRQSKLASIGVVCLQRLATSHAISPHRLNDTLSALRDITGLGQ 0 .|.|.|.|..||.||||.|..|.......|||.|.|...|...||...|.|....|.|.. gi|296147 0 ELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAM gi|242768 60 DVQLK 65 60 ..||| 65 gi|296147 60 EIQLK 65 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 65], [ 0, 65]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|242768840|ref|XM_002341608.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|242768840|ref|XM_002341608.1|" ) self.assertEqual(alignment.target.annotations["gi"], "242768840") self.assertEqual(alignment.target.annotations["gis"], "242768840") self.assertEqual(alignment.target.annotations["acc."], "XM_002341608") self.assertEqual(alignment.target.annotations["accs."], "XM_002341608") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_002341608.1") self.assertEqual(alignment.target.annotations["length"], 5181) self.assertEqual(alignment.query.annotations["start"], 153) self.assertEqual(alignment.query.annotations["end"], 348) self.assertEqual(alignment.target.annotations["start"], 144) self.assertEqual(alignment.target.annotations["end"], 339) self.assertEqual( alignment.target.seq, "DLIRRPHFVTPFILACQTRQSKLASIGVVCLQRLATSHAISPHRLNDTLSALRDITGLGQDVQLK", ) self.assertEqual( alignment.query.seq, "ELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAMEIQLK", ) self.assertAlmostEqual(alignment.annotations["evalue"], 2e-09, places=9) self.assertAlmostEqual(alignment.annotations["bit score"], 66.6) self.assertAlmostEqual(alignment.score, 139) self.assertEqual(alignment.shape, (2, 65)) self.assertAlmostEqual(alignment.annotations["% identity"], 41.54) self.assertEqual(alignment.annotations["identical"], 27) self.assertEqual(alignment.annotations["mismatches"], 38) self.assertEqual(alignment.annotations["positives"], 42) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 64.62) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "441959") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Talaromyces stipitatus ATCC 10500 endosomal peripheral membrane protein (Mon2), putative, mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "Talaromyces stipitatus ATCC 10500 endosomal peripheral membrane protein (Mon2), putative, mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 56) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 56) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|115391 0 DLARKPKFVDPFILACHTRHAKLAGIGVVCLQRLVASRALPSERLKDVLAGLKETTSLSL 0 .|.|.|.|..||.|||..|.||.......|||.|......|..||...|....|.|.|.. gi|296147 0 ELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAM gi|115391 60 DIQLK 65 60 .|||| 65 gi|296147 60 EIQLK 65 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 65], [ 0, 65]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|115391062|ref|XM_001213036.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|115391062|ref|XM_001213036.1|" ) self.assertEqual(alignment.target.annotations["gi"], "115391062") self.assertEqual(alignment.target.annotations["gis"], "115391062") self.assertEqual(alignment.target.annotations["acc."], "XM_001213036") self.assertEqual(alignment.target.annotations["accs."], "XM_001213036") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_001213036.1") self.assertEqual(alignment.target.annotations["length"], 4971) self.assertEqual(alignment.query.annotations["start"], 153) self.assertEqual(alignment.query.annotations["end"], 348) self.assertEqual(alignment.target.annotations["start"], 144) self.assertEqual(alignment.target.annotations["end"], 339) self.assertEqual( alignment.target.seq, "DLARKPKFVDPFILACHTRHAKLAGIGVVCLQRLVASRALPSERLKDVLAGLKETTSLSLDIQLK", ) self.assertEqual( alignment.query.seq, "ELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAMEIQLK", ) self.assertAlmostEqual(alignment.annotations["evalue"], 2e-09, places=9) self.assertAlmostEqual(alignment.annotations["bit score"], 66.6) self.assertAlmostEqual(alignment.score, 139) self.assertEqual(alignment.shape, (2, 65)) self.assertAlmostEqual(alignment.annotations["% identity"], 41.54) self.assertEqual(alignment.annotations["identical"], 27) self.assertEqual(alignment.annotations["mismatches"], 38) self.assertEqual(alignment.annotations["positives"], 41) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 63.08) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "341663") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Aspergillus terreus NIH2624 conserved hypothetical protein (ATEG_03858) partial mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "Aspergillus terreus NIH2624 conserved hypothetical protein (ATEG_03858) partial mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 56) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 56) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|261194 0 DLIRKPQFVKPFVIACQTRHGRLAAIGVVCIQRLVASRALPPELLRDVLDGLHETTNLGL 0 .|.|.|.|..|||.|||.|..........|.|.|......|...|...||...|.|.|.. gi|296147 0 ELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAM gi|261194 60 DVQLK 65 60 ..||| 65 gi|296147 60 EIQLK 65 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 65], [ 0, 65]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|261194600|ref|XM_002623659.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|261194600|ref|XM_002623659.1|" ) self.assertEqual(alignment.target.annotations["gi"], "261194600") self.assertEqual(alignment.target.annotations["gis"], "261194600") self.assertEqual(alignment.target.annotations["acc."], "XM_002623659") self.assertEqual(alignment.target.annotations["accs."], "XM_002623659") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_002623659.1") self.assertEqual(alignment.target.annotations["length"], 5331) self.assertEqual(alignment.query.annotations["start"], 153) self.assertEqual(alignment.query.annotations["end"], 348) self.assertEqual(alignment.target.annotations["start"], 246) self.assertEqual(alignment.target.annotations["end"], 441) self.assertEqual( alignment.target.seq, "DLIRKPQFVKPFVIACQTRHGRLAAIGVVCIQRLVASRALPPELLRDVLDGLHETTNLGLDVQLK", ) self.assertEqual( alignment.query.seq, "ELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAMEIQLK", ) self.assertAlmostEqual(alignment.annotations["evalue"], 5e-09, places=9) self.assertAlmostEqual(alignment.annotations["bit score"], 65.2) self.assertAlmostEqual(alignment.score, 136) self.assertEqual(alignment.shape, (2, 65)) self.assertAlmostEqual(alignment.annotations["% identity"], 36.92) self.assertEqual(alignment.annotations["identical"], 24) self.assertEqual(alignment.annotations["mismatches"], 41) self.assertEqual(alignment.annotations["positives"], 41) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 63.08) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "559298") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Ajellomyces dermatitidis SLH14081 endosomal peripheral membrane protein, mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "Ajellomyces dermatitidis SLH14081 endosomal peripheral membrane protein, mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 56) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 56) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|398410 0 DLSRRPAFIEPFLVACGTRNPKFAGPGIICLQKLVIVRGLPKARLQDALEAFNACTDLGQ 0 .|.|.|.|..||..||..||.|.......|||.|..|...|..||...|.||...|.|.. gi|296147 0 ELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAM gi|398410 60 DIQLK 65 60 .|||| 65 gi|296147 60 EIQLK 65 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 65], [ 0, 65]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|398410919|ref|XM_003856759.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|398410919|ref|XM_003856759.1|" ) self.assertEqual(alignment.target.annotations["gi"], "398410919") self.assertEqual(alignment.target.annotations["gis"], "398410919") self.assertEqual(alignment.target.annotations["acc."], "XM_003856759") self.assertEqual(alignment.target.annotations["accs."], "XM_003856759") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_003856759.1") self.assertEqual(alignment.target.annotations["length"], 5061) self.assertEqual(alignment.query.annotations["start"], 153) self.assertEqual(alignment.query.annotations["end"], 348) self.assertEqual(alignment.target.annotations["start"], 144) self.assertEqual(alignment.target.annotations["end"], 339) self.assertEqual( alignment.target.seq, "DLSRRPAFIEPFLVACGTRNPKFAGPGIICLQKLVIVRGLPKARLQDALEAFNACTDLGQDIQLK", ) self.assertEqual( alignment.query.seq, "ELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAMEIQLK", ) self.assertAlmostEqual(alignment.annotations["evalue"], 9e-09, places=9) self.assertAlmostEqual(alignment.annotations["bit score"], 64.3) self.assertAlmostEqual(alignment.score, 134) self.assertEqual(alignment.shape, (2, 65)) self.assertAlmostEqual(alignment.annotations["% identity"], 43.08) self.assertEqual(alignment.annotations["identical"], 28) self.assertEqual(alignment.annotations["mismatches"], 37) self.assertEqual(alignment.annotations["positives"], 39) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 60.00) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "336722") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Mycosphaerella graminicola IPO323 hypothetical protein (MYCGRDRAFT_67581) mRNA, complete cds", ) self.assertEqual( alignment.target.annotations["titles"], "Mycosphaerella graminicola IPO323 hypothetical protein (MYCGRDRAFT_67581) mRNA, complete cds", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 56) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 56) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|295669 0 DLLRKPHFVKPFVIACQTRHARLAAIGVVGVQRLVASRALPPERLRDVLNALQETTNLGL 0 .|.|.|.|..|||.|||.|.|..........|.|......|..||...|.|..|.|.|.. gi|296147 0 ELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAM gi|295669 60 DVQLK 65 60 ..||| 65 gi|296147 60 EIQLK 65 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 65], [ 0, 65]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|295669495|ref|XM_002795250.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|295669495|ref|XM_002795250.1|" ) self.assertEqual(alignment.target.annotations["gi"], "295669495") self.assertEqual(alignment.target.annotations["gis"], "295669495") self.assertEqual(alignment.target.annotations["acc."], "XM_002795250") self.assertEqual(alignment.target.annotations["accs."], "XM_002795250") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_002795250.1") self.assertEqual(alignment.target.annotations["length"], 5465) self.assertEqual(alignment.query.annotations["start"], 153) self.assertEqual(alignment.query.annotations["end"], 348) self.assertEqual(alignment.target.annotations["start"], 344) self.assertEqual(alignment.target.annotations["end"], 539) self.assertEqual( alignment.target.seq, "DLLRKPHFVKPFVIACQTRHARLAAIGVVGVQRLVASRALPPERLRDVLNALQETTNLGLDVQLK", ) self.assertEqual( alignment.query.seq, "ELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAMEIQLK", ) self.assertAlmostEqual(alignment.annotations["evalue"], 2e-08, places=8) self.assertAlmostEqual(alignment.annotations["bit score"], 63.4) self.assertAlmostEqual(alignment.score, 132) self.assertEqual(alignment.shape, (2, 65)) self.assertAlmostEqual(alignment.annotations["% identity"], 38.46) self.assertEqual(alignment.annotations["identical"], 25) self.assertEqual(alignment.annotations["mismatches"], 40) self.assertEqual(alignment.annotations["positives"], 43) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 66.15) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/3") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "3") self.assertEqual(alignment.target.annotations["tax ids"], "502779") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Paracoccidioides brasiliensis Pb01 conserved hypothetical protein, mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "Paracoccidioides brasiliensis Pb01 conserved hypothetical protein, mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 56) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 56) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|504227 0 KSYQPQEKIHDISQNEIKMDILKPFLISCNTGNAKFATISIPIIHKLIIGEIIPVECLNE 0 ||.......|.....|...|...||...|...|||..|........|.....||...|.| gi|296147 0 KSIEILKRVHSFEELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSE gi|504227 60 LLDSLKEATNLATDIQLR 78 60 .||...|||.||..|||. 78 gi|296147 60 ILDAFIEATHLAMEIQLK 78 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 78], [ 0, 78]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|50422728|ref|XM_459941.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|50422728|ref|XM_459941.1|" ) self.assertEqual(alignment.target.annotations["gi"], "50422728") self.assertEqual(alignment.target.annotations["gis"], "50422728") self.assertEqual(alignment.target.annotations["acc."], "XM_459941") self.assertEqual(alignment.target.annotations["accs."], "XM_459941") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_459941.1") self.assertEqual(alignment.target.annotations["length"], 4800) self.assertEqual(alignment.query.annotations["start"], 114) self.assertEqual(alignment.query.annotations["end"], 348) self.assertEqual(alignment.target.annotations["start"], 108) self.assertEqual(alignment.target.annotations["end"], 342) self.assertEqual( alignment.target.seq, "KSYQPQEKIHDISQNEIKMDILKPFLISCNTGNAKFATISIPIIHKLIIGEIIPVECLNELLDSLKEATNLATDIQLR", ) self.assertEqual( alignment.query.seq, "KSIEILKRVHSFEELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAMEIQLK", ) self.assertAlmostEqual(alignment.annotations["evalue"], 1e-07) self.assertAlmostEqual(alignment.annotations["bit score"], 60.6) self.assertAlmostEqual(alignment.score, 126) self.assertEqual(alignment.shape, (2, 78)) self.assertAlmostEqual(alignment.annotations["% identity"], 34.62) self.assertEqual(alignment.annotations["identical"], 27) self.assertEqual(alignment.annotations["mismatches"], 51) self.assertEqual(alignment.annotations["positives"], 46) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 58.97) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "284592") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Debaryomyces hansenii CBS767 DEHA2E14608p (DEHA2E14608g) mRNA, complete cds", ) self.assertEqual( alignment.target.annotations["titles"], "Debaryomyces hansenii CBS767 DEHA2E14608p (DEHA2E14608g) mRNA, complete cds", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 67) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 67) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|126258 0 KSIHDITNEQHRQHIIAPFVASCRTGNAKIATIAIPTIHKLIMAGVVPLGSLGSLVDSLM 0 |..|.............|||..|...|||..|.|......|......|...|....|... gi|296147 0 KRVHSFEELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFI gi|126258 60 EASHLAVDIQLR 72 60 ||.|||..|||. 72 gi|296147 60 EATHLAMEIQLK 72 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 72], [ 0, 72]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|126258058|ref|XM_001387099.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|126258058|ref|XM_001387099.1|" ) self.assertEqual(alignment.target.annotations["gi"], "126258058") self.assertEqual(alignment.target.annotations["gis"], "126258058") self.assertEqual(alignment.target.annotations["acc."], "XM_001387099") self.assertEqual(alignment.target.annotations["accs."], "XM_001387099") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_001387099.1") self.assertEqual(alignment.target.annotations["length"], 4755) self.assertEqual(alignment.query.annotations["start"], 132) self.assertEqual(alignment.query.annotations["end"], 348) self.assertEqual(alignment.target.annotations["start"], 126) self.assertEqual(alignment.target.annotations["end"], 342) self.assertEqual( alignment.target.seq, "KSIHDITNEQHRQHIIAPFVASCRTGNAKIATIAIPTIHKLIMAGVVPLGSLGSLVDSLMEASHLAVDIQLR", ) self.assertEqual( alignment.query.seq, "KRVHSFEELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAMEIQLK", ) self.assertAlmostEqual(alignment.annotations["evalue"], 2e-07) self.assertAlmostEqual(alignment.annotations["bit score"], 59.7) self.assertAlmostEqual(alignment.score, 124) self.assertEqual(alignment.shape, (2, 72)) self.assertAlmostEqual(alignment.annotations["% identity"], 31.94) self.assertEqual(alignment.annotations["identical"], 23) self.assertEqual(alignment.annotations["mismatches"], 49) self.assertEqual(alignment.annotations["positives"], 41) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 56.94) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "322104") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Scheffersomyces stipitis CBS 6054 chromosome 1", ) self.assertEqual( alignment.target.annotations["titles"], "Scheffersomyces stipitis CBS 6054 chromosome 1", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 62) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 62) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|302663 0 DLARKPQFARPFVLACQTRQTRLAAIGVTNLQRLVTIGALPHERLKDVLQGLHETANLS 0 .|.|.|.||.|||||||.|...........||.|.|....|..||...|....|...|. gi|296147 0 ELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLA gi|302663 59 59 gi|296147 59 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 59], [ 0, 59]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|302663055|ref|XM_003023130.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|302663055|ref|XM_003023130.1|" ) self.assertEqual(alignment.target.annotations["gi"], "302663055") self.assertEqual(alignment.target.annotations["gis"], "302663055") self.assertEqual(alignment.target.annotations["acc."], "XM_003023130") self.assertEqual(alignment.target.annotations["accs."], "XM_003023130") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_003023130.1") self.assertEqual(alignment.target.annotations["length"], 5163) self.assertEqual(alignment.query.annotations["start"], 153) self.assertEqual(alignment.query.annotations["end"], 330) self.assertEqual(alignment.target.annotations["start"], 108) self.assertEqual(alignment.target.annotations["end"], 285) self.assertEqual( alignment.target.seq, "DLARKPQFARPFVLACQTRQTRLAAIGVTNLQRLVTIGALPHERLKDVLQGLHETANLS", ) self.assertEqual( alignment.query.seq, "ELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLA", ) self.assertAlmostEqual(alignment.annotations["evalue"], 3e-07) self.assertAlmostEqual(alignment.annotations["bit score"], 59.3) self.assertAlmostEqual(alignment.score, 123) self.assertEqual(alignment.shape, (2, 59)) self.assertAlmostEqual(alignment.annotations["% identity"], 38.98) self.assertEqual(alignment.annotations["identical"], 23) self.assertEqual(alignment.annotations["mismatches"], 36) self.assertEqual(alignment.annotations["positives"], 36) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 61.02) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "663202") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Trichophyton verrucosum HKI 0517 endosomal peripheral membrane protein (Mon2), putative, mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "Trichophyton verrucosum HKI 0517 endosomal peripheral membrane protein (Mon2), putative, mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 51) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 51) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|255728 0 PFILACKSGNIKLTNTATPVIYKLILAHAIPEENIPELLQALLEASNLAIDIQLR 55 0 ||.|||.|.|.|.|..|......|.....||.....|.|.|..||..||..|||. 55 gi|296147 0 PFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAMEIQLK 55 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 55], [ 0, 55]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|255728730|ref|XM_002549245.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|255728730|ref|XM_002549245.1|" ) self.assertEqual(alignment.target.annotations["gi"], "255728730") self.assertEqual(alignment.target.annotations["gis"], "255728730") self.assertEqual(alignment.target.annotations["acc."], "XM_002549245") self.assertEqual(alignment.target.annotations["accs."], "XM_002549245") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_002549245.1") self.assertEqual(alignment.target.annotations["length"], 4671) self.assertEqual(alignment.query.annotations["start"], 183) self.assertEqual(alignment.query.annotations["end"], 348) self.assertEqual(alignment.target.annotations["start"], 177) self.assertEqual(alignment.target.annotations["end"], 342) self.assertEqual( alignment.target.seq, "PFILACKSGNIKLTNTATPVIYKLILAHAIPEENIPELLQALLEASNLAIDIQLR", ) self.assertEqual( alignment.query.seq, "PFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAMEIQLK", ) self.assertAlmostEqual(alignment.annotations["evalue"], 2e-06) self.assertAlmostEqual(alignment.annotations["bit score"], 57.0) self.assertAlmostEqual(alignment.score, 118) self.assertEqual(alignment.shape, (2, 55)) self.assertAlmostEqual(alignment.annotations["% identity"], 41.82) self.assertEqual(alignment.annotations["identical"], 23) self.assertEqual(alignment.annotations["mismatches"], 32) self.assertEqual(alignment.annotations["positives"], 36) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 65.45) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "294747") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Candida tropicalis MYA-3404 conserved hypothetical protein, mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "Candida tropicalis MYA-3404 conserved hypothetical protein, mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 47) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 47) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|171682 0 RQTYTIPELTQRPNFVNPFIIACGTKNVKFTGIAI 35 0 .......||...|.|..||..||...|.|.|..|. 35 gi|296147 0 KRVHSFEELERHPDFALPFVLACQSRNAKMTTLAM 35 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 35], [ 0, 35]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|171682617|ref|XM_001906217.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|171682617|ref|XM_001906217.1|" ) self.assertEqual(alignment.target.annotations["gi"], "171682617") self.assertEqual(alignment.target.annotations["gis"], "171682617") self.assertEqual(alignment.target.annotations["acc."], "XM_001906217") self.assertEqual(alignment.target.annotations["accs."], "XM_001906217") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_001906217.1") self.assertEqual(alignment.target.annotations["length"], 4959) self.assertEqual(alignment.query.annotations["start"], 132) self.assertEqual(alignment.query.annotations["end"], 237) self.assertEqual(alignment.target.annotations["start"], 10) self.assertEqual(alignment.target.annotations["end"], 115) self.assertEqual( alignment.target.seq, "RQTYTIPELTQRPNFVNPFIIACGTKNVKFTGIAI" ) self.assertEqual(alignment.query.seq, "KRVHSFEELERHPDFALPFVLACQSRNAKMTTLAM") self.assertAlmostEqual(alignment.annotations["evalue"], 2e-06) self.assertAlmostEqual(alignment.annotations["bit score"], 38.6) self.assertAlmostEqual(alignment.score, 78) self.assertEqual(alignment.shape, (2, 35)) self.assertAlmostEqual(alignment.annotations["% identity"], 34.29) self.assertEqual(alignment.annotations["identical"], 12) self.assertEqual(alignment.annotations["mismatches"], 23) self.assertEqual(alignment.annotations["positives"], 24) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 68.57) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/2") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "2") self.assertEqual(alignment.target.annotations["tax ids"], "515849") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Podospora anserina S mat+ hypothetical protein (PODANSg3280) partial mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "Podospora anserina S mat+ hypothetical protein (PODANSg3280) partial mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 52) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 30) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|171682 0 LPRSRLSQVLEALQQATSAGLDVQLK 26 0 .||||||..|.|...||......||| 26 gi|296147 0 IPRSRLSEILDAFIEATHLAMEIQLK 26 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 26], [ 0, 26]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|171682617|ref|XM_001906217.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|171682617|ref|XM_001906217.1|" ) self.assertEqual(alignment.target.annotations["gi"], "171682617") self.assertEqual(alignment.target.annotations["gis"], "171682617") self.assertEqual(alignment.target.annotations["acc."], "XM_001906217") self.assertEqual(alignment.target.annotations["accs."], "XM_001906217") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_001906217.1") self.assertEqual(alignment.target.annotations["length"], 4959) self.assertEqual(alignment.query.annotations["start"], 270) self.assertEqual(alignment.query.annotations["end"], 348) self.assertEqual(alignment.target.annotations["start"], 117) self.assertEqual(alignment.target.annotations["end"], 195) self.assertEqual(alignment.target.seq, "LPRSRLSQVLEALQQATSAGLDVQLK") self.assertEqual(alignment.query.seq, "IPRSRLSEILDAFIEATHLAMEIQLK") self.assertAlmostEqual(alignment.annotations["evalue"], 2e-06) self.assertAlmostEqual(alignment.annotations["bit score"], 36.3) self.assertAlmostEqual(alignment.score, 73) self.assertEqual(alignment.shape, (2, 26)) self.assertAlmostEqual(alignment.annotations["% identity"], 50.00) self.assertEqual(alignment.annotations["identical"], 13) self.assertEqual(alignment.annotations["mismatches"], 13) self.assertEqual(alignment.annotations["positives"], 21) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 80.77) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "515849") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Podospora anserina S mat+ hypothetical protein (PODANSg3280) partial mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "Podospora anserina S mat+ hypothetical protein (PODANSg3280) partial mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 52) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 22) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|460402 0 VKDAAEHAILKLRSLSSPSEIAHNEDILNIFLMACEVRNVKMSVIGLSCLQKLISHDVVA 0 ...|....|..|....|..|.....|....|..||..||.||......|||.|....... gi|296147 0 IRHASDKSIEILKRVHSFEELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIP gi|460402 60 TSALKEILDTLKDHGEMADE 80 60 .|.|.||||........|.| 80 gi|296147 60 RSRLSEILDAFIEATHLAME 80 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 80], [ 0, 80]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|460402609|ref|XM_004246756.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|460402609|ref|XM_004246756.1|" ) self.assertEqual(alignment.target.annotations["gi"], "460402609") self.assertEqual(alignment.target.annotations["gis"], "460402609") self.assertEqual(alignment.target.annotations["acc."], "XM_004246756") self.assertEqual(alignment.target.annotations["accs."], "XM_004246756") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_004246756.1") self.assertEqual(alignment.target.annotations["length"], 5431) self.assertEqual(alignment.query.annotations["start"], 96) self.assertEqual(alignment.query.annotations["end"], 336) self.assertEqual(alignment.target.annotations["start"], 402) self.assertEqual(alignment.target.annotations["end"], 642) self.assertEqual( alignment.target.seq, "VKDAAEHAILKLRSLSSPSEIAHNEDILNIFLMACEVRNVKMSVIGLSCLQKLISHDVVATSALKEILDTLKDHGEMADE", ) self.assertEqual( alignment.query.seq, "IRHASDKSIEILKRVHSFEELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAME", ) self.assertAlmostEqual(alignment.annotations["evalue"], 2e-05) self.assertAlmostEqual(alignment.annotations["bit score"], 53.3) self.assertAlmostEqual(alignment.score, 110) self.assertEqual(alignment.shape, (2, 80)) self.assertAlmostEqual(alignment.annotations["% identity"], 31.25) self.assertEqual(alignment.annotations["identical"], 25) self.assertEqual(alignment.annotations["mismatches"], 55) self.assertEqual(alignment.annotations["positives"], 44) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 55.00) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "4081") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "PREDICTED: Solanum lycopersicum protein MON2 homolog (LOC101244609), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "PREDICTED: Solanum lycopersicum protein MON2 homolog (LOC101244609), mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 69) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 69) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|684672 0 KSYSLVVPIQEINKEDHKEEILKPFILSCKSGNIKLTNISIPVIHKLILAHLIPELDITQ 0 ||.....................||.|.|.|.|.|.|.........|.....||...... gi|296147 0 KSIEILKRVHSFEELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSE gi|684672 60 VLLCLLEASNLAVDIQLR 78 60 .|....||..||..|||. 78 gi|296147 60 ILDAFIEATHLAMEIQLK 78 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 78], [ 0, 78]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|68467204|ref|XM_717171.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|68467204|ref|XM_717171.1|" ) self.assertEqual(alignment.target.annotations["gi"], "68467204") self.assertEqual(alignment.target.annotations["gis"], "68467204") self.assertEqual(alignment.target.annotations["acc."], "XM_717171") self.assertEqual(alignment.target.annotations["accs."], "XM_717171") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_717171.1") self.assertEqual(alignment.target.annotations["length"], 4905) self.assertEqual(alignment.query.annotations["start"], 114) self.assertEqual(alignment.query.annotations["end"], 348) self.assertEqual(alignment.target.annotations["start"], 108) self.assertEqual(alignment.target.annotations["end"], 342) self.assertEqual( alignment.target.seq, "KSYSLVVPIQEINKEDHKEEILKPFILSCKSGNIKLTNISIPVIHKLILAHLIPELDITQVLLCLLEASNLAVDIQLR", ) self.assertEqual( alignment.query.seq, "KSIEILKRVHSFEELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAMEIQLK", ) self.assertAlmostEqual(alignment.annotations["evalue"], 2e-05) self.assertAlmostEqual(alignment.annotations["bit score"], 53.3) self.assertAlmostEqual(alignment.score, 110) self.assertEqual(alignment.shape, (2, 78)) self.assertAlmostEqual(alignment.annotations["% identity"], 26.92) self.assertEqual(alignment.annotations["identical"], 21) self.assertEqual(alignment.annotations["mismatches"], 57) self.assertEqual(alignment.annotations["positives"], 45) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 57.69) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "237561") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Candida albicans SC5314 hypothetical protein (CaO19_12405) partial mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "Candida albicans SC5314 hypothetical protein (CaO19_12405) partial mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 67) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 67) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|684674 0 KSYSLVVPIQEINKEDHKEEILKPFILSCKSGNIKLTNISIPVIHKLILAHLIPELDITQ 0 ||.....................||.|.|.|.|.|.|.........|.....||...... gi|296147 0 KSIEILKRVHSFEELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSE gi|684674 60 VLLCLLEASNLAVDIQLR 78 60 .|....||..||..|||. 78 gi|296147 60 ILDAFIEATHLAMEIQLK 78 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 78], [ 0, 78]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|68467433|ref|XM_717057.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|68467433|ref|XM_717057.1|" ) self.assertEqual(alignment.target.annotations["gi"], "68467433") self.assertEqual(alignment.target.annotations["gis"], "68467433") self.assertEqual(alignment.target.annotations["acc."], "XM_717057") self.assertEqual(alignment.target.annotations["accs."], "XM_717057") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_717057.1") self.assertEqual(alignment.target.annotations["length"], 4905) self.assertEqual(alignment.query.annotations["start"], 114) self.assertEqual(alignment.query.annotations["end"], 348) self.assertEqual(alignment.target.annotations["start"], 108) self.assertEqual(alignment.target.annotations["end"], 342) self.assertEqual( alignment.target.seq, "KSYSLVVPIQEINKEDHKEEILKPFILSCKSGNIKLTNISIPVIHKLILAHLIPELDITQVLLCLLEASNLAVDIQLR", ) self.assertEqual( alignment.query.seq, "KSIEILKRVHSFEELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAMEIQLK", ) self.assertAlmostEqual(alignment.annotations["evalue"], 2e-05) self.assertAlmostEqual(alignment.annotations["bit score"], 53.3) self.assertAlmostEqual(alignment.score, 110) self.assertEqual(alignment.shape, (2, 78)) self.assertAlmostEqual(alignment.annotations["% identity"], 26.92) self.assertEqual(alignment.annotations["identical"], 21) self.assertEqual(alignment.annotations["mismatches"], 57) self.assertEqual(alignment.annotations["positives"], 45) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 57.69) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "237561") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Candida albicans SC5314 hypothetical protein (MON2) mRNA, complete cds", ) self.assertEqual( alignment.target.annotations["titles"], "Candida albicans SC5314 hypothetical protein (MON2) mRNA, complete cds", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 67) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 67) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|317144 0 ACHTRHAKLAGIGVVCLQRLVASRALPSERLKDVLSGLKETTNLSLDIQLK 51 0 ||..|.||.......|||.|......|..||...|....|.|.|...|||| 51 gi|296147 0 ACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAMEIQLK 51 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 51], [ 0, 51]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|317144425|ref|XM_001820059.2|") self.assertEqual( alignment.target.annotations["ids"], "gi|317144425|ref|XM_001820059.2|" ) self.assertEqual(alignment.target.annotations["gi"], "317144425") self.assertEqual(alignment.target.annotations["gis"], "317144425") self.assertEqual(alignment.target.annotations["acc."], "XM_001820059") self.assertEqual(alignment.target.annotations["accs."], "XM_001820059") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_001820059.2") self.assertEqual(alignment.target.annotations["length"], 5076) self.assertEqual(alignment.query.annotations["start"], 195) self.assertEqual(alignment.query.annotations["end"], 348) self.assertEqual(alignment.target.annotations["start"], 144) self.assertEqual(alignment.target.annotations["end"], 297) self.assertEqual( alignment.target.seq, "ACHTRHAKLAGIGVVCLQRLVASRALPSERLKDVLSGLKETTNLSLDIQLK", ) self.assertEqual( alignment.query.seq, "ACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAMEIQLK", ) self.assertAlmostEqual(alignment.annotations["evalue"], 7e-05) self.assertAlmostEqual(alignment.annotations["bit score"], 51.5) self.assertAlmostEqual(alignment.score, 106) self.assertEqual(alignment.shape, (2, 51)) self.assertAlmostEqual(alignment.annotations["% identity"], 39.22) self.assertEqual(alignment.annotations["identical"], 20) self.assertEqual(alignment.annotations["mismatches"], 31) self.assertEqual(alignment.annotations["positives"], 33) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 64.71) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "510516") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Aspergillus oryzae RIB40 endosomal peripheral membrane protein (Mon2), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "Aspergillus oryzae RIB40 endosomal peripheral membrane protein (Mon2), mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 44) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 44) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|241950 0 KSYSSVVPIQEINKENHREEVLKPFILSCKSGNIKLTNISIPVIYKLILAHLIPELDISQ 0 ||.....................||.|.|.|.|.|.|.........|.....||....|. gi|296147 0 KSIEILKRVHSFEELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSE gi|241950 60 VLLCLLEASNLAVDIQLR 78 60 .|....||..||..|||. 78 gi|296147 60 ILDAFIEATHLAMEIQLK 78 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 78], [ 0, 78]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|241950270|ref|XM_002417813.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|241950270|ref|XM_002417813.1|" ) self.assertEqual(alignment.target.annotations["gi"], "241950270") self.assertEqual(alignment.target.annotations["gis"], "241950270") self.assertEqual(alignment.target.annotations["acc."], "XM_002417813") self.assertEqual(alignment.target.annotations["accs."], "XM_002417813") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_002417813.1") self.assertEqual(alignment.target.annotations["length"], 4944) self.assertEqual(alignment.query.annotations["start"], 114) self.assertEqual(alignment.query.annotations["end"], 348) self.assertEqual(alignment.target.annotations["start"], 108) self.assertEqual(alignment.target.annotations["end"], 342) self.assertEqual( alignment.target.seq, "KSYSSVVPIQEINKENHREEVLKPFILSCKSGNIKLTNISIPVIYKLILAHLIPELDISQVLLCLLEASNLAVDIQLR", ) self.assertEqual( alignment.query.seq, "KSIEILKRVHSFEELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAMEIQLK", ) self.assertAlmostEqual(alignment.annotations["evalue"], 7e-05) self.assertAlmostEqual(alignment.annotations["bit score"], 51.5) self.assertAlmostEqual(alignment.score, 106) self.assertEqual(alignment.shape, (2, 78)) self.assertAlmostEqual(alignment.annotations["% identity"], 28.21) self.assertEqual(alignment.annotations["identical"], 22) self.assertEqual(alignment.annotations["mismatches"], 56) self.assertEqual(alignment.annotations["positives"], 43) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 55.13) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "573826") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Candida dubliniensis CD36 SEC7-family member, endocytosis and vacuole integrity protein, putative (CD36_12180) mRNA, complete cds", ) self.assertEqual( alignment.target.annotations["titles"], "Candida dubliniensis CD36 SEC7-family member, endocytosis and vacuole integrity protein, putative (CD36_12180) mRNA, complete cds", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 67) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 67) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|448082 0 PFILSSHNWNAKTATISIPIIHKLIISNAVSREDLEQLLHALKEASNLALDIQLR 55 0 ||.|.....|||..|........|.......|..|...|.|..||..||..|||. 55 gi|296147 0 PFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAMEIQLK 55 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 55], [ 0, 55]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|448082269|ref|XM_004195049.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|448082269|ref|XM_004195049.1|" ) self.assertEqual(alignment.target.annotations["gi"], "448082269") self.assertEqual(alignment.target.annotations["gis"], "448082269") self.assertEqual(alignment.target.annotations["acc."], "XM_004195049") self.assertEqual(alignment.target.annotations["accs."], "XM_004195049") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_004195049.1") self.assertEqual(alignment.target.annotations["length"], 4794) self.assertEqual(alignment.query.annotations["start"], 183) self.assertEqual(alignment.query.annotations["end"], 348) self.assertEqual(alignment.target.annotations["start"], 177) self.assertEqual(alignment.target.annotations["end"], 342) self.assertEqual( alignment.target.seq, "PFILSSHNWNAKTATISIPIIHKLIISNAVSREDLEQLLHALKEASNLALDIQLR", ) self.assertEqual( alignment.query.seq, "PFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAMEIQLK", ) self.assertAlmostEqual(alignment.annotations["evalue"], 3e-04) self.assertAlmostEqual(alignment.annotations["bit score"], 45.1) self.assertAlmostEqual(alignment.score, 92) self.assertEqual(alignment.shape, (2, 55)) self.assertAlmostEqual(alignment.annotations["% identity"], 34.55) self.assertEqual(alignment.annotations["identical"], 19) self.assertEqual(alignment.annotations["mismatches"], 36) self.assertEqual(alignment.annotations["positives"], 35) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 63.64) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "559304") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Millerozyma farinosa CBS 7064 hypothetical protein (Piso0_005640) mRNA, complete cds", ) self.assertEqual( alignment.target.annotations["titles"], "Millerozyma farinosa CBS 7064 hypothetical protein (Piso0_005640) mRNA, complete cds", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 62) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 47) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|448082 0 CIVFSVNRREETPVFVM 17 0 |.....||.||...|.| 17 gi|296147 0 CVLYLPNRKEEIQPFAM 17 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 17], [ 0, 17]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|448082269|ref|XM_004195049.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|448082269|ref|XM_004195049.1|" ) self.assertEqual(alignment.target.annotations["gi"], "448082269") self.assertEqual(alignment.target.annotations["gis"], "448082269") self.assertEqual(alignment.target.annotations["acc."], "XM_004195049") self.assertEqual(alignment.target.annotations["accs."], "XM_004195049") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_004195049.1") self.assertEqual(alignment.target.annotations["length"], 4794) self.assertEqual(alignment.query.annotations["start"], 55) self.assertEqual(alignment.query.annotations["end"], 106) self.assertEqual(alignment.target.annotations["start"], 31) self.assertEqual(alignment.target.annotations["end"], 82) self.assertEqual(alignment.target.seq, "CIVFSVNRREETPVFVM") self.assertEqual(alignment.query.seq, "CVLYLPNRKEEIQPFAM") self.assertAlmostEqual(alignment.annotations["evalue"], 3e-04) self.assertAlmostEqual(alignment.annotations["bit score"], 22.1) self.assertAlmostEqual(alignment.score, 42) self.assertEqual(alignment.shape, (2, 17)) self.assertAlmostEqual(alignment.annotations["% identity"], 41.18) self.assertEqual(alignment.annotations["identical"], 7) self.assertEqual(alignment.annotations["mismatches"], 10) self.assertEqual(alignment.annotations["positives"], 11) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 64.71) self.assertEqual(alignment.annotations["query/sbjct frames"], "2/2") self.assertEqual(alignment.query.annotations["frame"], "2") self.assertEqual(alignment.target.annotations["frame"], "2") self.assertEqual(alignment.target.annotations["tax ids"], "559304") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Millerozyma farinosa CBS 7064 hypothetical protein (Piso0_005640) mRNA, complete cds", ) self.assertEqual( alignment.target.annotations["titles"], "Millerozyma farinosa CBS 7064 hypothetical protein (Piso0_005640) mRNA, complete cds", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 62) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 15) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|359487 0 VKDGAEHGILKLRSLSSPSEIAHNEDILRIFLMACEVRNVKLSVIGLSCLQKLISHDAVA 0 ........|..|....|..|.....|....|..||..||.|.......|||.|....... gi|296147 0 IRHASDKSIEILKRVHSFEELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIP gi|359487 60 PSALKEILSTLKDHAEMADE 80 60 .|.|.|||.........|.| 80 gi|296147 60 RSRLSEILDAFIEATHLAME 80 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 80], [ 0, 80]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|359487908|ref|XM_003633625.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|359487908|ref|XM_003633625.1|" ) self.assertEqual(alignment.target.annotations["gi"], "359487908") self.assertEqual(alignment.target.annotations["gis"], "359487908") self.assertEqual(alignment.target.annotations["acc."], "XM_003633625") self.assertEqual(alignment.target.annotations["accs."], "XM_003633625") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_003633625.1") self.assertEqual(alignment.target.annotations["length"], 5238) self.assertEqual(alignment.query.annotations["start"], 96) self.assertEqual(alignment.query.annotations["end"], 336) self.assertEqual(alignment.target.annotations["start"], 72) self.assertEqual(alignment.target.annotations["end"], 312) self.assertEqual( alignment.target.seq, "VKDGAEHGILKLRSLSSPSEIAHNEDILRIFLMACEVRNVKLSVIGLSCLQKLISHDAVAPSALKEILSTLKDHAEMADE", ) self.assertEqual( alignment.query.seq, "IRHASDKSIEILKRVHSFEELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAME", ) self.assertAlmostEqual(alignment.annotations["evalue"], 3e-04) self.assertAlmostEqual(alignment.annotations["bit score"], 49.2) self.assertAlmostEqual(alignment.score, 101) self.assertEqual(alignment.shape, (2, 80)) self.assertAlmostEqual(alignment.annotations["% identity"], 27.50) self.assertEqual(alignment.annotations["identical"], 22) self.assertEqual(alignment.annotations["mismatches"], 58) self.assertEqual(alignment.annotations["positives"], 42) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 52.50) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "29760") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "PREDICTED: Vitis vinifera protein MON2 homolog (LOC100264068), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "PREDICTED: Vitis vinifera protein MON2 homolog (LOC100264068), mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 69) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 69) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|302795 0 VKDAAEHAILKLRTITDPSQISRNDDVLRLYMLACDTRNVKLSILGLSCLQKLLAHDAVP 0 ...|....|..|..........|..|......|||..||.|...|...|||.|......| gi|296147 0 IRHASDKSIEILKRVHSFEELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIP gi|302795 60 PLAFPQILETLQEHCEINDEI 81 60 ......||....|......|| 81 gi|296147 60 RSRLSEILDAFIEATHLAMEI 81 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 81], [ 0, 81]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|302795299|ref|XM_002979367.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|302795299|ref|XM_002979367.1|" ) self.assertEqual(alignment.target.annotations["gi"], "302795299") self.assertEqual(alignment.target.annotations["gis"], "302795299") self.assertEqual(alignment.target.annotations["acc."], "XM_002979367") self.assertEqual(alignment.target.annotations["accs."], "XM_002979367") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_002979367.1") self.assertEqual(alignment.target.annotations["length"], 5019) self.assertEqual(alignment.query.annotations["start"], 96) self.assertEqual(alignment.query.annotations["end"], 339) self.assertEqual(alignment.target.annotations["start"], 72) self.assertEqual(alignment.target.annotations["end"], 315) self.assertEqual( alignment.target.seq, "VKDAAEHAILKLRTITDPSQISRNDDVLRLYMLACDTRNVKLSILGLSCLQKLLAHDAVPPLAFPQILETLQEHCEINDEI", ) self.assertEqual( alignment.query.seq, "IRHASDKSIEILKRVHSFEELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAMEI", ) self.assertAlmostEqual(alignment.annotations["evalue"], 3e-04) self.assertAlmostEqual(alignment.annotations["bit score"], 49.2) self.assertAlmostEqual(alignment.score, 101) self.assertEqual(alignment.shape, (2, 81)) self.assertAlmostEqual(alignment.annotations["% identity"], 27.16) self.assertEqual(alignment.annotations["identical"], 22) self.assertEqual(alignment.annotations["mismatches"], 59) self.assertEqual(alignment.annotations["positives"], 43) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 53.09) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "88036") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Selaginella moellendorffii hypothetical protein, mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "Selaginella moellendorffii hypothetical protein, mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 69) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 69) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|302792 0 VKDAAEHAILKLRTVTDPSQIARNDDVLRLYMLACDTRNVKLSILGLSCLQKLLAHDAVP 0 ...|....|..|..|.......|..|......|||..||.|...|...|||.|......| gi|296147 0 IRHASDKSIEILKRVHSFEELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIP gi|302792 60 PLAFPQILETLQEHCEINDEI 81 60 ......||....|......|| 81 gi|296147 60 RSRLSEILDAFIEATHLAMEI 81 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 81], [ 0, 81]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|302792279|ref|XM_002977860.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|302792279|ref|XM_002977860.1|" ) self.assertEqual(alignment.target.annotations["gi"], "302792279") self.assertEqual(alignment.target.annotations["gis"], "302792279") self.assertEqual(alignment.target.annotations["acc."], "XM_002977860") self.assertEqual(alignment.target.annotations["accs."], "XM_002977860") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_002977860.1") self.assertEqual(alignment.target.annotations["length"], 5197) self.assertEqual(alignment.query.annotations["start"], 96) self.assertEqual(alignment.query.annotations["end"], 339) self.assertEqual(alignment.target.annotations["start"], 72) self.assertEqual(alignment.target.annotations["end"], 315) self.assertEqual( alignment.target.seq, "VKDAAEHAILKLRTVTDPSQIARNDDVLRLYMLACDTRNVKLSILGLSCLQKLLAHDAVPPLAFPQILETLQEHCEINDEI", ) self.assertEqual( alignment.query.seq, "IRHASDKSIEILKRVHSFEELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAMEI", ) self.assertAlmostEqual(alignment.annotations["evalue"], 3e-04) self.assertAlmostEqual(alignment.annotations["bit score"], 49.2) self.assertAlmostEqual(alignment.score, 101) self.assertEqual(alignment.shape, (2, 81)) self.assertAlmostEqual(alignment.annotations["% identity"], 28.40) self.assertEqual(alignment.annotations["identical"], 23) self.assertEqual(alignment.annotations["mismatches"], 58) self.assertEqual(alignment.annotations["positives"], 43) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 53.09) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "88036") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Selaginella moellendorffii hypothetical protein, mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "Selaginella moellendorffii hypothetical protein, mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 69) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 69) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|146416 0 AAPLVSTLASNNTKLVTISILAINRLAGTTAFSTATLGPLLDGLLEASHLAMDIQLR 57 0 |.|.|....|.|.|..|........|..........|...||...||.||||.|||. 57 gi|296147 0 ALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAMEIQLK 57 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 57], [ 0, 57]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|146416588|ref|XM_001484214.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|146416588|ref|XM_001484214.1|" ) self.assertEqual(alignment.target.annotations["gi"], "146416588") self.assertEqual(alignment.target.annotations["gis"], "146416588") self.assertEqual(alignment.target.annotations["acc."], "XM_001484214") self.assertEqual(alignment.target.annotations["accs."], "XM_001484214") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_001484214.1") self.assertEqual(alignment.target.annotations["length"], 1320) self.assertEqual(alignment.query.annotations["start"], 177) self.assertEqual(alignment.query.annotations["end"], 348) self.assertEqual(alignment.target.annotations["start"], 168) self.assertEqual(alignment.target.annotations["end"], 339) self.assertEqual( alignment.target.seq, "AAPLVSTLASNNTKLVTISILAINRLAGTTAFSTATLGPLLDGLLEASHLAMDIQLR", ) self.assertEqual( alignment.query.seq, "ALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAMEIQLK", ) self.assertAlmostEqual(alignment.annotations["evalue"], 5e-04) self.assertAlmostEqual(alignment.annotations["bit score"], 48.7) self.assertAlmostEqual(alignment.score, 100) self.assertEqual(alignment.shape, (2, 57)) self.assertAlmostEqual(alignment.annotations["% identity"], 35.09) self.assertEqual(alignment.annotations["identical"], 20) self.assertEqual(alignment.annotations["mismatches"], 37) self.assertEqual(alignment.annotations["positives"], 33) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 57.89) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "294746") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Meyerozyma guilliermondii ATCC 6260 hypothetical protein (PGUG_03645) partial mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "Meyerozyma guilliermondii ATCC 6260 hypothetical protein (PGUG_03645) partial mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 49) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 49) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|255542 0 VKDGAEHAILKLRSLSSPNEIAHNEDILRIFLMACEVRTVKLSVIGLSCLQKLISHDAVA 0 ........|..|....|..|.....|....|..||..|..|.......|||.|....... gi|296147 0 IRHASDKSIEILKRVHSFEELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIP gi|255542 60 PSALKEILSTLKDHAEMADE 80 60 .|.|.|||.........|.| 80 gi|296147 60 RSRLSEILDAFIEATHLAME 80 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 80], [ 0, 80]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|255542393|ref|XM_002512214.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|255542393|ref|XM_002512214.1|" ) self.assertEqual(alignment.target.annotations["gi"], "255542393") self.assertEqual(alignment.target.annotations["gis"], "255542393") self.assertEqual(alignment.target.annotations["acc."], "XM_002512214") self.assertEqual(alignment.target.annotations["accs."], "XM_002512214") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_002512214.1") self.assertEqual(alignment.target.annotations["length"], 4776) self.assertEqual(alignment.query.annotations["start"], 96) self.assertEqual(alignment.query.annotations["end"], 336) self.assertEqual(alignment.target.annotations["start"], 72) self.assertEqual(alignment.target.annotations["end"], 312) self.assertEqual( alignment.target.seq, "VKDGAEHAILKLRSLSSPNEIAHNEDILRIFLMACEVRTVKLSVIGLSCLQKLISHDAVAPSALKEILSTLKDHAEMADE", ) self.assertEqual( alignment.query.seq, "IRHASDKSIEILKRVHSFEELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAME", ) self.assertAlmostEqual(alignment.annotations["evalue"], 0.002) self.assertAlmostEqual(alignment.annotations["bit score"], 46.9) self.assertAlmostEqual(alignment.score, 96) self.assertEqual(alignment.shape, (2, 80)) self.assertAlmostEqual(alignment.annotations["% identity"], 26.25) self.assertEqual(alignment.annotations["identical"], 21) self.assertEqual(alignment.annotations["mismatches"], 59) self.assertEqual(alignment.annotations["positives"], 42) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 52.50) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "3988") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Ricinus communis guanine nucleotide-exchange, putative, mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "Ricinus communis guanine nucleotide-exchange, putative, mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 69) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 69) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|470133 0 VKDGAEHAILKLRSLSSPGEIAQNEDILRIFLMACEVRTVKLSVIGLSCLQKLISHDAVA 0 ........|..|....|..|.....|....|..||..|..|.......|||.|....... gi|296147 0 IRHASDKSIEILKRVHSFEELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIP gi|470133 60 SSALHEILSTLKDHAEMADE 80 60 .|.|.|||.........|.| 80 gi|296147 60 RSRLSEILDAFIEATHLAME 80 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 80], [ 0, 80]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|470133344|ref|XM_004302479.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|470133344|ref|XM_004302479.1|" ) self.assertEqual(alignment.target.annotations["gi"], "470133344") self.assertEqual(alignment.target.annotations["gis"], "470133344") self.assertEqual(alignment.target.annotations["acc."], "XM_004302479") self.assertEqual(alignment.target.annotations["accs."], "XM_004302479") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_004302479.1") self.assertEqual(alignment.target.annotations["length"], 5152) self.assertEqual(alignment.query.annotations["start"], 96) self.assertEqual(alignment.query.annotations["end"], 336) self.assertEqual(alignment.target.annotations["start"], 72) self.assertEqual(alignment.target.annotations["end"], 312) self.assertEqual( alignment.target.seq, "VKDGAEHAILKLRSLSSPGEIAQNEDILRIFLMACEVRTVKLSVIGLSCLQKLISHDAVASSALHEILSTLKDHAEMADE", ) self.assertEqual( alignment.query.seq, "IRHASDKSIEILKRVHSFEELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAME", ) self.assertAlmostEqual(alignment.annotations["evalue"], 0.002) self.assertAlmostEqual(alignment.annotations["bit score"], 46.4) self.assertAlmostEqual(alignment.score, 95) self.assertEqual(alignment.shape, (2, 80)) self.assertAlmostEqual(alignment.annotations["% identity"], 26.25) self.assertEqual(alignment.annotations["identical"], 21) self.assertEqual(alignment.annotations["mismatches"], 59) self.assertEqual(alignment.annotations["positives"], 43) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 53.75) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "101020") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "PREDICTED: Fragaria vesca subsp. vesca protein MON2 homolog (LOC101302372), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "PREDICTED: Fragaria vesca subsp. vesca protein MON2 homolog (LOC101302372), mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 69) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 69) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|356574 0 TVKDGAEHAILKLRTLSSPSEIAHNDDILRIFLMACEVRTVKLSVIGLSCLQKLISHDAV 0 |........|..|....|..|.....|....|..||..|..|.......|||.|...... gi|296147 0 TIRHASDKSIEILKRVHSFEELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSI gi|356574 60 SPSALREIL 69 60 ..|.|.||| 69 gi|296147 60 PRSRLSEIL 69 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 69], [ 0, 69]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|356574903|ref|XM_003555535.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|356574903|ref|XM_003555535.1|" ) self.assertEqual(alignment.target.annotations["gi"], "356574903") self.assertEqual(alignment.target.annotations["gis"], "356574903") self.assertEqual(alignment.target.annotations["acc."], "XM_003555535") self.assertEqual(alignment.target.annotations["accs."], "XM_003555535") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_003555535.1") self.assertEqual(alignment.target.annotations["length"], 4935) self.assertEqual(alignment.query.annotations["start"], 93) self.assertEqual(alignment.query.annotations["end"], 300) self.assertEqual(alignment.target.annotations["start"], 69) self.assertEqual(alignment.target.annotations["end"], 276) self.assertEqual( alignment.target.seq, "TVKDGAEHAILKLRTLSSPSEIAHNDDILRIFLMACEVRTVKLSVIGLSCLQKLISHDAVSPSALREIL", ) self.assertEqual( alignment.query.seq, "TIRHASDKSIEILKRVHSFEELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEIL", ) self.assertAlmostEqual(alignment.annotations["evalue"], 0.002) self.assertAlmostEqual(alignment.annotations["bit score"], 46.4) self.assertAlmostEqual(alignment.score, 95) self.assertEqual(alignment.shape, (2, 69)) self.assertAlmostEqual(alignment.annotations["% identity"], 28.99) self.assertEqual(alignment.annotations["identical"], 20) self.assertEqual(alignment.annotations["mismatches"], 49) self.assertEqual(alignment.annotations["positives"], 39) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 56.52) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "3847") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "PREDICTED: Glycine max protein MON2 homolog (LOC100777257), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "PREDICTED: Glycine max protein MON2 homolog (LOC100777257), mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 59) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 59) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|334187 0 VKDGAEHAILKLRSSSSASDLSSNEDILRIFLMACGVRNTKLSVIGLSCLQKLISHDAVE 0 ........|..|....|...|....|....|..||..||.|.......|||.|....... gi|296147 0 IRHASDKSIEILKRVHSFEELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIP gi|334187 60 PSSLKEILYTLKDHSEMAEE 80 60 .|.|.|||.........|.| 80 gi|296147 60 RSRLSEILDAFIEATHLAME 80 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 80], [ 0, 80]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|334187990|ref|NM_001203485.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|334187990|ref|NM_001203485.1|" ) self.assertEqual(alignment.target.annotations["gi"], "334187990") self.assertEqual(alignment.target.annotations["gis"], "334187990") self.assertEqual(alignment.target.annotations["acc."], "NM_001203485") self.assertEqual(alignment.target.annotations["accs."], "NM_001203485") self.assertEqual(alignment.target.annotations["acc.ver"], "NM_001203485.1") self.assertEqual(alignment.target.annotations["length"], 5026) self.assertEqual(alignment.query.annotations["start"], 96) self.assertEqual(alignment.query.annotations["end"], 336) self.assertEqual(alignment.target.annotations["start"], 72) self.assertEqual(alignment.target.annotations["end"], 312) self.assertEqual( alignment.target.seq, "VKDGAEHAILKLRSSSSASDLSSNEDILRIFLMACGVRNTKLSVIGLSCLQKLISHDAVEPSSLKEILYTLKDHSEMAEE", ) self.assertEqual( alignment.query.seq, "IRHASDKSIEILKRVHSFEELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAME", ) self.assertAlmostEqual(alignment.annotations["evalue"], 0.002) self.assertAlmostEqual(alignment.annotations["bit score"], 46.4) self.assertAlmostEqual(alignment.score, 95) self.assertEqual(alignment.shape, (2, 80)) self.assertAlmostEqual(alignment.annotations["% identity"], 27.50) self.assertEqual(alignment.annotations["identical"], 22) self.assertEqual(alignment.annotations["mismatches"], 58) self.assertEqual(alignment.annotations["positives"], 42) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 52.50) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "3702") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Arabidopsis thaliana armadillo/beta-catenin-like repeat-containing protein (AT5G27970) mRNA, complete cds", ) self.assertEqual( alignment.target.annotations["titles"], "Arabidopsis thaliana armadillo/beta-catenin-like repeat-containing protein (AT5G27970) mRNA, complete cds", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 69) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 69) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|334187 0 VKDGAEHAILKLRSSSSASDLSSNEDILRIFLMACGVRNTKLSVIGLSCLQKLISHDAVE 0 ........|..|....|...|....|....|..||..||.|.......|||.|....... gi|296147 0 IRHASDKSIEILKRVHSFEELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIP gi|334187 60 PSSLKEILYTLKDAKQLS 78 60 .|.|.|||.....|..|. 78 gi|296147 60 RSRLSEILDAFIEATHLA 78 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 78], [ 0, 78]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|334187988|ref|NM_122680.3|") self.assertEqual( alignment.target.annotations["ids"], "gi|334187988|ref|NM_122680.3|" ) self.assertEqual(alignment.target.annotations["gi"], "334187988") self.assertEqual(alignment.target.annotations["gis"], "334187988") self.assertEqual(alignment.target.annotations["acc."], "NM_122680") self.assertEqual(alignment.target.annotations["accs."], "NM_122680") self.assertEqual(alignment.target.annotations["acc.ver"], "NM_122680.3") self.assertEqual(alignment.target.annotations["length"], 5132) self.assertEqual(alignment.query.annotations["start"], 96) self.assertEqual(alignment.query.annotations["end"], 330) self.assertEqual(alignment.target.annotations["start"], 72) self.assertEqual(alignment.target.annotations["end"], 306) self.assertEqual( alignment.target.seq, "VKDGAEHAILKLRSSSSASDLSSNEDILRIFLMACGVRNTKLSVIGLSCLQKLISHDAVEPSSLKEILYTLKDAKQLS", ) self.assertEqual( alignment.query.seq, "IRHASDKSIEILKRVHSFEELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLA", ) self.assertAlmostEqual(alignment.annotations["evalue"], 0.002) self.assertAlmostEqual(alignment.annotations["bit score"], 46.4) self.assertAlmostEqual(alignment.score, 95) self.assertEqual(alignment.shape, (2, 78)) self.assertAlmostEqual(alignment.annotations["% identity"], 28.21) self.assertEqual(alignment.annotations["identical"], 22) self.assertEqual(alignment.annotations["mismatches"], 56) self.assertEqual(alignment.annotations["positives"], 41) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 52.56) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "3702") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Arabidopsis thaliana armadillo/beta-catenin-like repeat-containing protein (AT5G27970) mRNA, complete cds", ) self.assertEqual( alignment.target.annotations["titles"], "Arabidopsis thaliana armadillo/beta-catenin-like repeat-containing protein (AT5G27970) mRNA, complete cds", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 67) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 67) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|356535 0 VKDGAEHAILKLRTLSSPSEIAHNDDILRIFLMACEVRTVKLSIIGLSCLQKLISHDAVS 0 ........|..|....|..|.....|....|..||..|..|.......|||.|....... gi|296147 0 IRHASDKSIEILKRVHSFEELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIP gi|356535 60 PSALTEILSTLKDA 74 60 .|.|.|||.....| 74 gi|296147 60 RSRLSEILDAFIEA 74 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 74], [ 0, 74]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|356535140|ref|XM_003536059.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|356535140|ref|XM_003536059.1|" ) self.assertEqual(alignment.target.annotations["gi"], "356535140") self.assertEqual(alignment.target.annotations["gis"], "356535140") self.assertEqual(alignment.target.annotations["acc."], "XM_003536059") self.assertEqual(alignment.target.annotations["accs."], "XM_003536059") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_003536059.1") self.assertEqual(alignment.target.annotations["length"], 5612) self.assertEqual(alignment.query.annotations["start"], 96) self.assertEqual(alignment.query.annotations["end"], 318) self.assertEqual(alignment.target.annotations["start"], 72) self.assertEqual(alignment.target.annotations["end"], 294) self.assertEqual( alignment.target.seq, "VKDGAEHAILKLRTLSSPSEIAHNDDILRIFLMACEVRTVKLSIIGLSCLQKLISHDAVSPSALTEILSTLKDA", ) self.assertEqual( alignment.query.seq, "IRHASDKSIEILKRVHSFEELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFIEA", ) self.assertAlmostEqual(alignment.annotations["evalue"], 0.003) self.assertAlmostEqual(alignment.annotations["bit score"], 46.0) self.assertAlmostEqual(alignment.score, 94) self.assertEqual(alignment.shape, (2, 74)) self.assertAlmostEqual(alignment.annotations["% identity"], 27.03) self.assertEqual(alignment.annotations["identical"], 20) self.assertEqual(alignment.annotations["mismatches"], 54) self.assertEqual(alignment.annotations["positives"], 41) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 55.41) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "3847") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "PREDICTED: Glycine max protein MON2 homolog, transcript variant 2 (LOC100818893), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "PREDICTED: Glycine max protein MON2 homolog, transcript variant 2 (LOC100818893), mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 63) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 63) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|296414 0 ELSGRPQFIHPFLIACSTRNAKFSTIGVVCLQRLIVSQGLAKVCRQDIL 49 0 ||...|.|..||..||..||||..|....|||.|.............|| 49 gi|296147 0 ELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEIL 49 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 49], [ 0, 49]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|296414539|ref|XM_002836911.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|296414539|ref|XM_002836911.1|" ) self.assertEqual(alignment.target.annotations["gi"], "296414539") self.assertEqual(alignment.target.annotations["gis"], "296414539") self.assertEqual(alignment.target.annotations["acc."], "XM_002836911") self.assertEqual(alignment.target.annotations["accs."], "XM_002836911") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_002836911.1") self.assertEqual(alignment.target.annotations["length"], 5004) self.assertEqual(alignment.query.annotations["start"], 153) self.assertEqual(alignment.query.annotations["end"], 300) self.assertEqual(alignment.target.annotations["start"], 147) self.assertEqual(alignment.target.annotations["end"], 294) self.assertEqual( alignment.target.seq, "ELSGRPQFIHPFLIACSTRNAKFSTIGVVCLQRLIVSQGLAKVCRQDIL", ) self.assertEqual( alignment.query.seq, "ELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEIL" ) self.assertAlmostEqual(alignment.annotations["evalue"], 0.003) self.assertAlmostEqual(alignment.annotations["bit score"], 46.0) self.assertAlmostEqual(alignment.score, 94) self.assertEqual(alignment.shape, (2, 49)) self.assertAlmostEqual(alignment.annotations["% identity"], 38.78) self.assertEqual(alignment.annotations["identical"], 19) self.assertEqual(alignment.annotations["mismatches"], 30) self.assertEqual(alignment.annotations["positives"], 28) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 57.14) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "656061") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Tuber melanosporum Mel28 hypothetical protein (GSTUM_00003289001) mRNA, complete cds", ) self.assertEqual( alignment.target.annotations["titles"], "Tuber melanosporum Mel28 hypothetical protein (GSTUM_00003289001) mRNA, complete cds", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 42) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 42) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|297597 0 SVKDAAEHAILKLRSLSSPMEIAQNEDILRMFLVACSVKSVKLSVIGLSCLQKLISHDAV 0 ....|....|..|....|..|.....|....|..||.....|.......|||.|...... gi|296147 0 TIRHASDKSIEILKRVHSFEELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSI gi|297597 60 ASSALKDILTTLKDHAEMTDEI 82 60 ..|.|..||...........|| 82 gi|296147 60 PRSRLSEILDAFIEATHLAMEI 82 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 82], [ 0, 82]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|297597693|ref|NM_001050929.2|") self.assertEqual( alignment.target.annotations["ids"], "gi|297597693|ref|NM_001050929.2|" ) self.assertEqual(alignment.target.annotations["gi"], "297597693") self.assertEqual(alignment.target.annotations["gis"], "297597693") self.assertEqual(alignment.target.annotations["acc."], "NM_001050929") self.assertEqual(alignment.target.annotations["accs."], "NM_001050929") self.assertEqual(alignment.target.annotations["acc.ver"], "NM_001050929.2") self.assertEqual(alignment.target.annotations["length"], 3804) self.assertEqual(alignment.query.annotations["start"], 93) self.assertEqual(alignment.query.annotations["end"], 339) self.assertEqual(alignment.target.annotations["start"], 69) self.assertEqual(alignment.target.annotations["end"], 315) self.assertEqual( alignment.target.seq, "SVKDAAEHAILKLRSLSSPMEIAQNEDILRMFLVACSVKSVKLSVIGLSCLQKLISHDAVASSALKDILTTLKDHAEMTDEI", ) self.assertEqual( alignment.query.seq, "TIRHASDKSIEILKRVHSFEELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAMEI", ) self.assertAlmostEqual(alignment.annotations["evalue"], 0.004) self.assertAlmostEqual(alignment.annotations["bit score"], 45.5) self.assertAlmostEqual(alignment.score, 93) self.assertEqual(alignment.shape, (2, 82)) self.assertAlmostEqual(alignment.annotations["% identity"], 24.39) self.assertEqual(alignment.annotations["identical"], 20) self.assertEqual(alignment.annotations["mismatches"], 62) self.assertEqual(alignment.annotations["positives"], 45) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 54.88) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "39947") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Oryza sativa Japonica Group Os01g0772700 (Os01g0772700) mRNA, complete cds", ) self.assertEqual( alignment.target.annotations["titles"], "Oryza sativa Japonica Group Os01g0772700 (Os01g0772700) mRNA, complete cds", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 70) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 70) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|448086 0 PFILSSHNWNAKTATISIPIIHKLIISNAVSREDLEQLLHALKEASNLALDIQLR 55 0 ||.|.....|||..|........|.......|..|...|.|..||..||..|||. 55 gi|296147 0 PFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAMEIQLK 55 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 55], [ 0, 55]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|448086792|ref|XM_004196143.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|448086792|ref|XM_004196143.1|" ) self.assertEqual(alignment.target.annotations["gi"], "448086792") self.assertEqual(alignment.target.annotations["gis"], "448086792") self.assertEqual(alignment.target.annotations["acc."], "XM_004196143") self.assertEqual(alignment.target.annotations["accs."], "XM_004196143") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_004196143.1") self.assertEqual(alignment.target.annotations["length"], 4794) self.assertEqual(alignment.query.annotations["start"], 183) self.assertEqual(alignment.query.annotations["end"], 348) self.assertEqual(alignment.target.annotations["start"], 177) self.assertEqual(alignment.target.annotations["end"], 342) self.assertEqual( alignment.target.seq, "PFILSSHNWNAKTATISIPIIHKLIISNAVSREDLEQLLHALKEASNLALDIQLR", ) self.assertEqual( alignment.query.seq, "PFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAMEIQLK", ) self.assertAlmostEqual(alignment.annotations["evalue"], 0.006) self.assertAlmostEqual(alignment.annotations["bit score"], 45.1) self.assertAlmostEqual(alignment.score, 92) self.assertEqual(alignment.shape, (2, 55)) self.assertAlmostEqual(alignment.annotations["% identity"], 34.55) self.assertEqual(alignment.annotations["identical"], 19) self.assertEqual(alignment.annotations["mismatches"], 36) self.assertEqual(alignment.annotations["positives"], 35) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 63.64) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "559304") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Millerozyma farinosa CBS 7064 hypothetical protein (Piso0_005640) mRNA, complete cds", ) self.assertEqual( alignment.target.annotations["titles"], "Millerozyma farinosa CBS 7064 hypothetical protein (Piso0_005640) mRNA, complete cds", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 47) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 47) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|403176 0 DIFRPISMACATKNAKVVVIALGSLQRLIAMDAVPSCKIPQIVNLLSTVLPLGVEIQLR 0 |...|...||...|||....|...||.|......|......|.........|..||||. gi|296147 0 DFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAMEIQLK gi|403176 59 59 gi|296147 59 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 59], [ 0, 59]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|403176154|ref|XM_003334821.2|") self.assertEqual( alignment.target.annotations["ids"], "gi|403176154|ref|XM_003334821.2|" ) self.assertEqual(alignment.target.annotations["gi"], "403176154") self.assertEqual(alignment.target.annotations["gis"], "403176154") self.assertEqual(alignment.target.annotations["acc."], "XM_003334821") self.assertEqual(alignment.target.annotations["accs."], "XM_003334821") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_003334821.2") self.assertEqual(alignment.target.annotations["length"], 5427) self.assertEqual(alignment.query.annotations["start"], 171) self.assertEqual(alignment.query.annotations["end"], 348) self.assertEqual(alignment.target.annotations["start"], 186) self.assertEqual(alignment.target.annotations["end"], 363) self.assertEqual( alignment.target.seq, "DIFRPISMACATKNAKVVVIALGSLQRLIAMDAVPSCKIPQIVNLLSTVLPLGVEIQLR", ) self.assertEqual( alignment.query.seq, "DFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAMEIQLK", ) self.assertAlmostEqual(alignment.annotations["evalue"], 0.006) self.assertAlmostEqual(alignment.annotations["bit score"], 45.1) self.assertAlmostEqual(alignment.score, 92) self.assertEqual(alignment.shape, (2, 59)) self.assertAlmostEqual(alignment.annotations["% identity"], 30.51) self.assertEqual(alignment.annotations["identical"], 18) self.assertEqual(alignment.annotations["mismatches"], 41) self.assertEqual(alignment.annotations["positives"], 34) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 57.63) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "418459") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Puccinia graminis f. sp. tritici CRL 75-36-700-3 hypothetical protein (PGTG_16037), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "Puccinia graminis f. sp. tritici CRL 75-36-700-3 hypothetical protein (PGTG_16037), mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 51) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 51) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|356535 0 VKDGAEHAILKLRTLSSPSEIAHNDDILRIFLMACEVRTVKLSIIGLSCLQKLISHDAVS 0 ........|..|....|..|.....|....|..||..|..|.......|||.|....... gi|296147 0 IRHASDKSIEILKRVHSFEELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIP gi|356535 60 PSALTEILSTLKDHAEMVDE 80 60 .|.|.|||...........| 80 gi|296147 60 RSRLSEILDAFIEATHLAME 80 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 80], [ 0, 80]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|356535138|ref|XM_003536058.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|356535138|ref|XM_003536058.1|" ) self.assertEqual(alignment.target.annotations["gi"], "356535138") self.assertEqual(alignment.target.annotations["gis"], "356535138") self.assertEqual(alignment.target.annotations["acc."], "XM_003536058") self.assertEqual(alignment.target.annotations["accs."], "XM_003536058") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_003536058.1") self.assertEqual(alignment.target.annotations["length"], 5530) self.assertEqual(alignment.query.annotations["start"], 96) self.assertEqual(alignment.query.annotations["end"], 336) self.assertEqual(alignment.target.annotations["start"], 152) self.assertEqual(alignment.target.annotations["end"], 392) self.assertEqual( alignment.target.seq, "VKDGAEHAILKLRTLSSPSEIAHNDDILRIFLMACEVRTVKLSIIGLSCLQKLISHDAVSPSALTEILSTLKDHAEMVDE", ) self.assertEqual( alignment.query.seq, "IRHASDKSIEILKRVHSFEELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAME", ) self.assertAlmostEqual(alignment.annotations["evalue"], 0.006) self.assertAlmostEqual(alignment.annotations["bit score"], 45.1) self.assertAlmostEqual(alignment.score, 92) self.assertEqual(alignment.shape, (2, 80)) self.assertAlmostEqual(alignment.annotations["% identity"], 25.00) self.assertEqual(alignment.annotations["identical"], 20) self.assertEqual(alignment.annotations["mismatches"], 60) self.assertEqual(alignment.annotations["positives"], 42) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 52.50) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/3") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "3") self.assertEqual(alignment.target.annotations["tax ids"], "3847") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "PREDICTED: Glycine max protein MON2 homolog, transcript variant 1 (LOC100818893), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "PREDICTED: Glycine max protein MON2 homolog, transcript variant 1 (LOC100818893), mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 69) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 69) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|297808 0 VKDGAEHAILKLRSSSSASDLSSNEDILRIFLMACGVRNTKLSVIGLSCLQKLISHDAVE 0 ........|..|....|...|....|....|..||..||.|.......|||.|....... gi|296147 0 IRHASDKSIEILKRVHSFEELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIP gi|297808 60 PSSLKEIL 68 60 .|.|.||| 68 gi|296147 60 RSRLSEIL 68 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 68], [ 0, 68]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|297808820|ref|XM_002872248.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|297808820|ref|XM_002872248.1|" ) self.assertEqual(alignment.target.annotations["gi"], "297808820") self.assertEqual(alignment.target.annotations["gis"], "297808820") self.assertEqual(alignment.target.annotations["acc."], "XM_002872248") self.assertEqual(alignment.target.annotations["accs."], "XM_002872248") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_002872248.1") self.assertEqual(alignment.target.annotations["length"], 4854) self.assertEqual(alignment.query.annotations["start"], 96) self.assertEqual(alignment.query.annotations["end"], 300) self.assertEqual(alignment.target.annotations["start"], 72) self.assertEqual(alignment.target.annotations["end"], 276) self.assertEqual( alignment.target.seq, "VKDGAEHAILKLRSSSSASDLSSNEDILRIFLMACGVRNTKLSVIGLSCLQKLISHDAVEPSSLKEIL", ) self.assertEqual( alignment.query.seq, "IRHASDKSIEILKRVHSFEELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEIL", ) self.assertAlmostEqual(alignment.annotations["evalue"], 0.008) self.assertAlmostEqual(alignment.annotations["bit score"], 44.6) self.assertAlmostEqual(alignment.score, 91) self.assertEqual(alignment.shape, (2, 68)) self.assertAlmostEqual(alignment.annotations["% identity"], 29.41) self.assertEqual(alignment.annotations["identical"], 20) self.assertEqual(alignment.annotations["mismatches"], 48) self.assertEqual(alignment.annotations["positives"], 37) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 54.41) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "81972") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Arabidopsis lyrata subsp. lyrata binding protein, mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "Arabidopsis lyrata subsp. lyrata binding protein, mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 58) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 58) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|242054 0 VKDAAEHAVLKLRSLSGPSEIAQNEDILRMFLMACSVKSVKLSVIGLSCLQKLISHGAVA 0 ...|.......|.......|.....|....|..||.....|.......|||.|....... gi|296147 0 IRHASDKSIEILKRVHSFEELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIP gi|242054 60 SSALKEILATLKDHAEMTDEI 81 60 .|.|.|||...........|| 81 gi|296147 60 RSRLSEILDAFIEATHLAMEI 81 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 81], [ 0, 81]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|242054552|ref|XM_002456377.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|242054552|ref|XM_002456377.1|" ) self.assertEqual(alignment.target.annotations["gi"], "242054552") self.assertEqual(alignment.target.annotations["gis"], "242054552") self.assertEqual(alignment.target.annotations["acc."], "XM_002456377") self.assertEqual(alignment.target.annotations["accs."], "XM_002456377") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_002456377.1") self.assertEqual(alignment.target.annotations["length"], 414) self.assertEqual(alignment.query.annotations["start"], 96) self.assertEqual(alignment.query.annotations["end"], 339) self.assertEqual(alignment.target.annotations["start"], 72) self.assertEqual(alignment.target.annotations["end"], 315) self.assertEqual( alignment.target.seq, "VKDAAEHAVLKLRSLSGPSEIAQNEDILRMFLMACSVKSVKLSVIGLSCLQKLISHGAVASSALKEILATLKDHAEMTDEI", ) self.assertEqual( alignment.query.seq, "IRHASDKSIEILKRVHSFEELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAMEI", ) self.assertAlmostEqual(alignment.annotations["evalue"], 0.008) self.assertAlmostEqual(alignment.annotations["bit score"], 44.6) self.assertAlmostEqual(alignment.score, 91) self.assertEqual(alignment.shape, (2, 81)) self.assertAlmostEqual(alignment.annotations["% identity"], 23.46) self.assertEqual(alignment.annotations["identical"], 19) self.assertEqual(alignment.annotations["mismatches"], 62) self.assertEqual(alignment.annotations["positives"], 43) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 53.09) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "4558") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Sorghum bicolor hypothetical protein, mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "Sorghum bicolor hypothetical protein, mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 69) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 69) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|224125 0 VKDGAEHAILKLRSLSSPSEIADNEDILRIFLMACEVRTVKLSVIGLSCLQKLISHDAVA 0 ........|..|....|..|.....|....|..||..|..|.......|||.|....... gi|296147 0 IRHASDKSIEILKRVHSFEELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIP gi|224125 60 PSALKEIL 68 60 .|.|.||| 68 gi|296147 60 RSRLSEIL 68 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 68], [ 0, 68]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|224125555|ref|XM_002319579.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|224125555|ref|XM_002319579.1|" ) self.assertEqual(alignment.target.annotations["gi"], "224125555") self.assertEqual(alignment.target.annotations["gis"], "224125555") self.assertEqual(alignment.target.annotations["acc."], "XM_002319579") self.assertEqual(alignment.target.annotations["accs."], "XM_002319579") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_002319579.1") self.assertEqual(alignment.target.annotations["length"], 4914) self.assertEqual(alignment.query.annotations["start"], 96) self.assertEqual(alignment.query.annotations["end"], 300) self.assertEqual(alignment.target.annotations["start"], 72) self.assertEqual(alignment.target.annotations["end"], 276) self.assertEqual( alignment.target.seq, "VKDGAEHAILKLRSLSSPSEIADNEDILRIFLMACEVRTVKLSVIGLSCLQKLISHDAVAPSALKEIL", ) self.assertEqual( alignment.query.seq, "IRHASDKSIEILKRVHSFEELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEIL", ) self.assertAlmostEqual(alignment.annotations["evalue"], 0.015) self.assertAlmostEqual(alignment.annotations["bit score"], 43.7) self.assertAlmostEqual(alignment.score, 89) self.assertEqual(alignment.shape, (2, 68)) self.assertAlmostEqual(alignment.annotations["% identity"], 27.94) self.assertEqual(alignment.annotations["identical"], 19) self.assertEqual(alignment.annotations["mismatches"], 49) self.assertEqual(alignment.annotations["positives"], 38) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 55.88) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "3694") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Populus trichocarpa predicted protein, mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "Populus trichocarpa predicted protein, mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 58) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 58) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|357131 0 VKDAAEHATLKLRSLSNPSEIAQNGDILRMFLMACSVKSVKLSAIGLSCLQKLISHDAVA 0 ...|.......|.......|.....|....|..||.....|.......|||.|....... gi|296147 0 IRHASDKSIEILKRVHSFEELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIP gi|357131 60 SSALKEIL 68 60 .|.|.||| 68 gi|296147 60 RSRLSEIL 68 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 68], [ 0, 68]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|357131062|ref|XR_138050.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|357131062|ref|XR_138050.1|" ) self.assertEqual(alignment.target.annotations["gi"], "357131062") self.assertEqual(alignment.target.annotations["gis"], "357131062") self.assertEqual(alignment.target.annotations["acc."], "XR_138050") self.assertEqual(alignment.target.annotations["accs."], "XR_138050") self.assertEqual(alignment.target.annotations["acc.ver"], "XR_138050.1") self.assertEqual(alignment.target.annotations["length"], 3794) self.assertEqual(alignment.query.annotations["start"], 96) self.assertEqual(alignment.query.annotations["end"], 300) self.assertEqual(alignment.target.annotations["start"], 72) self.assertEqual(alignment.target.annotations["end"], 276) self.assertEqual( alignment.target.seq, "VKDAAEHATLKLRSLSNPSEIAQNGDILRMFLMACSVKSVKLSAIGLSCLQKLISHDAVASSALKEIL", ) self.assertEqual( alignment.query.seq, "IRHASDKSIEILKRVHSFEELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEIL", ) self.assertAlmostEqual(alignment.annotations["evalue"], 0.054) self.assertAlmostEqual(alignment.annotations["bit score"], 41.8) self.assertAlmostEqual(alignment.score, 85) self.assertEqual(alignment.shape, (2, 68)) self.assertAlmostEqual(alignment.annotations["% identity"], 25.00) self.assertEqual(alignment.annotations["identical"], 17) self.assertEqual(alignment.annotations["mismatches"], 51) self.assertEqual(alignment.annotations["positives"], 39) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 57.35) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "15368") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "PREDICTED: Brachypodium distachyon uncharacterized LOC100838086 (LOC100838086), miscRNA", ) self.assertEqual( alignment.target.annotations["titles"], "PREDICTED: Brachypodium distachyon uncharacterized LOC100838086 (LOC100838086), miscRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 58) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 58) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|403290 0 TLEVSCLQGLHTSPSLEDQGVSQITNAFNMVVHLSNTLELQ 41 0 ||...|||||.|.||......|.|..||....||.....|. 41 gi|296147 0 TLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAMEIQLK 41 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 41], [ 0, 41]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|403290914|ref|XM_003936502.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|403290914|ref|XM_003936502.1|" ) self.assertEqual(alignment.target.annotations["gi"], "403290914") self.assertEqual(alignment.target.annotations["gis"], "403290914") self.assertEqual(alignment.target.annotations["acc."], "XM_003936502") self.assertEqual(alignment.target.annotations["accs."], "XM_003936502") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_003936502.1") self.assertEqual(alignment.target.annotations["length"], 7255) self.assertEqual(alignment.query.annotations["start"], 225) self.assertEqual(alignment.query.annotations["end"], 348) self.assertEqual(alignment.target.annotations["start"], 6675) self.assertEqual(alignment.target.annotations["end"], 6552) self.assertEqual( alignment.target.seq, "TLEVSCLQGLHTSPSLEDQGVSQITNAFNMVVHLSNTLELQ" ) self.assertEqual( alignment.query.seq, "TLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAMEIQLK" ) self.assertAlmostEqual(alignment.annotations["evalue"], 0.14) self.assertAlmostEqual(alignment.annotations["bit score"], 40.5) self.assertAlmostEqual(alignment.score, 82) self.assertEqual(alignment.shape, (2, 41)) self.assertAlmostEqual(alignment.annotations["% identity"], 41.46) self.assertEqual(alignment.annotations["identical"], 17) self.assertEqual(alignment.annotations["mismatches"], 24) self.assertEqual(alignment.annotations["positives"], 26) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 63.41) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/-2") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "-2") self.assertEqual(alignment.target.annotations["tax ids"], "39432") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "PREDICTED: Saimiri boliviensis boliviensis Ral GTPase activating protein, beta subunit (non-catalytic) (RALGAPB), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "PREDICTED: Saimiri boliviensis boliviensis Ral GTPase activating protein, beta subunit (non-catalytic) (RALGAPB), mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 35) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 35) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|297707 0 TLGVSCLQGLHTLPSLEDKGVSQITNAFNMIVHVSNTLELQ 41 0 ||...|||||.|.||......|.|..||....|......|. 41 gi|296147 0 TLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAMEIQLK 41 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 41], [ 0, 41]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|297707079|ref|XM_002830297.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|297707079|ref|XM_002830297.1|" ) self.assertEqual(alignment.target.annotations["gi"], "297707079") self.assertEqual(alignment.target.annotations["gis"], "297707079") self.assertEqual(alignment.target.annotations["acc."], "XM_002830297") self.assertEqual(alignment.target.annotations["accs."], "XM_002830297") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_002830297.1") self.assertEqual(alignment.target.annotations["length"], 8045) self.assertEqual(alignment.query.annotations["start"], 225) self.assertEqual(alignment.query.annotations["end"], 348) self.assertEqual(alignment.target.annotations["start"], 6177) self.assertEqual(alignment.target.annotations["end"], 6054) self.assertEqual( alignment.target.seq, "TLGVSCLQGLHTLPSLEDKGVSQITNAFNMIVHVSNTLELQ" ) self.assertEqual( alignment.query.seq, "TLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAMEIQLK" ) self.assertAlmostEqual(alignment.annotations["evalue"], 0.14) self.assertAlmostEqual(alignment.annotations["bit score"], 40.5) self.assertAlmostEqual(alignment.score, 82) self.assertEqual(alignment.shape, (2, 41)) self.assertAlmostEqual(alignment.annotations["% identity"], 39.02) self.assertEqual(alignment.annotations["identical"], 16) self.assertEqual(alignment.annotations["mismatches"], 25) self.assertEqual(alignment.annotations["positives"], 27) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 65.85) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/-3") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "-3") self.assertEqual(alignment.target.annotations["tax ids"], "9601") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "PREDICTED: Pongo abelii Ral GTPase activating protein, beta subunit (non-catalytic) (RALGAPB), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "PREDICTED: Pongo abelii Ral GTPase activating protein, beta subunit (non-catalytic) (RALGAPB), mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 35) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 35) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|254567 0 ASIDMIRSFKQRVPIQELVKFESFVDPFLLSIQTRSLKLVNTGLACLQKLIIESAIADTK 0 ||...|...|......||.....|..||.|..|.|..|.......|||.|.....|.... gi|296147 0 ASDKSIEILKRVHSFEELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSR gi|254567 60 LESLVNSLL 69 60 |........ 69 gi|296147 60 LSEILDAFI 69 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 69], [ 0, 69]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|254567673|ref|XM_002490902.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|254567673|ref|XM_002490902.1|" ) self.assertEqual(alignment.target.annotations["gi"], "254567673") self.assertEqual(alignment.target.annotations["gis"], "254567673") self.assertEqual(alignment.target.annotations["acc."], "XM_002490902") self.assertEqual(alignment.target.annotations["accs."], "XM_002490902") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_002490902.1") self.assertEqual(alignment.target.annotations["length"], 4647) self.assertEqual(alignment.query.annotations["start"], 105) self.assertEqual(alignment.query.annotations["end"], 312) self.assertEqual(alignment.target.annotations["start"], 87) self.assertEqual(alignment.target.annotations["end"], 294) self.assertEqual( alignment.target.seq, "ASIDMIRSFKQRVPIQELVKFESFVDPFLLSIQTRSLKLVNTGLACLQKLIIESAIADTKLESLVNSLL", ) self.assertEqual( alignment.query.seq, "ASDKSIEILKRVHSFEELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFI", ) self.assertAlmostEqual(alignment.annotations["evalue"], 0.19) self.assertAlmostEqual(alignment.annotations["bit score"], 40.0) self.assertAlmostEqual(alignment.score, 81) self.assertEqual(alignment.shape, (2, 69)) self.assertAlmostEqual(alignment.annotations["% identity"], 27.54) self.assertEqual(alignment.annotations["identical"], 19) self.assertEqual(alignment.annotations["mismatches"], 50) self.assertEqual(alignment.annotations["positives"], 36) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 52.17) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "644223") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Pichia pastoris GS115 Peripheral membrane protein with a role in endocytosis and vacuole integrity, interacts with Arl1p a (PAS_chr2-1_0066) mRNA, complete cds", ) self.assertEqual( alignment.target.annotations["titles"], "Pichia pastoris GS115 Peripheral membrane protein with a role in endocytosis and vacuole integrity, interacts with Arl1p a (PAS_chr2-1_0066) mRNA, complete cds", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 59) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 59) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|302772 0 MLTCKTRNIKLSVLGLSCLQKLLAHDAIPPLAVPQILEILQEHSEIHYEV 50 0 .|.|..||.|...|...|||.|.....||......||....|......|. 50 gi|296147 0 VLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAMEI 50 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 50], [ 0, 50]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|302772536|ref|XM_002969640.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|302772536|ref|XM_002969640.1|" ) self.assertEqual(alignment.target.annotations["gi"], "302772536") self.assertEqual(alignment.target.annotations["gis"], "302772536") self.assertEqual(alignment.target.annotations["acc."], "XM_002969640") self.assertEqual(alignment.target.annotations["accs."], "XM_002969640") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_002969640.1") self.assertEqual(alignment.target.annotations["length"], 399) self.assertEqual(alignment.query.annotations["start"], 189) self.assertEqual(alignment.query.annotations["end"], 339) self.assertEqual(alignment.target.annotations["start"], 0) self.assertEqual(alignment.target.annotations["end"], 150) self.assertEqual( alignment.target.seq, "MLTCKTRNIKLSVLGLSCLQKLLAHDAIPPLAVPQILEILQEHSEIHYEV", ) self.assertEqual( alignment.query.seq, "VLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAMEI", ) self.assertAlmostEqual(alignment.annotations["evalue"], 0.27) self.assertAlmostEqual(alignment.annotations["bit score"], 39.6) self.assertAlmostEqual(alignment.score, 80) self.assertEqual(alignment.shape, (2, 50)) self.assertAlmostEqual(alignment.annotations["% identity"], 32.00) self.assertEqual(alignment.annotations["identical"], 16) self.assertEqual(alignment.annotations["mismatches"], 34) self.assertEqual(alignment.annotations["positives"], 29) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 58.00) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "88036") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Selaginella moellendorffii hypothetical protein, mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "Selaginella moellendorffii hypothetical protein, mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 43) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 43) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|189235 0 YFLPFELACQSRSARIVVTALDCLQKL 27 0 ..|||.||||||.|.....|..|||.| 27 gi|296147 0 FALPFVLACQSRNAKMTTLAMQCLQGL 27 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 27], [ 0, 27]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|189235995|ref|XM_967692.2|") self.assertEqual( alignment.target.annotations["ids"], "gi|189235995|ref|XM_967692.2|" ) self.assertEqual(alignment.target.annotations["gi"], "189235995") self.assertEqual(alignment.target.annotations["gis"], "189235995") self.assertEqual(alignment.target.annotations["acc."], "XM_967692") self.assertEqual(alignment.target.annotations["accs."], "XM_967692") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_967692.2") self.assertEqual(alignment.target.annotations["length"], 5169) self.assertEqual(alignment.query.annotations["start"], 174) self.assertEqual(alignment.query.annotations["end"], 255) self.assertEqual(alignment.target.annotations["start"], 231) self.assertEqual(alignment.target.annotations["end"], 312) self.assertEqual(alignment.target.seq, "YFLPFELACQSRSARIVVTALDCLQKL") self.assertEqual(alignment.query.seq, "FALPFVLACQSRNAKMTTLAMQCLQGL") self.assertAlmostEqual(alignment.annotations["evalue"], 0.27) self.assertAlmostEqual(alignment.annotations["bit score"], 39.6) self.assertAlmostEqual(alignment.score, 80) self.assertEqual(alignment.shape, (2, 27)) self.assertAlmostEqual(alignment.annotations["% identity"], 55.56) self.assertEqual(alignment.annotations["identical"], 15) self.assertEqual(alignment.annotations["mismatches"], 12) self.assertEqual(alignment.annotations["positives"], 20) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 74.07) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "7070") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "PREDICTED: Tribolium castaneum similar to AGAP008906-PA (LOC661541), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "PREDICTED: Tribolium castaneum similar to AGAP008906-PA (LOC661541), mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 23) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 23) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|238586 0 MACATKNAKVVAISLGSLQRLIALKAVPQSDVPLIIKTMSDSMSQGVDIQLK 52 0 .||...|||........||.|......|.|....|.............|||| 52 gi|296147 0 LACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAMEIQLK 52 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 52], [ 0, 52]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|238586708|ref|XM_002391211.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|238586708|ref|XM_002391211.1|" ) self.assertEqual(alignment.target.annotations["gi"], "238586708") self.assertEqual(alignment.target.annotations["gis"], "238586708") self.assertEqual(alignment.target.annotations["acc."], "XM_002391211") self.assertEqual(alignment.target.annotations["accs."], "XM_002391211") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_002391211.1") self.assertEqual(alignment.target.annotations["length"], 1557) self.assertEqual(alignment.query.annotations["start"], 192) self.assertEqual(alignment.query.annotations["end"], 348) self.assertEqual(alignment.target.annotations["start"], 0) self.assertEqual(alignment.target.annotations["end"], 156) self.assertEqual( alignment.target.seq, "MACATKNAKVVAISLGSLQRLIALKAVPQSDVPLIIKTMSDSMSQGVDIQLK", ) self.assertEqual( alignment.query.seq, "LACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAMEIQLK", ) self.assertAlmostEqual(alignment.annotations["evalue"], 0.50) self.assertAlmostEqual(alignment.annotations["bit score"], 38.6) self.assertAlmostEqual(alignment.score, 78) self.assertEqual(alignment.shape, (2, 52)) self.assertAlmostEqual(alignment.annotations["% identity"], 28.85) self.assertEqual(alignment.annotations["identical"], 15) self.assertEqual(alignment.annotations["mismatches"], 37) self.assertEqual(alignment.annotations["positives"], 32) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 61.54) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "554373") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Moniliophthora perniciosa FA553 hypothetical protein (MPER_09344) mRNA, partial cds", ) self.assertEqual( alignment.target.annotations["titles"], "Moniliophthora perniciosa FA553 hypothetical protein (MPER_09344) mRNA, partial cds", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 45) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 45) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|827342 0 TLGVSCLQGLHILPSLEDEEVSQITNAFNMIVHVSNTLELQ 41 0 ||...|||||...||......|.|..||....|......|. 41 gi|296147 0 TLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAMEIQLK 41 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 41], [ 0, 41]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|82734234|ref|NM_020336.2|") self.assertEqual( alignment.target.annotations["ids"], "gi|82734234|ref|NM_020336.2|" ) self.assertEqual(alignment.target.annotations["gi"], "82734234") self.assertEqual(alignment.target.annotations["gis"], "82734234") self.assertEqual(alignment.target.annotations["acc."], "NM_020336") self.assertEqual(alignment.target.annotations["accs."], "NM_020336") self.assertEqual(alignment.target.annotations["acc.ver"], "NM_020336.2") self.assertEqual(alignment.target.annotations["length"], 8636) self.assertEqual(alignment.query.annotations["start"], 225) self.assertEqual(alignment.query.annotations["end"], 348) self.assertEqual(alignment.target.annotations["start"], 6902) self.assertEqual(alignment.target.annotations["end"], 6779) self.assertEqual( alignment.target.seq, "TLGVSCLQGLHILPSLEDEEVSQITNAFNMIVHVSNTLELQ" ) self.assertEqual( alignment.query.seq, "TLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAMEIQLK" ) self.assertAlmostEqual(alignment.annotations["evalue"], 0.50) self.assertAlmostEqual(alignment.annotations["bit score"], 38.6) self.assertAlmostEqual(alignment.score, 78) self.assertEqual(alignment.shape, (2, 41)) self.assertAlmostEqual(alignment.annotations["% identity"], 36.59) self.assertEqual(alignment.annotations["identical"], 15) self.assertEqual(alignment.annotations["mismatches"], 26) self.assertEqual(alignment.annotations["positives"], 26) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 63.41) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/-1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "-1") self.assertEqual(alignment.target.annotations["tax ids"], "9606") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Homo sapiens Ral GTPase activating protein, beta subunit (non-catalytic) (RALGAPB), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "Homo sapiens Ral GTPase activating protein, beta subunit (non-catalytic) (RALGAPB), mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 35) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 35) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|391342 0 FMAPFELACQSKSPRLTVIALDCVQKL 27 0 |..||.|||||.....|..|..|.|.| 27 gi|296147 0 FALPFVLACQSRNAKMTTLAMQCLQGL 27 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 27], [ 0, 27]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|391342729|ref|XM_003745620.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|391342729|ref|XM_003745620.1|" ) self.assertEqual(alignment.target.annotations["gi"], "391342729") self.assertEqual(alignment.target.annotations["gis"], "391342729") self.assertEqual(alignment.target.annotations["acc."], "XM_003745620") self.assertEqual(alignment.target.annotations["accs."], "XM_003745620") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_003745620.1") self.assertEqual(alignment.target.annotations["length"], 4662) self.assertEqual(alignment.query.annotations["start"], 174) self.assertEqual(alignment.query.annotations["end"], 255) self.assertEqual(alignment.target.annotations["start"], 210) self.assertEqual(alignment.target.annotations["end"], 291) self.assertEqual(alignment.target.seq, "FMAPFELACQSKSPRLTVIALDCVQKL") self.assertEqual(alignment.query.seq, "FALPFVLACQSRNAKMTTLAMQCLQGL") self.assertAlmostEqual(alignment.annotations["evalue"], 0.69) self.assertAlmostEqual(alignment.annotations["bit score"], 38.2) self.assertAlmostEqual(alignment.score, 77) self.assertEqual(alignment.shape, (2, 27)) self.assertAlmostEqual(alignment.annotations["% identity"], 48.15) self.assertEqual(alignment.annotations["identical"], 13) self.assertEqual(alignment.annotations["mismatches"], 14) self.assertEqual(alignment.annotations["positives"], 20) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 74.07) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "34638") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "PREDICTED: Metaseiulus occidentalis brefeldin A-inhibited guanine nucleotide-exchange protein 1-like (LOC100907146), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "PREDICTED: Metaseiulus occidentalis brefeldin A-inhibited guanine nucleotide-exchange protein 1-like (LOC100907146), mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 23) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 23) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|291235 0 YFLPFELACQSKSARIVNTALDCLQKL 27 0 ..|||.|||||..|.....|..|||.| 27 gi|296147 0 FALPFVLACQSRNAKMTTLAMQCLQGL 27 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 27], [ 0, 27]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|291235727|ref|XM_002737750.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|291235727|ref|XM_002737750.1|" ) self.assertEqual(alignment.target.annotations["gi"], "291235727") self.assertEqual(alignment.target.annotations["gis"], "291235727") self.assertEqual(alignment.target.annotations["acc."], "XM_002737750") self.assertEqual(alignment.target.annotations["accs."], "XM_002737750") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_002737750.1") self.assertEqual(alignment.target.annotations["length"], 4743) self.assertEqual(alignment.query.annotations["start"], 174) self.assertEqual(alignment.query.annotations["end"], 255) self.assertEqual(alignment.target.annotations["start"], 198) self.assertEqual(alignment.target.annotations["end"], 279) self.assertEqual(alignment.target.seq, "YFLPFELACQSKSARIVNTALDCLQKL") self.assertEqual(alignment.query.seq, "FALPFVLACQSRNAKMTTLAMQCLQGL") self.assertAlmostEqual(alignment.annotations["evalue"], 0.69) self.assertAlmostEqual(alignment.annotations["bit score"], 38.2) self.assertAlmostEqual(alignment.score, 77) self.assertEqual(alignment.shape, (2, 27)) self.assertAlmostEqual(alignment.annotations["% identity"], 51.85) self.assertEqual(alignment.annotations["identical"], 14) self.assertEqual(alignment.annotations["mismatches"], 13) self.assertEqual(alignment.annotations["positives"], 20) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 74.07) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "10224") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "PREDICTED: Saccoglossus kowalevskii ADP-ribosylation factor guanine nucleotide-exchange factor 1(brefeldin A-inhibited)-like (LOC100366823), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "PREDICTED: Saccoglossus kowalevskii ADP-ribosylation factor guanine nucleotide-exchange factor 1(brefeldin A-inhibited)-like (LOC100366823), mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 23) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 23) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|330938 0 ISAMSPVPVLARVRLSDVDDAYFRISHVVSDL 32 0 ....|.||...|.|||...||.....|..... 32 gi|296147 0 LQGLSTVPSIPRSRLSEILDAFIEATHLAMEI 32 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 32], [ 0, 32]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|330938727|ref|XM_003305716.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|330938727|ref|XM_003305716.1|" ) self.assertEqual(alignment.target.annotations["gi"], "330938727") self.assertEqual(alignment.target.annotations["gis"], "330938727") self.assertEqual(alignment.target.annotations["acc."], "XM_003305716") self.assertEqual(alignment.target.annotations["accs."], "XM_003305716") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_003305716.1") self.assertEqual(alignment.target.annotations["length"], 459) self.assertEqual(alignment.query.annotations["start"], 243) self.assertEqual(alignment.query.annotations["end"], 339) self.assertEqual(alignment.target.annotations["start"], 164) self.assertEqual(alignment.target.annotations["end"], 68) self.assertEqual(alignment.target.seq, "ISAMSPVPVLARVRLSDVDDAYFRISHVVSDL") self.assertEqual(alignment.query.seq, "LQGLSTVPSIPRSRLSEILDAFIEATHLAMEI") self.assertAlmostEqual(alignment.annotations["evalue"], 0.77) self.assertAlmostEqual(alignment.annotations["bit score"], 29.9) self.assertAlmostEqual(alignment.score, 59) self.assertEqual(alignment.shape, (2, 32)) self.assertAlmostEqual(alignment.annotations["% identity"], 31.25) self.assertEqual(alignment.annotations["identical"], 10) self.assertEqual(alignment.annotations["mismatches"], 22) self.assertEqual(alignment.annotations["positives"], 20) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 62.50) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/-2") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "-2") self.assertEqual(alignment.target.annotations["tax ids"], "861557") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Pyrenophora teres f. teres 0-1 hypothetical protein, mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "Pyrenophora teres f. teres 0-1 hypothetical protein, mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 42) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 27) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|330938 0 SLPVIIRTHSLPQLERH 17 0 |.....|.||...|||| 17 gi|296147 0 SIEILKRVHSFEELERH 17 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 17], [ 0, 17]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|330938727|ref|XM_003305716.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|330938727|ref|XM_003305716.1|" ) self.assertEqual(alignment.target.annotations["gi"], "330938727") self.assertEqual(alignment.target.annotations["gis"], "330938727") self.assertEqual(alignment.target.annotations["acc."], "XM_003305716") self.assertEqual(alignment.target.annotations["accs."], "XM_003305716") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_003305716.1") self.assertEqual(alignment.target.annotations["length"], 459) self.assertEqual(alignment.query.annotations["start"], 117) self.assertEqual(alignment.query.annotations["end"], 168) self.assertEqual(alignment.target.annotations["start"], 447) self.assertEqual(alignment.target.annotations["end"], 396) self.assertEqual(alignment.target.seq, "SLPVIIRTHSLPQLERH") self.assertEqual(alignment.query.seq, "SIEILKRVHSFEELERH") self.assertAlmostEqual(alignment.annotations["evalue"], 0.77) self.assertAlmostEqual(alignment.annotations["bit score"], 24.4) self.assertAlmostEqual(alignment.score, 47) self.assertEqual(alignment.shape, (2, 17)) self.assertAlmostEqual(alignment.annotations["% identity"], 47.06) self.assertEqual(alignment.annotations["identical"], 8) self.assertEqual(alignment.annotations["mismatches"], 9) self.assertEqual(alignment.annotations["positives"], 12) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 70.59) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/-1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "-1") self.assertEqual(alignment.target.annotations["tax ids"], "861557") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Pyrenophora teres f. teres 0-1 hypothetical protein, mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "Pyrenophora teres f. teres 0-1 hypothetical protein, mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 42) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 15) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|397511 0 TLGVSCLQGLHILPSLEDEGVSQITNAFNMIVHVSNTLELQ 41 0 ||...|||||...||......|.|..||....|......|. 41 gi|296147 0 TLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAMEIQLK 41 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 41], [ 0, 41]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|397511126|ref|XM_003825883.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|397511126|ref|XM_003825883.1|" ) self.assertEqual(alignment.target.annotations["gi"], "397511126") self.assertEqual(alignment.target.annotations["gis"], "397511126") self.assertEqual(alignment.target.annotations["acc."], "XM_003825883") self.assertEqual(alignment.target.annotations["accs."], "XM_003825883") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_003825883.1") self.assertEqual(alignment.target.annotations["length"], 8056) self.assertEqual(alignment.query.annotations["start"], 225) self.assertEqual(alignment.query.annotations["end"], 348) self.assertEqual(alignment.target.annotations["start"], 6171) self.assertEqual(alignment.target.annotations["end"], 6048) self.assertEqual( alignment.target.seq, "TLGVSCLQGLHILPSLEDEGVSQITNAFNMIVHVSNTLELQ" ) self.assertEqual( alignment.query.seq, "TLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAMEIQLK" ) self.assertAlmostEqual(alignment.annotations["evalue"], 0.95) self.assertAlmostEqual(alignment.annotations["bit score"], 37.7) self.assertAlmostEqual(alignment.score, 76) self.assertEqual(alignment.shape, (2, 41)) self.assertAlmostEqual(alignment.annotations["% identity"], 36.59) self.assertEqual(alignment.annotations["identical"], 15) self.assertEqual(alignment.annotations["mismatches"], 26) self.assertEqual(alignment.annotations["positives"], 26) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 63.41) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/-2") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "-2") self.assertEqual(alignment.target.annotations["tax ids"], "9597") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "PREDICTED: Pan paniscus Ral GTPase activating protein, beta subunit (non-catalytic), transcript variant 2 (RALGAPB), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "PREDICTED: Pan paniscus Ral GTPase activating protein, beta subunit (non-catalytic), transcript variant 2 (RALGAPB), mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 35) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 35) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|397511 0 TLGVSCLQGLHILPSLEDEGVSQITNAFNMIVHVSNTLELQ 41 0 ||...|||||...||......|.|..||....|......|. 41 gi|296147 0 TLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAMEIQLK 41 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 41], [ 0, 41]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|397511124|ref|XM_003825882.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|397511124|ref|XM_003825882.1|" ) self.assertEqual(alignment.target.annotations["gi"], "397511124") self.assertEqual(alignment.target.annotations["gis"], "397511124") self.assertEqual(alignment.target.annotations["acc."], "XM_003825882") self.assertEqual(alignment.target.annotations["accs."], "XM_003825882") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_003825882.1") self.assertEqual(alignment.target.annotations["length"], 8831) self.assertEqual(alignment.query.annotations["start"], 225) self.assertEqual(alignment.query.annotations["end"], 348) self.assertEqual(alignment.target.annotations["start"], 6946) self.assertEqual(alignment.target.annotations["end"], 6823) self.assertEqual( alignment.target.seq, "TLGVSCLQGLHILPSLEDEGVSQITNAFNMIVHVSNTLELQ" ) self.assertEqual( alignment.query.seq, "TLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAMEIQLK" ) self.assertAlmostEqual(alignment.annotations["evalue"], 0.95) self.assertAlmostEqual(alignment.annotations["bit score"], 37.7) self.assertAlmostEqual(alignment.score, 76) self.assertEqual(alignment.shape, (2, 41)) self.assertAlmostEqual(alignment.annotations["% identity"], 36.59) self.assertEqual(alignment.annotations["identical"], 15) self.assertEqual(alignment.annotations["mismatches"], 26) self.assertEqual(alignment.annotations["positives"], 26) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 63.41) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/-2") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "-2") self.assertEqual(alignment.target.annotations["tax ids"], "9597") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "PREDICTED: Pan paniscus Ral GTPase activating protein, beta subunit (non-catalytic), transcript variant 1 (RALGAPB), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "PREDICTED: Pan paniscus Ral GTPase activating protein, beta subunit (non-catalytic), transcript variant 1 (RALGAPB), mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 35) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 35) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|390362 0 LPFELACQSKSARIVNTALDCLQKL 25 0 |||.|||||..|.....|..|||.| 25 gi|296147 0 LPFVLACQSRNAKMTTLAMQCLQGL 25 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 25], [ 0, 25]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|390362724|ref|XR_025702.2|") self.assertEqual( alignment.target.annotations["ids"], "gi|390362724|ref|XR_025702.2|" ) self.assertEqual(alignment.target.annotations["gi"], "390362724") self.assertEqual(alignment.target.annotations["gis"], "390362724") self.assertEqual(alignment.target.annotations["acc."], "XR_025702") self.assertEqual(alignment.target.annotations["accs."], "XR_025702") self.assertEqual(alignment.target.annotations["acc.ver"], "XR_025702.2") self.assertEqual(alignment.target.annotations["length"], 5049) self.assertEqual(alignment.query.annotations["start"], 180) self.assertEqual(alignment.query.annotations["end"], 255) self.assertEqual(alignment.target.annotations["start"], 243) self.assertEqual(alignment.target.annotations["end"], 318) self.assertEqual(alignment.target.seq, "LPFELACQSKSARIVNTALDCLQKL") self.assertEqual(alignment.query.seq, "LPFVLACQSRNAKMTTLAMQCLQGL") self.assertAlmostEqual(alignment.annotations["evalue"], 0.95) self.assertAlmostEqual(alignment.annotations["bit score"], 37.7) self.assertAlmostEqual(alignment.score, 76) self.assertEqual(alignment.shape, (2, 25)) self.assertAlmostEqual(alignment.annotations["% identity"], 56.00) self.assertEqual(alignment.annotations["identical"], 14) self.assertEqual(alignment.annotations["mismatches"], 11) self.assertEqual(alignment.annotations["positives"], 19) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 76.00) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "7668") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "PREDICTED: Strongylocentrotus purpuratus brefeldin A-inhibited guanine nucleotide-exchange protein 1-like (LOC754128), misc_RNA", ) self.assertEqual( alignment.target.annotations["titles"], "PREDICTED: Strongylocentrotus purpuratus brefeldin A-inhibited guanine nucleotide-exchange protein 1-like (LOC754128), misc_RNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 21) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 21) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|390341 0 LPFELACQSKSARIVNTALDCLQKL 25 0 |||.|||||..|.....|..|||.| 25 gi|296147 0 LPFVLACQSRNAKMTTLAMQCLQGL 25 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 25], [ 0, 25]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|390341406|ref|XR_143615.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|390341406|ref|XR_143615.1|" ) self.assertEqual(alignment.target.annotations["gi"], "390341406") self.assertEqual(alignment.target.annotations["gis"], "390341406") self.assertEqual(alignment.target.annotations["acc."], "XR_143615") self.assertEqual(alignment.target.annotations["accs."], "XR_143615") self.assertEqual(alignment.target.annotations["acc.ver"], "XR_143615.1") self.assertEqual(alignment.target.annotations["length"], 4439) self.assertEqual(alignment.query.annotations["start"], 180) self.assertEqual(alignment.query.annotations["end"], 255) self.assertEqual(alignment.target.annotations["start"], 791) self.assertEqual(alignment.target.annotations["end"], 866) self.assertEqual(alignment.target.seq, "LPFELACQSKSARIVNTALDCLQKL") self.assertEqual(alignment.query.seq, "LPFVLACQSRNAKMTTLAMQCLQGL") self.assertAlmostEqual(alignment.annotations["evalue"], 0.95) self.assertAlmostEqual(alignment.annotations["bit score"], 37.7) self.assertAlmostEqual(alignment.score, 76) self.assertEqual(alignment.shape, (2, 25)) self.assertAlmostEqual(alignment.annotations["% identity"], 56.00) self.assertEqual(alignment.annotations["identical"], 14) self.assertEqual(alignment.annotations["mismatches"], 11) self.assertEqual(alignment.annotations["positives"], 19) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 76.00) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/3") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "3") self.assertEqual(alignment.target.annotations["tax ids"], "7668") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "PREDICTED: Strongylocentrotus purpuratus brefeldin A-inhibited guanine nucleotide-exchange protein 1-like (LOC586243), misc_RNA", ) self.assertEqual( alignment.target.annotations["titles"], "PREDICTED: Strongylocentrotus purpuratus brefeldin A-inhibited guanine nucleotide-exchange protein 1-like (LOC586243), misc_RNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 21) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 21) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|332858 0 TLGVSCLQGLHILPSLEDEGVSQITNAFNMIVHVSNTLELQ 41 0 ||...|||||...||......|.|..||....|......|. 41 gi|296147 0 TLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAMEIQLK 41 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 41], [ 0, 41]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|332858441|ref|XM_003316935.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|332858441|ref|XM_003316935.1|" ) self.assertEqual(alignment.target.annotations["gi"], "332858441") self.assertEqual(alignment.target.annotations["gis"], "332858441") self.assertEqual(alignment.target.annotations["acc."], "XM_003316935") self.assertEqual(alignment.target.annotations["accs."], "XM_003316935") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_003316935.1") self.assertEqual(alignment.target.annotations["length"], 8054) self.assertEqual(alignment.query.annotations["start"], 225) self.assertEqual(alignment.query.annotations["end"], 348) self.assertEqual(alignment.target.annotations["start"], 6171) self.assertEqual(alignment.target.annotations["end"], 6048) self.assertEqual( alignment.target.seq, "TLGVSCLQGLHILPSLEDEGVSQITNAFNMIVHVSNTLELQ" ) self.assertEqual( alignment.query.seq, "TLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAMEIQLK" ) self.assertAlmostEqual(alignment.annotations["evalue"], 0.95) self.assertAlmostEqual(alignment.annotations["bit score"], 37.7) self.assertAlmostEqual(alignment.score, 76) self.assertEqual(alignment.shape, (2, 41)) self.assertAlmostEqual(alignment.annotations["% identity"], 36.59) self.assertEqual(alignment.annotations["identical"], 15) self.assertEqual(alignment.annotations["mismatches"], 26) self.assertEqual(alignment.annotations["positives"], 26) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 63.41) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/-3") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "-3") self.assertEqual(alignment.target.annotations["tax ids"], "9598") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "PREDICTED: Pan troglodytes Ral GTPase activating protein, beta subunit (non-catalytic), transcript variant 2 (RALGAPB), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "PREDICTED: Pan troglodytes Ral GTPase activating protein, beta subunit (non-catalytic), transcript variant 2 (RALGAPB), mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 35) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 35) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|332858 0 TLGVSCLQGLHILPSLEDEGVSQITNAFNMIVHVSNTLELQ 41 0 ||...|||||...||......|.|..||....|......|. 41 gi|296147 0 TLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAMEIQLK 41 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 41], [ 0, 41]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|332858439|ref|XM_003316934.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|332858439|ref|XM_003316934.1|" ) self.assertEqual(alignment.target.annotations["gi"], "332858439") self.assertEqual(alignment.target.annotations["gis"], "332858439") self.assertEqual(alignment.target.annotations["acc."], "XM_003316934") self.assertEqual(alignment.target.annotations["accs."], "XM_003316934") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_003316934.1") self.assertEqual(alignment.target.annotations["length"], 8593) self.assertEqual(alignment.query.annotations["start"], 225) self.assertEqual(alignment.query.annotations["end"], 348) self.assertEqual(alignment.target.annotations["start"], 6710) self.assertEqual(alignment.target.annotations["end"], 6587) self.assertEqual( alignment.target.seq, "TLGVSCLQGLHILPSLEDEGVSQITNAFNMIVHVSNTLELQ" ) self.assertEqual( alignment.query.seq, "TLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAMEIQLK" ) self.assertAlmostEqual(alignment.annotations["evalue"], 0.95) self.assertAlmostEqual(alignment.annotations["bit score"], 37.7) self.assertAlmostEqual(alignment.score, 76) self.assertEqual(alignment.shape, (2, 41)) self.assertAlmostEqual(alignment.annotations["% identity"], 36.59) self.assertEqual(alignment.annotations["identical"], 15) self.assertEqual(alignment.annotations["mismatches"], 26) self.assertEqual(alignment.annotations["positives"], 26) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 63.41) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/-3") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "-3") self.assertEqual(alignment.target.annotations["tax ids"], "9598") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "PREDICTED: Pan troglodytes Ral GTPase activating protein, beta subunit (non-catalytic), transcript variant 1 (RALGAPB), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "PREDICTED: Pan troglodytes Ral GTPase activating protein, beta subunit (non-catalytic), transcript variant 1 (RALGAPB), mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 35) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 35) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|332858 0 TLGVSCLQGLHILPSLEDEGVSQITNAFNMIVHVSNTLELQ 41 0 ||...|||||...||......|.|..||....|......|. 41 gi|296147 0 TLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAMEIQLK 41 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 41], [ 0, 41]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|332858437|ref|XM_514640.3|") self.assertEqual( alignment.target.annotations["ids"], "gi|332858437|ref|XM_514640.3|" ) self.assertEqual(alignment.target.annotations["gi"], "332858437") self.assertEqual(alignment.target.annotations["gis"], "332858437") self.assertEqual(alignment.target.annotations["acc."], "XM_514640") self.assertEqual(alignment.target.annotations["accs."], "XM_514640") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_514640.3") self.assertEqual(alignment.target.annotations["length"], 8829) self.assertEqual(alignment.query.annotations["start"], 225) self.assertEqual(alignment.query.annotations["end"], 348) self.assertEqual(alignment.target.annotations["start"], 6946) self.assertEqual(alignment.target.annotations["end"], 6823) self.assertEqual( alignment.target.seq, "TLGVSCLQGLHILPSLEDEGVSQITNAFNMIVHVSNTLELQ" ) self.assertEqual( alignment.query.seq, "TLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAMEIQLK" ) self.assertAlmostEqual(alignment.annotations["evalue"], 0.95) self.assertAlmostEqual(alignment.annotations["bit score"], 37.7) self.assertAlmostEqual(alignment.score, 76) self.assertEqual(alignment.shape, (2, 41)) self.assertAlmostEqual(alignment.annotations["% identity"], 36.59) self.assertEqual(alignment.annotations["identical"], 15) self.assertEqual(alignment.annotations["mismatches"], 26) self.assertEqual(alignment.annotations["positives"], 26) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 63.41) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/-3") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "-3") self.assertEqual(alignment.target.annotations["tax ids"], "9598") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "PREDICTED: Pan troglodytes Ral GTPase activating protein, beta subunit (non-catalytic), transcript variant 3 (RALGAPB), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "PREDICTED: Pan troglodytes Ral GTPase activating protein, beta subunit (non-catalytic), transcript variant 3 (RALGAPB), mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 35) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 35) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|470302 0 YFLPFQLACETQNVKITVTTLDCLQKL 27 0 ..|||.|||...|.|.|.....|||.| 27 gi|296147 0 FALPFVLACQSRNAKMTTLAMQCLQGL 27 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 27], [ 0, 27]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|470302053|ref|XM_004347467.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|470302053|ref|XM_004347467.1|" ) self.assertEqual(alignment.target.annotations["gi"], "470302053") self.assertEqual(alignment.target.annotations["gis"], "470302053") self.assertEqual(alignment.target.annotations["acc."], "XM_004347467") self.assertEqual(alignment.target.annotations["accs."], "XM_004347467") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_004347467.1") self.assertEqual(alignment.target.annotations["length"], 6093) self.assertEqual(alignment.query.annotations["start"], 174) self.assertEqual(alignment.query.annotations["end"], 255) self.assertEqual(alignment.target.annotations["start"], 231) self.assertEqual(alignment.target.annotations["end"], 312) self.assertEqual(alignment.target.seq, "YFLPFQLACETQNVKITVTTLDCLQKL") self.assertEqual(alignment.query.seq, "FALPFVLACQSRNAKMTTLAMQCLQGL") self.assertAlmostEqual(alignment.annotations["evalue"], 1.3) self.assertAlmostEqual(alignment.annotations["bit score"], 37.3) self.assertAlmostEqual(alignment.score, 75) self.assertEqual(alignment.shape, (2, 27)) self.assertAlmostEqual(alignment.annotations["% identity"], 48.15) self.assertEqual(alignment.annotations["identical"], 13) self.assertEqual(alignment.annotations["mismatches"], 14) self.assertEqual(alignment.annotations["positives"], 19) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 70.37) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "595528") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Capsaspora owczarzaki ATCC 30864 guanine nucleotide-exchange protein (CAOG_04766) mRNA, complete cds", ) self.assertEqual( alignment.target.annotations["titles"], "Capsaspora owczarzaki ATCC 30864 guanine nucleotide-exchange protein (CAOG_04766) mRNA, complete cds", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 23) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 23) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|449435 0 VKDGAEHAILKLRTMSCPSDIAENEDILRIFLLACEAKTIKLSVIGLSSLQKLISHDAVT 0 ........|..|.............|....|.|||.....|........||.|....... gi|296147 0 IRHASDKSIEILKRVHSFEELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIP gi|449435 60 PSALKEIL 68 60 .|.|.||| 68 gi|296147 60 RSRLSEIL 68 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 68], [ 0, 68]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|449435759|ref|XM_004135614.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|449435759|ref|XM_004135614.1|" ) self.assertEqual(alignment.target.annotations["gi"], "449435759") self.assertEqual(alignment.target.annotations["gis"], "449435759") self.assertEqual(alignment.target.annotations["acc."], "XM_004135614") self.assertEqual(alignment.target.annotations["accs."], "XM_004135614") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_004135614.1") self.assertEqual(alignment.target.annotations["length"], 4903) self.assertEqual(alignment.query.annotations["start"], 96) self.assertEqual(alignment.query.annotations["end"], 300) self.assertEqual(alignment.target.annotations["start"], 72) self.assertEqual(alignment.target.annotations["end"], 276) self.assertEqual( alignment.target.seq, "VKDGAEHAILKLRTMSCPSDIAENEDILRIFLLACEAKTIKLSVIGLSSLQKLISHDAVTPSALKEIL", ) self.assertEqual( alignment.query.seq, "IRHASDKSIEILKRVHSFEELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEIL", ) self.assertAlmostEqual(alignment.annotations["evalue"], 1.8) self.assertAlmostEqual(alignment.annotations["bit score"], 36.8) self.assertAlmostEqual(alignment.score, 74) self.assertEqual(alignment.shape, (2, 68)) self.assertAlmostEqual(alignment.annotations["% identity"], 23.53) self.assertEqual(alignment.annotations["identical"], 16) self.assertEqual(alignment.annotations["mismatches"], 52) self.assertEqual(alignment.annotations["positives"], 37) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 54.41) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "3659") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "PREDICTED: Cucumis sativus protein MON2 homolog (LOC101218514), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "PREDICTED: Cucumis sativus protein MON2 homolog (LOC101218514), mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 58) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 58) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|426391 0 TLGVSCLQGLHILPSLEDEGVSQITNAFNMIVHVSNILELQ 41 0 ||...|||||...||......|.|..||....|......|. 41 gi|296147 0 TLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAMEIQLK 41 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 41], [ 0, 41]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|426391663|ref|XM_004062140.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|426391663|ref|XM_004062140.1|" ) self.assertEqual(alignment.target.annotations["gi"], "426391663") self.assertEqual(alignment.target.annotations["gis"], "426391663") self.assertEqual(alignment.target.annotations["acc."], "XM_004062140") self.assertEqual(alignment.target.annotations["accs."], "XM_004062140") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_004062140.1") self.assertEqual(alignment.target.annotations["length"], 8057) self.assertEqual(alignment.query.annotations["start"], 225) self.assertEqual(alignment.query.annotations["end"], 348) self.assertEqual(alignment.target.annotations["start"], 6172) self.assertEqual(alignment.target.annotations["end"], 6049) self.assertEqual( alignment.target.seq, "TLGVSCLQGLHILPSLEDEGVSQITNAFNMIVHVSNILELQ" ) self.assertEqual( alignment.query.seq, "TLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAMEIQLK" ) self.assertAlmostEqual(alignment.annotations["evalue"], 1.8) self.assertAlmostEqual(alignment.annotations["bit score"], 36.8) self.assertAlmostEqual(alignment.score, 74) self.assertEqual(alignment.shape, (2, 41)) self.assertAlmostEqual(alignment.annotations["% identity"], 36.59) self.assertEqual(alignment.annotations["identical"], 15) self.assertEqual(alignment.annotations["mismatches"], 26) self.assertEqual(alignment.annotations["positives"], 26) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 63.41) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/-2") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "-2") self.assertEqual(alignment.target.annotations["tax ids"], "9595") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "PREDICTED: Gorilla gorilla gorilla Ral GTPase activating protein, beta subunit (non-catalytic), transcript variant 2 (RALGAPB), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "PREDICTED: Gorilla gorilla gorilla Ral GTPase activating protein, beta subunit (non-catalytic), transcript variant 2 (RALGAPB), mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 35) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 35) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|426391 0 TLGVSCLQGLHILPSLEDEGVSQITNAFNMIVHVSNILELQ 41 0 ||...|||||...||......|.|..||....|......|. 41 gi|296147 0 TLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAMEIQLK 41 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 41], [ 0, 41]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|426391661|ref|XM_004062139.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|426391661|ref|XM_004062139.1|" ) self.assertEqual(alignment.target.annotations["gi"], "426391661") self.assertEqual(alignment.target.annotations["gis"], "426391661") self.assertEqual(alignment.target.annotations["acc."], "XM_004062139") self.assertEqual(alignment.target.annotations["accs."], "XM_004062139") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_004062139.1") self.assertEqual(alignment.target.annotations["length"], 8832) self.assertEqual(alignment.query.annotations["start"], 225) self.assertEqual(alignment.query.annotations["end"], 348) self.assertEqual(alignment.target.annotations["start"], 6947) self.assertEqual(alignment.target.annotations["end"], 6824) self.assertEqual( alignment.target.seq, "TLGVSCLQGLHILPSLEDEGVSQITNAFNMIVHVSNILELQ" ) self.assertEqual( alignment.query.seq, "TLAMQCLQGLSTVPSIPRSRLSEILDAFIEATHLAMEIQLK" ) self.assertAlmostEqual(alignment.annotations["evalue"], 1.8) self.assertAlmostEqual(alignment.annotations["bit score"], 36.8) self.assertAlmostEqual(alignment.score, 74) self.assertEqual(alignment.shape, (2, 41)) self.assertAlmostEqual(alignment.annotations["% identity"], 36.59) self.assertEqual(alignment.annotations["identical"], 15) self.assertEqual(alignment.annotations["mismatches"], 26) self.assertEqual(alignment.annotations["positives"], 26) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 63.41) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/-2") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "-2") self.assertEqual(alignment.target.annotations["tax ids"], "9595") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "PREDICTED: Gorilla gorilla gorilla Ral GTPase activating protein, beta subunit (non-catalytic), transcript variant 1 (RALGAPB), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "PREDICTED: Gorilla gorilla gorilla Ral GTPase activating protein, beta subunit (non-catalytic), transcript variant 1 (RALGAPB), mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 35) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 35) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|347973 0 YFLPFELACQSRTPRIVVTALDCLQKL 27 0 ..|||.||||||.......|..|||.| 27 gi|296147 0 FALPFVLACQSRNAKMTTLAMQCLQGL 27 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 27], [ 0, 27]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|347973012|ref|XM_319652.4|") self.assertEqual( alignment.target.annotations["ids"], "gi|347973012|ref|XM_319652.4|" ) self.assertEqual(alignment.target.annotations["gi"], "347973012") self.assertEqual(alignment.target.annotations["gis"], "347973012") self.assertEqual(alignment.target.annotations["acc."], "XM_319652") self.assertEqual(alignment.target.annotations["accs."], "XM_319652") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_319652.4") self.assertEqual(alignment.target.annotations["length"], 5006) self.assertEqual(alignment.query.annotations["start"], 174) self.assertEqual(alignment.query.annotations["end"], 255) self.assertEqual(alignment.target.annotations["start"], 246) self.assertEqual(alignment.target.annotations["end"], 327) self.assertEqual(alignment.target.seq, "YFLPFELACQSRTPRIVVTALDCLQKL") self.assertEqual(alignment.query.seq, "FALPFVLACQSRNAKMTTLAMQCLQGL") self.assertAlmostEqual(alignment.annotations["evalue"], 1.8) self.assertAlmostEqual(alignment.annotations["bit score"], 36.8) self.assertAlmostEqual(alignment.score, 74) self.assertEqual(alignment.shape, (2, 27)) self.assertAlmostEqual(alignment.annotations["% identity"], 51.85) self.assertEqual(alignment.annotations["identical"], 14) self.assertEqual(alignment.annotations["mismatches"], 13) self.assertEqual(alignment.annotations["positives"], 18) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 66.67) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "180454") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Anopheles gambiae str. PEST AGAP008906-PA (AgaP_AGAP008906) mRNA, partial cds", ) self.assertEqual( alignment.target.annotations["titles"], "Anopheles gambiae str. PEST AGAP008906-PA (AgaP_AGAP008906) mRNA, partial cds", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 23) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 23) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|339252 0 YFLPFELACSSKSTKIVVIALDCLQKL 27 0 ..|||.|||.|...|....|..|||.| 27 gi|296147 0 FALPFVLACQSRNAKMTTLAMQCLQGL 27 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 27], [ 0, 27]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|339252087|ref|XM_003371219.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|339252087|ref|XM_003371219.1|" ) self.assertEqual(alignment.target.annotations["gi"], "339252087") self.assertEqual(alignment.target.annotations["gis"], "339252087") self.assertEqual(alignment.target.annotations["acc."], "XM_003371219") self.assertEqual(alignment.target.annotations["accs."], "XM_003371219") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_003371219.1") self.assertEqual(alignment.target.annotations["length"], 3699) self.assertEqual(alignment.query.annotations["start"], 174) self.assertEqual(alignment.query.annotations["end"], 255) self.assertEqual(alignment.target.annotations["start"], 222) self.assertEqual(alignment.target.annotations["end"], 303) self.assertEqual(alignment.target.seq, "YFLPFELACSSKSTKIVVIALDCLQKL") self.assertEqual(alignment.query.seq, "FALPFVLACQSRNAKMTTLAMQCLQGL") self.assertAlmostEqual(alignment.annotations["evalue"], 1.8) self.assertAlmostEqual(alignment.annotations["bit score"], 36.8) self.assertAlmostEqual(alignment.score, 74) self.assertEqual(alignment.shape, (2, 27)) self.assertAlmostEqual(alignment.annotations["% identity"], 48.15) self.assertEqual(alignment.annotations["identical"], 13) self.assertEqual(alignment.annotations["mismatches"], 14) self.assertEqual(alignment.annotations["positives"], 19) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 70.37) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "6334") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Trichinella spiralis putative Sec7 domain protein (Tsp_09497) mRNA, complete cds", ) self.assertEqual( alignment.target.annotations["titles"], "Trichinella spiralis putative Sec7 domain protein (Tsp_09497) mRNA, complete cds", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 23) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 23) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|189192 0 ISAMSPVPVLARVRLSDVADAYFRINHVVSDL 32 0 ....|.||...|.|||...||.....|..... 32 gi|296147 0 LQGLSTVPSIPRSRLSEILDAFIEATHLAMEI 32 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 32], [ 0, 32]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|189192213|ref|XM_001932411.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|189192213|ref|XM_001932411.1|" ) self.assertEqual(alignment.target.annotations["gi"], "189192213") self.assertEqual(alignment.target.annotations["gis"], "189192213") self.assertEqual(alignment.target.annotations["acc."], "XM_001932411") self.assertEqual(alignment.target.annotations["accs."], "XM_001932411") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_001932411.1") self.assertEqual(alignment.target.annotations["length"], 769) self.assertEqual(alignment.query.annotations["start"], 243) self.assertEqual(alignment.query.annotations["end"], 339) self.assertEqual(alignment.target.annotations["start"], 335) self.assertEqual(alignment.target.annotations["end"], 239) self.assertEqual(alignment.target.seq, "ISAMSPVPVLARVRLSDVADAYFRINHVVSDL") self.assertEqual(alignment.query.seq, "LQGLSTVPSIPRSRLSEILDAFIEATHLAMEI") self.assertAlmostEqual(alignment.annotations["evalue"], 1.9) self.assertAlmostEqual(alignment.annotations["bit score"], 30.9) self.assertAlmostEqual(alignment.score, 61) self.assertEqual(alignment.shape, (2, 32)) self.assertAlmostEqual(alignment.annotations["% identity"], 31.25) self.assertEqual(alignment.annotations["identical"], 10) self.assertEqual(alignment.annotations["mismatches"], 22) self.assertEqual(alignment.annotations["positives"], 19) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 59.38) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/-3") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "-3") self.assertEqual(alignment.target.annotations["tax ids"], "426418") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Pyrenophora tritici-repentis Pt-1C-BFP conserved hypothetical protein, mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "Pyrenophora tritici-repentis Pt-1C-BFP conserved hypothetical protein, mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 43) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 27) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|189192 0 RSLPIIIRAHGLPQLERH 18 0 .|..|..|.|....|||| 18 gi|296147 0 KSIEILKRVHSFEELERH 18 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 18], [ 0, 18]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|189192213|ref|XM_001932411.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|189192213|ref|XM_001932411.1|" ) self.assertEqual(alignment.target.annotations["gi"], "189192213") self.assertEqual(alignment.target.annotations["gis"], "189192213") self.assertEqual(alignment.target.annotations["acc."], "XM_001932411") self.assertEqual(alignment.target.annotations["accs."], "XM_001932411") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_001932411.1") self.assertEqual(alignment.target.annotations["length"], 769) self.assertEqual(alignment.query.annotations["start"], 114) self.assertEqual(alignment.query.annotations["end"], 168) self.assertEqual(alignment.target.annotations["start"], 621) self.assertEqual(alignment.target.annotations["end"], 567) self.assertEqual(alignment.target.seq, "RSLPIIIRAHGLPQLERH") self.assertEqual(alignment.query.seq, "KSIEILKRVHSFEELERH") self.assertAlmostEqual(alignment.annotations["evalue"], 1.9) self.assertAlmostEqual(alignment.annotations["bit score"], 24.0) self.assertAlmostEqual(alignment.score, 46) self.assertEqual(alignment.shape, (2, 18)) self.assertAlmostEqual(alignment.annotations["% identity"], 44.44) self.assertEqual(alignment.annotations["identical"], 8) self.assertEqual(alignment.annotations["mismatches"], 10) self.assertEqual(alignment.annotations["positives"], 12) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 66.67) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/-2") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "-2") self.assertEqual(alignment.target.annotations["tax ids"], "426418") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Pyrenophora tritici-repentis Pt-1C-BFP conserved hypothetical protein, mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "Pyrenophora tritici-repentis Pt-1C-BFP conserved hypothetical protein, mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 43) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 15) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|426242 0 YFLPFELACQSRSPRVVSTSLDCLQKL 27 0 ..|||.||||||..........|||.| 27 gi|296147 0 FALPFVLACQSRNAKMTTLAMQCLQGL 27 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 27], [ 0, 27]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|426242124|ref|XM_004014876.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|426242124|ref|XM_004014876.1|" ) self.assertEqual(alignment.target.annotations["gi"], "426242124") self.assertEqual(alignment.target.annotations["gis"], "426242124") self.assertEqual(alignment.target.annotations["acc."], "XM_004014876") self.assertEqual(alignment.target.annotations["accs."], "XM_004014876") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_004014876.1") self.assertEqual(alignment.target.annotations["length"], 5780) self.assertEqual(alignment.query.annotations["start"], 174) self.assertEqual(alignment.query.annotations["end"], 255) self.assertEqual(alignment.target.annotations["start"], 240) self.assertEqual(alignment.target.annotations["end"], 321) self.assertEqual(alignment.target.seq, "YFLPFELACQSRSPRVVSTSLDCLQKL") self.assertEqual(alignment.query.seq, "FALPFVLACQSRNAKMTTLAMQCLQGL") self.assertAlmostEqual(alignment.annotations["evalue"], 2.5) self.assertAlmostEqual(alignment.annotations["bit score"], 36.3) self.assertAlmostEqual(alignment.score, 73) self.assertEqual(alignment.shape, (2, 27)) self.assertAlmostEqual(alignment.annotations["% identity"], 48.15) self.assertEqual(alignment.annotations["identical"], 13) self.assertEqual(alignment.annotations["mismatches"], 14) self.assertEqual(alignment.annotations["positives"], 20) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 74.07) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "9940") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "PREDICTED: Ovis aries ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited) (ARFGEF2), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "PREDICTED: Ovis aries ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited) (ARFGEF2), mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 23) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 23) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|329663 0 YFLPFELACQSRSPRVVSTSLDCLQKL 27 0 ..|||.||||||..........|||.| 27 gi|296147 0 FALPFVLACQSRNAKMTTLAMQCLQGL 27 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 27], [ 0, 27]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|329663901|ref|NM_001205652.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|329663901|ref|NM_001205652.1|" ) self.assertEqual(alignment.target.annotations["gi"], "329663901") self.assertEqual(alignment.target.annotations["gis"], "329663901") self.assertEqual(alignment.target.annotations["acc."], "NM_001205652") self.assertEqual(alignment.target.annotations["accs."], "NM_001205652") self.assertEqual(alignment.target.annotations["acc.ver"], "NM_001205652.1") self.assertEqual(alignment.target.annotations["length"], 8869) self.assertEqual(alignment.query.annotations["start"], 174) self.assertEqual(alignment.query.annotations["end"], 255) self.assertEqual(alignment.target.annotations["start"], 201) self.assertEqual(alignment.target.annotations["end"], 282) self.assertEqual(alignment.target.seq, "YFLPFELACQSRSPRVVSTSLDCLQKL") self.assertEqual(alignment.query.seq, "FALPFVLACQSRNAKMTTLAMQCLQGL") self.assertAlmostEqual(alignment.annotations["evalue"], 2.5) self.assertAlmostEqual(alignment.annotations["bit score"], 36.3) self.assertAlmostEqual(alignment.score, 73) self.assertEqual(alignment.shape, (2, 27)) self.assertAlmostEqual(alignment.annotations["% identity"], 48.15) self.assertEqual(alignment.annotations["identical"], 13) self.assertEqual(alignment.annotations["mismatches"], 14) self.assertEqual(alignment.annotations["positives"], 20) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 74.07) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "9913") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Bos taurus ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited) (ARFGEF2), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "Bos taurus ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited) (ARFGEF2), mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 23) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 23) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|167533 0 PFRLACECKSAKVTRTALDCLQKMMAYGHINSHMMAEV 38 0 ||.|||....||.|..|..|||.......|......|. 38 gi|296147 0 PFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEI 38 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 38], [ 0, 38]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|167533856|ref|XM_001748555.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|167533856|ref|XM_001748555.1|" ) self.assertEqual(alignment.target.annotations["gi"], "167533856") self.assertEqual(alignment.target.annotations["gis"], "167533856") self.assertEqual(alignment.target.annotations["acc."], "XM_001748555") self.assertEqual(alignment.target.annotations["accs."], "XM_001748555") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_001748555.1") self.assertEqual(alignment.target.annotations["length"], 5818) self.assertEqual(alignment.query.annotations["start"], 183) self.assertEqual(alignment.query.annotations["end"], 297) self.assertEqual(alignment.target.annotations["start"], 619) self.assertEqual(alignment.target.annotations["end"], 733) self.assertEqual( alignment.target.seq, "PFRLACECKSAKVTRTALDCLQKMMAYGHINSHMMAEV" ) self.assertEqual( alignment.query.seq, "PFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEI" ) self.assertAlmostEqual(alignment.annotations["evalue"], 2.5) self.assertAlmostEqual(alignment.annotations["bit score"], 36.3) self.assertAlmostEqual(alignment.score, 73) self.assertEqual(alignment.shape, (2, 38)) self.assertAlmostEqual(alignment.annotations["% identity"], 36.84) self.assertEqual(alignment.annotations["identical"], 14) self.assertEqual(alignment.annotations["mismatches"], 24) self.assertEqual(alignment.annotations["positives"], 23) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 60.53) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/2") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "2") self.assertEqual(alignment.target.annotations["tax ids"], "431895") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Monosiga brevicollis MX1 predicted protein MONBRDRAFT_33770 mRNA, complete cds", ) self.assertEqual( alignment.target.annotations["titles"], "Monosiga brevicollis MX1 predicted protein MONBRDRAFT_33770 mRNA, complete cds", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 33) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 33) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|410970 0 AGLLDFWMPGLRLWPRRWKF 20 0 ||.|.||||.|||...||.| 20 gi|296147 0 AGCLKFWMPSLRLLISRWRF 20 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 20], [ 0, 20]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|410970929|ref|XM_003991879.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|410970929|ref|XM_003991879.1|" ) self.assertEqual(alignment.target.annotations["gi"], "410970929") self.assertEqual(alignment.target.annotations["gis"], "410970929") self.assertEqual(alignment.target.annotations["acc."], "XM_003991879") self.assertEqual(alignment.target.annotations["accs."], "XM_003991879") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_003991879.1") self.assertEqual(alignment.target.annotations["length"], 3983) self.assertEqual(alignment.query.annotations["start"], 280) self.assertEqual(alignment.query.annotations["end"], 340) self.assertEqual(alignment.target.annotations["start"], 3234) self.assertEqual(alignment.target.annotations["end"], 3294) self.assertEqual(alignment.target.seq, "AGLLDFWMPGLRLWPRRWKF") self.assertEqual(alignment.query.seq, "AGCLKFWMPSLRLLISRWRF") self.assertAlmostEqual(alignment.annotations["evalue"], 3.4) self.assertAlmostEqual(alignment.annotations["bit score"], 35.9) self.assertAlmostEqual(alignment.score, 72) self.assertEqual(alignment.shape, (2, 20)) self.assertAlmostEqual(alignment.annotations["% identity"], 65.00) self.assertEqual(alignment.annotations["identical"], 13) self.assertEqual(alignment.annotations["mismatches"], 7) self.assertEqual(alignment.annotations["positives"], 14) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 70.00) self.assertEqual(alignment.annotations["query/sbjct frames"], "2/1") self.assertEqual(alignment.query.annotations["frame"], "2") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "9685") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "PREDICTED: Felis catus EPH receptor B3 (EPHB3), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "PREDICTED: Felis catus EPH receptor B3 (EPHB3), mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 17) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 17) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|410929 0 YVLPFELACQSKSPRIVSTSLDCLQKL 27 0 ..|||.|||||...........|||.| 27 gi|296147 0 FALPFVLACQSRNAKMTTLAMQCLQGL 27 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 27], [ 0, 27]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|410929672|ref|XM_003978175.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|410929672|ref|XM_003978175.1|" ) self.assertEqual(alignment.target.annotations["gi"], "410929672") self.assertEqual(alignment.target.annotations["gis"], "410929672") self.assertEqual(alignment.target.annotations["acc."], "XM_003978175") self.assertEqual(alignment.target.annotations["accs."], "XM_003978175") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_003978175.1") self.assertEqual(alignment.target.annotations["length"], 4929) self.assertEqual(alignment.query.annotations["start"], 174) self.assertEqual(alignment.query.annotations["end"], 255) self.assertEqual(alignment.target.annotations["start"], 231) self.assertEqual(alignment.target.annotations["end"], 312) self.assertEqual(alignment.target.seq, "YVLPFELACQSKSPRIVSTSLDCLQKL") self.assertEqual(alignment.query.seq, "FALPFVLACQSRNAKMTTLAMQCLQGL") self.assertAlmostEqual(alignment.annotations["evalue"], 3.4) self.assertAlmostEqual(alignment.annotations["bit score"], 35.9) self.assertAlmostEqual(alignment.score, 72) self.assertEqual(alignment.shape, (2, 27)) self.assertAlmostEqual(alignment.annotations["% identity"], 44.44) self.assertEqual(alignment.annotations["identical"], 12) self.assertEqual(alignment.annotations["mismatches"], 15) self.assertEqual(alignment.annotations["positives"], 20) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 74.07) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "31033") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "PREDICTED: Takifugu rubripes brefeldin A-inhibited guanine nucleotide-exchange protein 2-like (LOC101076459), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "PREDICTED: Takifugu rubripes brefeldin A-inhibited guanine nucleotide-exchange protein 2-like (LOC101076459), mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 23) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 23) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|402903 0 DSISSFEKTGARSQWRGTQDSSGDPCRGRSFQLP*LAT 38 0 ..|..|.....|..|.|.|......|.||.|..||||. 38 gi|296147 0 EGIQNFRQPASRNRWNG*QSL*ALHCQGRHFSIP*LAS 38 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 38], [ 0, 38]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|402903089|ref|XM_003914364.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|402903089|ref|XM_003914364.1|" ) self.assertEqual(alignment.target.annotations["gi"], "402903089") self.assertEqual(alignment.target.annotations["gis"], "402903089") self.assertEqual(alignment.target.annotations["acc."], "XM_003914364") self.assertEqual(alignment.target.annotations["accs."], "XM_003914364") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_003914364.1") self.assertEqual(alignment.target.annotations["length"], 3776) self.assertEqual(alignment.query.annotations["start"], 309) self.assertEqual(alignment.query.annotations["end"], 195) self.assertEqual(alignment.target.annotations["start"], 2581) self.assertEqual(alignment.target.annotations["end"], 2467) self.assertEqual( alignment.target.seq, "DSISSFEKTGARSQWRGTQDSSGDPCRGRSFQLP*LAT" ) self.assertEqual( alignment.query.seq, "EGIQNFRQPASRNRWNG*QSL*ALHCQGRHFSIP*LAS" ) self.assertAlmostEqual(alignment.annotations["evalue"], 3.4) self.assertAlmostEqual(alignment.annotations["bit score"], 35.9) self.assertAlmostEqual(alignment.score, 72) self.assertEqual(alignment.shape, (2, 38)) self.assertAlmostEqual(alignment.annotations["% identity"], 36.84) self.assertEqual(alignment.annotations["identical"], 14) self.assertEqual(alignment.annotations["mismatches"], 24) self.assertEqual(alignment.annotations["positives"], 23) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 60.53) self.assertEqual(alignment.annotations["query/sbjct frames"], "-3/-2") self.assertEqual(alignment.query.annotations["frame"], "-3") self.assertEqual(alignment.target.annotations["frame"], "-2") self.assertEqual(alignment.target.annotations["tax ids"], "9555") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "PREDICTED: Papio anubis CBP80/20-dependent translation initiation factor-like (LOC101009629), partial mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "PREDICTED: Papio anubis CBP80/20-dependent translation initiation factor-like (LOC101009629), partial mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 33) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 33) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|383853 0 YFLPFELACQSKSPRIVVTALDCLQKL 27 0 ..|||.|||||........|..|||.| 27 gi|296147 0 FALPFVLACQSRNAKMTTLAMQCLQGL 27 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 27], [ 0, 27]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|383853967|ref|XM_003702446.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|383853967|ref|XM_003702446.1|" ) self.assertEqual(alignment.target.annotations["gi"], "383853967") self.assertEqual(alignment.target.annotations["gis"], "383853967") self.assertEqual(alignment.target.annotations["acc."], "XM_003702446") self.assertEqual(alignment.target.annotations["accs."], "XM_003702446") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_003702446.1") self.assertEqual(alignment.target.annotations["length"], 5094) self.assertEqual(alignment.query.annotations["start"], 174) self.assertEqual(alignment.query.annotations["end"], 255) self.assertEqual(alignment.target.annotations["start"], 216) self.assertEqual(alignment.target.annotations["end"], 297) self.assertEqual(alignment.target.seq, "YFLPFELACQSKSPRIVVTALDCLQKL") self.assertEqual(alignment.query.seq, "FALPFVLACQSRNAKMTTLAMQCLQGL") self.assertAlmostEqual(alignment.annotations["evalue"], 3.4) self.assertAlmostEqual(alignment.annotations["bit score"], 35.9) self.assertAlmostEqual(alignment.score, 72) self.assertEqual(alignment.shape, (2, 27)) self.assertAlmostEqual(alignment.annotations["% identity"], 48.15) self.assertEqual(alignment.annotations["identical"], 13) self.assertEqual(alignment.annotations["mismatches"], 14) self.assertEqual(alignment.annotations["positives"], 19) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 70.37) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "143995") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "PREDICTED: Megachile rotundata ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited) (Arfgef2), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "PREDICTED: Megachile rotundata ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited) (Arfgef2), mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 23) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 23) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|380017 0 YFLPFELACQSKSPRIVVTALDCLQKL 27 0 ..|||.|||||........|..|||.| 27 gi|296147 0 FALPFVLACQSRNAKMTTLAMQCLQGL 27 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 27], [ 0, 27]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|380017270|ref|XM_003692535.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|380017270|ref|XM_003692535.1|" ) self.assertEqual(alignment.target.annotations["gi"], "380017270") self.assertEqual(alignment.target.annotations["gis"], "380017270") self.assertEqual(alignment.target.annotations["acc."], "XM_003692535") self.assertEqual(alignment.target.annotations["accs."], "XM_003692535") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_003692535.1") self.assertEqual(alignment.target.annotations["length"], 5723) self.assertEqual(alignment.query.annotations["start"], 174) self.assertEqual(alignment.query.annotations["end"], 255) self.assertEqual(alignment.target.annotations["start"], 521) self.assertEqual(alignment.target.annotations["end"], 602) self.assertEqual(alignment.target.seq, "YFLPFELACQSKSPRIVVTALDCLQKL") self.assertEqual(alignment.query.seq, "FALPFVLACQSRNAKMTTLAMQCLQGL") self.assertAlmostEqual(alignment.annotations["evalue"], 3.4) self.assertAlmostEqual(alignment.annotations["bit score"], 35.9) self.assertAlmostEqual(alignment.score, 72) self.assertEqual(alignment.shape, (2, 27)) self.assertAlmostEqual(alignment.annotations["% identity"], 48.15) self.assertEqual(alignment.annotations["identical"], 13) self.assertEqual(alignment.annotations["mismatches"], 14) self.assertEqual(alignment.annotations["positives"], 19) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 70.37) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/3") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "3") self.assertEqual(alignment.target.annotations["tax ids"], "7463") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "PREDICTED: Apis florea ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited) (Arfgef2), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "PREDICTED: Apis florea ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited) (Arfgef2), mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 23) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 23) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|350411 0 YFLPFELACQSKSPRIVVTALDCLQKL 27 0 ..|||.|||||........|..|||.| 27 gi|296147 0 FALPFVLACQSRNAKMTTLAMQCLQGL 27 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 27], [ 0, 27]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|350411438|ref|XM_003489304.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|350411438|ref|XM_003489304.1|" ) self.assertEqual(alignment.target.annotations["gi"], "350411438") self.assertEqual(alignment.target.annotations["gis"], "350411438") self.assertEqual(alignment.target.annotations["acc."], "XM_003489304") self.assertEqual(alignment.target.annotations["accs."], "XM_003489304") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_003489304.1") self.assertEqual(alignment.target.annotations["length"], 5094) self.assertEqual(alignment.query.annotations["start"], 174) self.assertEqual(alignment.query.annotations["end"], 255) self.assertEqual(alignment.target.annotations["start"], 216) self.assertEqual(alignment.target.annotations["end"], 297) self.assertEqual(alignment.target.seq, "YFLPFELACQSKSPRIVVTALDCLQKL") self.assertEqual(alignment.query.seq, "FALPFVLACQSRNAKMTTLAMQCLQGL") self.assertAlmostEqual(alignment.annotations["evalue"], 3.4) self.assertAlmostEqual(alignment.annotations["bit score"], 35.9) self.assertAlmostEqual(alignment.score, 72) self.assertEqual(alignment.shape, (2, 27)) self.assertAlmostEqual(alignment.annotations["% identity"], 48.15) self.assertEqual(alignment.annotations["identical"], 13) self.assertEqual(alignment.annotations["mismatches"], 14) self.assertEqual(alignment.annotations["positives"], 19) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 70.37) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "132113") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "PREDICTED: Bombus impatiens brefeldin A-inhibited guanine nucleotide-exchange protein 1-like (LOC100743555), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "PREDICTED: Bombus impatiens brefeldin A-inhibited guanine nucleotide-exchange protein 1-like (LOC100743555), mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 23) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 23) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|348539 0 YVLPFELACQSKSPRIVSTSLDCLQKL 27 0 ..|||.|||||...........|||.| 27 gi|296147 0 FALPFVLACQSRNAKMTTLAMQCLQGL 27 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 27], [ 0, 27]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|348539090|ref|XM_003456975.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|348539090|ref|XM_003456975.1|" ) self.assertEqual(alignment.target.annotations["gi"], "348539090") self.assertEqual(alignment.target.annotations["gis"], "348539090") self.assertEqual(alignment.target.annotations["acc."], "XM_003456975") self.assertEqual(alignment.target.annotations["accs."], "XM_003456975") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_003456975.1") self.assertEqual(alignment.target.annotations["length"], 5589) self.assertEqual(alignment.query.annotations["start"], 174) self.assertEqual(alignment.query.annotations["end"], 255) self.assertEqual(alignment.target.annotations["start"], 306) self.assertEqual(alignment.target.annotations["end"], 387) self.assertEqual(alignment.target.seq, "YVLPFELACQSKSPRIVSTSLDCLQKL") self.assertEqual(alignment.query.seq, "FALPFVLACQSRNAKMTTLAMQCLQGL") self.assertAlmostEqual(alignment.annotations["evalue"], 3.4) self.assertAlmostEqual(alignment.annotations["bit score"], 35.9) self.assertAlmostEqual(alignment.score, 72) self.assertEqual(alignment.shape, (2, 27)) self.assertAlmostEqual(alignment.annotations["% identity"], 44.44) self.assertEqual(alignment.annotations["identical"], 12) self.assertEqual(alignment.annotations["mismatches"], 15) self.assertEqual(alignment.annotations["positives"], 20) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 74.07) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "8128") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "PREDICTED: Oreochromis niloticus ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited) (ARFGEF2), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "PREDICTED: Oreochromis niloticus ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited) (ARFGEF2), mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 23) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 23) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|345796 0 AGLLDFWMPGLRLWPRRWKF 20 0 ||.|.||||.|||...||.| 20 gi|296147 0 AGCLKFWMPSLRLLISRWRF 20 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 20], [ 0, 20]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|345796385|ref|XM_003434116.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|345796385|ref|XM_003434116.1|" ) self.assertEqual(alignment.target.annotations["gi"], "345796385") self.assertEqual(alignment.target.annotations["gis"], "345796385") self.assertEqual(alignment.target.annotations["acc."], "XM_003434116") self.assertEqual(alignment.target.annotations["accs."], "XM_003434116") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_003434116.1") self.assertEqual(alignment.target.annotations["length"], 3664) self.assertEqual(alignment.query.annotations["start"], 280) self.assertEqual(alignment.query.annotations["end"], 340) self.assertEqual(alignment.target.annotations["start"], 2945) self.assertEqual(alignment.target.annotations["end"], 3005) self.assertEqual(alignment.target.seq, "AGLLDFWMPGLRLWPRRWKF") self.assertEqual(alignment.query.seq, "AGCLKFWMPSLRLLISRWRF") self.assertAlmostEqual(alignment.annotations["evalue"], 3.4) self.assertAlmostEqual(alignment.annotations["bit score"], 35.9) self.assertAlmostEqual(alignment.score, 72) self.assertEqual(alignment.shape, (2, 20)) self.assertAlmostEqual(alignment.annotations["% identity"], 65.00) self.assertEqual(alignment.annotations["identical"], 13) self.assertEqual(alignment.annotations["mismatches"], 7) self.assertEqual(alignment.annotations["positives"], 14) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 70.00) self.assertEqual(alignment.annotations["query/sbjct frames"], "2/3") self.assertEqual(alignment.query.annotations["frame"], "2") self.assertEqual(alignment.target.annotations["frame"], "3") self.assertEqual(alignment.target.annotations["tax ids"], "9615") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "PREDICTED: Canis lupus familiaris EPH receptor B3, transcript variant 1 (EPHB3), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "PREDICTED: Canis lupus familiaris EPH receptor B3, transcript variant 1 (EPHB3), mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 17) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 17) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|345796 0 AGLLDFWMPGLRLWPRRWKF 20 0 ||.|.||||.|||...||.| 20 gi|296147 0 AGCLKFWMPSLRLLISRWRF 20 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 20], [ 0, 20]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|345796383|ref|XM_545232.3|") self.assertEqual( alignment.target.annotations["ids"], "gi|345796383|ref|XM_545232.3|" ) self.assertEqual(alignment.target.annotations["gi"], "345796383") self.assertEqual(alignment.target.annotations["gis"], "345796383") self.assertEqual(alignment.target.annotations["acc."], "XM_545232") self.assertEqual(alignment.target.annotations["accs."], "XM_545232") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_545232.3") self.assertEqual(alignment.target.annotations["length"], 3660) self.assertEqual(alignment.query.annotations["start"], 280) self.assertEqual(alignment.query.annotations["end"], 340) self.assertEqual(alignment.target.annotations["start"], 2941) self.assertEqual(alignment.target.annotations["end"], 3001) self.assertEqual(alignment.target.seq, "AGLLDFWMPGLRLWPRRWKF") self.assertEqual(alignment.query.seq, "AGCLKFWMPSLRLLISRWRF") self.assertAlmostEqual(alignment.annotations["evalue"], 3.4) self.assertAlmostEqual(alignment.annotations["bit score"], 35.9) self.assertAlmostEqual(alignment.score, 72) self.assertEqual(alignment.shape, (2, 20)) self.assertAlmostEqual(alignment.annotations["% identity"], 65.00) self.assertEqual(alignment.annotations["identical"], 13) self.assertEqual(alignment.annotations["mismatches"], 7) self.assertEqual(alignment.annotations["positives"], 14) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 70.00) self.assertEqual(alignment.annotations["query/sbjct frames"], "2/2") self.assertEqual(alignment.query.annotations["frame"], "2") self.assertEqual(alignment.target.annotations["frame"], "2") self.assertEqual(alignment.target.annotations["tax ids"], "9615") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "PREDICTED: Canis lupus familiaris EPH receptor B3, transcript variant 2 (EPHB3), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "PREDICTED: Canis lupus familiaris EPH receptor B3, transcript variant 2 (EPHB3), mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 17) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 17) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|340729 0 YFLPFELACQSKSPRIVVTALDCLQKL 27 0 ..|||.|||||........|..|||.| 27 gi|296147 0 FALPFVLACQSRNAKMTTLAMQCLQGL 27 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 27], [ 0, 27]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|340729748|ref|XM_003403110.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|340729748|ref|XM_003403110.1|" ) self.assertEqual(alignment.target.annotations["gi"], "340729748") self.assertEqual(alignment.target.annotations["gis"], "340729748") self.assertEqual(alignment.target.annotations["acc."], "XM_003403110") self.assertEqual(alignment.target.annotations["accs."], "XM_003403110") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_003403110.1") self.assertEqual(alignment.target.annotations["length"], 7331) self.assertEqual(alignment.query.annotations["start"], 174) self.assertEqual(alignment.query.annotations["end"], 255) self.assertEqual(alignment.target.annotations["start"], 621) self.assertEqual(alignment.target.annotations["end"], 702) self.assertEqual(alignment.target.seq, "YFLPFELACQSKSPRIVVTALDCLQKL") self.assertEqual(alignment.query.seq, "FALPFVLACQSRNAKMTTLAMQCLQGL") self.assertAlmostEqual(alignment.annotations["evalue"], 3.4) self.assertAlmostEqual(alignment.annotations["bit score"], 35.9) self.assertAlmostEqual(alignment.score, 72) self.assertEqual(alignment.shape, (2, 27)) self.assertAlmostEqual(alignment.annotations["% identity"], 48.15) self.assertEqual(alignment.annotations["identical"], 13) self.assertEqual(alignment.annotations["mismatches"], 14) self.assertEqual(alignment.annotations["positives"], 19) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 70.37) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "30195") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "PREDICTED: Bombus terrestris brefeldin A-inhibited guanine nucleotide-exchange protein 2-like (LOC100648040), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "PREDICTED: Bombus terrestris brefeldin A-inhibited guanine nucleotide-exchange protein 2-like (LOC100648040), mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 23) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 23) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|338716 0 AGLLDFWMPGLRLWPRRWKF 20 0 ||.|.||||.|||...||.| 20 gi|296147 0 AGCLKFWMPSLRLLISRWRF 20 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 20], [ 0, 20]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|338716130|ref|XM_001497451.3|") self.assertEqual( alignment.target.annotations["ids"], "gi|338716130|ref|XM_001497451.3|" ) self.assertEqual(alignment.target.annotations["gi"], "338716130") self.assertEqual(alignment.target.annotations["gis"], "338716130") self.assertEqual(alignment.target.annotations["acc."], "XM_001497451") self.assertEqual(alignment.target.annotations["accs."], "XM_001497451") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_001497451.3") self.assertEqual(alignment.target.annotations["length"], 3659) self.assertEqual(alignment.query.annotations["start"], 280) self.assertEqual(alignment.query.annotations["end"], 340) self.assertEqual(alignment.target.annotations["start"], 2940) self.assertEqual(alignment.target.annotations["end"], 3000) self.assertEqual(alignment.target.seq, "AGLLDFWMPGLRLWPRRWKF") self.assertEqual(alignment.query.seq, "AGCLKFWMPSLRLLISRWRF") self.assertAlmostEqual(alignment.annotations["evalue"], 3.4) self.assertAlmostEqual(alignment.annotations["bit score"], 35.9) self.assertAlmostEqual(alignment.score, 72) self.assertEqual(alignment.shape, (2, 20)) self.assertAlmostEqual(alignment.annotations["% identity"], 65.00) self.assertEqual(alignment.annotations["identical"], 13) self.assertEqual(alignment.annotations["mismatches"], 7) self.assertEqual(alignment.annotations["positives"], 14) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 70.00) self.assertEqual(alignment.annotations["query/sbjct frames"], "2/1") self.assertEqual(alignment.query.annotations["frame"], "2") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "9796") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "PREDICTED: Equus caballus EPH receptor B3 (EPHB3), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "PREDICTED: Equus caballus EPH receptor B3 (EPHB3), mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 17) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 17) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|328778 0 YFLPFELACQSKSPRIVVTALDCLQKL 27 0 ..|||.|||||........|..|||.| 27 gi|296147 0 FALPFVLACQSRNAKMTTLAMQCLQGL 27 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 27], [ 0, 27]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|328778548|ref|XM_003249467.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|328778548|ref|XM_003249467.1|" ) self.assertEqual(alignment.target.annotations["gi"], "328778548") self.assertEqual(alignment.target.annotations["gis"], "328778548") self.assertEqual(alignment.target.annotations["acc."], "XM_003249467") self.assertEqual(alignment.target.annotations["accs."], "XM_003249467") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_003249467.1") self.assertEqual(alignment.target.annotations["length"], 5773) self.assertEqual(alignment.query.annotations["start"], 174) self.assertEqual(alignment.query.annotations["end"], 255) self.assertEqual(alignment.target.annotations["start"], 519) self.assertEqual(alignment.target.annotations["end"], 600) self.assertEqual(alignment.target.seq, "YFLPFELACQSKSPRIVVTALDCLQKL") self.assertEqual(alignment.query.seq, "FALPFVLACQSRNAKMTTLAMQCLQGL") self.assertAlmostEqual(alignment.annotations["evalue"], 3.4) self.assertAlmostEqual(alignment.annotations["bit score"], 35.9) self.assertAlmostEqual(alignment.score, 72) self.assertEqual(alignment.shape, (2, 27)) self.assertAlmostEqual(alignment.annotations["% identity"], 48.15) self.assertEqual(alignment.annotations["identical"], 13) self.assertEqual(alignment.annotations["mismatches"], 14) self.assertEqual(alignment.annotations["positives"], 19) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 70.37) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "7460") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "PREDICTED: Apis mellifera sec71 protein (sec71), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "PREDICTED: Apis mellifera sec71 protein (sec71), mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 23) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 23) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|301759 0 AGLLDFWMPGLRLWPRRWKF 20 0 ||.|.||||.|||...||.| 20 gi|296147 0 AGCLKFWMPSLRLLISRWRF 20 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 20], [ 0, 20]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|301759744|ref|XM_002915676.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|301759744|ref|XM_002915676.1|" ) self.assertEqual(alignment.target.annotations["gi"], "301759744") self.assertEqual(alignment.target.annotations["gis"], "301759744") self.assertEqual(alignment.target.annotations["acc."], "XM_002915676") self.assertEqual(alignment.target.annotations["accs."], "XM_002915676") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_002915676.1") self.assertEqual(alignment.target.annotations["length"], 3673) self.assertEqual(alignment.query.annotations["start"], 280) self.assertEqual(alignment.query.annotations["end"], 340) self.assertEqual(alignment.target.annotations["start"], 2954) self.assertEqual(alignment.target.annotations["end"], 3014) self.assertEqual(alignment.target.seq, "AGLLDFWMPGLRLWPRRWKF") self.assertEqual(alignment.query.seq, "AGCLKFWMPSLRLLISRWRF") self.assertAlmostEqual(alignment.annotations["evalue"], 3.4) self.assertAlmostEqual(alignment.annotations["bit score"], 35.9) self.assertAlmostEqual(alignment.score, 72) self.assertEqual(alignment.shape, (2, 20)) self.assertAlmostEqual(alignment.annotations["% identity"], 65.00) self.assertEqual(alignment.annotations["identical"], 13) self.assertEqual(alignment.annotations["mismatches"], 7) self.assertEqual(alignment.annotations["positives"], 14) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 70.00) self.assertEqual(alignment.annotations["query/sbjct frames"], "2/3") self.assertEqual(alignment.query.annotations["frame"], "2") self.assertEqual(alignment.target.annotations["frame"], "3") self.assertEqual(alignment.target.annotations["tax ids"], "9646") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "PREDICTED: Ailuropoda melanoleuca EPH receptor B3, transcript variant 2 (EPHB3), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "PREDICTED: Ailuropoda melanoleuca EPH receptor B3, transcript variant 2 (EPHB3), mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 17) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 17) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|301759 0 AGLLDFWMPGLRLWPRRWKF 20 0 ||.|.||||.|||...||.| 20 gi|296147 0 AGCLKFWMPSLRLLISRWRF 20 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 20], [ 0, 20]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|301759742|ref|XM_002915675.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|301759742|ref|XM_002915675.1|" ) self.assertEqual(alignment.target.annotations["gi"], "301759742") self.assertEqual(alignment.target.annotations["gis"], "301759742") self.assertEqual(alignment.target.annotations["acc."], "XM_002915675") self.assertEqual(alignment.target.annotations["accs."], "XM_002915675") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_002915675.1") self.assertEqual(alignment.target.annotations["length"], 3658) self.assertEqual(alignment.query.annotations["start"], 280) self.assertEqual(alignment.query.annotations["end"], 340) self.assertEqual(alignment.target.annotations["start"], 2939) self.assertEqual(alignment.target.annotations["end"], 2999) self.assertEqual(alignment.target.seq, "AGLLDFWMPGLRLWPRRWKF") self.assertEqual(alignment.query.seq, "AGCLKFWMPSLRLLISRWRF") self.assertAlmostEqual(alignment.annotations["evalue"], 3.4) self.assertAlmostEqual(alignment.annotations["bit score"], 35.9) self.assertAlmostEqual(alignment.score, 72) self.assertEqual(alignment.shape, (2, 20)) self.assertAlmostEqual(alignment.annotations["% identity"], 65.00) self.assertEqual(alignment.annotations["identical"], 13) self.assertEqual(alignment.annotations["mismatches"], 7) self.assertEqual(alignment.annotations["positives"], 14) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 70.00) self.assertEqual(alignment.annotations["query/sbjct frames"], "2/3") self.assertEqual(alignment.query.annotations["frame"], "2") self.assertEqual(alignment.target.annotations["frame"], "3") self.assertEqual(alignment.target.annotations["tax ids"], "9646") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "PREDICTED: Ailuropoda melanoleuca EPH receptor B3, transcript variant 1 (EPHB3), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "PREDICTED: Ailuropoda melanoleuca EPH receptor B3, transcript variant 1 (EPHB3), mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 17) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 17) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|292626 0 YVLPFELACQSKSPRIVSTSLDCLQKL 27 0 ..|||.|||||...........|||.| 27 gi|296147 0 FALPFVLACQSRNAKMTTLAMQCLQGL 27 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 27], [ 0, 27]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|292626951|ref|XM_002666467.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|292626951|ref|XM_002666467.1|" ) self.assertEqual(alignment.target.annotations["gi"], "292626951") self.assertEqual(alignment.target.annotations["gis"], "292626951") self.assertEqual(alignment.target.annotations["acc."], "XM_002666467") self.assertEqual(alignment.target.annotations["accs."], "XM_002666467") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_002666467.1") self.assertEqual(alignment.target.annotations["length"], 5942) self.assertEqual(alignment.query.annotations["start"], 174) self.assertEqual(alignment.query.annotations["end"], 255) self.assertEqual(alignment.target.annotations["start"], 405) self.assertEqual(alignment.target.annotations["end"], 486) self.assertEqual(alignment.target.seq, "YVLPFELACQSKSPRIVSTSLDCLQKL") self.assertEqual(alignment.query.seq, "FALPFVLACQSRNAKMTTLAMQCLQGL") self.assertAlmostEqual(alignment.annotations["evalue"], 3.4) self.assertAlmostEqual(alignment.annotations["bit score"], 35.9) self.assertAlmostEqual(alignment.score, 72) self.assertEqual(alignment.shape, (2, 27)) self.assertAlmostEqual(alignment.annotations["% identity"], 44.44) self.assertEqual(alignment.annotations["identical"], 12) self.assertEqual(alignment.annotations["mismatches"], 15) self.assertEqual(alignment.annotations["positives"], 20) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 74.07) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "7955") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "PREDICTED: Danio rerio ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited) (arfgef2), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "PREDICTED: Danio rerio ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited) (arfgef2), mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 23) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 23) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|237836 0 PWCRDAQRECRPFSFFVR*RCKRFFSPGL 29 0 ||...|.|.|.||..|....|..|..|.| 29 gi|296147 0 PWQCNAYRDCQPFHLFLEAGCLKFWMPSL 29 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 29], [ 0, 29]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|237836078|ref|XM_002367296.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|237836078|ref|XM_002367296.1|" ) self.assertEqual(alignment.target.annotations["gi"], "237836078") self.assertEqual(alignment.target.annotations["gis"], "237836078") self.assertEqual(alignment.target.annotations["acc."], "XM_002367296") self.assertEqual(alignment.target.annotations["accs."], "XM_002367296") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_002367296.1") self.assertEqual(alignment.target.annotations["length"], 6159) self.assertEqual(alignment.query.annotations["start"], 226) self.assertEqual(alignment.query.annotations["end"], 313) self.assertEqual(alignment.target.annotations["start"], 1016) self.assertEqual(alignment.target.annotations["end"], 1103) self.assertEqual(alignment.target.seq, "PWCRDAQRECRPFSFFVR*RCKRFFSPGL") self.assertEqual(alignment.query.seq, "PWQCNAYRDCQPFHLFLEAGCLKFWMPSL") self.assertAlmostEqual(alignment.annotations["evalue"], 3.4) self.assertAlmostEqual(alignment.annotations["bit score"], 35.9) self.assertAlmostEqual(alignment.score, 72) self.assertEqual(alignment.shape, (2, 29)) self.assertAlmostEqual(alignment.annotations["% identity"], 41.38) self.assertEqual(alignment.annotations["identical"], 12) self.assertEqual(alignment.annotations["mismatches"], 17) self.assertEqual(alignment.annotations["positives"], 18) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 62.07) self.assertEqual(alignment.annotations["query/sbjct frames"], "2/3") self.assertEqual(alignment.query.annotations["frame"], "2") self.assertEqual(alignment.target.annotations["frame"], "3") self.assertEqual(alignment.target.annotations["tax ids"], "508771") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Toxoplasma gondii ME49 hypothetical protein, mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "Toxoplasma gondii ME49 hypothetical protein, mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 25) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 25) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|396462 0 SRKDLSRRPHFISPFLIACGTRNAKV 26 0 |...|.|.|.|..||..||..||||. 26 gi|296147 0 SFEELERHPDFALPFVLACQSRNAKM 26 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 26], [ 0, 26]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|396462349|ref|XM_003835738.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|396462349|ref|XM_003835738.1|" ) self.assertEqual(alignment.target.annotations["gi"], "396462349") self.assertEqual(alignment.target.annotations["gis"], "396462349") self.assertEqual(alignment.target.annotations["acc."], "XM_003835738") self.assertEqual(alignment.target.annotations["accs."], "XM_003835738") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_003835738.1") self.assertEqual(alignment.target.annotations["length"], 6858) self.assertEqual(alignment.query.annotations["start"], 144) self.assertEqual(alignment.query.annotations["end"], 222) self.assertEqual(alignment.target.annotations["start"], 402) self.assertEqual(alignment.target.annotations["end"], 480) self.assertEqual(alignment.target.seq, "SRKDLSRRPHFISPFLIACGTRNAKV") self.assertEqual(alignment.query.seq, "SFEELERHPDFALPFVLACQSRNAKM") self.assertAlmostEqual(alignment.annotations["evalue"], 4.6) self.assertAlmostEqual(alignment.annotations["bit score"], 35.4) self.assertAlmostEqual(alignment.score, 71) self.assertEqual(alignment.shape, (2, 26)) self.assertAlmostEqual(alignment.annotations["% identity"], 50.00) self.assertEqual(alignment.annotations["identical"], 13) self.assertEqual(alignment.annotations["mismatches"], 13) self.assertEqual(alignment.annotations["positives"], 19) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 73.08) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "985895") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Leptosphaeria maculans JN3 hypothetical protein (LEMA_P051270.1) mRNA, complete cds", ) self.assertEqual( alignment.target.annotations["titles"], "Leptosphaeria maculans JN3 hypothetical protein (LEMA_P051270.1) mRNA, complete cds", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 22) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 22) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|268570 0 YFLPFELACNSKNPRVVITALDCLQKL 27 0 ..|||.|||.|.|......|..|||.| 27 gi|296147 0 FALPFVLACQSRNAKMTTLAMQCLQGL 27 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 27], [ 0, 27]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|268570183|ref|XM_002640666.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|268570183|ref|XM_002640666.1|" ) self.assertEqual(alignment.target.annotations["gi"], "268570183") self.assertEqual(alignment.target.annotations["gis"], "268570183") self.assertEqual(alignment.target.annotations["acc."], "XM_002640666") self.assertEqual(alignment.target.annotations["accs."], "XM_002640666") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_002640666.1") self.assertEqual(alignment.target.annotations["length"], 4782) self.assertEqual(alignment.query.annotations["start"], 174) self.assertEqual(alignment.query.annotations["end"], 255) self.assertEqual(alignment.target.annotations["start"], 249) self.assertEqual(alignment.target.annotations["end"], 330) self.assertEqual(alignment.target.seq, "YFLPFELACNSKNPRVVITALDCLQKL") self.assertEqual(alignment.query.seq, "FALPFVLACQSRNAKMTTLAMQCLQGL") self.assertAlmostEqual(alignment.annotations["evalue"], 4.6) self.assertAlmostEqual(alignment.annotations["bit score"], 35.4) self.assertAlmostEqual(alignment.score, 71) self.assertEqual(alignment.shape, (2, 27)) self.assertAlmostEqual(alignment.annotations["% identity"], 48.15) self.assertEqual(alignment.annotations["identical"], 13) self.assertEqual(alignment.annotations["mismatches"], 14) self.assertEqual(alignment.annotations["positives"], 18) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 66.67) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "6238") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Caenorhabditis briggsae C. briggsae CBR-AGEF-1 protein (Cbr-agef-1) mRNA, complete cds", ) self.assertEqual( alignment.target.annotations["titles"], "Caenorhabditis briggsae C. briggsae CBR-AGEF-1 protein (Cbr-agef-1) mRNA, complete cds", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 23) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 23) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|198473 0 YFLPFELACKSRSPRIVVTALDCLQKL 27 0 ..|||.|||.||.......|..|||.| 27 gi|296147 0 FALPFVLACQSRNAKMTTLAMQCLQGL 27 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 27], [ 0, 27]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|198473316|ref|XM_001356210.2|") self.assertEqual( alignment.target.annotations["ids"], "gi|198473316|ref|XM_001356210.2|" ) self.assertEqual(alignment.target.annotations["gi"], "198473316") self.assertEqual(alignment.target.annotations["gis"], "198473316") self.assertEqual(alignment.target.annotations["acc."], "XM_001356210") self.assertEqual(alignment.target.annotations["accs."], "XM_001356210") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_001356210.2") self.assertEqual(alignment.target.annotations["length"], 4935) self.assertEqual(alignment.query.annotations["start"], 174) self.assertEqual(alignment.query.annotations["end"], 255) self.assertEqual(alignment.target.annotations["start"], 243) self.assertEqual(alignment.target.annotations["end"], 324) self.assertEqual(alignment.target.seq, "YFLPFELACKSRSPRIVVTALDCLQKL") self.assertEqual(alignment.query.seq, "FALPFVLACQSRNAKMTTLAMQCLQGL") self.assertAlmostEqual(alignment.annotations["evalue"], 4.6) self.assertAlmostEqual(alignment.annotations["bit score"], 35.4) self.assertAlmostEqual(alignment.score, 71) self.assertEqual(alignment.shape, (2, 27)) self.assertAlmostEqual(alignment.annotations["% identity"], 48.15) self.assertEqual(alignment.annotations["identical"], 13) self.assertEqual(alignment.annotations["mismatches"], 14) self.assertEqual(alignment.annotations["positives"], 19) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 70.37) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "46245") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], r"Drosophila pseudoobscura pseudoobscura GA20452 (Dpse\GA20452), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], r"Drosophila pseudoobscura pseudoobscura GA20452 (Dpse\GA20452), mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 23) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 23) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|196008 0 DYFLPFELACKSRCSRIVIASLDCLQKL 28 0 |..|||.|||.||..........|||.| 28 gi|296147 0 DFALPFVLACQSRNAKMTTLAMQCLQGL 28 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 28], [ 0, 28]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|196008366|ref|XM_002114013.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|196008366|ref|XM_002114013.1|" ) self.assertEqual(alignment.target.annotations["gi"], "196008366") self.assertEqual(alignment.target.annotations["gis"], "196008366") self.assertEqual(alignment.target.annotations["acc."], "XM_002114013") self.assertEqual(alignment.target.annotations["accs."], "XM_002114013") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_002114013.1") self.assertEqual(alignment.target.annotations["length"], 5498) self.assertEqual(alignment.query.annotations["start"], 171) self.assertEqual(alignment.query.annotations["end"], 255) self.assertEqual(alignment.target.annotations["start"], 225) self.assertEqual(alignment.target.annotations["end"], 309) self.assertEqual(alignment.target.seq, "DYFLPFELACKSRCSRIVIASLDCLQKL") self.assertEqual(alignment.query.seq, "DFALPFVLACQSRNAKMTTLAMQCLQGL") self.assertAlmostEqual(alignment.annotations["evalue"], 4.6) self.assertAlmostEqual(alignment.annotations["bit score"], 35.4) self.assertAlmostEqual(alignment.score, 71) self.assertEqual(alignment.shape, (2, 28)) self.assertAlmostEqual(alignment.annotations["% identity"], 46.43) self.assertEqual(alignment.annotations["identical"], 13) self.assertEqual(alignment.annotations["mismatches"], 15) self.assertEqual(alignment.annotations["positives"], 20) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 71.43) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "10228") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Trichoplax adhaerens hypothetical protein, mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "Trichoplax adhaerens hypothetical protein, mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 24) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 24) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|195579 0 YFLPFELACKSRSPRIVVTALDCLQKL 27 0 ..|||.|||.||.......|..|||.| 27 gi|296147 0 FALPFVLACQSRNAKMTTLAMQCLQGL 27 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 27], [ 0, 27]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|195579057|ref|XM_002079343.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|195579057|ref|XM_002079343.1|" ) self.assertEqual(alignment.target.annotations["gi"], "195579057") self.assertEqual(alignment.target.annotations["gis"], "195579057") self.assertEqual(alignment.target.annotations["acc."], "XM_002079343") self.assertEqual(alignment.target.annotations["accs."], "XM_002079343") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_002079343.1") self.assertEqual(alignment.target.annotations["length"], 4869) self.assertEqual(alignment.query.annotations["start"], 174) self.assertEqual(alignment.query.annotations["end"], 255) self.assertEqual(alignment.target.annotations["start"], 219) self.assertEqual(alignment.target.annotations["end"], 300) self.assertEqual(alignment.target.seq, "YFLPFELACKSRSPRIVVTALDCLQKL") self.assertEqual(alignment.query.seq, "FALPFVLACQSRNAKMTTLAMQCLQGL") self.assertAlmostEqual(alignment.annotations["evalue"], 4.6) self.assertAlmostEqual(alignment.annotations["bit score"], 35.4) self.assertAlmostEqual(alignment.score, 71) self.assertEqual(alignment.shape, (2, 27)) self.assertAlmostEqual(alignment.annotations["% identity"], 48.15) self.assertEqual(alignment.annotations["identical"], 13) self.assertEqual(alignment.annotations["mismatches"], 14) self.assertEqual(alignment.annotations["positives"], 19) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 70.37) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "7240") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], r"Drosophila simulans GD23923 (Dsim\GD23923), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], r"Drosophila simulans GD23923 (Dsim\GD23923), mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 23) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 23) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|195472 0 YFLPFELACKSRSPRIVVTALDCLQKL 27 0 ..|||.|||.||.......|..|||.| 27 gi|296147 0 FALPFVLACQSRNAKMTTLAMQCLQGL 27 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 27], [ 0, 27]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|195472698|ref|XM_002088601.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|195472698|ref|XM_002088601.1|" ) self.assertEqual(alignment.target.annotations["gi"], "195472698") self.assertEqual(alignment.target.annotations["gis"], "195472698") self.assertEqual(alignment.target.annotations["acc."], "XM_002088601") self.assertEqual(alignment.target.annotations["accs."], "XM_002088601") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_002088601.1") self.assertEqual(alignment.target.annotations["length"], 4962) self.assertEqual(alignment.query.annotations["start"], 174) self.assertEqual(alignment.query.annotations["end"], 255) self.assertEqual(alignment.target.annotations["start"], 243) self.assertEqual(alignment.target.annotations["end"], 324) self.assertEqual(alignment.target.seq, "YFLPFELACKSRSPRIVVTALDCLQKL") self.assertEqual(alignment.query.seq, "FALPFVLACQSRNAKMTTLAMQCLQGL") self.assertAlmostEqual(alignment.annotations["evalue"], 4.6) self.assertAlmostEqual(alignment.annotations["bit score"], 35.4) self.assertAlmostEqual(alignment.score, 71) self.assertEqual(alignment.shape, (2, 27)) self.assertAlmostEqual(alignment.annotations["% identity"], 48.15) self.assertEqual(alignment.annotations["identical"], 13) self.assertEqual(alignment.annotations["mismatches"], 14) self.assertEqual(alignment.annotations["positives"], 19) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 70.37) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "7245") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], r"Drosophila yakuba GE18681 (Dyak\GE18681), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], r"Drosophila yakuba GE18681 (Dyak\GE18681), mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 23) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 23) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|195438 0 YFLPFELACKSRSPRIVVTALDCLQKL 27 0 ..|||.|||.||.......|..|||.| 27 gi|296147 0 FALPFVLACQSRNAKMTTLAMQCLQGL 27 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 27], [ 0, 27]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|195438259|ref|XM_002067019.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|195438259|ref|XM_002067019.1|" ) self.assertEqual(alignment.target.annotations["gi"], "195438259") self.assertEqual(alignment.target.annotations["gis"], "195438259") self.assertEqual(alignment.target.annotations["acc."], "XM_002067019") self.assertEqual(alignment.target.annotations["accs."], "XM_002067019") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_002067019.1") self.assertEqual(alignment.target.annotations["length"], 5019) self.assertEqual(alignment.query.annotations["start"], 174) self.assertEqual(alignment.query.annotations["end"], 255) self.assertEqual(alignment.target.annotations["start"], 243) self.assertEqual(alignment.target.annotations["end"], 324) self.assertEqual(alignment.target.seq, "YFLPFELACKSRSPRIVVTALDCLQKL") self.assertEqual(alignment.query.seq, "FALPFVLACQSRNAKMTTLAMQCLQGL") self.assertAlmostEqual(alignment.annotations["evalue"], 4.6) self.assertAlmostEqual(alignment.annotations["bit score"], 35.4) self.assertAlmostEqual(alignment.score, 71) self.assertEqual(alignment.shape, (2, 27)) self.assertAlmostEqual(alignment.annotations["% identity"], 48.15) self.assertEqual(alignment.annotations["identical"], 13) self.assertEqual(alignment.annotations["mismatches"], 14) self.assertEqual(alignment.annotations["positives"], 19) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 70.37) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "7260") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], r"Drosophila willistoni GK24228 (Dwil\GK24228), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], r"Drosophila willistoni GK24228 (Dwil\GK24228), mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 23) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 23) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|195397 0 YFLPFELACKSRSPRIVVTALDCLQKL 27 0 ..|||.|||.||.......|..|||.| 27 gi|296147 0 FALPFVLACQSRNAKMTTLAMQCLQGL 27 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 27], [ 0, 27]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|195397689|ref|XM_002057425.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|195397689|ref|XM_002057425.1|" ) self.assertEqual(alignment.target.annotations["gi"], "195397689") self.assertEqual(alignment.target.annotations["gis"], "195397689") self.assertEqual(alignment.target.annotations["acc."], "XM_002057425") self.assertEqual(alignment.target.annotations["accs."], "XM_002057425") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_002057425.1") self.assertEqual(alignment.target.annotations["length"], 5145) self.assertEqual(alignment.query.annotations["start"], 174) self.assertEqual(alignment.query.annotations["end"], 255) self.assertEqual(alignment.target.annotations["start"], 243) self.assertEqual(alignment.target.annotations["end"], 324) self.assertEqual(alignment.target.seq, "YFLPFELACKSRSPRIVVTALDCLQKL") self.assertEqual(alignment.query.seq, "FALPFVLACQSRNAKMTTLAMQCLQGL") self.assertAlmostEqual(alignment.annotations["evalue"], 4.6) self.assertAlmostEqual(alignment.annotations["bit score"], 35.4) self.assertAlmostEqual(alignment.score, 71) self.assertEqual(alignment.shape, (2, 27)) self.assertAlmostEqual(alignment.annotations["% identity"], 48.15) self.assertEqual(alignment.annotations["identical"], 13) self.assertEqual(alignment.annotations["mismatches"], 14) self.assertEqual(alignment.annotations["positives"], 19) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 70.37) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "7244") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], r"Drosophila virilis GJ18143 (Dvir\GJ18143), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], r"Drosophila virilis GJ18143 (Dvir\GJ18143), mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 23) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 23) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|195338 0 YFLPFELACKSRSPRIVVTALDCLQKL 27 0 ..|||.|||.||.......|..|||.| 27 gi|296147 0 FALPFVLACQSRNAKMTTLAMQCLQGL 27 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 27], [ 0, 27]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|195338276|ref|XM_002035715.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|195338276|ref|XM_002035715.1|" ) self.assertEqual(alignment.target.annotations["gi"], "195338276") self.assertEqual(alignment.target.annotations["gis"], "195338276") self.assertEqual(alignment.target.annotations["acc."], "XM_002035715") self.assertEqual(alignment.target.annotations["accs."], "XM_002035715") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_002035715.1") self.assertEqual(alignment.target.annotations["length"], 4962) self.assertEqual(alignment.query.annotations["start"], 174) self.assertEqual(alignment.query.annotations["end"], 255) self.assertEqual(alignment.target.annotations["start"], 243) self.assertEqual(alignment.target.annotations["end"], 324) self.assertEqual(alignment.target.seq, "YFLPFELACKSRSPRIVVTALDCLQKL") self.assertEqual(alignment.query.seq, "FALPFVLACQSRNAKMTTLAMQCLQGL") self.assertAlmostEqual(alignment.annotations["evalue"], 4.6) self.assertAlmostEqual(alignment.annotations["bit score"], 35.4) self.assertAlmostEqual(alignment.score, 71) self.assertEqual(alignment.shape, (2, 27)) self.assertAlmostEqual(alignment.annotations["% identity"], 48.15) self.assertEqual(alignment.annotations["identical"], 13) self.assertEqual(alignment.annotations["mismatches"], 14) self.assertEqual(alignment.annotations["positives"], 19) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 70.37) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "7238") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], r"Drosophila sechellia GM15214 (Dsec\GM15214), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], r"Drosophila sechellia GM15214 (Dsec\GM15214), mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 23) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 23) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|195164 0 YFLPFELACKSRSPRIVVTALDCLQKL 27 0 ..|||.|||.||.......|..|||.| 27 gi|296147 0 FALPFVLACQSRNAKMTTLAMQCLQGL 27 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 27], [ 0, 27]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|195164721|ref|XM_002023159.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|195164721|ref|XM_002023159.1|" ) self.assertEqual(alignment.target.annotations["gi"], "195164721") self.assertEqual(alignment.target.annotations["gis"], "195164721") self.assertEqual(alignment.target.annotations["acc."], "XM_002023159") self.assertEqual(alignment.target.annotations["accs."], "XM_002023159") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_002023159.1") self.assertEqual(alignment.target.annotations["length"], 4935) self.assertEqual(alignment.query.annotations["start"], 174) self.assertEqual(alignment.query.annotations["end"], 255) self.assertEqual(alignment.target.annotations["start"], 243) self.assertEqual(alignment.target.annotations["end"], 324) self.assertEqual(alignment.target.seq, "YFLPFELACKSRSPRIVVTALDCLQKL") self.assertEqual(alignment.query.seq, "FALPFVLACQSRNAKMTTLAMQCLQGL") self.assertAlmostEqual(alignment.annotations["evalue"], 4.6) self.assertAlmostEqual(alignment.annotations["bit score"], 35.4) self.assertAlmostEqual(alignment.score, 71) self.assertEqual(alignment.shape, (2, 27)) self.assertAlmostEqual(alignment.annotations["% identity"], 48.15) self.assertEqual(alignment.annotations["identical"], 13) self.assertEqual(alignment.annotations["mismatches"], 14) self.assertEqual(alignment.annotations["positives"], 19) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 70.37) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "7234") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], r"Drosophila persimilis GL21229 (Dper\GL21229), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], r"Drosophila persimilis GL21229 (Dper\GL21229), mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 23) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 23) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|195119 0 YFLPFELACKSRSPRIVVTALDCLQKL 27 0 ..|||.|||.||.......|..|||.| 27 gi|296147 0 FALPFVLACQSRNAKMTTLAMQCLQGL 27 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 27], [ 0, 27]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|195119048|ref|XM_002004008.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|195119048|ref|XM_002004008.1|" ) self.assertEqual(alignment.target.annotations["gi"], "195119048") self.assertEqual(alignment.target.annotations["gis"], "195119048") self.assertEqual(alignment.target.annotations["acc."], "XM_002004008") self.assertEqual(alignment.target.annotations["accs."], "XM_002004008") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_002004008.1") self.assertEqual(alignment.target.annotations["length"], 5133) self.assertEqual(alignment.query.annotations["start"], 174) self.assertEqual(alignment.query.annotations["end"], 255) self.assertEqual(alignment.target.annotations["start"], 243) self.assertEqual(alignment.target.annotations["end"], 324) self.assertEqual(alignment.target.seq, "YFLPFELACKSRSPRIVVTALDCLQKL") self.assertEqual(alignment.query.seq, "FALPFVLACQSRNAKMTTLAMQCLQGL") self.assertAlmostEqual(alignment.annotations["evalue"], 4.6) self.assertAlmostEqual(alignment.annotations["bit score"], 35.4) self.assertAlmostEqual(alignment.score, 71) self.assertEqual(alignment.shape, (2, 27)) self.assertAlmostEqual(alignment.annotations["% identity"], 48.15) self.assertEqual(alignment.annotations["identical"], 13) self.assertEqual(alignment.annotations["mismatches"], 14) self.assertEqual(alignment.annotations["positives"], 19) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 70.37) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "7230") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], r"Drosophila mojavensis GI18236 (Dmoj\GI18236), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], r"Drosophila mojavensis GI18236 (Dmoj\GI18236), mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 23) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 23) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|195031 0 YFLPFELACKSRSPRIVVTALDCLQKL 27 0 ..|||.|||.||.......|..|||.| 27 gi|296147 0 FALPFVLACQSRNAKMTTLAMQCLQGL 27 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 27], [ 0, 27]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|195031427|ref|XM_001988304.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|195031427|ref|XM_001988304.1|" ) self.assertEqual(alignment.target.annotations["gi"], "195031427") self.assertEqual(alignment.target.annotations["gis"], "195031427") self.assertEqual(alignment.target.annotations["acc."], "XM_001988304") self.assertEqual(alignment.target.annotations["accs."], "XM_001988304") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_001988304.1") self.assertEqual(alignment.target.annotations["length"], 5130) self.assertEqual(alignment.query.annotations["start"], 174) self.assertEqual(alignment.query.annotations["end"], 255) self.assertEqual(alignment.target.annotations["start"], 243) self.assertEqual(alignment.target.annotations["end"], 324) self.assertEqual(alignment.target.seq, "YFLPFELACKSRSPRIVVTALDCLQKL") self.assertEqual(alignment.query.seq, "FALPFVLACQSRNAKMTTLAMQCLQGL") self.assertAlmostEqual(alignment.annotations["evalue"], 4.6) self.assertAlmostEqual(alignment.annotations["bit score"], 35.4) self.assertAlmostEqual(alignment.score, 71) self.assertEqual(alignment.shape, (2, 27)) self.assertAlmostEqual(alignment.annotations["% identity"], 48.15) self.assertEqual(alignment.annotations["identical"], 13) self.assertEqual(alignment.annotations["mismatches"], 14) self.assertEqual(alignment.annotations["positives"], 19) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 70.37) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "7222") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], r"Drosophila grimshawi GH11113 (Dgri\GH11113), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], r"Drosophila grimshawi GH11113 (Dgri\GH11113), mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 23) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 23) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|194860 0 YFLPFELACKSRSPRIVVTALDCLQKL 27 0 ..|||.|||.||.......|..|||.| 27 gi|296147 0 FALPFVLACQSRNAKMTTLAMQCLQGL 27 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 27], [ 0, 27]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|194860432|ref|XM_001969546.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|194860432|ref|XM_001969546.1|" ) self.assertEqual(alignment.target.annotations["gi"], "194860432") self.assertEqual(alignment.target.annotations["gis"], "194860432") self.assertEqual(alignment.target.annotations["acc."], "XM_001969546") self.assertEqual(alignment.target.annotations["accs."], "XM_001969546") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_001969546.1") self.assertEqual(alignment.target.annotations["length"], 4962) self.assertEqual(alignment.query.annotations["start"], 174) self.assertEqual(alignment.query.annotations["end"], 255) self.assertEqual(alignment.target.annotations["start"], 243) self.assertEqual(alignment.target.annotations["end"], 324) self.assertEqual(alignment.target.seq, "YFLPFELACKSRSPRIVVTALDCLQKL") self.assertEqual(alignment.query.seq, "FALPFVLACQSRNAKMTTLAMQCLQGL") self.assertAlmostEqual(alignment.annotations["evalue"], 4.6) self.assertAlmostEqual(alignment.annotations["bit score"], 35.4) self.assertAlmostEqual(alignment.score, 71) self.assertEqual(alignment.shape, (2, 27)) self.assertAlmostEqual(alignment.annotations["% identity"], 48.15) self.assertEqual(alignment.annotations["identical"], 13) self.assertEqual(alignment.annotations["mismatches"], 14) self.assertEqual(alignment.annotations["positives"], 19) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 70.37) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "7220") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], r"Drosophila erecta GG23880 (Dere\GG23880), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], r"Drosophila erecta GG23880 (Dere\GG23880), mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 23) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 23) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|194761 0 YFLPFELACKSRSPRIVVTALDCLQKL 27 0 ..|||.|||.||.......|..|||.| 27 gi|296147 0 FALPFVLACQSRNAKMTTLAMQCLQGL 27 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 27], [ 0, 27]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|194761139|ref|XM_001962754.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|194761139|ref|XM_001962754.1|" ) self.assertEqual(alignment.target.annotations["gi"], "194761139") self.assertEqual(alignment.target.annotations["gis"], "194761139") self.assertEqual(alignment.target.annotations["acc."], "XM_001962754") self.assertEqual(alignment.target.annotations["accs."], "XM_001962754") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_001962754.1") self.assertEqual(alignment.target.annotations["length"], 4971) self.assertEqual(alignment.query.annotations["start"], 174) self.assertEqual(alignment.query.annotations["end"], 255) self.assertEqual(alignment.target.annotations["start"], 246) self.assertEqual(alignment.target.annotations["end"], 327) self.assertEqual(alignment.target.seq, "YFLPFELACKSRSPRIVVTALDCLQKL") self.assertEqual(alignment.query.seq, "FALPFVLACQSRNAKMTTLAMQCLQGL") self.assertAlmostEqual(alignment.annotations["evalue"], 4.6) self.assertAlmostEqual(alignment.annotations["bit score"], 35.4) self.assertAlmostEqual(alignment.score, 71) self.assertEqual(alignment.shape, (2, 27)) self.assertAlmostEqual(alignment.annotations["% identity"], 48.15) self.assertEqual(alignment.annotations["identical"], 13) self.assertEqual(alignment.annotations["mismatches"], 14) self.assertEqual(alignment.annotations["positives"], 19) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 70.37) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "7217") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], r"Drosophila ananassae GF14256 (Dana\GF14256), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], r"Drosophila ananassae GF14256 (Dana\GF14256), mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 23) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 23) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|170037 0 YFLPFELACQSKTPRIVVTALDCLQKL 27 0 ..|||.|||||........|..|||.| 27 gi|296147 0 FALPFVLACQSRNAKMTTLAMQCLQGL 27 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 27], [ 0, 27]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|170037186|ref|XM_001846389.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|170037186|ref|XM_001846389.1|" ) self.assertEqual(alignment.target.annotations["gi"], "170037186") self.assertEqual(alignment.target.annotations["gis"], "170037186") self.assertEqual(alignment.target.annotations["acc."], "XM_001846389") self.assertEqual(alignment.target.annotations["accs."], "XM_001846389") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_001846389.1") self.assertEqual(alignment.target.annotations["length"], 6192) self.assertEqual(alignment.query.annotations["start"], 174) self.assertEqual(alignment.query.annotations["end"], 255) self.assertEqual(alignment.target.annotations["start"], 1356) self.assertEqual(alignment.target.annotations["end"], 1437) self.assertEqual(alignment.target.seq, "YFLPFELACQSKTPRIVVTALDCLQKL") self.assertEqual(alignment.query.seq, "FALPFVLACQSRNAKMTTLAMQCLQGL") self.assertAlmostEqual(alignment.annotations["evalue"], 4.6) self.assertAlmostEqual(alignment.annotations["bit score"], 35.4) self.assertAlmostEqual(alignment.score, 71) self.assertEqual(alignment.shape, (2, 27)) self.assertAlmostEqual(alignment.annotations["% identity"], 48.15) self.assertEqual(alignment.annotations["identical"], 13) self.assertEqual(alignment.annotations["mismatches"], 14) self.assertEqual(alignment.annotations["positives"], 18) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 66.67) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "7176") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Culex quinquefasciatus brefeldin A-inhibited guanine nucleotide-exchange protein 1, mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "Culex quinquefasciatus brefeldin A-inhibited guanine nucleotide-exchange protein 1, mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 23) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 23) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|157134 0 YFLPFELACQSKTPRIVVTALDCLQKL 27 0 ..|||.|||||........|..|||.| 27 gi|296147 0 FALPFVLACQSRNAKMTTLAMQCLQGL 27 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 27], [ 0, 27]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|157134230|ref|XM_001663149.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|157134230|ref|XM_001663149.1|" ) self.assertEqual(alignment.target.annotations["gi"], "157134230") self.assertEqual(alignment.target.annotations["gis"], "157134230") self.assertEqual(alignment.target.annotations["acc."], "XM_001663149") self.assertEqual(alignment.target.annotations["accs."], "XM_001663149") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_001663149.1") self.assertEqual(alignment.target.annotations["length"], 5320) self.assertEqual(alignment.query.annotations["start"], 174) self.assertEqual(alignment.query.annotations["end"], 255) self.assertEqual(alignment.target.annotations["start"], 132) self.assertEqual(alignment.target.annotations["end"], 213) self.assertEqual(alignment.target.seq, "YFLPFELACQSKTPRIVVTALDCLQKL") self.assertEqual(alignment.query.seq, "FALPFVLACQSRNAKMTTLAMQCLQGL") self.assertAlmostEqual(alignment.annotations["evalue"], 4.6) self.assertAlmostEqual(alignment.annotations["bit score"], 35.4) self.assertAlmostEqual(alignment.score, 71) self.assertEqual(alignment.shape, (2, 27)) self.assertAlmostEqual(alignment.annotations["% identity"], 48.15) self.assertEqual(alignment.annotations["identical"], 13) self.assertEqual(alignment.annotations["mismatches"], 14) self.assertEqual(alignment.annotations["positives"], 18) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 66.67) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "7159") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Aedes aegypti brefeldin a-inhibited guanine nucleotide-exchange protein partial mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "Aedes aegypti brefeldin a-inhibited guanine nucleotide-exchange protein partial mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 23) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 23) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|156386 0 YLLPFELACQSKCPRIVTTSLDCLQKL 27 0 ..|||.|||||......|....|||.| 27 gi|296147 0 FALPFVLACQSRNAKMTTLAMQCLQGL 27 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 27], [ 0, 27]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|156386529|ref|XM_001633915.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|156386529|ref|XM_001633915.1|" ) self.assertEqual(alignment.target.annotations["gi"], "156386529") self.assertEqual(alignment.target.annotations["gis"], "156386529") self.assertEqual(alignment.target.annotations["acc."], "XM_001633915") self.assertEqual(alignment.target.annotations["accs."], "XM_001633915") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_001633915.1") self.assertEqual(alignment.target.annotations["length"], 5502) self.assertEqual(alignment.query.annotations["start"], 174) self.assertEqual(alignment.query.annotations["end"], 255) self.assertEqual(alignment.target.annotations["start"], 213) self.assertEqual(alignment.target.annotations["end"], 294) self.assertEqual(alignment.target.seq, "YLLPFELACQSKCPRIVTTSLDCLQKL") self.assertEqual(alignment.query.seq, "FALPFVLACQSRNAKMTTLAMQCLQGL") self.assertAlmostEqual(alignment.annotations["evalue"], 4.6) self.assertAlmostEqual(alignment.annotations["bit score"], 35.4) self.assertAlmostEqual(alignment.score, 71) self.assertEqual(alignment.shape, (2, 27)) self.assertAlmostEqual(alignment.annotations["% identity"], 48.15) self.assertEqual(alignment.annotations["identical"], 13) self.assertEqual(alignment.annotations["mismatches"], 14) self.assertEqual(alignment.annotations["positives"], 19) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 70.37) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "45351") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Nematostella vectensis predicted protein (NEMVEDRAFT_v1g102625) partial mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "Nematostella vectensis predicted protein (NEMVEDRAFT_v1g102625) partial mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 23) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 23) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|245841 0 YFLPFELACKSRSPRIVVTALDCLQKL 27 0 ..|||.|||.||.......|..|||.| 27 gi|296147 0 FALPFVLACQSRNAKMTTLAMQCLQGL 27 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 27], [ 0, 27]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|24584188|ref|NM_165059.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|24584188|ref|NM_165059.1|" ) self.assertEqual(alignment.target.annotations["gi"], "24584188") self.assertEqual(alignment.target.annotations["gis"], "24584188") self.assertEqual(alignment.target.annotations["acc."], "NM_165059") self.assertEqual(alignment.target.annotations["accs."], "NM_165059") self.assertEqual(alignment.target.annotations["acc.ver"], "NM_165059.1") self.assertEqual(alignment.target.annotations["length"], 5672) self.assertEqual(alignment.query.annotations["start"], 174) self.assertEqual(alignment.query.annotations["end"], 255) self.assertEqual(alignment.target.annotations["start"], 541) self.assertEqual(alignment.target.annotations["end"], 622) self.assertEqual(alignment.target.seq, "YFLPFELACKSRSPRIVVTALDCLQKL") self.assertEqual(alignment.query.seq, "FALPFVLACQSRNAKMTTLAMQCLQGL") self.assertAlmostEqual(alignment.annotations["evalue"], 4.6) self.assertAlmostEqual(alignment.annotations["bit score"], 35.4) self.assertAlmostEqual(alignment.score, 71) self.assertEqual(alignment.shape, (2, 27)) self.assertAlmostEqual(alignment.annotations["% identity"], 48.15) self.assertEqual(alignment.annotations["identical"], 13) self.assertEqual(alignment.annotations["mismatches"], 14) self.assertEqual(alignment.annotations["positives"], 19) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 70.37) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/2") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "2") self.assertEqual(alignment.target.annotations["tax ids"], "7227") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Drosophila melanogaster sec71 (sec71), transcript variant B, mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "Drosophila melanogaster sec71 (sec71), transcript variant B, mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 23) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 23) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|245841 0 YFLPFELACKSRSPRIVVTALDCLQKL 27 0 ..|||.|||.||.......|..|||.| 27 gi|296147 0 FALPFVLACQSRNAKMTTLAMQCLQGL 27 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 27], [ 0, 27]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|24584186|ref|NM_135831.2|") self.assertEqual( alignment.target.annotations["ids"], "gi|24584186|ref|NM_135831.2|" ) self.assertEqual(alignment.target.annotations["gi"], "24584186") self.assertEqual(alignment.target.annotations["gis"], "24584186") self.assertEqual(alignment.target.annotations["acc."], "NM_135831") self.assertEqual(alignment.target.annotations["accs."], "NM_135831") self.assertEqual(alignment.target.annotations["acc.ver"], "NM_135831.2") self.assertEqual(alignment.target.annotations["length"], 5799) self.assertEqual(alignment.query.annotations["start"], 174) self.assertEqual(alignment.query.annotations["end"], 255) self.assertEqual(alignment.target.annotations["start"], 544) self.assertEqual(alignment.target.annotations["end"], 625) self.assertEqual(alignment.target.seq, "YFLPFELACKSRSPRIVVTALDCLQKL") self.assertEqual(alignment.query.seq, "FALPFVLACQSRNAKMTTLAMQCLQGL") self.assertAlmostEqual(alignment.annotations["evalue"], 4.6) self.assertAlmostEqual(alignment.annotations["bit score"], 35.4) self.assertAlmostEqual(alignment.score, 71) self.assertEqual(alignment.shape, (2, 27)) self.assertAlmostEqual(alignment.annotations["% identity"], 48.15) self.assertEqual(alignment.annotations["identical"], 13) self.assertEqual(alignment.annotations["mismatches"], 14) self.assertEqual(alignment.annotations["positives"], 19) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 70.37) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/2") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "2") self.assertEqual(alignment.target.annotations["tax ids"], "7227") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Drosophila melanogaster sec71 (sec71), transcript variant A, mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "Drosophila melanogaster sec71 (sec71), transcript variant A, mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 23) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 23) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|157110 0 FLIVGSNCWLFIVSSDWLNFFFS 23 0 ........|.......||||||| 23 gi|296147 0 YVLFSISQWIYH*HGEWLNFFFS 23 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 23], [ 0, 23]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|157110325|ref|XM_001651005.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|157110325|ref|XM_001651005.1|" ) self.assertEqual(alignment.target.annotations["gi"], "157110325") self.assertEqual(alignment.target.annotations["gis"], "157110325") self.assertEqual(alignment.target.annotations["acc."], "XM_001651005") self.assertEqual(alignment.target.annotations["accs."], "XM_001651005") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_001651005.1") self.assertEqual(alignment.target.annotations["length"], 9654) self.assertEqual(alignment.query.annotations["start"], 145) self.assertEqual(alignment.query.annotations["end"], 76) self.assertEqual(alignment.target.annotations["start"], 5691) self.assertEqual(alignment.target.annotations["end"], 5622) self.assertEqual(alignment.target.seq, "FLIVGSNCWLFIVSSDWLNFFFS") self.assertEqual(alignment.query.seq, "YVLFSISQWIYH*HGEWLNFFFS") self.assertAlmostEqual(alignment.annotations["evalue"], 5.2) self.assertAlmostEqual(alignment.annotations["bit score"], 27.6) self.assertAlmostEqual(alignment.score, 54) self.assertEqual(alignment.shape, (2, 23)) self.assertAlmostEqual(alignment.annotations["% identity"], 34.78) self.assertEqual(alignment.annotations["identical"], 8) self.assertEqual(alignment.annotations["mismatches"], 15) self.assertEqual(alignment.annotations["positives"], 15) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 65.22) self.assertEqual(alignment.annotations["query/sbjct frames"], "-2/-1") self.assertEqual(alignment.query.annotations["frame"], "-2") self.assertEqual(alignment.target.annotations["frame"], "-1") self.assertEqual(alignment.target.annotations["tax ids"], "7159") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Aedes aegypti hypothetical protein AaeL_AAEL005529 partial mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "Aedes aegypti hypothetical protein AaeL_AAEL005529 partial mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 40) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 20) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|157110 0 GNWFHFFFSWFLIVGSNWLNFFLSWFFIISRNW 33 0 |.|..||||...|.....|.....|.......| 33 gi|296147 0 GEWLNFFFSIRKIKNAILLQVAFAWSQTLQCSW 33 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 33], [ 0, 33]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|157110325|ref|XM_001651005.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|157110325|ref|XM_001651005.1|" ) self.assertEqual(alignment.target.annotations["gi"], "157110325") self.assertEqual(alignment.target.annotations["gis"], "157110325") self.assertEqual(alignment.target.annotations["acc."], "XM_001651005") self.assertEqual(alignment.target.annotations["accs."], "XM_001651005") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_001651005.1") self.assertEqual(alignment.target.annotations["length"], 9654) self.assertEqual(alignment.query.annotations["start"], 103) self.assertEqual(alignment.query.annotations["end"], 4) self.assertEqual(alignment.target.annotations["start"], 5517) self.assertEqual(alignment.target.annotations["end"], 5418) self.assertEqual(alignment.target.seq, "GNWFHFFFSWFLIVGSNWLNFFLSWFFIISRNW") self.assertEqual(alignment.query.seq, "GEWLNFFFSIRKIKNAILLQVAFAWSQTLQCSW") self.assertAlmostEqual(alignment.annotations["evalue"], 5.2) self.assertAlmostEqual(alignment.annotations["bit score"], 24.9) self.assertAlmostEqual(alignment.score, 48) self.assertEqual(alignment.shape, (2, 33)) self.assertAlmostEqual(alignment.annotations["% identity"], 30.30) self.assertEqual(alignment.annotations["identical"], 10) self.assertEqual(alignment.annotations["mismatches"], 23) self.assertEqual(alignment.annotations["positives"], 15) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 45.45) self.assertEqual(alignment.annotations["query/sbjct frames"], "-2/-1") self.assertEqual(alignment.query.annotations["frame"], "-2") self.assertEqual(alignment.target.annotations["frame"], "-1") self.assertEqual(alignment.target.annotations["tax ids"], "7159") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Aedes aegypti hypothetical protein AaeL_AAEL005529 partial mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "Aedes aegypti hypothetical protein AaeL_AAEL005529 partial mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 40) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 28) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|156388 0 CQPFLRFLEWGNMDL*LPALLVL 23 0 ||||..|||.|......|.|..| 23 gi|296147 0 CQPFHLFLEAGCLKFWMPSLRLL 23 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 23], [ 0, 23]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|156388828|ref|XM_001634645.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|156388828|ref|XM_001634645.1|" ) self.assertEqual(alignment.target.annotations["gi"], "156388828") self.assertEqual(alignment.target.annotations["gis"], "156388828") self.assertEqual(alignment.target.annotations["acc."], "XM_001634645") self.assertEqual(alignment.target.annotations["accs."], "XM_001634645") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_001634645.1") self.assertEqual(alignment.target.annotations["length"], 528) self.assertEqual(alignment.query.annotations["start"], 253) self.assertEqual(alignment.query.annotations["end"], 322) self.assertEqual(alignment.target.annotations["start"], 352) self.assertEqual(alignment.target.annotations["end"], 421) self.assertEqual(alignment.target.seq, "CQPFLRFLEWGNMDL*LPALLVL") self.assertEqual(alignment.query.seq, "CQPFHLFLEAGCLKFWMPSLRLL") self.assertAlmostEqual(alignment.annotations["evalue"], 5.4) self.assertAlmostEqual(alignment.annotations["bit score"], 26.3) self.assertAlmostEqual(alignment.score, 51) self.assertEqual(alignment.shape, (2, 23)) self.assertAlmostEqual(alignment.annotations["% identity"], 47.83) self.assertEqual(alignment.annotations["identical"], 11) self.assertEqual(alignment.annotations["mismatches"], 12) self.assertEqual(alignment.annotations["positives"], 15) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 65.22) self.assertEqual(alignment.annotations["query/sbjct frames"], "2/2") self.assertEqual(alignment.query.annotations["frame"], "2") self.assertEqual(alignment.target.annotations["frame"], "2") self.assertEqual(alignment.target.annotations["tax ids"], "45351") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Nematostella vectensis predicted protein (NEMVEDRAFT_v1g26815) partial mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "Nematostella vectensis predicted protein (NEMVEDRAFT_v1g26815) partial mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 33) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 20) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|156388 0 RNAKVMVIFLWCLSLLSAIPPV 22 0 ||||.......||..||..|.. 22 gi|296147 0 RNAKMTTLAMQCLQGLSTVPSI 22 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 22], [ 0, 22]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|156388828|ref|XM_001634645.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|156388828|ref|XM_001634645.1|" ) self.assertEqual(alignment.target.annotations["gi"], "156388828") self.assertEqual(alignment.target.annotations["gis"], "156388828") self.assertEqual(alignment.target.annotations["acc."], "XM_001634645") self.assertEqual(alignment.target.annotations["accs."], "XM_001634645") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_001634645.1") self.assertEqual(alignment.target.annotations["length"], 528) self.assertEqual(alignment.query.annotations["start"], 207) self.assertEqual(alignment.query.annotations["end"], 273) self.assertEqual(alignment.target.annotations["start"], 306) self.assertEqual(alignment.target.annotations["end"], 372) self.assertEqual(alignment.target.seq, "RNAKVMVIFLWCLSLLSAIPPV") self.assertEqual(alignment.query.seq, "RNAKMTTLAMQCLQGLSTVPSI") self.assertAlmostEqual(alignment.annotations["evalue"], 5.4) self.assertAlmostEqual(alignment.annotations["bit score"], 25.4) self.assertAlmostEqual(alignment.score, 49) self.assertEqual(alignment.shape, (2, 22)) self.assertAlmostEqual(alignment.annotations["% identity"], 40.91) self.assertEqual(alignment.annotations["identical"], 9) self.assertEqual(alignment.annotations["mismatches"], 13) self.assertEqual(alignment.annotations["positives"], 14) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 63.64) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "45351") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Nematostella vectensis predicted protein (NEMVEDRAFT_v1g26815) partial mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "Nematostella vectensis predicted protein (NEMVEDRAFT_v1g26815) partial mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 33) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 19) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|156359 0 CQPFLRFLEWGNMDL*LPALLVL 23 0 ||||..|||.|......|.|..| 23 gi|296147 0 CQPFHLFLEAGCLKFWMPSLRLL 23 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 23], [ 0, 23]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|156359702|ref|XM_001624855.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|156359702|ref|XM_001624855.1|" ) self.assertEqual(alignment.target.annotations["gi"], "156359702") self.assertEqual(alignment.target.annotations["gis"], "156359702") self.assertEqual(alignment.target.annotations["acc."], "XM_001624855") self.assertEqual(alignment.target.annotations["accs."], "XM_001624855") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_001624855.1") self.assertEqual(alignment.target.annotations["length"], 528) self.assertEqual(alignment.query.annotations["start"], 253) self.assertEqual(alignment.query.annotations["end"], 322) self.assertEqual(alignment.target.annotations["start"], 352) self.assertEqual(alignment.target.annotations["end"], 421) self.assertEqual(alignment.target.seq, "CQPFLRFLEWGNMDL*LPALLVL") self.assertEqual(alignment.query.seq, "CQPFHLFLEAGCLKFWMPSLRLL") self.assertAlmostEqual(alignment.annotations["evalue"], 5.4) self.assertAlmostEqual(alignment.annotations["bit score"], 26.3) self.assertAlmostEqual(alignment.score, 51) self.assertEqual(alignment.shape, (2, 23)) self.assertAlmostEqual(alignment.annotations["% identity"], 47.83) self.assertEqual(alignment.annotations["identical"], 11) self.assertEqual(alignment.annotations["mismatches"], 12) self.assertEqual(alignment.annotations["positives"], 15) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 65.22) self.assertEqual(alignment.annotations["query/sbjct frames"], "2/2") self.assertEqual(alignment.query.annotations["frame"], "2") self.assertEqual(alignment.target.annotations["frame"], "2") self.assertEqual(alignment.target.annotations["tax ids"], "45351") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Nematostella vectensis predicted protein (NEMVEDRAFT_v1g16273) partial mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "Nematostella vectensis predicted protein (NEMVEDRAFT_v1g16273) partial mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 33) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 20) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|156359 0 RNAKVMVIFLWCLSLLSAIPPV 22 0 ||||.......||..||..|.. 22 gi|296147 0 RNAKMTTLAMQCLQGLSTVPSI 22 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 22], [ 0, 22]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|156359702|ref|XM_001624855.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|156359702|ref|XM_001624855.1|" ) self.assertEqual(alignment.target.annotations["gi"], "156359702") self.assertEqual(alignment.target.annotations["gis"], "156359702") self.assertEqual(alignment.target.annotations["acc."], "XM_001624855") self.assertEqual(alignment.target.annotations["accs."], "XM_001624855") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_001624855.1") self.assertEqual(alignment.target.annotations["length"], 528) self.assertEqual(alignment.query.annotations["start"], 207) self.assertEqual(alignment.query.annotations["end"], 273) self.assertEqual(alignment.target.annotations["start"], 306) self.assertEqual(alignment.target.annotations["end"], 372) self.assertEqual(alignment.target.seq, "RNAKVMVIFLWCLSLLSAIPPV") self.assertEqual(alignment.query.seq, "RNAKMTTLAMQCLQGLSTVPSI") self.assertAlmostEqual(alignment.annotations["evalue"], 5.4) self.assertAlmostEqual(alignment.annotations["bit score"], 25.4) self.assertAlmostEqual(alignment.score, 49) self.assertEqual(alignment.shape, (2, 22)) self.assertAlmostEqual(alignment.annotations["% identity"], 40.91) self.assertEqual(alignment.annotations["identical"], 9) self.assertEqual(alignment.annotations["mismatches"], 13) self.assertEqual(alignment.annotations["positives"], 14) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 63.64) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "45351") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Nematostella vectensis predicted protein (NEMVEDRAFT_v1g16273) partial mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "Nematostella vectensis predicted protein (NEMVEDRAFT_v1g16273) partial mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 33) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 19) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|471359 0 YFLPFELACQSKSPRVVSTSLDCLQKL 27 0 ..|||.|||||...........|||.| 27 gi|296147 0 FALPFVLACQSRNAKMTTLAMQCLQGL 27 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 27], [ 0, 27]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|471359494|ref|XM_004370266.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|471359494|ref|XM_004370266.1|" ) self.assertEqual(alignment.target.annotations["gi"], "471359494") self.assertEqual(alignment.target.annotations["gis"], "471359494") self.assertEqual(alignment.target.annotations["acc."], "XM_004370266") self.assertEqual(alignment.target.annotations["accs."], "XM_004370266") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_004370266.1") self.assertEqual(alignment.target.annotations["length"], 9039) self.assertEqual(alignment.query.annotations["start"], 174) self.assertEqual(alignment.query.annotations["end"], 255) self.assertEqual(alignment.target.annotations["start"], 352) self.assertEqual(alignment.target.annotations["end"], 433) self.assertEqual(alignment.target.seq, "YFLPFELACQSKSPRVVSTSLDCLQKL") self.assertEqual(alignment.query.seq, "FALPFVLACQSRNAKMTTLAMQCLQGL") self.assertAlmostEqual(alignment.annotations["evalue"], 6.4) self.assertAlmostEqual(alignment.annotations["bit score"], 35.0) self.assertAlmostEqual(alignment.score, 70) self.assertEqual(alignment.shape, (2, 27)) self.assertAlmostEqual(alignment.annotations["% identity"], 44.44) self.assertEqual(alignment.annotations["identical"], 12) self.assertEqual(alignment.annotations["mismatches"], 15) self.assertEqual(alignment.annotations["positives"], 20) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 74.07) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/2") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "2") self.assertEqual(alignment.target.annotations["tax ids"], "127582") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "PREDICTED: Trichechus manatus latirostris ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited) (ARFGEF2), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "PREDICTED: Trichechus manatus latirostris ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited) (ARFGEF2), mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 23) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 23) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|470652 0 YFLPFELACQSKSPRVVSTSLDCLQKL 27 0 ..|||.|||||...........|||.| 27 gi|296147 0 FALPFVLACQSRNAKMTTLAMQCLQGL 27 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 27], [ 0, 27]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|470652205|ref|XM_004329148.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|470652205|ref|XM_004329148.1|" ) self.assertEqual(alignment.target.annotations["gi"], "470652205") self.assertEqual(alignment.target.annotations["gis"], "470652205") self.assertEqual(alignment.target.annotations["acc."], "XM_004329148") self.assertEqual(alignment.target.annotations["accs."], "XM_004329148") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_004329148.1") self.assertEqual(alignment.target.annotations["length"], 3458) self.assertEqual(alignment.query.annotations["start"], 174) self.assertEqual(alignment.query.annotations["end"], 255) self.assertEqual(alignment.target.annotations["start"], 75) self.assertEqual(alignment.target.annotations["end"], 156) self.assertEqual(alignment.target.seq, "YFLPFELACQSKSPRVVSTSLDCLQKL") self.assertEqual(alignment.query.seq, "FALPFVLACQSRNAKMTTLAMQCLQGL") self.assertAlmostEqual(alignment.annotations["evalue"], 6.4) self.assertAlmostEqual(alignment.annotations["bit score"], 35.0) self.assertAlmostEqual(alignment.score, 70) self.assertEqual(alignment.shape, (2, 27)) self.assertAlmostEqual(alignment.annotations["% identity"], 44.44) self.assertEqual(alignment.annotations["identical"], 12) self.assertEqual(alignment.annotations["mismatches"], 15) self.assertEqual(alignment.annotations["positives"], 20) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 74.07) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "9739") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "PREDICTED: Tursiops truncatus ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited) (ARFGEF2), partial mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "PREDICTED: Tursiops truncatus ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited) (ARFGEF2), partial mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 23) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 23) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|470125 0 FVQSCSSPNFKFSTSSSEHSQGSSNSKSIPRLRVSD 36 0 ||..|.|.|.|..|......||.|...||||.|.|. 36 gi|296147 0 FVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSE 36 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 36], [ 0, 36]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|470125017|ref|XM_004298456.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|470125017|ref|XM_004298456.1|" ) self.assertEqual(alignment.target.annotations["gi"], "470125017") self.assertEqual(alignment.target.annotations["gis"], "470125017") self.assertEqual(alignment.target.annotations["acc."], "XM_004298456") self.assertEqual(alignment.target.annotations["accs."], "XM_004298456") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_004298456.1") self.assertEqual(alignment.target.annotations["length"], 3617) self.assertEqual(alignment.query.annotations["start"], 186) self.assertEqual(alignment.query.annotations["end"], 294) self.assertEqual(alignment.target.annotations["start"], 1362) self.assertEqual(alignment.target.annotations["end"], 1470) self.assertEqual( alignment.target.seq, "FVQSCSSPNFKFSTSSSEHSQGSSNSKSIPRLRVSD" ) self.assertEqual( alignment.query.seq, "FVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSE" ) self.assertAlmostEqual(alignment.annotations["evalue"], 6.4) self.assertAlmostEqual(alignment.annotations["bit score"], 35.0) self.assertAlmostEqual(alignment.score, 70) self.assertEqual(alignment.shape, (2, 36)) self.assertAlmostEqual(alignment.annotations["% identity"], 44.44) self.assertEqual(alignment.annotations["identical"], 16) self.assertEqual(alignment.annotations["mismatches"], 20) self.assertEqual(alignment.annotations["positives"], 22) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 61.11) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "101020") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "PREDICTED: Fragaria vesca subsp. vesca cleavage and polyadenylation specificity factor subunit 3-II-like (LOC101304092), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "PREDICTED: Fragaria vesca subsp. vesca cleavage and polyadenylation specificity factor subunit 3-II-like (LOC101304092), mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 31) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 31) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|466073 0 YFLPFELACQSKSPRVVSTSLDCLQKL 27 0 ..|||.|||||...........|||.| 27 gi|296147 0 FALPFVLACQSRNAKMTTLAMQCLQGL 27 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 27], [ 0, 27]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|466073472|ref|XM_004282882.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|466073472|ref|XM_004282882.1|" ) self.assertEqual(alignment.target.annotations["gi"], "466073472") self.assertEqual(alignment.target.annotations["gis"], "466073472") self.assertEqual(alignment.target.annotations["acc."], "XM_004282882") self.assertEqual(alignment.target.annotations["accs."], "XM_004282882") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_004282882.1") self.assertEqual(alignment.target.annotations["length"], 9027) self.assertEqual(alignment.query.annotations["start"], 174) self.assertEqual(alignment.query.annotations["end"], 255) self.assertEqual(alignment.target.annotations["start"], 347) self.assertEqual(alignment.target.annotations["end"], 428) self.assertEqual(alignment.target.seq, "YFLPFELACQSKSPRVVSTSLDCLQKL") self.assertEqual(alignment.query.seq, "FALPFVLACQSRNAKMTTLAMQCLQGL") self.assertAlmostEqual(alignment.annotations["evalue"], 6.4) self.assertAlmostEqual(alignment.annotations["bit score"], 35.0) self.assertAlmostEqual(alignment.score, 70) self.assertEqual(alignment.shape, (2, 27)) self.assertAlmostEqual(alignment.annotations["% identity"], 44.44) self.assertEqual(alignment.annotations["identical"], 12) self.assertEqual(alignment.annotations["mismatches"], 15) self.assertEqual(alignment.annotations["positives"], 20) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 74.07) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/3") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "3") self.assertEqual(alignment.target.annotations["tax ids"], "9733") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "PREDICTED: Orcinus orca ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited) (ARFGEF2), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "PREDICTED: Orcinus orca ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited) (ARFGEF2), mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 23) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 23) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|449492 0 RLEEVSPLGSLLTGQLNRAREFIILKS*KTVRLSIEL 37 0 |.||..|...|....|....|.|.|.|||..|.|..| 37 gi|296147 0 RKEEIQPFAMLVINPLRY*KEYIVLRS*KDIRISHSL 37 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 37], [ 0, 37]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|449492807|ref|XM_004159059.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|449492807|ref|XM_004159059.1|" ) self.assertEqual(alignment.target.annotations["gi"], "449492807") self.assertEqual(alignment.target.annotations["gis"], "449492807") self.assertEqual(alignment.target.annotations["acc."], "XM_004159059") self.assertEqual(alignment.target.annotations["accs."], "XM_004159059") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_004159059.1") self.assertEqual(alignment.target.annotations["length"], 1991) self.assertEqual(alignment.query.annotations["start"], 76) self.assertEqual(alignment.query.annotations["end"], 187) self.assertEqual(alignment.target.annotations["start"], 533) self.assertEqual(alignment.target.annotations["end"], 644) self.assertEqual( alignment.target.seq, "RLEEVSPLGSLLTGQLNRAREFIILKS*KTVRLSIEL" ) self.assertEqual( alignment.query.seq, "RKEEIQPFAMLVINPLRY*KEYIVLRS*KDIRISHSL" ) self.assertAlmostEqual(alignment.annotations["evalue"], 6.4) self.assertAlmostEqual(alignment.annotations["bit score"], 35.0) self.assertAlmostEqual(alignment.score, 70) self.assertEqual(alignment.shape, (2, 37)) self.assertAlmostEqual(alignment.annotations["% identity"], 40.54) self.assertEqual(alignment.annotations["identical"], 15) self.assertEqual(alignment.annotations["mismatches"], 22) self.assertEqual(alignment.annotations["positives"], 23) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 62.16) self.assertEqual(alignment.annotations["query/sbjct frames"], "2/3") self.assertEqual(alignment.query.annotations["frame"], "2") self.assertEqual(alignment.target.annotations["frame"], "3") self.assertEqual(alignment.target.annotations["tax ids"], "3659") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "PREDICTED: Cucumis sativus uncharacterized LOC101210909, transcript variant 2 (LOC101210909), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "PREDICTED: Cucumis sativus uncharacterized LOC101210909, transcript variant 2 (LOC101210909), mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 32) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 32) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|449492 0 RLEEVSPLGSLLTGQLNRAREFIILKS*KTVRLSIEL 37 0 |.||..|...|....|....|.|.|.|||..|.|..| 37 gi|296147 0 RKEEIQPFAMLVINPLRY*KEYIVLRS*KDIRISHSL 37 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 37], [ 0, 37]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|449492804|ref|XM_004159058.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|449492804|ref|XM_004159058.1|" ) self.assertEqual(alignment.target.annotations["gi"], "449492804") self.assertEqual(alignment.target.annotations["gis"], "449492804") self.assertEqual(alignment.target.annotations["acc."], "XM_004159058") self.assertEqual(alignment.target.annotations["accs."], "XM_004159058") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_004159058.1") self.assertEqual(alignment.target.annotations["length"], 2110) self.assertEqual(alignment.query.annotations["start"], 76) self.assertEqual(alignment.query.annotations["end"], 187) self.assertEqual(alignment.target.annotations["start"], 652) self.assertEqual(alignment.target.annotations["end"], 763) self.assertEqual( alignment.target.seq, "RLEEVSPLGSLLTGQLNRAREFIILKS*KTVRLSIEL" ) self.assertEqual( alignment.query.seq, "RKEEIQPFAMLVINPLRY*KEYIVLRS*KDIRISHSL" ) self.assertAlmostEqual(alignment.annotations["evalue"], 6.4) self.assertAlmostEqual(alignment.annotations["bit score"], 35.0) self.assertAlmostEqual(alignment.score, 70) self.assertEqual(alignment.shape, (2, 37)) self.assertAlmostEqual(alignment.annotations["% identity"], 40.54) self.assertEqual(alignment.annotations["identical"], 15) self.assertEqual(alignment.annotations["mismatches"], 22) self.assertEqual(alignment.annotations["positives"], 23) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 62.16) self.assertEqual(alignment.annotations["query/sbjct frames"], "2/2") self.assertEqual(alignment.query.annotations["frame"], "2") self.assertEqual(alignment.target.annotations["frame"], "2") self.assertEqual(alignment.target.annotations["tax ids"], "3659") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "PREDICTED: Cucumis sativus uncharacterized LOC101210909, transcript variant 1 (LOC101210909), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "PREDICTED: Cucumis sativus uncharacterized LOC101210909, transcript variant 1 (LOC101210909), mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 32) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 32) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|449443 0 RLEEVSPLGSLLTGQLNRAREFIILKS*KTVRLSIEL 37 0 |.||..|...|....|....|.|.|.|||..|.|..| 37 gi|296147 0 RKEEIQPFAMLVINPLRY*KEYIVLRS*KDIRISHSL 37 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 37], [ 0, 37]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|449443485|ref|XM_004139460.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|449443485|ref|XM_004139460.1|" ) self.assertEqual(alignment.target.annotations["gi"], "449443485") self.assertEqual(alignment.target.annotations["gis"], "449443485") self.assertEqual(alignment.target.annotations["acc."], "XM_004139460") self.assertEqual(alignment.target.annotations["accs."], "XM_004139460") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_004139460.1") self.assertEqual(alignment.target.annotations["length"], 1989) self.assertEqual(alignment.query.annotations["start"], 76) self.assertEqual(alignment.query.annotations["end"], 187) self.assertEqual(alignment.target.annotations["start"], 533) self.assertEqual(alignment.target.annotations["end"], 644) self.assertEqual( alignment.target.seq, "RLEEVSPLGSLLTGQLNRAREFIILKS*KTVRLSIEL" ) self.assertEqual( alignment.query.seq, "RKEEIQPFAMLVINPLRY*KEYIVLRS*KDIRISHSL" ) self.assertAlmostEqual(alignment.annotations["evalue"], 6.4) self.assertAlmostEqual(alignment.annotations["bit score"], 35.0) self.assertAlmostEqual(alignment.score, 70) self.assertEqual(alignment.shape, (2, 37)) self.assertAlmostEqual(alignment.annotations["% identity"], 40.54) self.assertEqual(alignment.annotations["identical"], 15) self.assertEqual(alignment.annotations["mismatches"], 22) self.assertEqual(alignment.annotations["positives"], 23) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 62.16) self.assertEqual(alignment.annotations["query/sbjct frames"], "2/3") self.assertEqual(alignment.query.annotations["frame"], "2") self.assertEqual(alignment.target.annotations["frame"], "3") self.assertEqual(alignment.target.annotations["tax ids"], "3659") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "PREDICTED: Cucumis sativus uncharacterized LOC101210909, transcript variant 2 (LOC101210909), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "PREDICTED: Cucumis sativus uncharacterized LOC101210909, transcript variant 2 (LOC101210909), mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 32) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 32) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|449443 0 RLEEVSPLGSLLTGQLNRAREFIILKS*KTVRLSIEL 37 0 |.||..|...|....|....|.|.|.|||..|.|..| 37 gi|296147 0 RKEEIQPFAMLVINPLRY*KEYIVLRS*KDIRISHSL 37 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 37], [ 0, 37]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|449443483|ref|XM_004139459.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|449443483|ref|XM_004139459.1|" ) self.assertEqual(alignment.target.annotations["gi"], "449443483") self.assertEqual(alignment.target.annotations["gis"], "449443483") self.assertEqual(alignment.target.annotations["acc."], "XM_004139459") self.assertEqual(alignment.target.annotations["accs."], "XM_004139459") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_004139459.1") self.assertEqual(alignment.target.annotations["length"], 2108) self.assertEqual(alignment.query.annotations["start"], 76) self.assertEqual(alignment.query.annotations["end"], 187) self.assertEqual(alignment.target.annotations["start"], 652) self.assertEqual(alignment.target.annotations["end"], 763) self.assertEqual( alignment.target.seq, "RLEEVSPLGSLLTGQLNRAREFIILKS*KTVRLSIEL" ) self.assertEqual( alignment.query.seq, "RKEEIQPFAMLVINPLRY*KEYIVLRS*KDIRISHSL" ) self.assertAlmostEqual(alignment.annotations["evalue"], 6.4) self.assertAlmostEqual(alignment.annotations["bit score"], 35.0) self.assertAlmostEqual(alignment.score, 70) self.assertEqual(alignment.shape, (2, 37)) self.assertAlmostEqual(alignment.annotations["% identity"], 40.54) self.assertEqual(alignment.annotations["identical"], 15) self.assertEqual(alignment.annotations["mismatches"], 22) self.assertEqual(alignment.annotations["positives"], 23) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 62.16) self.assertEqual(alignment.annotations["query/sbjct frames"], "2/2") self.assertEqual(alignment.query.annotations["frame"], "2") self.assertEqual(alignment.target.annotations["frame"], "2") self.assertEqual(alignment.target.annotations["tax ids"], "3659") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "PREDICTED: Cucumis sativus uncharacterized LOC101210909, transcript variant 1 (LOC101210909), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "PREDICTED: Cucumis sativus uncharacterized LOC101210909, transcript variant 1 (LOC101210909), mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 32) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 32) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|432873 0 CWLRSQGTTERRPLQMRSSADRAPSHFQMETAYLVFQM 38 0 |||..||....||.|.....|..|.|...|...|.|.| 38 gi|296147 0 CWLANQGMLK*RPWQCNAYRDCQPFHLFLEAGCLKFWM 38 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 38], [ 0, 38]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|432873290|ref|XM_004072130.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|432873290|ref|XM_004072130.1|" ) self.assertEqual(alignment.target.annotations["gi"], "432873290") self.assertEqual(alignment.target.annotations["gis"], "432873290") self.assertEqual(alignment.target.annotations["acc."], "XM_004072130") self.assertEqual(alignment.target.annotations["accs."], "XM_004072130") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_004072130.1") self.assertEqual(alignment.target.annotations["length"], 6378) self.assertEqual(alignment.query.annotations["start"], 190) self.assertEqual(alignment.query.annotations["end"], 304) self.assertEqual(alignment.target.annotations["start"], 4027) self.assertEqual(alignment.target.annotations["end"], 3913) self.assertEqual( alignment.target.seq, "CWLRSQGTTERRPLQMRSSADRAPSHFQMETAYLVFQM" ) self.assertEqual( alignment.query.seq, "CWLANQGMLK*RPWQCNAYRDCQPFHLFLEAGCLKFWM" ) self.assertAlmostEqual(alignment.annotations["evalue"], 6.4) self.assertAlmostEqual(alignment.annotations["bit score"], 35.0) self.assertAlmostEqual(alignment.score, 70) self.assertEqual(alignment.shape, (2, 38)) self.assertAlmostEqual(alignment.annotations["% identity"], 39.47) self.assertEqual(alignment.annotations["identical"], 15) self.assertEqual(alignment.annotations["mismatches"], 23) self.assertEqual(alignment.annotations["positives"], 19) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 50.00) self.assertEqual(alignment.annotations["query/sbjct frames"], "2/-3") self.assertEqual(alignment.query.annotations["frame"], "2") self.assertEqual(alignment.target.annotations["frame"], "-3") self.assertEqual(alignment.target.annotations["tax ids"], "8090") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "PREDICTED: Oryzias latipes zinc finger protein 462-like (LOC101161246), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "PREDICTED: Oryzias latipes zinc finger protein 462-like (LOC101161246), mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 33) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 33) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|426392 0 YFLPFELACQSKSPRVVSTSLDCLQKL 27 0 ..|||.|||||...........|||.| 27 gi|296147 0 FALPFVLACQSRNAKMTTLAMQCLQGL 27 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 27], [ 0, 27]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|426392076|ref|XM_004062338.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|426392076|ref|XM_004062338.1|" ) self.assertEqual(alignment.target.annotations["gi"], "426392076") self.assertEqual(alignment.target.annotations["gis"], "426392076") self.assertEqual(alignment.target.annotations["acc."], "XM_004062338") self.assertEqual(alignment.target.annotations["accs."], "XM_004062338") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_004062338.1") self.assertEqual(alignment.target.annotations["length"], 9002) self.assertEqual(alignment.query.annotations["start"], 174) self.assertEqual(alignment.query.annotations["end"], 255) self.assertEqual(alignment.target.annotations["start"], 345) self.assertEqual(alignment.target.annotations["end"], 426) self.assertEqual(alignment.target.seq, "YFLPFELACQSKSPRVVSTSLDCLQKL") self.assertEqual(alignment.query.seq, "FALPFVLACQSRNAKMTTLAMQCLQGL") self.assertAlmostEqual(alignment.annotations["evalue"], 6.4) self.assertAlmostEqual(alignment.annotations["bit score"], 35.0) self.assertAlmostEqual(alignment.score, 70) self.assertEqual(alignment.shape, (2, 27)) self.assertAlmostEqual(alignment.annotations["% identity"], 44.44) self.assertEqual(alignment.annotations["identical"], 12) self.assertEqual(alignment.annotations["mismatches"], 15) self.assertEqual(alignment.annotations["positives"], 20) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 74.07) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "9595") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "PREDICTED: Gorilla gorilla gorilla ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited) (ARFGEF2), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "PREDICTED: Gorilla gorilla gorilla ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited) (ARFGEF2), mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 23) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 23) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|410953 0 YFLPFELACQSKSPRVVSTSLDCLQKL 27 0 ..|||.|||||...........|||.| 27 gi|296147 0 FALPFVLACQSRNAKMTTLAMQCLQGL 27 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 27], [ 0, 27]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|410953779|ref|XM_003983499.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|410953779|ref|XM_003983499.1|" ) self.assertEqual(alignment.target.annotations["gi"], "410953779") self.assertEqual(alignment.target.annotations["gis"], "410953779") self.assertEqual(alignment.target.annotations["acc."], "XM_003983499") self.assertEqual(alignment.target.annotations["accs."], "XM_003983499") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_003983499.1") self.assertEqual(alignment.target.annotations["length"], 6297) self.assertEqual(alignment.query.annotations["start"], 174) self.assertEqual(alignment.query.annotations["end"], 255) self.assertEqual(alignment.target.annotations["start"], 129) self.assertEqual(alignment.target.annotations["end"], 210) self.assertEqual(alignment.target.seq, "YFLPFELACQSKSPRVVSTSLDCLQKL") self.assertEqual(alignment.query.seq, "FALPFVLACQSRNAKMTTLAMQCLQGL") self.assertAlmostEqual(alignment.annotations["evalue"], 6.4) self.assertAlmostEqual(alignment.annotations["bit score"], 35.0) self.assertAlmostEqual(alignment.score, 70) self.assertEqual(alignment.shape, (2, 27)) self.assertAlmostEqual(alignment.annotations["% identity"], 44.44) self.assertEqual(alignment.annotations["identical"], 12) self.assertEqual(alignment.annotations["mismatches"], 15) self.assertEqual(alignment.annotations["positives"], 20) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 74.07) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "9685") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "PREDICTED: Felis catus ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited) (ARFGEF2), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "PREDICTED: Felis catus ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited) (ARFGEF2), mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 23) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 23) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|403282 0 YFLPFELACQSKSPRVVSTSLDCLQKL 27 0 ..|||.|||||...........|||.| 27 gi|296147 0 FALPFVLACQSRNAKMTTLAMQCLQGL 27 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 27], [ 0, 27]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|403282318|ref|XM_003932550.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|403282318|ref|XM_003932550.1|" ) self.assertEqual(alignment.target.annotations["gi"], "403282318") self.assertEqual(alignment.target.annotations["gis"], "403282318") self.assertEqual(alignment.target.annotations["acc."], "XM_003932550") self.assertEqual(alignment.target.annotations["accs."], "XM_003932550") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_003932550.1") self.assertEqual(alignment.target.annotations["length"], 7122) self.assertEqual(alignment.query.annotations["start"], 174) self.assertEqual(alignment.query.annotations["end"], 255) self.assertEqual(alignment.target.annotations["start"], 378) self.assertEqual(alignment.target.annotations["end"], 459) self.assertEqual(alignment.target.seq, "YFLPFELACQSKSPRVVSTSLDCLQKL") self.assertEqual(alignment.query.seq, "FALPFVLACQSRNAKMTTLAMQCLQGL") self.assertAlmostEqual(alignment.annotations["evalue"], 6.4) self.assertAlmostEqual(alignment.annotations["bit score"], 35.0) self.assertAlmostEqual(alignment.score, 70) self.assertEqual(alignment.shape, (2, 27)) self.assertAlmostEqual(alignment.annotations["% identity"], 44.44) self.assertEqual(alignment.annotations["identical"], 12) self.assertEqual(alignment.annotations["mismatches"], 15) self.assertEqual(alignment.annotations["positives"], 20) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 74.07) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "39432") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "PREDICTED: Saimiri boliviensis boliviensis ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited) (ARFGEF2), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "PREDICTED: Saimiri boliviensis boliviensis ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited) (ARFGEF2), mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 23) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 23) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|402882 0 YFLPFELACQSKSPRVVSTSLDCLQKL 27 0 ..|||.|||||...........|||.| 27 gi|296147 0 FALPFVLACQSRNAKMTTLAMQCLQGL 27 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 27], [ 0, 27]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|402882302|ref|XM_003904638.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|402882302|ref|XM_003904638.1|" ) self.assertEqual(alignment.target.annotations["gi"], "402882302") self.assertEqual(alignment.target.annotations["gis"], "402882302") self.assertEqual(alignment.target.annotations["acc."], "XM_003904638") self.assertEqual(alignment.target.annotations["accs."], "XM_003904638") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_003904638.1") self.assertEqual(alignment.target.annotations["length"], 9027) self.assertEqual(alignment.query.annotations["start"], 174) self.assertEqual(alignment.query.annotations["end"], 255) self.assertEqual(alignment.target.annotations["start"], 378) self.assertEqual(alignment.target.annotations["end"], 459) self.assertEqual(alignment.target.seq, "YFLPFELACQSKSPRVVSTSLDCLQKL") self.assertEqual(alignment.query.seq, "FALPFVLACQSRNAKMTTLAMQCLQGL") self.assertAlmostEqual(alignment.annotations["evalue"], 6.4) self.assertAlmostEqual(alignment.annotations["bit score"], 35.0) self.assertAlmostEqual(alignment.score, 70) self.assertEqual(alignment.shape, (2, 27)) self.assertAlmostEqual(alignment.annotations["% identity"], 44.44) self.assertEqual(alignment.annotations["identical"], 12) self.assertEqual(alignment.annotations["mismatches"], 15) self.assertEqual(alignment.annotations["positives"], 20) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 74.07) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "9555") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "PREDICTED: Papio anubis ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited) (ARFGEF2), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "PREDICTED: Papio anubis ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited) (ARFGEF2), mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 23) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 23) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|397475 0 YFLPFELACQSKSPRVVSTSLDCLQKL 27 0 ..|||.|||||...........|||.| 27 gi|296147 0 FALPFVLACQSRNAKMTTLAMQCLQGL 27 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 27], [ 0, 27]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|397475827|ref|XM_003809272.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|397475827|ref|XM_003809272.1|" ) self.assertEqual(alignment.target.annotations["gi"], "397475827") self.assertEqual(alignment.target.annotations["gis"], "397475827") self.assertEqual(alignment.target.annotations["acc."], "XM_003809272") self.assertEqual(alignment.target.annotations["accs."], "XM_003809272") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_003809272.1") self.assertEqual(alignment.target.annotations["length"], 8939) self.assertEqual(alignment.query.annotations["start"], 174) self.assertEqual(alignment.query.annotations["end"], 255) self.assertEqual(alignment.target.annotations["start"], 282) self.assertEqual(alignment.target.annotations["end"], 363) self.assertEqual(alignment.target.seq, "YFLPFELACQSKSPRVVSTSLDCLQKL") self.assertEqual(alignment.query.seq, "FALPFVLACQSRNAKMTTLAMQCLQGL") self.assertAlmostEqual(alignment.annotations["evalue"], 6.4) self.assertAlmostEqual(alignment.annotations["bit score"], 35.0) self.assertAlmostEqual(alignment.score, 70) self.assertEqual(alignment.shape, (2, 27)) self.assertAlmostEqual(alignment.annotations["% identity"], 44.44) self.assertEqual(alignment.annotations["identical"], 12) self.assertEqual(alignment.annotations["mismatches"], 15) self.assertEqual(alignment.annotations["positives"], 20) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 74.07) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "9597") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "PREDICTED: Pan paniscus ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited) (ARFGEF2), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "PREDICTED: Pan paniscus ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited) (ARFGEF2), mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 23) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 23) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|395752 0 YFLPFELACQSKSPRVVSTSLDCLQKL 27 0 ..|||.|||||...........|||.| 27 gi|296147 0 FALPFVLACQSRNAKMTTLAMQCLQGL 27 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 27], [ 0, 27]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|395752429|ref|XM_002830404.2|") self.assertEqual( alignment.target.annotations["ids"], "gi|395752429|ref|XM_002830404.2|" ) self.assertEqual(alignment.target.annotations["gi"], "395752429") self.assertEqual(alignment.target.annotations["gis"], "395752429") self.assertEqual(alignment.target.annotations["acc."], "XM_002830404") self.assertEqual(alignment.target.annotations["accs."], "XM_002830404") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_002830404.2") self.assertEqual(alignment.target.annotations["length"], 5544) self.assertEqual(alignment.query.annotations["start"], 174) self.assertEqual(alignment.query.annotations["end"], 255) self.assertEqual(alignment.target.annotations["start"], 345) self.assertEqual(alignment.target.annotations["end"], 426) self.assertEqual(alignment.target.seq, "YFLPFELACQSKSPRVVSTSLDCLQKL") self.assertEqual(alignment.query.seq, "FALPFVLACQSRNAKMTTLAMQCLQGL") self.assertAlmostEqual(alignment.annotations["evalue"], 6.4) self.assertAlmostEqual(alignment.annotations["bit score"], 35.0) self.assertAlmostEqual(alignment.score, 70) self.assertEqual(alignment.shape, (2, 27)) self.assertAlmostEqual(alignment.annotations["% identity"], 44.44) self.assertEqual(alignment.annotations["identical"], 12) self.assertEqual(alignment.annotations["mismatches"], 15) self.assertEqual(alignment.annotations["positives"], 20) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 74.07) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "9601") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "PREDICTED: Pongo abelii ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited) (ARFGEF2), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "PREDICTED: Pongo abelii ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited) (ARFGEF2), mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 23) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 23) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|395506 0 YFLPFELACQSKSPRVVSTSLDCLQKL 27 0 ..|||.|||||...........|||.| 27 gi|296147 0 FALPFVLACQSRNAKMTTLAMQCLQGL 27 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 27], [ 0, 27]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|395506884|ref|XM_003757711.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|395506884|ref|XM_003757711.1|" ) self.assertEqual(alignment.target.annotations["gi"], "395506884") self.assertEqual(alignment.target.annotations["gis"], "395506884") self.assertEqual(alignment.target.annotations["acc."], "XM_003757711") self.assertEqual(alignment.target.annotations["accs."], "XM_003757711") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_003757711.1") self.assertEqual(alignment.target.annotations["length"], 5767) self.assertEqual(alignment.query.annotations["start"], 174) self.assertEqual(alignment.query.annotations["end"], 255) self.assertEqual(alignment.target.annotations["start"], 153) self.assertEqual(alignment.target.annotations["end"], 234) self.assertEqual(alignment.target.seq, "YFLPFELACQSKSPRVVSTSLDCLQKL") self.assertEqual(alignment.query.seq, "FALPFVLACQSRNAKMTTLAMQCLQGL") self.assertAlmostEqual(alignment.annotations["evalue"], 6.4) self.assertAlmostEqual(alignment.annotations["bit score"], 35.0) self.assertAlmostEqual(alignment.score, 70) self.assertEqual(alignment.shape, (2, 27)) self.assertAlmostEqual(alignment.annotations["% identity"], 44.44) self.assertEqual(alignment.annotations["identical"], 12) self.assertEqual(alignment.annotations["mismatches"], 15) self.assertEqual(alignment.annotations["positives"], 20) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 74.07) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "9305") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "PREDICTED: Sarcophilus harrisii ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited) (ARFGEF2), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "PREDICTED: Sarcophilus harrisii ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited) (ARFGEF2), mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 23) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 23) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|363741 0 YFLPFELACQSKSPRIVSTSLDCLQKL 27 0 ..|||.|||||...........|||.| 27 gi|296147 0 FALPFVLACQSRNAKMTTLAMQCLQGL 27 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 27], [ 0, 27]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|363741618|ref|XM_417388.3|") self.assertEqual( alignment.target.annotations["ids"], "gi|363741618|ref|XM_417388.3|" ) self.assertEqual(alignment.target.annotations["gi"], "363741618") self.assertEqual(alignment.target.annotations["gis"], "363741618") self.assertEqual(alignment.target.annotations["acc."], "XM_417388") self.assertEqual(alignment.target.annotations["accs."], "XM_417388") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_417388.3") self.assertEqual(alignment.target.annotations["length"], 5934) self.assertEqual(alignment.query.annotations["start"], 174) self.assertEqual(alignment.query.annotations["end"], 255) self.assertEqual(alignment.target.annotations["start"], 313) self.assertEqual(alignment.target.annotations["end"], 394) self.assertEqual(alignment.target.seq, "YFLPFELACQSKSPRIVSTSLDCLQKL") self.assertEqual(alignment.query.seq, "FALPFVLACQSRNAKMTTLAMQCLQGL") self.assertAlmostEqual(alignment.annotations["evalue"], 6.4) self.assertAlmostEqual(alignment.annotations["bit score"], 35.0) self.assertAlmostEqual(alignment.score, 70) self.assertEqual(alignment.shape, (2, 27)) self.assertAlmostEqual(alignment.annotations["% identity"], 44.44) self.assertEqual(alignment.annotations["identical"], 12) self.assertEqual(alignment.annotations["mismatches"], 15) self.assertEqual(alignment.annotations["positives"], 20) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 74.07) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/2") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "2") self.assertEqual(alignment.target.annotations["tax ids"], "9031") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "PREDICTED: Gallus gallus ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited) (ARFGEF2), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "PREDICTED: Gallus gallus ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited) (ARFGEF2), mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 23) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 23) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|359322 0 YFLPFELACQSKSPRVVSTSLDCLQKL 27 0 ..|||.|||||...........|||.| 27 gi|296147 0 FALPFVLACQSRNAKMTTLAMQCLQGL 27 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 27], [ 0, 27]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|359322761|ref|XM_534448.4|") self.assertEqual( alignment.target.annotations["ids"], "gi|359322761|ref|XM_534448.4|" ) self.assertEqual(alignment.target.annotations["gi"], "359322761") self.assertEqual(alignment.target.annotations["gis"], "359322761") self.assertEqual(alignment.target.annotations["acc."], "XM_534448") self.assertEqual(alignment.target.annotations["accs."], "XM_534448") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_534448.4") self.assertEqual(alignment.target.annotations["length"], 6505) self.assertEqual(alignment.query.annotations["start"], 174) self.assertEqual(alignment.query.annotations["end"], 255) self.assertEqual(alignment.target.annotations["start"], 353) self.assertEqual(alignment.target.annotations["end"], 434) self.assertEqual(alignment.target.seq, "YFLPFELACQSKSPRVVSTSLDCLQKL") self.assertEqual(alignment.query.seq, "FALPFVLACQSRNAKMTTLAMQCLQGL") self.assertAlmostEqual(alignment.annotations["evalue"], 6.4) self.assertAlmostEqual(alignment.annotations["bit score"], 35.0) self.assertAlmostEqual(alignment.score, 70) self.assertEqual(alignment.shape, (2, 27)) self.assertAlmostEqual(alignment.annotations["% identity"], 44.44) self.assertEqual(alignment.annotations["identical"], 12) self.assertEqual(alignment.annotations["mismatches"], 15) self.assertEqual(alignment.annotations["positives"], 20) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 74.07) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/3") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "3") self.assertEqual(alignment.target.annotations["tax ids"], "9615") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "PREDICTED: Canis lupus familiaris ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited) (ARFGEF2), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "PREDICTED: Canis lupus familiaris ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited) (ARFGEF2), mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 23) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 23) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|354476 0 YFLPFELACQSKSPRVVSTSLDCLQKL 27 0 ..|||.|||||...........|||.| 27 gi|296147 0 FALPFVLACQSRNAKMTTLAMQCLQGL 27 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 27], [ 0, 27]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|354476751|ref|XM_003500539.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|354476751|ref|XM_003500539.1|" ) self.assertEqual(alignment.target.annotations["gi"], "354476751") self.assertEqual(alignment.target.annotations["gis"], "354476751") self.assertEqual(alignment.target.annotations["acc."], "XM_003500539") self.assertEqual(alignment.target.annotations["accs."], "XM_003500539") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_003500539.1") self.assertEqual(alignment.target.annotations["length"], 6829) self.assertEqual(alignment.query.annotations["start"], 174) self.assertEqual(alignment.query.annotations["end"], 255) self.assertEqual(alignment.target.annotations["start"], 207) self.assertEqual(alignment.target.annotations["end"], 288) self.assertEqual(alignment.target.seq, "YFLPFELACQSKSPRVVSTSLDCLQKL") self.assertEqual(alignment.query.seq, "FALPFVLACQSRNAKMTTLAMQCLQGL") self.assertAlmostEqual(alignment.annotations["evalue"], 6.4) self.assertAlmostEqual(alignment.annotations["bit score"], 35.0) self.assertAlmostEqual(alignment.score, 70) self.assertEqual(alignment.shape, (2, 27)) self.assertAlmostEqual(alignment.annotations["% identity"], 44.44) self.assertEqual(alignment.annotations["identical"], 12) self.assertEqual(alignment.annotations["mismatches"], 15) self.assertEqual(alignment.annotations["positives"], 20) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 74.07) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "10029") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "PREDICTED: Cricetulus griseus brefeldin A-inhibited guanine nucleotide-exchange protein 2-like (LOC100773989), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "PREDICTED: Cricetulus griseus brefeldin A-inhibited guanine nucleotide-exchange protein 2-like (LOC100773989), mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 23) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 23) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|350595 0 YFLPFELACQSKSPRVVSTSLDCLQKL 27 0 ..|||.|||||...........|||.| 27 gi|296147 0 FALPFVLACQSRNAKMTTLAMQCLQGL 27 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 27], [ 0, 27]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|350595022|ref|XM_003483981.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|350595022|ref|XM_003483981.1|" ) self.assertEqual(alignment.target.annotations["gi"], "350595022") self.assertEqual(alignment.target.annotations["gis"], "350595022") self.assertEqual(alignment.target.annotations["acc."], "XM_003483981") self.assertEqual(alignment.target.annotations["accs."], "XM_003483981") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_003483981.1") self.assertEqual(alignment.target.annotations["length"], 6052) self.assertEqual(alignment.query.annotations["start"], 174) self.assertEqual(alignment.query.annotations["end"], 255) self.assertEqual(alignment.target.annotations["start"], 351) self.assertEqual(alignment.target.annotations["end"], 432) self.assertEqual(alignment.target.seq, "YFLPFELACQSKSPRVVSTSLDCLQKL") self.assertEqual(alignment.query.seq, "FALPFVLACQSRNAKMTTLAMQCLQGL") self.assertAlmostEqual(alignment.annotations["evalue"], 6.4) self.assertAlmostEqual(alignment.annotations["bit score"], 35.0) self.assertAlmostEqual(alignment.score, 70) self.assertEqual(alignment.shape, (2, 27)) self.assertAlmostEqual(alignment.annotations["% identity"], 44.44) self.assertEqual(alignment.annotations["identical"], 12) self.assertEqual(alignment.annotations["mismatches"], 15) self.assertEqual(alignment.annotations["positives"], 20) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 74.07) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "9823") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "PREDICTED: Sus scrofa ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited) (ARFGEF2), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "PREDICTED: Sus scrofa ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited) (ARFGEF2), mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 23) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 23) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|350591 0 AGRVDFWMPGLRLWPRRWRF 20 0 ||...||||.|||...|||| 20 gi|296147 0 AGCLKFWMPSLRLLISRWRF 20 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 20], [ 0, 20]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|350591776|ref|XM_003132566.3|") self.assertEqual( alignment.target.annotations["ids"], "gi|350591776|ref|XM_003132566.3|" ) self.assertEqual(alignment.target.annotations["gi"], "350591776") self.assertEqual(alignment.target.annotations["gis"], "350591776") self.assertEqual(alignment.target.annotations["acc."], "XM_003132566") self.assertEqual(alignment.target.annotations["accs."], "XM_003132566") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_003132566.3") self.assertEqual(alignment.target.annotations["length"], 1870) self.assertEqual(alignment.query.annotations["start"], 280) self.assertEqual(alignment.query.annotations["end"], 340) self.assertEqual(alignment.target.annotations["start"], 1159) self.assertEqual(alignment.target.annotations["end"], 1219) self.assertEqual(alignment.target.seq, "AGRVDFWMPGLRLWPRRWRF") self.assertEqual(alignment.query.seq, "AGCLKFWMPSLRLLISRWRF") self.assertAlmostEqual(alignment.annotations["evalue"], 6.4) self.assertAlmostEqual(alignment.annotations["bit score"], 35.0) self.assertAlmostEqual(alignment.score, 70) self.assertEqual(alignment.shape, (2, 20)) self.assertAlmostEqual(alignment.annotations["% identity"], 65.00) self.assertEqual(alignment.annotations["identical"], 13) self.assertEqual(alignment.annotations["mismatches"], 7) self.assertEqual(alignment.annotations["positives"], 14) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 70.00) self.assertEqual(alignment.annotations["query/sbjct frames"], "2/2") self.assertEqual(alignment.query.annotations["frame"], "2") self.assertEqual(alignment.target.annotations["frame"], "2") self.assertEqual(alignment.target.annotations["tax ids"], "9823") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "PREDICTED: Sus scrofa ephrin type-B receptor 3-like (LOC100514541), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "PREDICTED: Sus scrofa ephrin type-B receptor 3-like (LOC100514541), mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 17) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 17) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|350591 0 AGRVDFWMPGLRLWPRRWRF 20 0 ||...||||.|||...|||| 20 gi|296147 0 AGCLKFWMPSLRLLISRWRF 20 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 20], [ 0, 20]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|350591772|ref|XM_003358733.2|") self.assertEqual( alignment.target.annotations["ids"], "gi|350591772|ref|XM_003358733.2|" ) self.assertEqual(alignment.target.annotations["gi"], "350591772") self.assertEqual(alignment.target.annotations["gis"], "350591772") self.assertEqual(alignment.target.annotations["acc."], "XM_003358733") self.assertEqual(alignment.target.annotations["accs."], "XM_003358733") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_003358733.2") self.assertEqual(alignment.target.annotations["length"], 3776) self.assertEqual(alignment.query.annotations["start"], 280) self.assertEqual(alignment.query.annotations["end"], 340) self.assertEqual(alignment.target.annotations["start"], 3064) self.assertEqual(alignment.target.annotations["end"], 3124) self.assertEqual(alignment.target.seq, "AGRVDFWMPGLRLWPRRWRF") self.assertEqual(alignment.query.seq, "AGCLKFWMPSLRLLISRWRF") self.assertAlmostEqual(alignment.annotations["evalue"], 6.4) self.assertAlmostEqual(alignment.annotations["bit score"], 35.0) self.assertAlmostEqual(alignment.score, 70) self.assertEqual(alignment.shape, (2, 20)) self.assertAlmostEqual(alignment.annotations["% identity"], 65.00) self.assertEqual(alignment.annotations["identical"], 13) self.assertEqual(alignment.annotations["mismatches"], 7) self.assertEqual(alignment.annotations["positives"], 14) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 70.00) self.assertEqual(alignment.annotations["query/sbjct frames"], "2/2") self.assertEqual(alignment.query.annotations["frame"], "2") self.assertEqual(alignment.target.annotations["frame"], "2") self.assertEqual(alignment.target.annotations["tax ids"], "9823") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "PREDICTED: Sus scrofa EPH receptor B3, transcript variant 2 (EPHB3), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "PREDICTED: Sus scrofa EPH receptor B3, transcript variant 2 (EPHB3), mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 17) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 17) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|348563 0 YFLPFELACQSKSPRVVSTSLDCLQKL 27 0 ..|||.|||||...........|||.| 27 gi|296147 0 FALPFVLACQSRNAKMTTLAMQCLQGL 27 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 27], [ 0, 27]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|348563932|ref|XM_003467713.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|348563932|ref|XM_003467713.1|" ) self.assertEqual(alignment.target.annotations["gi"], "348563932") self.assertEqual(alignment.target.annotations["gis"], "348563932") self.assertEqual(alignment.target.annotations["acc."], "XM_003467713") self.assertEqual(alignment.target.annotations["accs."], "XM_003467713") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_003467713.1") self.assertEqual(alignment.target.annotations["length"], 5355) self.assertEqual(alignment.query.annotations["start"], 174) self.assertEqual(alignment.query.annotations["end"], 255) self.assertEqual(alignment.target.annotations["start"], 201) self.assertEqual(alignment.target.annotations["end"], 282) self.assertEqual(alignment.target.seq, "YFLPFELACQSKSPRVVSTSLDCLQKL") self.assertEqual(alignment.query.seq, "FALPFVLACQSRNAKMTTLAMQCLQGL") self.assertAlmostEqual(alignment.annotations["evalue"], 6.4) self.assertAlmostEqual(alignment.annotations["bit score"], 35.0) self.assertAlmostEqual(alignment.score, 70) self.assertEqual(alignment.shape, (2, 27)) self.assertAlmostEqual(alignment.annotations["% identity"], 44.44) self.assertEqual(alignment.annotations["identical"], 12) self.assertEqual(alignment.annotations["mismatches"], 15) self.assertEqual(alignment.annotations["positives"], 20) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 74.07) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "10141") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "PREDICTED: Cavia porcellus brefeldin A-inhibited guanine nucleotide-exchange protein 2-like (LOC100724838), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "PREDICTED: Cavia porcellus brefeldin A-inhibited guanine nucleotide-exchange protein 2-like (LOC100724838), mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 23) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 23) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|344280 0 YFLPFELACQSKSPRVVSTSLDCLQKL 27 0 ..|||.|||||...........|||.| 27 gi|296147 0 FALPFVLACQSRNAKMTTLAMQCLQGL 27 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 27], [ 0, 27]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|344280063|ref|XM_003411757.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|344280063|ref|XM_003411757.1|" ) self.assertEqual(alignment.target.annotations["gi"], "344280063") self.assertEqual(alignment.target.annotations["gis"], "344280063") self.assertEqual(alignment.target.annotations["acc."], "XM_003411757") self.assertEqual(alignment.target.annotations["accs."], "XM_003411757") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_003411757.1") self.assertEqual(alignment.target.annotations["length"], 5452) self.assertEqual(alignment.query.annotations["start"], 174) self.assertEqual(alignment.query.annotations["end"], 255) self.assertEqual(alignment.target.annotations["start"], 201) self.assertEqual(alignment.target.annotations["end"], 282) self.assertEqual(alignment.target.seq, "YFLPFELACQSKSPRVVSTSLDCLQKL") self.assertEqual(alignment.query.seq, "FALPFVLACQSRNAKMTTLAMQCLQGL") self.assertAlmostEqual(alignment.annotations["evalue"], 6.4) self.assertAlmostEqual(alignment.annotations["bit score"], 35.0) self.assertAlmostEqual(alignment.score, 70) self.assertEqual(alignment.shape, (2, 27)) self.assertAlmostEqual(alignment.annotations["% identity"], 44.44) self.assertEqual(alignment.annotations["identical"], 12) self.assertEqual(alignment.annotations["mismatches"], 15) self.assertEqual(alignment.annotations["positives"], 20) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 74.07) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "9785") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "PREDICTED: Loxodonta africana ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited) (ARFGEF2), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "PREDICTED: Loxodonta africana ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited) (ARFGEF2), mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 23) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 23) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|338719 0 YFLPFELACQSKSPRVVSTSLDCLQKL 27 0 ..|||.|||||...........|||.| 27 gi|296147 0 FALPFVLACQSRNAKMTTLAMQCLQGL 27 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 27], [ 0, 27]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|338719107|ref|XM_001916930.2|") self.assertEqual( alignment.target.annotations["ids"], "gi|338719107|ref|XM_001916930.2|" ) self.assertEqual(alignment.target.annotations["gi"], "338719107") self.assertEqual(alignment.target.annotations["gis"], "338719107") self.assertEqual(alignment.target.annotations["acc."], "XM_001916930") self.assertEqual(alignment.target.annotations["accs."], "XM_001916930") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_001916930.2") self.assertEqual(alignment.target.annotations["length"], 5782) self.assertEqual(alignment.query.annotations["start"], 174) self.assertEqual(alignment.query.annotations["end"], 255) self.assertEqual(alignment.target.annotations["start"], 342) self.assertEqual(alignment.target.annotations["end"], 423) self.assertEqual(alignment.target.seq, "YFLPFELACQSKSPRVVSTSLDCLQKL") self.assertEqual(alignment.query.seq, "FALPFVLACQSRNAKMTTLAMQCLQGL") self.assertAlmostEqual(alignment.annotations["evalue"], 6.4) self.assertAlmostEqual(alignment.annotations["bit score"], 35.0) self.assertAlmostEqual(alignment.score, 70) self.assertEqual(alignment.shape, (2, 27)) self.assertAlmostEqual(alignment.annotations["% identity"], 44.44) self.assertEqual(alignment.annotations["identical"], 12) self.assertEqual(alignment.annotations["mismatches"], 15) self.assertEqual(alignment.annotations["positives"], 20) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 74.07) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "9796") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "PREDICTED: Equus caballus ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited) (ARFGEF2), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "PREDICTED: Equus caballus ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited) (ARFGEF2), mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 23) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 23) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|335300 0 AGRVDFWMPGLRLWPRRWRF 20 0 ||...||||.|||...|||| 20 gi|296147 0 AGCLKFWMPSLRLLISRWRF 20 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 20], [ 0, 20]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|335300059|ref|XM_003132565.2|") self.assertEqual( alignment.target.annotations["ids"], "gi|335300059|ref|XM_003132565.2|" ) self.assertEqual(alignment.target.annotations["gi"], "335300059") self.assertEqual(alignment.target.annotations["gis"], "335300059") self.assertEqual(alignment.target.annotations["acc."], "XM_003132565") self.assertEqual(alignment.target.annotations["accs."], "XM_003132565") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_003132565.2") self.assertEqual(alignment.target.annotations["length"], 3667) self.assertEqual(alignment.query.annotations["start"], 280) self.assertEqual(alignment.query.annotations["end"], 340) self.assertEqual(alignment.target.annotations["start"], 2956) self.assertEqual(alignment.target.annotations["end"], 3016) self.assertEqual(alignment.target.seq, "AGRVDFWMPGLRLWPRRWRF") self.assertEqual(alignment.query.seq, "AGCLKFWMPSLRLLISRWRF") self.assertAlmostEqual(alignment.annotations["evalue"], 6.4) self.assertAlmostEqual(alignment.annotations["bit score"], 35.0) self.assertAlmostEqual(alignment.score, 70) self.assertEqual(alignment.shape, (2, 20)) self.assertAlmostEqual(alignment.annotations["% identity"], 65.00) self.assertEqual(alignment.annotations["identical"], 13) self.assertEqual(alignment.annotations["mismatches"], 7) self.assertEqual(alignment.annotations["positives"], 14) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 70.00) self.assertEqual(alignment.annotations["query/sbjct frames"], "2/2") self.assertEqual(alignment.query.annotations["frame"], "2") self.assertEqual(alignment.target.annotations["frame"], "2") self.assertEqual(alignment.target.annotations["tax ids"], "9823") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "PREDICTED: Sus scrofa EPH receptor B3, transcript variant 1 (EPHB3), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "PREDICTED: Sus scrofa EPH receptor B3, transcript variant 1 (EPHB3), mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 17) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 17) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|334312 0 YFLPFELACQSKSPRVVSTSLDCLQKL 27 0 ..|||.|||||...........|||.| 27 gi|296147 0 FALPFVLACQSRNAKMTTLAMQCLQGL 27 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 27], [ 0, 27]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|334312365|ref|XM_001379067.2|") self.assertEqual( alignment.target.annotations["ids"], "gi|334312365|ref|XM_001379067.2|" ) self.assertEqual(alignment.target.annotations["gi"], "334312365") self.assertEqual(alignment.target.annotations["gis"], "334312365") self.assertEqual(alignment.target.annotations["acc."], "XM_001379067") self.assertEqual(alignment.target.annotations["accs."], "XM_001379067") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_001379067.2") self.assertEqual(alignment.target.annotations["length"], 5511) self.assertEqual(alignment.query.annotations["start"], 174) self.assertEqual(alignment.query.annotations["end"], 255) self.assertEqual(alignment.target.annotations["start"], 201) self.assertEqual(alignment.target.annotations["end"], 282) self.assertEqual(alignment.target.seq, "YFLPFELACQSKSPRVVSTSLDCLQKL") self.assertEqual(alignment.query.seq, "FALPFVLACQSRNAKMTTLAMQCLQGL") self.assertAlmostEqual(alignment.annotations["evalue"], 6.4) self.assertAlmostEqual(alignment.annotations["bit score"], 35.0) self.assertAlmostEqual(alignment.score, 70) self.assertEqual(alignment.shape, (2, 27)) self.assertAlmostEqual(alignment.annotations["% identity"], 44.44) self.assertEqual(alignment.annotations["identical"], 12) self.assertEqual(alignment.annotations["mismatches"], 15) self.assertEqual(alignment.annotations["positives"], 20) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 74.07) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "13616") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "PREDICTED: Monodelphis domestica ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited) (ARFGEF2), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "PREDICTED: Monodelphis domestica ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited) (ARFGEF2), mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 23) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 23) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|332858 0 YFLPFELACQSKSPRVVSTSLDCLQKL 27 0 ..|||.|||||...........|||.| 27 gi|296147 0 FALPFVLACQSRNAKMTTLAMQCLQGL 27 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 27], [ 0, 27]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|332858727|ref|XM_001165517.2|") self.assertEqual( alignment.target.annotations["ids"], "gi|332858727|ref|XM_001165517.2|" ) self.assertEqual(alignment.target.annotations["gi"], "332858727") self.assertEqual(alignment.target.annotations["gis"], "332858727") self.assertEqual(alignment.target.annotations["acc."], "XM_001165517") self.assertEqual(alignment.target.annotations["accs."], "XM_001165517") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_001165517.2") self.assertEqual(alignment.target.annotations["length"], 8850) self.assertEqual(alignment.query.annotations["start"], 174) self.assertEqual(alignment.query.annotations["end"], 255) self.assertEqual(alignment.target.annotations["start"], 201) self.assertEqual(alignment.target.annotations["end"], 282) self.assertEqual(alignment.target.seq, "YFLPFELACQSKSPRVVSTSLDCLQKL") self.assertEqual(alignment.query.seq, "FALPFVLACQSRNAKMTTLAMQCLQGL") self.assertAlmostEqual(alignment.annotations["evalue"], 6.4) self.assertAlmostEqual(alignment.annotations["bit score"], 35.0) self.assertAlmostEqual(alignment.score, 70) self.assertEqual(alignment.shape, (2, 27)) self.assertAlmostEqual(alignment.annotations["% identity"], 44.44) self.assertEqual(alignment.annotations["identical"], 12) self.assertEqual(alignment.annotations["mismatches"], 15) self.assertEqual(alignment.annotations["positives"], 20) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 74.07) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "9598") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "PREDICTED: Pan troglodytes ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited), transcript variant 1 (ARFGEF2), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "PREDICTED: Pan troglodytes ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited), transcript variant 1 (ARFGEF2), mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 23) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 23) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|332207 0 YFLPFELACQSKSPRVVSTSLDCLQKL 27 0 ..|||.|||||...........|||.| 27 gi|296147 0 FALPFVLACQSRNAKMTTLAMQCLQGL 27 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 27], [ 0, 27]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|332207745|ref|XM_003252909.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|332207745|ref|XM_003252909.1|" ) self.assertEqual(alignment.target.annotations["gi"], "332207745") self.assertEqual(alignment.target.annotations["gis"], "332207745") self.assertEqual(alignment.target.annotations["acc."], "XM_003252909") self.assertEqual(alignment.target.annotations["accs."], "XM_003252909") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_003252909.1") self.assertEqual(alignment.target.annotations["length"], 9022) self.assertEqual(alignment.query.annotations["start"], 174) self.assertEqual(alignment.query.annotations["end"], 255) self.assertEqual(alignment.target.annotations["start"], 369) self.assertEqual(alignment.target.annotations["end"], 450) self.assertEqual(alignment.target.seq, "YFLPFELACQSKSPRVVSTSLDCLQKL") self.assertEqual(alignment.query.seq, "FALPFVLACQSRNAKMTTLAMQCLQGL") self.assertAlmostEqual(alignment.annotations["evalue"], 6.4) self.assertAlmostEqual(alignment.annotations["bit score"], 35.0) self.assertAlmostEqual(alignment.score, 70) self.assertEqual(alignment.shape, (2, 27)) self.assertAlmostEqual(alignment.annotations["% identity"], 44.44) self.assertEqual(alignment.annotations["identical"], 12) self.assertEqual(alignment.annotations["mismatches"], 15) self.assertEqual(alignment.annotations["positives"], 20) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 74.07) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "61853") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "PREDICTED: Nomascus leucogenys ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited), transcript variant 2 (ARFGEF2), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "PREDICTED: Nomascus leucogenys ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited), transcript variant 2 (ARFGEF2), mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 23) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 23) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|332207 0 YFLPFELACQSKSPRVVSTSLDCLQKL 27 0 ..|||.|||||...........|||.| 27 gi|296147 0 FALPFVLACQSRNAKMTTLAMQCLQGL 27 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 27], [ 0, 27]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|332207743|ref|XM_003252908.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|332207743|ref|XM_003252908.1|" ) self.assertEqual(alignment.target.annotations["gi"], "332207743") self.assertEqual(alignment.target.annotations["gis"], "332207743") self.assertEqual(alignment.target.annotations["acc."], "XM_003252908") self.assertEqual(alignment.target.annotations["accs."], "XM_003252908") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_003252908.1") self.assertEqual(alignment.target.annotations["length"], 9031) self.assertEqual(alignment.query.annotations["start"], 174) self.assertEqual(alignment.query.annotations["end"], 255) self.assertEqual(alignment.target.annotations["start"], 369) self.assertEqual(alignment.target.annotations["end"], 450) self.assertEqual(alignment.target.seq, "YFLPFELACQSKSPRVVSTSLDCLQKL") self.assertEqual(alignment.query.seq, "FALPFVLACQSRNAKMTTLAMQCLQGL") self.assertAlmostEqual(alignment.annotations["evalue"], 6.4) self.assertAlmostEqual(alignment.annotations["bit score"], 35.0) self.assertAlmostEqual(alignment.score, 70) self.assertEqual(alignment.shape, (2, 27)) self.assertAlmostEqual(alignment.annotations["% identity"], 44.44) self.assertEqual(alignment.annotations["identical"], 12) self.assertEqual(alignment.annotations["mismatches"], 15) self.assertEqual(alignment.annotations["positives"], 20) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 74.07) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "61853") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "PREDICTED: Nomascus leucogenys ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited), transcript variant 1 (ARFGEF2), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "PREDICTED: Nomascus leucogenys ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited), transcript variant 1 (ARFGEF2), mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 23) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 23) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|326931 0 YFLPFELACQSKSPRIVSTSLDCLQKL 27 0 ..|||.|||||...........|||.| 27 gi|296147 0 FALPFVLACQSRNAKMTTLAMQCLQGL 27 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 27], [ 0, 27]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|326931872|ref|XM_003212000.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|326931872|ref|XM_003212000.1|" ) self.assertEqual(alignment.target.annotations["gi"], "326931872") self.assertEqual(alignment.target.annotations["gis"], "326931872") self.assertEqual(alignment.target.annotations["acc."], "XM_003212000") self.assertEqual(alignment.target.annotations["accs."], "XM_003212000") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_003212000.1") self.assertEqual(alignment.target.annotations["length"], 5240) self.assertEqual(alignment.query.annotations["start"], 174) self.assertEqual(alignment.query.annotations["end"], 255) self.assertEqual(alignment.target.annotations["start"], 80) self.assertEqual(alignment.target.annotations["end"], 161) self.assertEqual(alignment.target.seq, "YFLPFELACQSKSPRIVSTSLDCLQKL") self.assertEqual(alignment.query.seq, "FALPFVLACQSRNAKMTTLAMQCLQGL") self.assertAlmostEqual(alignment.annotations["evalue"], 6.4) self.assertAlmostEqual(alignment.annotations["bit score"], 35.0) self.assertAlmostEqual(alignment.score, 70) self.assertEqual(alignment.shape, (2, 27)) self.assertAlmostEqual(alignment.annotations["% identity"], 44.44) self.assertEqual(alignment.annotations["identical"], 12) self.assertEqual(alignment.annotations["mismatches"], 15) self.assertEqual(alignment.annotations["positives"], 20) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 74.07) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/3") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "3") self.assertEqual(alignment.target.annotations["tax ids"], "9103") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "PREDICTED: Meleagris gallopavo ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited) (ARFGEF2), partial mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "PREDICTED: Meleagris gallopavo ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited) (ARFGEF2), partial mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 23) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 23) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|327271 0 YFLPFELACQSKSPRIVSTSLDCLQKL 27 0 ..|||.|||||...........|||.| 27 gi|296147 0 FALPFVLACQSRNAKMTTLAMQCLQGL 27 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 27], [ 0, 27]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|327271833|ref|XM_003220644.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|327271833|ref|XM_003220644.1|" ) self.assertEqual(alignment.target.annotations["gi"], "327271833") self.assertEqual(alignment.target.annotations["gis"], "327271833") self.assertEqual(alignment.target.annotations["acc."], "XM_003220644") self.assertEqual(alignment.target.annotations["accs."], "XM_003220644") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_003220644.1") self.assertEqual(alignment.target.annotations["length"], 5379) self.assertEqual(alignment.query.annotations["start"], 174) self.assertEqual(alignment.query.annotations["end"], 255) self.assertEqual(alignment.target.annotations["start"], 219) self.assertEqual(alignment.target.annotations["end"], 300) self.assertEqual(alignment.target.seq, "YFLPFELACQSKSPRIVSTSLDCLQKL") self.assertEqual(alignment.query.seq, "FALPFVLACQSRNAKMTTLAMQCLQGL") self.assertAlmostEqual(alignment.annotations["evalue"], 6.4) self.assertAlmostEqual(alignment.annotations["bit score"], 35.0) self.assertAlmostEqual(alignment.score, 70) self.assertEqual(alignment.shape, (2, 27)) self.assertAlmostEqual(alignment.annotations["% identity"], 44.44) self.assertEqual(alignment.annotations["identical"], 12) self.assertEqual(alignment.annotations["mismatches"], 15) self.assertEqual(alignment.annotations["positives"], 20) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 74.07) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "28377") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "PREDICTED: Anolis carolinensis ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited) (arfgef2), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "PREDICTED: Anolis carolinensis ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited) (arfgef2), mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 23) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 23) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|301754 0 YFLPFELACQSKSPRVVSTSLDCLQKL 27 0 ..|||.|||||...........|||.| 27 gi|296147 0 FALPFVLACQSRNAKMTTLAMQCLQGL 27 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 27], [ 0, 27]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|301754408|ref|XM_002912990.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|301754408|ref|XM_002912990.1|" ) self.assertEqual(alignment.target.annotations["gi"], "301754408") self.assertEqual(alignment.target.annotations["gis"], "301754408") self.assertEqual(alignment.target.annotations["acc."], "XM_002912990") self.assertEqual(alignment.target.annotations["accs."], "XM_002912990") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_002912990.1") self.assertEqual(alignment.target.annotations["length"], 6451) self.assertEqual(alignment.query.annotations["start"], 174) self.assertEqual(alignment.query.annotations["end"], 255) self.assertEqual(alignment.target.annotations["start"], 201) self.assertEqual(alignment.target.annotations["end"], 282) self.assertEqual(alignment.target.seq, "YFLPFELACQSKSPRVVSTSLDCLQKL") self.assertEqual(alignment.query.seq, "FALPFVLACQSRNAKMTTLAMQCLQGL") self.assertAlmostEqual(alignment.annotations["evalue"], 6.4) self.assertAlmostEqual(alignment.annotations["bit score"], 35.0) self.assertAlmostEqual(alignment.score, 70) self.assertEqual(alignment.shape, (2, 27)) self.assertAlmostEqual(alignment.annotations["% identity"], 44.44) self.assertEqual(alignment.annotations["identical"], 12) self.assertEqual(alignment.annotations["mismatches"], 15) self.assertEqual(alignment.annotations["positives"], 20) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 74.07) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "9646") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "PREDICTED: Ailuropoda melanoleuca ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited) (ARFGEF2), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "PREDICTED: Ailuropoda melanoleuca ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited) (ARFGEF2), mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 23) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 23) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|297259 0 YFLPFELACQSKSPRVVSTSLDCLQKL 27 0 ..|||.|||||...........|||.| 27 gi|296147 0 FALPFVLACQSRNAKMTTLAMQCLQGL 27 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 27], [ 0, 27]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|297259620|ref|XM_002798127.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|297259620|ref|XM_002798127.1|" ) self.assertEqual(alignment.target.annotations["gi"], "297259620") self.assertEqual(alignment.target.annotations["gis"], "297259620") self.assertEqual(alignment.target.annotations["acc."], "XM_002798127") self.assertEqual(alignment.target.annotations["accs."], "XM_002798127") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_002798127.1") self.assertEqual(alignment.target.annotations["length"], 5801) self.assertEqual(alignment.query.annotations["start"], 174) self.assertEqual(alignment.query.annotations["end"], 255) self.assertEqual(alignment.target.annotations["start"], 378) self.assertEqual(alignment.target.annotations["end"], 459) self.assertEqual(alignment.target.seq, "YFLPFELACQSKSPRVVSTSLDCLQKL") self.assertEqual(alignment.query.seq, "FALPFVLACQSRNAKMTTLAMQCLQGL") self.assertAlmostEqual(alignment.annotations["evalue"], 6.4) self.assertAlmostEqual(alignment.annotations["bit score"], 35.0) self.assertAlmostEqual(alignment.score, 70) self.assertEqual(alignment.shape, (2, 27)) self.assertAlmostEqual(alignment.annotations["% identity"], 44.44) self.assertEqual(alignment.annotations["identical"], 12) self.assertEqual(alignment.annotations["mismatches"], 15) self.assertEqual(alignment.annotations["positives"], 20) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 74.07) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "9544") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "PREDICTED: Macaca mulatta ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited) (ARFGEF2), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "PREDICTED: Macaca mulatta ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited) (ARFGEF2), mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 23) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 23) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|296200 0 YFLPFELACQSKSPRVVSTSLDCLQKL 27 0 ..|||.|||||...........|||.| 27 gi|296147 0 FALPFVLACQSRNAKMTTLAMQCLQGL 27 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 27], [ 0, 27]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|296200663|ref|XM_002806776.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|296200663|ref|XM_002806776.1|" ) self.assertEqual(alignment.target.annotations["gi"], "296200663") self.assertEqual(alignment.target.annotations["gis"], "296200663") self.assertEqual(alignment.target.annotations["acc."], "XM_002806776") self.assertEqual(alignment.target.annotations["accs."], "XM_002806776") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_002806776.1") self.assertEqual(alignment.target.annotations["length"], 5612) self.assertEqual(alignment.query.annotations["start"], 174) self.assertEqual(alignment.query.annotations["end"], 255) self.assertEqual(alignment.target.annotations["start"], 240) self.assertEqual(alignment.target.annotations["end"], 321) self.assertEqual(alignment.target.seq, "YFLPFELACQSKSPRVVSTSLDCLQKL") self.assertEqual(alignment.query.seq, "FALPFVLACQSRNAKMTTLAMQCLQGL") self.assertAlmostEqual(alignment.annotations["evalue"], 6.4) self.assertAlmostEqual(alignment.annotations["bit score"], 35.0) self.assertAlmostEqual(alignment.score, 70) self.assertEqual(alignment.shape, (2, 27)) self.assertAlmostEqual(alignment.annotations["% identity"], 44.44) self.assertEqual(alignment.annotations["identical"], 12) self.assertEqual(alignment.annotations["mismatches"], 15) self.assertEqual(alignment.annotations["positives"], 20) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 74.07) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "9483") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "PREDICTED: Callithrix jacchus ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited) (ARFGEF2), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "PREDICTED: Callithrix jacchus ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited) (ARFGEF2), mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 23) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 23) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|242009 0 YFLPFELVCQSKSSRIVVTALDCLQKL 27 0 ..|||.|.|||........|..|||.| 27 gi|296147 0 FALPFVLACQSRNAKMTTLAMQCLQGL 27 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 27], [ 0, 27]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|242009078|ref|XM_002425275.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|242009078|ref|XM_002425275.1|" ) self.assertEqual(alignment.target.annotations["gi"], "242009078") self.assertEqual(alignment.target.annotations["gis"], "242009078") self.assertEqual(alignment.target.annotations["acc."], "XM_002425275") self.assertEqual(alignment.target.annotations["accs."], "XM_002425275") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_002425275.1") self.assertEqual(alignment.target.annotations["length"], 5343) self.assertEqual(alignment.query.annotations["start"], 174) self.assertEqual(alignment.query.annotations["end"], 255) self.assertEqual(alignment.target.annotations["start"], 225) self.assertEqual(alignment.target.annotations["end"], 306) self.assertEqual(alignment.target.seq, "YFLPFELVCQSKSSRIVVTALDCLQKL") self.assertEqual(alignment.query.seq, "FALPFVLACQSRNAKMTTLAMQCLQGL") self.assertAlmostEqual(alignment.annotations["evalue"], 6.4) self.assertAlmostEqual(alignment.annotations["bit score"], 35.0) self.assertAlmostEqual(alignment.score, 70) self.assertEqual(alignment.shape, (2, 27)) self.assertAlmostEqual(alignment.annotations["% identity"], 44.44) self.assertEqual(alignment.annotations["identical"], 12) self.assertEqual(alignment.annotations["mismatches"], 15) self.assertEqual(alignment.annotations["positives"], 19) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 70.37) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "121224") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Pediculus humanus corporis Brefeldin A-inhibited guanine nucleotide-exchange protein, putative, mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "Pediculus humanus corporis Brefeldin A-inhibited guanine nucleotide-exchange protein, putative, mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 23) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 23) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|224078 0 YFLPFELACQSKSPRIVSTSLDCLQKL 27 0 ..|||.|||||...........|||.| 27 gi|296147 0 FALPFVLACQSRNAKMTTLAMQCLQGL 27 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 27], [ 0, 27]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|224078727|ref|XM_002187178.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|224078727|ref|XM_002187178.1|" ) self.assertEqual(alignment.target.annotations["gi"], "224078727") self.assertEqual(alignment.target.annotations["gis"], "224078727") self.assertEqual(alignment.target.annotations["acc."], "XM_002187178") self.assertEqual(alignment.target.annotations["accs."], "XM_002187178") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_002187178.1") self.assertEqual(alignment.target.annotations["length"], 5406) self.assertEqual(alignment.query.annotations["start"], 174) self.assertEqual(alignment.query.annotations["end"], 255) self.assertEqual(alignment.target.annotations["start"], 219) self.assertEqual(alignment.target.annotations["end"], 300) self.assertEqual(alignment.target.seq, "YFLPFELACQSKSPRIVSTSLDCLQKL") self.assertEqual(alignment.query.seq, "FALPFVLACQSRNAKMTTLAMQCLQGL") self.assertAlmostEqual(alignment.annotations["evalue"], 6.4) self.assertAlmostEqual(alignment.annotations["bit score"], 35.0) self.assertAlmostEqual(alignment.score, 70) self.assertEqual(alignment.shape, (2, 27)) self.assertAlmostEqual(alignment.annotations["% identity"], 44.44) self.assertEqual(alignment.annotations["identical"], 12) self.assertEqual(alignment.annotations["mismatches"], 15) self.assertEqual(alignment.annotations["positives"], 20) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 74.07) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "59729") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "PREDICTED: Taeniopygia guttata ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited) (ARFGEF2), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "PREDICTED: Taeniopygia guttata ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited) (ARFGEF2), mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 23) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 23) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|167736 0 YFLPFELACQSKSPRVVSTSLDCLQKL 27 0 ..|||.|||||...........|||.| 27 gi|296147 0 FALPFVLACQSRNAKMTTLAMQCLQGL 27 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 27], [ 0, 27]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|167736368|ref|NM_001085495.2|") self.assertEqual( alignment.target.annotations["ids"], "gi|167736368|ref|NM_001085495.2|" ) self.assertEqual(alignment.target.annotations["gi"], "167736368") self.assertEqual(alignment.target.annotations["gis"], "167736368") self.assertEqual(alignment.target.annotations["acc."], "NM_001085495") self.assertEqual(alignment.target.annotations["accs."], "NM_001085495") self.assertEqual(alignment.target.annotations["acc.ver"], "NM_001085495.2") self.assertEqual(alignment.target.annotations["length"], 8777) self.assertEqual(alignment.query.annotations["start"], 174) self.assertEqual(alignment.query.annotations["end"], 255) self.assertEqual(alignment.target.annotations["start"], 335) self.assertEqual(alignment.target.annotations["end"], 416) self.assertEqual(alignment.target.seq, "YFLPFELACQSKSPRVVSTSLDCLQKL") self.assertEqual(alignment.query.seq, "FALPFVLACQSRNAKMTTLAMQCLQGL") self.assertAlmostEqual(alignment.annotations["evalue"], 6.4) self.assertAlmostEqual(alignment.annotations["bit score"], 35.0) self.assertAlmostEqual(alignment.score, 70) self.assertEqual(alignment.shape, (2, 27)) self.assertAlmostEqual(alignment.annotations["% identity"], 44.44) self.assertEqual(alignment.annotations["identical"], 12) self.assertEqual(alignment.annotations["mismatches"], 15) self.assertEqual(alignment.annotations["positives"], 20) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 74.07) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/3") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "3") self.assertEqual(alignment.target.annotations["tax ids"], "10090") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Mus musculus ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited) (Arfgef2), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "Mus musculus ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited) (Arfgef2), mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 23) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 23) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|150417 0 YFLPFELACQSKSPRVVSTSLDCLQKL 27 0 ..|||.|||||...........|||.| 27 gi|296147 0 FALPFVLACQSRNAKMTTLAMQCLQGL 27 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 27], [ 0, 27]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|150417985|ref|NM_006420.2|") self.assertEqual( alignment.target.annotations["ids"], "gi|150417985|ref|NM_006420.2|" ) self.assertEqual(alignment.target.annotations["gi"], "150417985") self.assertEqual(alignment.target.annotations["gis"], "150417985") self.assertEqual(alignment.target.annotations["acc."], "NM_006420") self.assertEqual(alignment.target.annotations["accs."], "NM_006420") self.assertEqual(alignment.target.annotations["acc.ver"], "NM_006420.2") self.assertEqual(alignment.target.annotations["length"], 9004) self.assertEqual(alignment.query.annotations["start"], 174) self.assertEqual(alignment.query.annotations["end"], 255) self.assertEqual(alignment.target.annotations["start"], 353) self.assertEqual(alignment.target.annotations["end"], 434) self.assertEqual(alignment.target.seq, "YFLPFELACQSKSPRVVSTSLDCLQKL") self.assertEqual(alignment.query.seq, "FALPFVLACQSRNAKMTTLAMQCLQGL") self.assertAlmostEqual(alignment.annotations["evalue"], 6.4) self.assertAlmostEqual(alignment.annotations["bit score"], 35.0) self.assertAlmostEqual(alignment.score, 70) self.assertEqual(alignment.shape, (2, 27)) self.assertAlmostEqual(alignment.annotations["% identity"], 44.44) self.assertEqual(alignment.annotations["identical"], 12) self.assertEqual(alignment.annotations["mismatches"], 15) self.assertEqual(alignment.annotations["positives"], 20) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 74.07) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/3") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "3") self.assertEqual(alignment.target.annotations["tax ids"], "9606") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Homo sapiens ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited) (ARFGEF2), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "Homo sapiens ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited) (ARFGEF2), mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 23) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 23) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|149639 0 YFLPFELACQSKSPRVVSTSLDCLQKL 27 0 ..|||.|||||...........|||.| 27 gi|296147 0 FALPFVLACQSRNAKMTTLAMQCLQGL 27 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 27], [ 0, 27]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|149639802|ref|XM_001506842.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|149639802|ref|XM_001506842.1|" ) self.assertEqual(alignment.target.annotations["gi"], "149639802") self.assertEqual(alignment.target.annotations["gis"], "149639802") self.assertEqual(alignment.target.annotations["acc."], "XM_001506842") self.assertEqual(alignment.target.annotations["accs."], "XM_001506842") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_001506842.1") self.assertEqual(alignment.target.annotations["length"], 5268) self.assertEqual(alignment.query.annotations["start"], 174) self.assertEqual(alignment.query.annotations["end"], 255) self.assertEqual(alignment.target.annotations["start"], 105) self.assertEqual(alignment.target.annotations["end"], 186) self.assertEqual(alignment.target.seq, "YFLPFELACQSKSPRVVSTSLDCLQKL") self.assertEqual(alignment.query.seq, "FALPFVLACQSRNAKMTTLAMQCLQGL") self.assertAlmostEqual(alignment.annotations["evalue"], 6.4) self.assertAlmostEqual(alignment.annotations["bit score"], 35.0) self.assertAlmostEqual(alignment.score, 70) self.assertEqual(alignment.shape, (2, 27)) self.assertAlmostEqual(alignment.annotations["% identity"], 44.44) self.assertEqual(alignment.annotations["identical"], 12) self.assertEqual(alignment.annotations["mismatches"], 15) self.assertEqual(alignment.annotations["positives"], 20) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 74.07) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "9258") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "PREDICTED: Ornithorhynchus anatinus ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited) (ARFGEF2), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "PREDICTED: Ornithorhynchus anatinus ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited) (ARFGEF2), mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 23) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 23) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|114682 0 YFLPFELACQSKSPRVVSTSLDCLQKL 27 0 ..|||.|||||...........|||.| 27 gi|296147 0 FALPFVLACQSRNAKMTTLAMQCLQGL 27 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 27], [ 0, 27]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|114682530|ref|XM_001165584.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|114682530|ref|XM_001165584.1|" ) self.assertEqual(alignment.target.annotations["gi"], "114682530") self.assertEqual(alignment.target.annotations["gis"], "114682530") self.assertEqual(alignment.target.annotations["acc."], "XM_001165584") self.assertEqual(alignment.target.annotations["accs."], "XM_001165584") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_001165584.1") self.assertEqual(alignment.target.annotations["length"], 8859) self.assertEqual(alignment.query.annotations["start"], 174) self.assertEqual(alignment.query.annotations["end"], 255) self.assertEqual(alignment.target.annotations["start"], 201) self.assertEqual(alignment.target.annotations["end"], 282) self.assertEqual(alignment.target.seq, "YFLPFELACQSKSPRVVSTSLDCLQKL") self.assertEqual(alignment.query.seq, "FALPFVLACQSRNAKMTTLAMQCLQGL") self.assertAlmostEqual(alignment.annotations["evalue"], 6.4) self.assertAlmostEqual(alignment.annotations["bit score"], 35.0) self.assertAlmostEqual(alignment.score, 70) self.assertEqual(alignment.shape, (2, 27)) self.assertAlmostEqual(alignment.annotations["% identity"], 44.44) self.assertEqual(alignment.annotations["identical"], 12) self.assertEqual(alignment.annotations["mismatches"], 15) self.assertEqual(alignment.annotations["positives"], 20) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 74.07) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "9598") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "PREDICTED: Pan troglodytes ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited), transcript variant 3 (ARFGEF2), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "PREDICTED: Pan troglodytes ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited), transcript variant 3 (ARFGEF2), mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 23) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 23) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|313420 0 YFLPFELACQSKSPRVVSTSLDCLQKL 27 0 ..|||.|||||...........|||.| 27 gi|296147 0 FALPFVLACQSRNAKMTTLAMQCLQGL 27 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 27], [ 0, 27]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|31342050|ref|NM_181083.2|") self.assertEqual( alignment.target.annotations["ids"], "gi|31342050|ref|NM_181083.2|;gi|31126987|gb|AY255526.2|", ) self.assertEqual(alignment.target.annotations["gi"], "31342050") self.assertEqual(alignment.target.annotations["gis"], "31342050;31126987") self.assertEqual(alignment.target.annotations["acc."], "NM_181083") self.assertEqual( alignment.target.annotations["accs."], "NM_181083;AY255526" ) self.assertEqual(alignment.target.annotations["acc.ver"], "NM_181083.2") self.assertEqual(alignment.target.annotations["length"], 5784) self.assertEqual(alignment.query.annotations["start"], 174) self.assertEqual(alignment.query.annotations["end"], 255) self.assertEqual(alignment.target.annotations["start"], 201) self.assertEqual(alignment.target.annotations["end"], 282) self.assertEqual(alignment.target.seq, "YFLPFELACQSKSPRVVSTSLDCLQKL") self.assertEqual(alignment.query.seq, "FALPFVLACQSRNAKMTTLAMQCLQGL") self.assertAlmostEqual(alignment.annotations["evalue"], 6.4) self.assertAlmostEqual(alignment.annotations["bit score"], 35.0) self.assertAlmostEqual(alignment.score, 70) self.assertEqual(alignment.shape, (2, 27)) self.assertAlmostEqual(alignment.annotations["% identity"], 44.44) self.assertEqual(alignment.annotations["identical"], 12) self.assertEqual(alignment.annotations["mismatches"], 15) self.assertEqual(alignment.annotations["positives"], 20) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 74.07) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "10116") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Rattus norvegicus ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited) (Arfgef2), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "Rattus norvegicus ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited) (Arfgef2), mRNA<>Rattus norvegicus Brefeldin A-inhibited guanine nucleotide-exchange factor 2 (Big2) mRNA, complete cds", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 23) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 23) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|410036 0 RVHLSPLRQLWPGSSQPAVFPVQIKDSSPTCVACVRGQGKTTVPSPPRNRTSATL 55 0 |||........|....|.|...|......|..|....||..||||.||.|.|..| 55 gi|296147 0 RVHSFEELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEIL 55 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 55], [ 0, 55]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|410036861|ref|XM_001150377.3|") self.assertEqual( alignment.target.annotations["ids"], "gi|410036861|ref|XM_001150377.3|" ) self.assertEqual(alignment.target.annotations["gi"], "410036861") self.assertEqual(alignment.target.annotations["gis"], "410036861") self.assertEqual(alignment.target.annotations["acc."], "XM_001150377") self.assertEqual(alignment.target.annotations["accs."], "XM_001150377") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_001150377.3") self.assertEqual(alignment.target.annotations["length"], 3555) self.assertEqual(alignment.query.annotations["start"], 135) self.assertEqual(alignment.query.annotations["end"], 300) self.assertEqual(alignment.target.annotations["start"], 660) self.assertEqual(alignment.target.annotations["end"], 825) self.assertEqual( alignment.target.seq, "RVHLSPLRQLWPGSSQPAVFPVQIKDSSPTCVACVRGQGKTTVPSPPRNRTSATL", ) self.assertEqual( alignment.query.seq, "RVHSFEELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEIL", ) self.assertAlmostEqual(alignment.annotations["evalue"], 8.7) self.assertAlmostEqual(alignment.annotations["bit score"], 34.5) self.assertAlmostEqual(alignment.score, 69) self.assertEqual(alignment.shape, (2, 55)) self.assertAlmostEqual(alignment.annotations["% identity"], 36.36) self.assertEqual(alignment.annotations["identical"], 20) self.assertEqual(alignment.annotations["mismatches"], 35) self.assertEqual(alignment.annotations["positives"], 28) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 50.91) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "9598") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "PREDICTED: Pan troglodytes lactotransferrin, transcript variant 3 (LTF), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "PREDICTED: Pan troglodytes lactotransferrin, transcript variant 3 (LTF), mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 47) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 47) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|410036 0 RVHLSPLRQLWPGSSQPAVFPVQIKDSSPTCVACVRGQGKTTVPSPPRNRTSATL 55 0 |||........|....|.|...|......|..|....||..||||.||.|.|..| 55 gi|296147 0 RVHSFEELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEIL 55 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 55], [ 0, 55]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|410036860|ref|XM_516417.4|") self.assertEqual( alignment.target.annotations["ids"], "gi|410036860|ref|XM_516417.4|" ) self.assertEqual(alignment.target.annotations["gi"], "410036860") self.assertEqual(alignment.target.annotations["gis"], "410036860") self.assertEqual(alignment.target.annotations["acc."], "XM_516417") self.assertEqual(alignment.target.annotations["accs."], "XM_516417") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_516417.4") self.assertEqual(alignment.target.annotations["length"], 3660) self.assertEqual(alignment.query.annotations["start"], 135) self.assertEqual(alignment.query.annotations["end"], 300) self.assertEqual(alignment.target.annotations["start"], 765) self.assertEqual(alignment.target.annotations["end"], 930) self.assertEqual( alignment.target.seq, "RVHLSPLRQLWPGSSQPAVFPVQIKDSSPTCVACVRGQGKTTVPSPPRNRTSATL", ) self.assertEqual( alignment.query.seq, "RVHSFEELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEIL", ) self.assertAlmostEqual(alignment.annotations["evalue"], 8.7) self.assertAlmostEqual(alignment.annotations["bit score"], 34.5) self.assertAlmostEqual(alignment.score, 69) self.assertEqual(alignment.shape, (2, 55)) self.assertAlmostEqual(alignment.annotations["% identity"], 36.36) self.assertEqual(alignment.annotations["identical"], 20) self.assertEqual(alignment.annotations["mismatches"], 35) self.assertEqual(alignment.annotations["positives"], 28) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 50.91) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "9598") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "PREDICTED: Pan troglodytes lactotransferrin, transcript variant 8 (LTF), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "PREDICTED: Pan troglodytes lactotransferrin, transcript variant 8 (LTF), mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 47) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 47) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|397495 0 RVHLSPLRQLWPGSSQPAVFPVQIKDSSPTCVACVRGQGKTTVPSPPRNRTSATL 55 0 |||........|....|.|...|......|..|....||..||||.||.|.|..| 55 gi|296147 0 RVHSFEELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEIL 55 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 55], [ 0, 55]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|397495317|ref|XM_003818457.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|397495317|ref|XM_003818457.1|" ) self.assertEqual(alignment.target.annotations["gi"], "397495317") self.assertEqual(alignment.target.annotations["gis"], "397495317") self.assertEqual(alignment.target.annotations["acc."], "XM_003818457") self.assertEqual(alignment.target.annotations["accs."], "XM_003818457") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_003818457.1") self.assertEqual(alignment.target.annotations["length"], 2515) self.assertEqual(alignment.query.annotations["start"], 135) self.assertEqual(alignment.query.annotations["end"], 300) self.assertEqual(alignment.target.annotations["start"], 660) self.assertEqual(alignment.target.annotations["end"], 825) self.assertEqual( alignment.target.seq, "RVHLSPLRQLWPGSSQPAVFPVQIKDSSPTCVACVRGQGKTTVPSPPRNRTSATL", ) self.assertEqual( alignment.query.seq, "RVHSFEELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEIL", ) self.assertAlmostEqual(alignment.annotations["evalue"], 8.7) self.assertAlmostEqual(alignment.annotations["bit score"], 34.5) self.assertAlmostEqual(alignment.score, 69) self.assertEqual(alignment.shape, (2, 55)) self.assertAlmostEqual(alignment.annotations["% identity"], 36.36) self.assertEqual(alignment.annotations["identical"], 20) self.assertEqual(alignment.annotations["mismatches"], 35) self.assertEqual(alignment.annotations["positives"], 28) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 50.91) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "9597") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "PREDICTED: Pan paniscus lactotransferrin, transcript variant 2 (LTF), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "PREDICTED: Pan paniscus lactotransferrin, transcript variant 2 (LTF), mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 47) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 47) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|397495 0 RVHLSPLRQLWPGSSQPAVFPVQIKDSSPTCVACVRGQGKTTVPSPPRNRTSATL 55 0 |||........|....|.|...|......|..|....||..||||.||.|.|..| 55 gi|296147 0 RVHSFEELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEIL 55 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 55], [ 0, 55]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|397495315|ref|XM_003818456.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|397495315|ref|XM_003818456.1|" ) self.assertEqual(alignment.target.annotations["gi"], "397495315") self.assertEqual(alignment.target.annotations["gis"], "397495315") self.assertEqual(alignment.target.annotations["acc."], "XM_003818456") self.assertEqual(alignment.target.annotations["accs."], "XM_003818456") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_003818456.1") self.assertEqual(alignment.target.annotations["length"], 2620) self.assertEqual(alignment.query.annotations["start"], 135) self.assertEqual(alignment.query.annotations["end"], 300) self.assertEqual(alignment.target.annotations["start"], 765) self.assertEqual(alignment.target.annotations["end"], 930) self.assertEqual( alignment.target.seq, "RVHLSPLRQLWPGSSQPAVFPVQIKDSSPTCVACVRGQGKTTVPSPPRNRTSATL", ) self.assertEqual( alignment.query.seq, "RVHSFEELERHPDFALPFVLACQSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEIL", ) self.assertAlmostEqual(alignment.annotations["evalue"], 8.7) self.assertAlmostEqual(alignment.annotations["bit score"], 34.5) self.assertAlmostEqual(alignment.score, 69) self.assertEqual(alignment.shape, (2, 55)) self.assertAlmostEqual(alignment.annotations["% identity"], 36.36) self.assertEqual(alignment.annotations["identical"], 20) self.assertEqual(alignment.annotations["mismatches"], 35) self.assertEqual(alignment.annotations["positives"], 28) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 50.91) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "9597") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "PREDICTED: Pan paniscus lactotransferrin, transcript variant 1 (LTF), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "PREDICTED: Pan paniscus lactotransferrin, transcript variant 1 (LTF), mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 47) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 47) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|392887 0 YFLPFELACNSKSPKIVITALDCLQKL 27 0 ..|||.|||.|...|....|..|||.| 27 gi|296147 0 FALPFVLACQSRNAKMTTLAMQCLQGL 27 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 27], [ 0, 27]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|392887648|ref|NM_001026628.3|") self.assertEqual( alignment.target.annotations["ids"], "gi|392887648|ref|NM_001026628.3|" ) self.assertEqual(alignment.target.annotations["gi"], "392887648") self.assertEqual(alignment.target.annotations["gis"], "392887648") self.assertEqual(alignment.target.annotations["acc."], "NM_001026628") self.assertEqual(alignment.target.annotations["accs."], "NM_001026628") self.assertEqual(alignment.target.annotations["acc.ver"], "NM_001026628.3") self.assertEqual(alignment.target.annotations["length"], 1656) self.assertEqual(alignment.query.annotations["start"], 174) self.assertEqual(alignment.query.annotations["end"], 255) self.assertEqual(alignment.target.annotations["start"], 234) self.assertEqual(alignment.target.annotations["end"], 315) self.assertEqual(alignment.target.seq, "YFLPFELACNSKSPKIVITALDCLQKL") self.assertEqual(alignment.query.seq, "FALPFVLACQSRNAKMTTLAMQCLQGL") self.assertAlmostEqual(alignment.annotations["evalue"], 8.7) self.assertAlmostEqual(alignment.annotations["bit score"], 34.5) self.assertAlmostEqual(alignment.score, 69) self.assertEqual(alignment.shape, (2, 27)) self.assertAlmostEqual(alignment.annotations["% identity"], 48.15) self.assertEqual(alignment.annotations["identical"], 13) self.assertEqual(alignment.annotations["mismatches"], 14) self.assertEqual(alignment.annotations["positives"], 18) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 66.67) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "6239") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Caenorhabditis elegans Protein AGEF-1, isoform b (agef-1) mRNA, complete cds", ) self.assertEqual( alignment.target.annotations["titles"], "Caenorhabditis elegans Protein AGEF-1, isoform b (agef-1) mRNA, complete cds", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 23) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 23) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|392887 0 YFLPFELACNSKSPKIVITALDCLQKL 27 0 ..|||.|||.|...|....|..|||.| 27 gi|296147 0 FALPFVLACQSRNAKMTTLAMQCLQGL 27 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 27], [ 0, 27]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|392887646|ref|NM_001026627.5|") self.assertEqual( alignment.target.annotations["ids"], "gi|392887646|ref|NM_001026627.5|" ) self.assertEqual(alignment.target.annotations["gi"], "392887646") self.assertEqual(alignment.target.annotations["gis"], "392887646") self.assertEqual(alignment.target.annotations["acc."], "NM_001026627") self.assertEqual(alignment.target.annotations["accs."], "NM_001026627") self.assertEqual(alignment.target.annotations["acc.ver"], "NM_001026627.5") self.assertEqual(alignment.target.annotations["length"], 4785) self.assertEqual(alignment.query.annotations["start"], 174) self.assertEqual(alignment.query.annotations["end"], 255) self.assertEqual(alignment.target.annotations["start"], 234) self.assertEqual(alignment.target.annotations["end"], 315) self.assertEqual(alignment.target.seq, "YFLPFELACNSKSPKIVITALDCLQKL") self.assertEqual(alignment.query.seq, "FALPFVLACQSRNAKMTTLAMQCLQGL") self.assertAlmostEqual(alignment.annotations["evalue"], 8.7) self.assertAlmostEqual(alignment.annotations["bit score"], 34.5) self.assertAlmostEqual(alignment.score, 69) self.assertEqual(alignment.shape, (2, 27)) self.assertAlmostEqual(alignment.annotations["% identity"], 48.15) self.assertEqual(alignment.annotations["identical"], 13) self.assertEqual(alignment.annotations["mismatches"], 14) self.assertEqual(alignment.annotations["positives"], 18) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 66.67) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "6239") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Caenorhabditis elegans Protein AGEF-1, isoform a", ) self.assertEqual( alignment.target.annotations["titles"], "Caenorhabditis elegans Protein AGEF-1, isoform a", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 23) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 23) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|363727 0 NIGTMWNLQWEFKR*FSFSSRDDRRDPATSCQCMEGFLSLFCA 43 0 ||.....|.|.......|.|.|..|..|.||.|||.....|.| 43 gi|296147 0 NISMDLSLAWRMVEFLLFDSEDKERNSASSCLCMESNPPVFMA 43 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 43], [ 0, 43]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|363727654|ref|XM_001235329.2|") self.assertEqual( alignment.target.annotations["ids"], "gi|363727654|ref|XM_001235329.2|" ) self.assertEqual(alignment.target.annotations["gi"], "363727654") self.assertEqual(alignment.target.annotations["gis"], "363727654") self.assertEqual(alignment.target.annotations["acc."], "XM_001235329") self.assertEqual(alignment.target.annotations["accs."], "XM_001235329") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_001235329.2") self.assertEqual(alignment.target.annotations["length"], 8058) self.assertEqual(alignment.query.annotations["start"], 131) self.assertEqual(alignment.query.annotations["end"], 2) self.assertEqual(alignment.target.annotations["start"], 1805) self.assertEqual(alignment.target.annotations["end"], 1934) self.assertEqual( alignment.target.seq, "NIGTMWNLQWEFKR*FSFSSRDDRRDPATSCQCMEGFLSLFCA" ) self.assertEqual( alignment.query.seq, "NISMDLSLAWRMVEFLLFDSEDKERNSASSCLCMESNPPVFMA" ) self.assertAlmostEqual(alignment.annotations["evalue"], 8.7) self.assertAlmostEqual(alignment.annotations["bit score"], 34.5) self.assertAlmostEqual(alignment.score, 69) self.assertEqual(alignment.shape, (2, 43)) self.assertAlmostEqual(alignment.annotations["% identity"], 37.21) self.assertEqual(alignment.annotations["identical"], 16) self.assertEqual(alignment.annotations["mismatches"], 27) self.assertEqual(alignment.annotations["positives"], 20) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 46.51) self.assertEqual(alignment.annotations["query/sbjct frames"], "-1/3") self.assertEqual(alignment.query.annotations["frame"], "-1") self.assertEqual(alignment.target.annotations["frame"], "3") self.assertEqual(alignment.target.annotations["tax ids"], "9031") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "PREDICTED: Gallus gallus otogelin-like (LOC772154), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "PREDICTED: Gallus gallus otogelin-like (LOC772154), mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 37) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 37) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|350583 0 YFLPFELACQSRCPRIVSTSLDCLQKL 27 0 ..|||.||||||..........|||.| 27 gi|296147 0 FALPFVLACQSRNAKMTTLAMQCLQGL 27 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 27], [ 0, 27]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|350583133|ref|XM_001928010.4|") self.assertEqual( alignment.target.annotations["ids"], "gi|350583133|ref|XM_001928010.4|" ) self.assertEqual(alignment.target.annotations["gi"], "350583133") self.assertEqual(alignment.target.annotations["gis"], "350583133") self.assertEqual(alignment.target.annotations["acc."], "XM_001928010") self.assertEqual(alignment.target.annotations["accs."], "XM_001928010") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_001928010.4") self.assertEqual(alignment.target.annotations["length"], 7207) self.assertEqual(alignment.query.annotations["start"], 174) self.assertEqual(alignment.query.annotations["end"], 255) self.assertEqual(alignment.target.annotations["start"], 584) self.assertEqual(alignment.target.annotations["end"], 665) self.assertEqual(alignment.target.seq, "YFLPFELACQSRCPRIVSTSLDCLQKL") self.assertEqual(alignment.query.seq, "FALPFVLACQSRNAKMTTLAMQCLQGL") self.assertAlmostEqual(alignment.annotations["evalue"], 8.7) self.assertAlmostEqual(alignment.annotations["bit score"], 34.5) self.assertAlmostEqual(alignment.score, 69) self.assertEqual(alignment.shape, (2, 27)) self.assertAlmostEqual(alignment.annotations["% identity"], 48.15) self.assertEqual(alignment.annotations["identical"], 13) self.assertEqual(alignment.annotations["mismatches"], 14) self.assertEqual(alignment.annotations["positives"], 19) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 70.37) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/3") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "3") self.assertEqual(alignment.target.annotations["tax ids"], "9823") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "PREDICTED: Sus scrofa guanine nucleotide-exchange protein (LOC100156861), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "PREDICTED: Sus scrofa guanine nucleotide-exchange protein (LOC100156861), mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 23) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 23) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|345486 0 YFLPFELACQSKSPRIVVTSLDCLQKL 27 0 ..|||.|||||...........|||.| 27 gi|296147 0 FALPFVLACQSRNAKMTTLAMQCLQGL 27 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 27], [ 0, 27]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|345486369|ref|XM_001605920.2|") self.assertEqual( alignment.target.annotations["ids"], "gi|345486369|ref|XM_001605920.2|" ) self.assertEqual(alignment.target.annotations["gi"], "345486369") self.assertEqual(alignment.target.annotations["gis"], "345486369") self.assertEqual(alignment.target.annotations["acc."], "XM_001605920") self.assertEqual(alignment.target.annotations["accs."], "XM_001605920") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_001605920.2") self.assertEqual(alignment.target.annotations["length"], 7150) self.assertEqual(alignment.query.annotations["start"], 174) self.assertEqual(alignment.query.annotations["end"], 255) self.assertEqual(alignment.target.annotations["start"], 234) self.assertEqual(alignment.target.annotations["end"], 315) self.assertEqual(alignment.target.seq, "YFLPFELACQSKSPRIVVTSLDCLQKL") self.assertEqual(alignment.query.seq, "FALPFVLACQSRNAKMTTLAMQCLQGL") self.assertAlmostEqual(alignment.annotations["evalue"], 8.7) self.assertAlmostEqual(alignment.annotations["bit score"], 34.5) self.assertAlmostEqual(alignment.score, 69) self.assertEqual(alignment.shape, (2, 27)) self.assertAlmostEqual(alignment.annotations["% identity"], 44.44) self.assertEqual(alignment.annotations["identical"], 12) self.assertEqual(alignment.annotations["mismatches"], 15) self.assertEqual(alignment.annotations["positives"], 19) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 70.37) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "7425") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "PREDICTED: Nasonia vitripennis brefeldin A-inhibited guanine nucleotide-exchange protein 1-like (LOC100122365), mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "PREDICTED: Nasonia vitripennis brefeldin A-inhibited guanine nucleotide-exchange protein 1-like (LOC100122365), mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 23) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 23) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|344272 0 YFLPFELACQSRCPRIVSTSLDCLQKL 27 0 ..|||.||||||..........|||.| 27 gi|296147 0 FALPFVLACQSRNAKMTTLAMQCLQGL 27 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 27], [ 0, 27]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|344272888|ref|XR_133687.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|344272888|ref|XR_133687.1|" ) self.assertEqual(alignment.target.annotations["gi"], "344272888") self.assertEqual(alignment.target.annotations["gis"], "344272888") self.assertEqual(alignment.target.annotations["acc."], "XR_133687") self.assertEqual(alignment.target.annotations["accs."], "XR_133687") self.assertEqual(alignment.target.annotations["acc.ver"], "XR_133687.1") self.assertEqual(alignment.target.annotations["length"], 5928) self.assertEqual(alignment.query.annotations["start"], 174) self.assertEqual(alignment.query.annotations["end"], 255) self.assertEqual(alignment.target.annotations["start"], 237) self.assertEqual(alignment.target.annotations["end"], 318) self.assertEqual(alignment.target.seq, "YFLPFELACQSRCPRIVSTSLDCLQKL") self.assertEqual(alignment.query.seq, "FALPFVLACQSRNAKMTTLAMQCLQGL") self.assertAlmostEqual(alignment.annotations["evalue"], 8.7) self.assertAlmostEqual(alignment.annotations["bit score"], 34.5) self.assertAlmostEqual(alignment.score, 69) self.assertEqual(alignment.shape, (2, 27)) self.assertAlmostEqual(alignment.annotations["% identity"], 48.15) self.assertEqual(alignment.annotations["identical"], 13) self.assertEqual(alignment.annotations["mismatches"], 14) self.assertEqual(alignment.annotations["positives"], 19) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 70.37) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "9785") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "PREDICTED: Loxodonta africana brefeldin A-inhibited guanine nucleotide-exchange protein 1-like (LOC100676028), miscRNA", ) self.assertEqual( alignment.target.annotations["titles"], "PREDICTED: Loxodonta africana brefeldin A-inhibited guanine nucleotide-exchange protein 1-like (LOC100676028), miscRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 23) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 23) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|241632 0 YLMPFELACQSKSPRIVVTALDCIQKL 27 0 ...||.|||||........|..|.|.| 27 gi|296147 0 FALPFVLACQSRNAKMTTLAMQCLQGL 27 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 27], [ 0, 27]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|241632443|ref|XM_002408552.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|241632443|ref|XM_002408552.1|" ) self.assertEqual(alignment.target.annotations["gi"], "241632443") self.assertEqual(alignment.target.annotations["gis"], "241632443") self.assertEqual(alignment.target.annotations["acc."], "XM_002408552") self.assertEqual(alignment.target.annotations["accs."], "XM_002408552") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_002408552.1") self.assertEqual(alignment.target.annotations["length"], 4938) self.assertEqual(alignment.query.annotations["start"], 174) self.assertEqual(alignment.query.annotations["end"], 255) self.assertEqual(alignment.target.annotations["start"], 231) self.assertEqual(alignment.target.annotations["end"], 312) self.assertEqual(alignment.target.seq, "YLMPFELACQSKSPRIVVTALDCIQKL") self.assertEqual(alignment.query.seq, "FALPFVLACQSRNAKMTTLAMQCLQGL") self.assertAlmostEqual(alignment.annotations["evalue"], 8.7) self.assertAlmostEqual(alignment.annotations["bit score"], 34.5) self.assertAlmostEqual(alignment.score, 69) self.assertEqual(alignment.shape, (2, 27)) self.assertAlmostEqual(alignment.annotations["% identity"], 40.74) self.assertEqual(alignment.annotations["identical"], 11) self.assertEqual(alignment.annotations["mismatches"], 16) self.assertEqual(alignment.annotations["positives"], 19) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 70.37) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "6945") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Ixodes scapularis brefeldin A-inhibited guanine nucleotide-exchange protein, putative, mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "Ixodes scapularis brefeldin A-inhibited guanine nucleotide-exchange protein, putative, mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 23) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 23) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|157129 0 QAYNMSVTDLAIKSIQGIASLHTLPRSRAIIAFQAFV 37 0 |..|...|.||....||.......||||......||. 37 gi|296147 0 QSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFI 37 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 37], [ 0, 37]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|157129065|ref|XM_001655210.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|157129065|ref|XM_001655210.1|" ) self.assertEqual(alignment.target.annotations["gi"], "157129065") self.assertEqual(alignment.target.annotations["gis"], "157129065") self.assertEqual(alignment.target.annotations["acc."], "XM_001655210") self.assertEqual(alignment.target.annotations["accs."], "XM_001655210") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_001655210.1") self.assertEqual(alignment.target.annotations["length"], 3194) self.assertEqual(alignment.query.annotations["start"], 201) self.assertEqual(alignment.query.annotations["end"], 312) self.assertEqual(alignment.target.annotations["start"], 1116) self.assertEqual(alignment.target.annotations["end"], 1227) self.assertEqual( alignment.target.seq, "QAYNMSVTDLAIKSIQGIASLHTLPRSRAIIAFQAFV" ) self.assertEqual( alignment.query.seq, "QSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFI" ) self.assertAlmostEqual(alignment.annotations["evalue"], 8.7) self.assertAlmostEqual(alignment.annotations["bit score"], 34.5) self.assertAlmostEqual(alignment.score, 69) self.assertEqual(alignment.shape, (2, 37)) self.assertAlmostEqual(alignment.annotations["% identity"], 35.14) self.assertEqual(alignment.annotations["identical"], 13) self.assertEqual(alignment.annotations["mismatches"], 24) self.assertEqual(alignment.annotations["positives"], 25) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 67.57) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "7159") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Aedes aegypti hypothetical protein partial mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "Aedes aegypti hypothetical protein partial mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 32) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 32) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|157129 0 QAYNMSVTDLAIKSIQGIASLHTLPRSRAIIAFQAFV 37 0 |..|...|.||....||.......||||......||. 37 gi|296147 0 QSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFI 37 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 37], [ 0, 37]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|157129063|ref|XM_001655209.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|157129063|ref|XM_001655209.1|" ) self.assertEqual(alignment.target.annotations["gi"], "157129063") self.assertEqual(alignment.target.annotations["gis"], "157129063") self.assertEqual(alignment.target.annotations["acc."], "XM_001655209") self.assertEqual(alignment.target.annotations["accs."], "XM_001655209") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_001655209.1") self.assertEqual(alignment.target.annotations["length"], 3108) self.assertEqual(alignment.query.annotations["start"], 201) self.assertEqual(alignment.query.annotations["end"], 312) self.assertEqual(alignment.target.annotations["start"], 1116) self.assertEqual(alignment.target.annotations["end"], 1227) self.assertEqual( alignment.target.seq, "QAYNMSVTDLAIKSIQGIASLHTLPRSRAIIAFQAFV" ) self.assertEqual( alignment.query.seq, "QSRNAKMTTLAMQCLQGLSTVPSIPRSRLSEILDAFI" ) self.assertAlmostEqual(alignment.annotations["evalue"], 8.7) self.assertAlmostEqual(alignment.annotations["bit score"], 34.5) self.assertAlmostEqual(alignment.score, 69) self.assertEqual(alignment.shape, (2, 37)) self.assertAlmostEqual(alignment.annotations["% identity"], 35.14) self.assertEqual(alignment.annotations["identical"], 13) self.assertEqual(alignment.annotations["mismatches"], 24) self.assertEqual(alignment.annotations["positives"], 25) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 67.57) self.assertEqual(alignment.annotations["query/sbjct frames"], "1/1") self.assertEqual(alignment.query.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "7159") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Aedes aegypti hypothetical protein partial mRNA", ) self.assertEqual( alignment.target.annotations["titles"], "Aedes aegypti hypothetical protein partial mRNA", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 32) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 32) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|470250 0 HSQIGNPSTNNNNNQNLITQPQNYEMYKIN 30 0 ||.||.|......|......||||....|. 30 gi|296147 0 HSLIGKPTRKGVRNPDVFLAPQNYVLFSIS 30 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 30], [ 0, 30]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|470250072|ref|XM_004367211.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|470250072|ref|XM_004367211.1|" ) self.assertEqual(alignment.target.annotations["gi"], "470250072") self.assertEqual(alignment.target.annotations["gis"], "470250072") self.assertEqual(alignment.target.annotations["acc."], "XM_004367211") self.assertEqual(alignment.target.annotations["accs."], "XM_004367211") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_004367211.1") self.assertEqual(alignment.target.annotations["length"], 1509) self.assertEqual(alignment.query.annotations["start"], 214) self.assertEqual(alignment.query.annotations["end"], 124) self.assertEqual(alignment.target.annotations["start"], 1083) self.assertEqual(alignment.target.annotations["end"], 1173) self.assertEqual(alignment.target.seq, "HSQIGNPSTNNNNNQNLITQPQNYEMYKIN") self.assertEqual(alignment.query.seq, "HSLIGKPTRKGVRNPDVFLAPQNYVLFSIS") self.assertAlmostEqual(alignment.annotations["evalue"], 8.8) self.assertAlmostEqual(alignment.annotations["bit score"], 31.3) self.assertAlmostEqual(alignment.score, 62) self.assertEqual(alignment.shape, (2, 30)) self.assertAlmostEqual(alignment.annotations["% identity"], 36.67) self.assertEqual(alignment.annotations["identical"], 11) self.assertEqual(alignment.annotations["mismatches"], 19) self.assertEqual(alignment.annotations["positives"], 17) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 56.67) self.assertEqual(alignment.annotations["query/sbjct frames"], "-2/1") self.assertEqual(alignment.query.annotations["frame"], "-2") self.assertEqual(alignment.target.annotations["frame"], "1") self.assertEqual(alignment.target.annotations["tax ids"], "261658") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Dictyostelium fasciculatum hypothetical protein (DFA_07408) mRNA, complete cds", ) self.assertEqual( alignment.target.annotations["titles"], "Dictyostelium fasciculatum hypothetical protein (DFA_07408) mRNA, complete cds", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 55) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 26) alignment = next(alignments) self.assertEqual( str(alignment), """\ gi|470250 0 LFQEKTSLS*LWKVILFTML*SPSHCTRLPTQCPCLRS 38 0 ||.....||..|....|....|..........|.|..| 38 gi|296147 0 LFNISMDLSLAWRMVEFLLFDSEDKERNSASSCLCMES 38 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 38], [ 0, 38]]) # fmt: on ) ) self.assertEqual(alignment.query.id, "gi|296147483:1-350") self.assertEqual( alignment.query.description, "Saccharomyces cerevisiae S288c Mon2p (MON2) mRNA, complete cds", ) self.assertEqual(alignment.query.annotations["gi"], "0") self.assertEqual(alignment.query.annotations["acc."], "gi|296147483:1-350") self.assertEqual( alignment.query.annotations["acc.ver"], "gi|296147483:1-350" ) self.assertEqual(alignment.target.id, "gi|470250072|ref|XM_004367211.1|") self.assertEqual( alignment.target.annotations["ids"], "gi|470250072|ref|XM_004367211.1|" ) self.assertEqual(alignment.target.annotations["gi"], "470250072") self.assertEqual(alignment.target.annotations["gis"], "470250072") self.assertEqual(alignment.target.annotations["acc."], "XM_004367211") self.assertEqual(alignment.target.annotations["accs."], "XM_004367211") self.assertEqual(alignment.target.annotations["acc.ver"], "XM_004367211.1") self.assertEqual(alignment.target.annotations["length"], 1509) self.assertEqual(alignment.query.annotations["start"], 137) self.assertEqual(alignment.query.annotations["end"], 23) self.assertEqual(alignment.target.annotations["start"], 1298) self.assertEqual(alignment.target.annotations["end"], 1412) self.assertEqual( alignment.target.seq, "LFQEKTSLS*LWKVILFTML*SPSHCTRLPTQCPCLRS" ) self.assertEqual( alignment.query.seq, "LFNISMDLSLAWRMVEFLLFDSEDKERNSASSCLCMES" ) self.assertAlmostEqual(alignment.annotations["evalue"], 8.8) self.assertAlmostEqual(alignment.annotations["bit score"], 22.1) self.assertAlmostEqual(alignment.score, 42) self.assertEqual(alignment.shape, (2, 38)) self.assertAlmostEqual(alignment.annotations["% identity"], 26.32) self.assertEqual(alignment.annotations["identical"], 10) self.assertEqual(alignment.annotations["mismatches"], 28) self.assertEqual(alignment.annotations["positives"], 16) self.assertEqual(alignment.annotations["gap opens"], 0) self.assertEqual(alignment.annotations["gaps"], 0) self.assertAlmostEqual(alignment.annotations["% positives"], 42.11) self.assertEqual(alignment.annotations["query/sbjct frames"], "-1/3") self.assertEqual(alignment.query.annotations["frame"], "-1") self.assertEqual(alignment.target.annotations["frame"], "3") self.assertEqual(alignment.target.annotations["tax ids"], "261658") self.assertEqual(alignment.target.annotations["sci names"], "N/A") self.assertEqual(alignment.target.annotations["com names"], "N/A") self.assertEqual(alignment.target.annotations["blast names"], "N/A") self.assertEqual(alignment.target.annotations["super kingdoms"], "N/A") self.assertEqual( alignment.target.annotations["title"], "Dictyostelium fasciculatum hypothetical protein (DFA_07408) mRNA, complete cds", ) self.assertEqual( alignment.target.annotations["titles"], "Dictyostelium fasciculatum hypothetical protein (DFA_07408) mRNA, complete cds", ) self.assertEqual(alignment.target.annotations["strand"], "N/A") self.assertAlmostEqual(alignment.target.annotations["% coverage"], 55) self.assertAlmostEqual(alignment.annotations["% hsp coverage"], 33) with self.assertRaises(StopIteration): next(alignments) if __name__ == "__main__": runner = unittest.TextTestRunner(verbosity=2) unittest.main(testRunner=runner)