# Copyright 2008-2014 by Peter Cock. 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.emboss module.""" import unittest from io import StringIO from Bio import Align 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 TestEmboss(unittest.TestCase): def test_pair_example(self): # Alignment file obtained from EMBOSS: # http://emboss.sourceforge.net/docs/themes/alnformats/align.pair path = "Emboss/water.txt" alignments = Align.parse(path, "emboss") self.assertEqual(alignments.metadata["Program"], "water") self.assertEqual(alignments.metadata["Rundate"], "Wed Jan 16 17:23:19 2002") self.assertEqual(alignments.metadata["Report_file"], "stdout") alignment = next(alignments) self.assertEqual(alignment.annotations["Matrix"], "EBLOSUM62") self.assertAlmostEqual(alignment.annotations["Gap_penalty"], 10.0) self.assertAlmostEqual(alignment.annotations["Extend_penalty"], 0.5) self.assertEqual(alignment.annotations["Identity"], 112) self.assertEqual(alignment.annotations["Similarity"], 112) self.assertEqual(alignment.annotations["Gaps"], 19) self.assertAlmostEqual(alignment.annotations["Score"], 591.5) self.assertEqual(len(alignment), 2) self.assertEqual(alignment.shape, (2, 131)) self.assertEqual(alignment.sequences[0].id, "IXI_234") self.assertEqual(alignment.sequences[1].id, "IXI_235") self.assertEqual( alignment.sequences[0].seq, "TSPASIRPPAGPSSRPAMVSSRRTRPSPPGPRRPTGRPCCSAAPRRPQATGGWKTCSGTCTTSTSTRHRGRSGWSARTTTAACLRASRKSMRAACSRSAGSRPNRFAPTLMSSCITSTTGPPAWAGDRSHE", ) self.assertEqual( alignment.sequences[1].seq, "TSPASIRPPAGPSSRRPSPPGPRRPTGRPCCSAAPRRPQATGGWKTCSGTCTTSTSTRHRGRSGWRASRKSMRAACSRSAGSRPNRFAPTLMSSCITSTTGPPAWAGDRSHE", ) self.assertTrue( np.array_equal( alignment.coordinates, np.array([[0, 15, 24, 74, 84, 131], [0, 15, 15, 65, 65, 112]]), ) ) self.assertEqual( alignment[0], "TSPASIRPPAGPSSRPAMVSSRRTRPSPPGPRRPTGRPCCSAAPRRPQATGGWKTCSGTCTTSTSTRHRGRSGWSARTTTAACLRASRKSMRAACSRSAGSRPNRFAPTLMSSCITSTTGPPAWAGDRSHE", ) self.assertEqual( alignment[1], "TSPASIRPPAGPSSR---------RPSPPGPRRPTGRPCCSAAPRRPQATGGWKTCSGTCTTSTSTRHRGRSGW----------RASRKSMRAACSRSAGSRPNRFAPTLMSSCITSTTGPPAWAGDRSHE", ) self.assertEqual( alignment.column_annotations["emboss_consensus"], "||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||", ) self.assertEqual( str(alignment), """\ IXI_234 0 TSPASIRPPAGPSSRPAMVSSRRTRPSPPGPRRPTGRPCCSAAPRRPQATGGWKTCSGTC 0 |||||||||||||||---------|||||||||||||||||||||||||||||||||||| IXI_235 0 TSPASIRPPAGPSSR---------RPSPPGPRRPTGRPCCSAAPRRPQATGGWKTCSGTC IXI_234 60 TTSTSTRHRGRSGWSARTTTAACLRASRKSMRAACSRSAGSRPNRFAPTLMSSCITSTTG 60 ||||||||||||||----------|||||||||||||||||||||||||||||||||||| IXI_235 51 TTSTSTRHRGRSGW----------RASRKSMRAACSRSAGSRPNRFAPTLMSSCITSTTG IXI_234 120 PPAWAGDRSHE 131 120 ||||||||||| 131 IXI_235 101 PPAWAGDRSHE 112 """, ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['T', 'S', 'P', 'A', 'S', 'I', 'R', 'P', 'P', 'A', 'G', 'P', 'S', 'S', 'R', 'P', 'A', 'M', 'V', 'S', 'S', 'R', 'R', 'T', 'R', 'P', 'S', 'P', 'P', 'G', 'P', 'R', 'R', 'P', 'T', 'G', 'R', 'P', 'C', 'C', 'S', 'A', 'A', 'P', 'R', 'R', 'P', 'Q', 'A', 'T', 'G', 'G', 'W', 'K', 'T', 'C', 'S', 'G', 'T', 'C', 'T', 'T', 'S', 'T', 'S', 'T', 'R', 'H', 'R', 'G', 'R', 'S', 'G', 'W', 'S', 'A', 'R', 'T', 'T', 'T', 'A', 'A', 'C', 'L', 'R', 'A', 'S', 'R', 'K', 'S', 'M', 'R', 'A', 'A', 'C', 'S', 'R', 'S', 'A', 'G', 'S', 'R', 'P', 'N', 'R', 'F', 'A', 'P', 'T', 'L', 'M', 'S', 'S', 'C', 'I', 'T', 'S', 'T', 'T', 'G', 'P', 'P', 'A', 'W', 'A', 'G', 'D', 'R', 'S', 'H', 'E'], ['T', 'S', 'P', 'A', 'S', 'I', 'R', 'P', 'P', 'A', 'G', 'P', 'S', 'S', 'R', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'R', 'P', 'S', 'P', 'P', 'G', 'P', 'R', 'R', 'P', 'T', 'G', 'R', 'P', 'C', 'C', 'S', 'A', 'A', 'P', 'R', 'R', 'P', 'Q', 'A', 'T', 'G', 'G', 'W', 'K', 'T', 'C', 'S', 'G', 'T', 'C', 'T', 'T', 'S', 'T', 'S', 'T', 'R', 'H', 'R', 'G', 'R', 'S', 'G', 'W', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'R', 'A', 'S', 'R', 'K', 'S', 'M', 'R', 'A', 'A', 'C', 'S', 'R', 'S', 'A', 'G', 'S', 'R', 'P', 'N', 'R', 'F', 'A', 'P', 'T', 'L', 'M', 'S', 'S', 'C', 'I', 'T', 'S', 'T', 'T', 'G', 'P', 'P', 'A', 'W', 'A', 'G', 'D', 'R', 'S', 'H', 'E']], dtype='U') # fmt: on ) ) with self.assertRaises(StopIteration): next(alignments) def test_local_water2(self): """Test parsing a local alignment.""" path = "Emboss/water2.txt" alignments = Align.parse(path, "emboss") self.assertEqual(alignments.metadata["Program"], "water") self.assertEqual(alignments.metadata["Rundate"], "Sat Apr 04 2009 22:08:44") self.assertEqual( alignments.metadata["Command line"], "water -asequence asis:ACACACTCACACACACTTGGTCAGAGATGCTGTGCTTCTTGGAAGCAAGGNCTCAAAGGCAAGGTGCACGCAGAGGGACGTTTGAGTCTGGGATGAAGCATGTNCGTATTATTTATATGATGGAATTTCACGTTTTTATG -bsequence asis:CGTTTGAGTACTGGGATG -gapopen 10 -gapextend 0.5 -filter", ) self.assertEqual(alignments.metadata["Align_format"], "srspair") self.assertEqual(alignments.metadata["Report_file"], "stdout") alignment = next(alignments) self.assertEqual(alignment.annotations["Matrix"], "EDNAFULL") self.assertAlmostEqual(alignment.annotations["Gap_penalty"], 10.0) self.assertAlmostEqual(alignment.annotations["Extend_penalty"], 0.5) self.assertEqual(alignment.annotations["Identity"], 17) self.assertEqual(alignment.annotations["Similarity"], 17) self.assertEqual(alignment.annotations["Gaps"], 1) self.assertAlmostEqual(alignment.annotations["Score"], 75.0) self.assertEqual(len(alignment), 2) self.assertEqual(alignment.shape, (2, 18)) self.assertEqual(alignment.sequences[0].id, "asis") self.assertEqual(alignment.sequences[1].id, "asis") self.assertEqual( repr(alignment.sequences[0].seq), "Seq({78: 'CGTTTGAGTCTGGGATG'}, length=95)", ) self.assertEqual(alignment.sequences[0].seq[78:95], "CGTTTGAGTCTGGGATG") self.assertEqual(alignment.sequences[1].seq[0:18], "CGTTTGAGTACTGGGATG") self.assertTrue( np.array_equal( alignment.coordinates, np.array([[78, 87, 87, 95], [0, 9, 10, 18]]) ) ) self.assertEqual(alignment[0], "CGTTTGAGT-CTGGGATG") self.assertEqual(alignment[1], "CGTTTGAGTACTGGGATG") self.assertEqual( alignment.column_annotations["emboss_consensus"], "||||||||| ||||||||" ) self.assertEqual( str(alignment), """\ asis 78 CGTTTGAGT-CTGGGATG 95 0 |||||||||-|||||||| 18 asis 0 CGTTTGAGTACTGGGATG 18 """, ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['C', 'G', 'T', 'T', 'T', 'G', 'A', 'G', 'T', '-', 'C', 'T', 'G', 'G', 'G', 'A', 'T', 'G'], ['C', 'G', 'T', 'T', 'T', 'G', 'A', 'G', 'T', 'A', 'C', 'T', 'G', 'G', 'G', 'A', 'T', 'G']], dtype='U') # fmt: on ) ) with self.assertRaises(StopIteration): next(alignments) def test_matcher_simple(self): path = "Emboss/matcher_simple.txt" alignments = Align.parse(path, "emboss") self.assertEqual(alignments.metadata["Program"], "matcher") self.assertEqual(alignments.metadata["Rundate"], "Tue 8 Dec 2009 11:48:35") self.assertEqual( alignments.metadata["Command line"], "matcher [-asequence] rose.pro [-bsequence] rosemary.pro [-outfile] matcher_simple.txt -auto -sprotein -aformat simple", ) self.assertEqual(alignments.metadata["Align_format"], "simple") self.assertEqual(alignments.metadata["Report_file"], "matcher_simple.txt") alignment = next(alignments) self.assertEqual(alignment.annotations["Matrix"], "EBLOSUM62") self.assertAlmostEqual(alignment.annotations["Gap_penalty"], 14) self.assertAlmostEqual(alignment.annotations["Extend_penalty"], 4) self.assertEqual(alignment.annotations["Identity"], 7) self.assertEqual(alignment.annotations["Similarity"], 8) self.assertEqual(alignment.annotations["Gaps"], 0) self.assertAlmostEqual(alignment.annotations["Score"], 29) self.assertEqual(len(alignment), 2) self.assertEqual(alignment.shape, (2, 16)) self.assertEqual(alignment.sequences[0].id, "AF069992_1") self.assertEqual(alignment.sequences[1].id, "CAA85685.1") self.assertEqual( repr(alignment.sequences[0].seq), "Seq({72: 'GPPPQSPDENRAGESS'}, length=88)", ) self.assertEqual( repr(alignment.sequences[1].seq), "Seq({46: 'GVPPEEAGAAVAAESS'}, length=62)", ) self.assertEqual(alignment.sequences[0].seq[72:88], "GPPPQSPDENRAGESS") self.assertEqual(alignment.sequences[1].seq[46:62], "GVPPEEAGAAVAAESS") self.assertTrue( np.array_equal(alignment.coordinates, np.array([[72, 88], [46, 62]])) ) self.assertEqual(alignment[0], "GPPPQSPDENRAGESS") self.assertEqual(alignment[1], "GVPPEEAGAAVAAESS") self.assertEqual( alignment.column_annotations["emboss_consensus"], "|.||:......|.|||" ) self.assertEqual( str(alignment), """\ AF069992_ 72 GPPPQSPDENRAGESS 88 0 |.||.......|.||| 16 CAA85685. 46 GVPPEEAGAAVAAESS 62 """, ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['G', 'P', 'P', 'P', 'Q', 'S', 'P', 'D', 'E', 'N', 'R', 'A', 'G', 'E', 'S', 'S'], ['G', 'V', 'P', 'P', 'E', 'E', 'A', 'G', 'A', 'A', 'V', 'A', 'A', 'E', 'S', 'S']], dtype='U') # fmt: on ) ) with self.assertRaises(StopIteration): next(alignments) def test_matcher_pair(self): path = "Emboss/matcher_pair.txt" alignments = Align.parse(path, "emboss") self.check_matcher_pair(alignments) alignments = iter(alignments) self.check_matcher_pair(alignments) with Align.parse(path, "emboss") as alignments: self.check_matcher_pair(alignments) with self.assertRaises(AttributeError): alignments._stream with Align.parse(path, "emboss") as alignments: pass with self.assertRaises(AttributeError): alignments._stream def check_matcher_pair(self, alignments): self.assertEqual(alignments.metadata["Program"], "matcher") self.assertEqual(alignments.metadata["Rundate"], "Tue 8 Dec 2009 12:01:34") self.assertEqual( alignments.metadata["Command line"], "matcher [-asequence] hba_human.fasta [-bsequence] hbb_human.fasta [-outfile] matcher_pair.txt -alternatives 5 -aformat pair -sprotein", ) self.assertEqual(alignments.metadata["Align_format"], "pair") self.assertEqual(alignments.metadata["Report_file"], "matcher_pair.txt") alignment = next(alignments) self.assertEqual(alignment.annotations["Matrix"], "EBLOSUM62") self.assertAlmostEqual(alignment.annotations["Gap_penalty"], 14) self.assertAlmostEqual(alignment.annotations["Extend_penalty"], 4) self.assertEqual(alignment.annotations["Identity"], 63) self.assertEqual(alignment.annotations["Similarity"], 88) self.assertEqual(alignment.annotations["Gaps"], 8) self.assertAlmostEqual(alignment.annotations["Score"], 264) self.assertEqual(len(alignment), 2) self.assertEqual(alignment.shape, (2, 145)) self.assertEqual(alignment.sequences[0].id, "HBA_HUMAN") self.assertEqual(alignment.sequences[1].id, "HBB_HUMAN") self.assertEqual( repr(alignment.sequences[0].seq), "Seq({2: 'LSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQV...SKY'}, length=141)", ) self.assertEqual( repr(alignment.sequences[1].seq), "Seq({3: 'LTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMG...HKY'}, length=146)", ) self.assertEqual( alignment.sequences[0].seq[2:141], "LSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKY", ) self.assertEqual( alignment.sequences[1].seq[3:146], "LTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKY", ) self.assertTrue( np.array_equal( alignment.coordinates, np.array( [[2, 18, 20, 47, 47, 51, 51, 141], [3, 19, 19, 46, 47, 51, 56, 146]] ), ) ) self.assertEqual( alignment[0], "LSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHF-DLSH-----GSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKY", ) self.assertEqual( alignment[1], "LTPEEKSAVTALWGKV--NVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKY", ) self.assertEqual( alignment.column_annotations["emboss_consensus"], "|:|.:|:.|.|.|||| :..|.|.|||.|:.:.:|.|:.:|..| |||. |:.:||.|||||..|.::.:||:|::....:.||:||..||.|||.||:||.:.|:..||.|...||||.|.|:..|.:|.|:..|..||", ) self.assertEqual( str(alignment), """\ HBA_HUMAN 2 LSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHF-DLSH-----GSAQV 0 |.|..|..|.|.||||--...|.|.|||.|.....|.|...|..|-|||.-----|...| HBB_HUMAN 3 LTPEEKSAVTALWGKV--NVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKV HBA_HUMAN 56 KGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPA 60 |.|||||..|.....||.|........||.||..||.|||.||.||...|...||.|... HBB_HUMAN 61 KAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGK HBA_HUMAN 116 EFTPAVHASLDKFLASVSTVLTSKY 141 120 ||||.|.|...|..|.|...|..|| 145 HBB_HUMAN 121 EFTPPVQAAYQKVVAGVANALAHKY 146 """, ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['L', 'S', 'P', 'A', 'D', 'K', 'T', 'N', 'V', 'K', 'A', 'A', 'W', 'G', 'K', 'V', 'G', 'A', 'H', 'A', 'G', 'E', 'Y', 'G', 'A', 'E', 'A', 'L', 'E', 'R', 'M', 'F', 'L', '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', 'V', 'D', 'D', 'M', 'P', 'N', 'A', 'L', 'S', 'A', 'L', 'S', 'D', 'L', 'H', 'A', 'H', 'K', 'L', 'R', 'V', 'D', 'P', 'V', 'N', 'F', 'K', 'L', 'L', 'S', 'H', 'C', 'L', 'L', 'V', 'T', 'L', 'A', 'A', 'H', 'L', 'P', 'A', 'E', 'F', 'T', 'P', 'A', 'V', 'H', 'A', 'S', 'L', 'D', 'K', 'F', 'L', 'A', 'S', 'V', 'S', 'T', 'V', 'L', 'T', 'S', 'K', 'Y'], ['L', 'T', 'P', 'E', 'E', 'K', 'S', 'A', 'V', 'T', 'A', 'L', 'W', 'G', 'K', 'V', '-', '-', 'N', 'V', 'D', 'E', 'V', 'G', 'G', 'E', 'A', 'L', 'G', 'R', 'L', 'L', 'V', 'V', 'Y', 'P', 'W', 'T', 'Q', 'R', 'F', 'F', 'E', 'S', 'F', 'G', 'D', 'L', 'S', 'T', 'P', 'D', 'A', 'V', 'M', 'G', 'N', 'P', 'K', 'V', 'K', 'A', 'H', 'G', 'K', 'K', 'V', 'L', 'G', 'A', 'F', 'S', 'D', 'G', 'L', 'A', 'H', 'L', 'D', 'N', 'L', 'K', 'G', 'T', 'F', 'A', 'T', 'L', 'S', 'E', 'L', 'H', 'C', 'D', 'K', 'L', 'H', 'V', 'D', 'P', 'E', 'N', 'F', 'R', 'L', 'L', 'G', 'N', 'V', 'L', 'V', 'C', 'V', 'L', 'A', 'H', 'H', 'F', 'G', 'K', 'E', 'F', 'T', 'P', 'P', 'V', 'Q', 'A', 'A', 'Y', 'Q', 'K', 'V', 'V', 'A', 'G', 'V', 'A', 'N', 'A', 'L', 'A', 'H', 'K', 'Y']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertEqual(alignment.annotations["Matrix"], "EBLOSUM62") self.assertAlmostEqual(alignment.annotations["Gap_penalty"], 14) self.assertAlmostEqual(alignment.annotations["Extend_penalty"], 4) self.assertEqual(alignment.annotations["Identity"], 6) self.assertEqual(alignment.annotations["Similarity"], 9) self.assertEqual(alignment.annotations["Gaps"], 0) self.assertAlmostEqual(alignment.annotations["Score"], 32) self.assertEqual(len(alignment), 2) self.assertEqual(alignment.shape, (2, 13)) self.assertEqual(alignment.sequences[0].id, "HBA_HUMAN") self.assertEqual(alignment.sequences[1].id, "HBB_HUMAN") self.assertEqual( repr(alignment.sequences[0].seq), "Seq({60: 'KKVADALTNAVAH'}, length=73)", ) self.assertEqual( repr(alignment.sequences[1].seq), "Seq({131: 'QKVVAGVANALAH'}, length=144)", ) self.assertEqual(alignment.sequences[0].seq[60:73], "KKVADALTNAVAH") self.assertEqual(alignment.sequences[1].seq[131:144], "QKVVAGVANALAH") self.assertTrue( np.array_equal(alignment.coordinates, np.array([[60, 73], [131, 144]])) ) self.assertEqual(alignment[0], "KKVADALTNAVAH") self.assertEqual(alignment[1], "QKVVAGVANALAH") self.assertEqual( alignment.column_annotations["emboss_consensus"], ":||...:.||:||" ) self.assertEqual( str(alignment), """\ HBA_HUMAN 60 KKVADALTNAVAH 73 0 .||.....||.|| 13 HBB_HUMAN 131 QKVVAGVANALAH 144 """, ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['K', 'K', 'V', 'A', 'D', 'A', 'L', 'T', 'N', 'A', 'V', 'A', 'H'], ['Q', 'K', 'V', 'V', 'A', 'G', 'V', 'A', 'N', 'A', 'L', 'A', 'H']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertEqual(alignment.annotations["Matrix"], "EBLOSUM62") self.assertAlmostEqual(alignment.annotations["Gap_penalty"], 14) self.assertAlmostEqual(alignment.annotations["Extend_penalty"], 4) self.assertEqual(alignment.annotations["Identity"], 7) self.assertEqual(alignment.annotations["Similarity"], 10) self.assertEqual(alignment.annotations["Gaps"], 0) self.assertAlmostEqual(alignment.annotations["Score"], 28) self.assertEqual(len(alignment), 2) self.assertEqual(alignment.shape, (2, 18)) self.assertEqual(alignment.sequences[0].id, "HBA_HUMAN") self.assertEqual(alignment.sequences[1].id, "HBB_HUMAN") self.assertEqual( repr(alignment.sequences[0].seq), "Seq({90: 'KLRVDPVNFKLLSHCLLV'}, length=108)", ) self.assertEqual( repr(alignment.sequences[1].seq), "Seq({17: 'KVNVDEVGGEALGRLLVV'}, length=35)", ) self.assertEqual(alignment.sequences[0].seq[90:108], "KLRVDPVNFKLLSHCLLV") self.assertEqual(alignment.sequences[1].seq[17:35], "KVNVDEVGGEALGRLLVV") self.assertTrue( np.array_equal(alignment.coordinates, np.array([[90, 108], [17, 35]])) ) self.assertEqual(alignment[0], "KLRVDPVNFKLLSHCLLV") self.assertEqual(alignment[1], "KVNVDEVGGEALGRLLVV") self.assertEqual( alignment.column_annotations["emboss_consensus"], "|:.||.|..:.|...|:|" ) self.assertEqual( str(alignment), """\ HBA_HUMAN 90 KLRVDPVNFKLLSHCLLV 108 0 |..||.|....|...|.| 18 HBB_HUMAN 17 KVNVDEVGGEALGRLLVV 35 """, ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['K', 'L', 'R', 'V', 'D', 'P', 'V', 'N', 'F', 'K', 'L', 'L', 'S', 'H', 'C', 'L', 'L', 'V'], ['K', 'V', 'N', 'V', 'D', 'E', 'V', 'G', 'G', 'E', 'A', 'L', 'G', 'R', 'L', 'L', 'V', 'V']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertEqual(alignment.annotations["Matrix"], "EBLOSUM62") self.assertAlmostEqual(alignment.annotations["Gap_penalty"], 14) self.assertAlmostEqual(alignment.annotations["Extend_penalty"], 4) self.assertEqual(alignment.annotations["Identity"], 6) self.assertEqual(alignment.annotations["Similarity"], 6) self.assertEqual(alignment.annotations["Gaps"], 0) self.assertAlmostEqual(alignment.annotations["Score"], 23) self.assertEqual(len(alignment), 2) self.assertEqual(alignment.shape, (2, 10)) self.assertEqual(alignment.sequences[0].id, "HBA_HUMAN") self.assertEqual(alignment.sequences[1].id, "HBB_HUMAN") self.assertEqual( repr(alignment.sequences[0].seq), "Seq({80: 'LSALSDLHAH'}, length=90)", ) self.assertEqual( repr(alignment.sequences[1].seq), "Seq({68: 'LGAFSDGLAH'}, length=78)", ) self.assertEqual(alignment.sequences[0].seq[80:90], "LSALSDLHAH") self.assertEqual(alignment.sequences[1].seq[68:78], "LGAFSDGLAH") self.assertTrue( np.array_equal(alignment.coordinates, np.array([[80, 90], [68, 78]])) ) self.assertEqual(alignment[0], "LSALSDLHAH") self.assertEqual(alignment[1], "LGAFSDGLAH") self.assertEqual(alignment.column_annotations["emboss_consensus"], "|.|.||..||") self.assertEqual( str(alignment), """\ HBA_HUMAN 80 LSALSDLHAH 90 0 |.|.||..|| 10 HBB_HUMAN 68 LGAFSDGLAH 78 """, ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['L', 'S', 'A', 'L', 'S', 'D', 'L', 'H', 'A', 'H'], ['L', 'G', 'A', 'F', 'S', 'D', 'G', 'L', 'A', 'H']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertEqual(alignment.annotations["Matrix"], "EBLOSUM62") self.assertAlmostEqual(alignment.annotations["Gap_penalty"], 14) self.assertAlmostEqual(alignment.annotations["Extend_penalty"], 4) self.assertEqual(alignment.annotations["Identity"], 6) self.assertEqual(alignment.annotations["Similarity"], 8) self.assertEqual(alignment.annotations["Gaps"], 0) self.assertAlmostEqual(alignment.annotations["Score"], 23) self.assertEqual(len(alignment), 2) self.assertEqual(alignment.shape, (2, 10)) self.assertEqual(alignment.sequences[0].id, "HBA_HUMAN") self.assertEqual(alignment.sequences[1].id, "HBB_HUMAN") self.assertEqual( repr(alignment.sequences[0].seq), "Seq({10: 'VKAAWGKVGA'}, length=20)", ) self.assertEqual( repr(alignment.sequences[1].seq), "Seq({126: 'VQAAYQKVVA'}, length=136)", ) self.assertEqual(alignment.sequences[0].seq[10:20], "VKAAWGKVGA") self.assertEqual(alignment.sequences[1].seq[126:136], "VQAAYQKVVA") self.assertTrue( np.array_equal(alignment.coordinates, np.array([[10, 20], [126, 136]])) ) self.assertEqual(alignment[0], "VKAAWGKVGA") self.assertEqual(alignment[1], "VQAAYQKVVA") self.assertEqual(alignment.column_annotations["emboss_consensus"], "|:||:.||.|") self.assertEqual( str(alignment), """\ HBA_HUMAN 10 VKAAWGKVGA 20 0 |.||..||.| 10 HBB_HUMAN 126 VQAAYQKVVA 136 """, ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['V', 'K', 'A', 'A', 'W', 'G', 'K', 'V', 'G', 'A'], ['V', 'Q', 'A', 'A', 'Y', 'Q', 'K', 'V', 'V', 'A']], dtype='U') # fmt: on ) ) with self.assertRaises(StopIteration): next(alignments) def test_pair_example_nobrief(self): # Variation on the alignment file obtained from EMBOSS # (http://emboss.sourceforge.net/docs/themes/alnformats/align.pair) # if we include 3 sequences to align against, and we use the -nobrief # command line option. path = "Emboss/needle_nobrief_multiple.pair" alignments = Align.parse(path, "emboss") self.assertEqual(alignments.metadata["Program"], "needle") self.assertEqual(alignments.metadata["Rundate"], "Fri 23 Jul 2021 22:45:41") self.assertEqual( alignments.metadata["Command line"], "needle -asequence seqa.fa -bsequence seqb.fa -datafile EBLOSUM62 -gapopen 10 -gapextend 0.5 -nobrief -outfile stdout", ) self.assertEqual(alignments.metadata["Align_format"], "srspair") self.assertEqual(alignments.metadata["Report_file"], "stdout") alignment = next(alignments) self.assertEqual(alignment.annotations["Matrix"], "EBLOSUM62") self.assertAlmostEqual(alignment.annotations["Gap_penalty"], 10.0) self.assertAlmostEqual(alignment.annotations["Extend_penalty"], 0.5) self.assertEqual(alignment.annotations["Identity"], 112) self.assertEqual(alignment.annotations["Similarity"], 112) self.assertEqual(alignment.annotations["Gaps"], 19) self.assertAlmostEqual(alignment.annotations["Score"], 591.5) self.assertEqual(alignment.annotations["Longest_Identity"], "100.00%") self.assertEqual(alignment.annotations["Longest_Similarity"], "100.00%") self.assertEqual(alignment.annotations["Shortest_Identity"], "85.50%") self.assertEqual(alignment.annotations["Shortest_Similarity"], "85.50%") self.assertEqual(len(alignment), 2) self.assertEqual(alignment.shape, (2, 131)) self.assertEqual(alignment.sequences[0].id, "IXI_234") self.assertEqual(alignment.sequences[1].id, "IXI_235") self.assertEqual( alignment.sequences[0].seq, "TSPASIRPPAGPSSRPAMVSSRRTRPSPPGPRRPTGRPCCSAAPRRPQATGGWKTCSGTCTTSTSTRHRGRSGWSARTTTAACLRASRKSMRAACSRSAGSRPNRFAPTLMSSCITSTTGPPAWAGDRSHE", ) self.assertEqual( alignment.sequences[1].seq, "TSPASIRPPAGPSSRRPSPPGPRRPTGRPCCSAAPRRPQATGGWKTCSGTCTTSTSTRHRGRSGWRASRKSMRAACSRSAGSRPNRFAPTLMSSCITSTTGPPAWAGDRSHE", ) self.assertTrue( np.array_equal( alignment.coordinates, np.array([[0, 15, 24, 74, 84, 131], [0, 15, 15, 65, 65, 112]]), ) ) self.assertEqual( alignment[0], "TSPASIRPPAGPSSRPAMVSSRRTRPSPPGPRRPTGRPCCSAAPRRPQATGGWKTCSGTCTTSTSTRHRGRSGWSARTTTAACLRASRKSMRAACSRSAGSRPNRFAPTLMSSCITSTTGPPAWAGDRSHE", ) self.assertEqual( alignment[1], "TSPASIRPPAGPSSR---------RPSPPGPRRPTGRPCCSAAPRRPQATGGWKTCSGTCTTSTSTRHRGRSGW----------RASRKSMRAACSRSAGSRPNRFAPTLMSSCITSTTGPPAWAGDRSHE", ) self.assertEqual( alignment.column_annotations["emboss_consensus"], "||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||", ) self.assertEqual( str(alignment), """\ IXI_234 0 TSPASIRPPAGPSSRPAMVSSRRTRPSPPGPRRPTGRPCCSAAPRRPQATGGWKTCSGTC 0 |||||||||||||||---------|||||||||||||||||||||||||||||||||||| IXI_235 0 TSPASIRPPAGPSSR---------RPSPPGPRRPTGRPCCSAAPRRPQATGGWKTCSGTC IXI_234 60 TTSTSTRHRGRSGWSARTTTAACLRASRKSMRAACSRSAGSRPNRFAPTLMSSCITSTTG 60 ||||||||||||||----------|||||||||||||||||||||||||||||||||||| IXI_235 51 TTSTSTRHRGRSGW----------RASRKSMRAACSRSAGSRPNRFAPTLMSSCITSTTG IXI_234 120 PPAWAGDRSHE 131 120 ||||||||||| 131 IXI_235 101 PPAWAGDRSHE 112 """, ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['T', 'S', 'P', 'A', 'S', 'I', 'R', 'P', 'P', 'A', 'G', 'P', 'S', 'S', 'R', 'P', 'A', 'M', 'V', 'S', 'S', 'R', 'R', 'T', 'R', 'P', 'S', 'P', 'P', 'G', 'P', 'R', 'R', 'P', 'T', 'G', 'R', 'P', 'C', 'C', 'S', 'A', 'A', 'P', 'R', 'R', 'P', 'Q', 'A', 'T', 'G', 'G', 'W', 'K', 'T', 'C', 'S', 'G', 'T', 'C', 'T', 'T', 'S', 'T', 'S', 'T', 'R', 'H', 'R', 'G', 'R', 'S', 'G', 'W', 'S', 'A', 'R', 'T', 'T', 'T', 'A', 'A', 'C', 'L', 'R', 'A', 'S', 'R', 'K', 'S', 'M', 'R', 'A', 'A', 'C', 'S', 'R', 'S', 'A', 'G', 'S', 'R', 'P', 'N', 'R', 'F', 'A', 'P', 'T', 'L', 'M', 'S', 'S', 'C', 'I', 'T', 'S', 'T', 'T', 'G', 'P', 'P', 'A', 'W', 'A', 'G', 'D', 'R', 'S', 'H', 'E'], ['T', 'S', 'P', 'A', 'S', 'I', 'R', 'P', 'P', 'A', 'G', 'P', 'S', 'S', 'R', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'R', 'P', 'S', 'P', 'P', 'G', 'P', 'R', 'R', 'P', 'T', 'G', 'R', 'P', 'C', 'C', 'S', 'A', 'A', 'P', 'R', 'R', 'P', 'Q', 'A', 'T', 'G', 'G', 'W', 'K', 'T', 'C', 'S', 'G', 'T', 'C', 'T', 'T', 'S', 'T', 'S', 'T', 'R', 'H', 'R', 'G', 'R', 'S', 'G', 'W', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'R', 'A', 'S', 'R', 'K', 'S', 'M', 'R', 'A', 'A', 'C', 'S', 'R', 'S', 'A', 'G', 'S', 'R', 'P', 'N', 'R', 'F', 'A', 'P', 'T', 'L', 'M', 'S', 'S', 'C', 'I', 'T', 'S', 'T', 'T', 'G', 'P', 'P', 'A', 'W', 'A', 'G', 'D', 'R', 'S', 'H', 'E']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertEqual(alignment.annotations["Matrix"], "EBLOSUM62") self.assertAlmostEqual(alignment.annotations["Gap_penalty"], 10.0) self.assertAlmostEqual(alignment.annotations["Extend_penalty"], 0.5) self.assertEqual(alignment.annotations["Identity"], 120) self.assertEqual(alignment.annotations["Similarity"], 120) self.assertEqual(alignment.annotations["Gaps"], 4) self.assertAlmostEqual(alignment.annotations["Score"], 618.0) self.assertEqual(alignment.annotations["Longest_Identity"], "94.49%") self.assertEqual(alignment.annotations["Longest_Similarity"], "94.49%") self.assertEqual(alignment.annotations["Shortest_Identity"], "91.60%") self.assertEqual(alignment.annotations["Shortest_Similarity"], "91.60%") self.assertEqual(len(alignment), 2) self.assertEqual(alignment.shape, (2, 131)) self.assertEqual(alignment.sequences[0].id, "IXI_234") self.assertEqual(alignment.sequences[1].id, "IXI_236") self.assertEqual( alignment.sequences[0].seq, "TSPASIRPPAGPSSRPAMVSSRRTRPSPPGPRRPTGRPCCSAAPRRPQATGGWKTCSGTCTTSTSTRHRGRSGWSARTTTAACLRASRKSMRAACSRSAGSRPNRFAPTLMSSCITSTTGPPAWAGDRSHE", ) self.assertEqual( alignment.sequences[1].seq, "TSPASIRPPAGPSSRPAMVSSRRPSPPPPRRPPGRPCCSAAPPRPQATGGWKTCSGTCTTSTSTRHRGRSGWSARTTTAACLRASRKSMRAACSRGSRPPRFAPPLMSSCITSTTGPPPPAGDRSHE", ) self.assertTrue( np.array_equal( alignment.coordinates, np.array([[0, 22, 24, 97, 99, 131], [0, 22, 22, 95, 95, 127]]), ) ) self.assertEqual( alignment[0], "TSPASIRPPAGPSSRPAMVSSRRTRPSPPGPRRPTGRPCCSAAPRRPQATGGWKTCSGTCTTSTSTRHRGRSGWSARTTTAACLRASRKSMRAACSRSAGSRPNRFAPTLMSSCITSTTGPPAWAGDRSHE", ) self.assertEqual( alignment[1], "TSPASIRPPAGPSSRPAMVSSR--RPSPPPPRRPPGRPCCSAAPPRPQATGGWKTCSGTCTTSTSTRHRGRSGWSARTTTAACLRASRKSMRAACSR--GSRPPRFAPPLMSSCITSTTGPPPPAGDRSHE", ) self.assertEqual( alignment.column_annotations["emboss_consensus"], "|||||||||||||||||||||| |||||.||||.|||||||||.|||||||||||||||||||||||||||||||||||||||||||||||||||| ||||.||||.|||||||||||||..|||||||", ) self.assertEqual( str(alignment), """\ IXI_234 0 TSPASIRPPAGPSSRPAMVSSRRTRPSPPGPRRPTGRPCCSAAPRRPQATGGWKTCSGTC 0 ||||||||||||||||||||||--|||||.||||.|||||||||.||||||||||||||| IXI_236 0 TSPASIRPPAGPSSRPAMVSSR--RPSPPPPRRPPGRPCCSAAPPRPQATGGWKTCSGTC IXI_234 60 TTSTSTRHRGRSGWSARTTTAACLRASRKSMRAACSRSAGSRPNRFAPTLMSSCITSTTG 60 |||||||||||||||||||||||||||||||||||||--||||.||||.||||||||||| IXI_236 58 TTSTSTRHRGRSGWSARTTTAACLRASRKSMRAACSR--GSRPPRFAPPLMSSCITSTTG IXI_234 120 PPAWAGDRSHE 131 120 ||..||||||| 131 IXI_236 116 PPPPAGDRSHE 127 """, ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['T', 'S', 'P', 'A', 'S', 'I', 'R', 'P', 'P', 'A', 'G', 'P', 'S', 'S', 'R', 'P', 'A', 'M', 'V', 'S', 'S', 'R', 'R', 'T', 'R', 'P', 'S', 'P', 'P', 'G', 'P', 'R', 'R', 'P', 'T', 'G', 'R', 'P', 'C', 'C', 'S', 'A', 'A', 'P', 'R', 'R', 'P', 'Q', 'A', 'T', 'G', 'G', 'W', 'K', 'T', 'C', 'S', 'G', 'T', 'C', 'T', 'T', 'S', 'T', 'S', 'T', 'R', 'H', 'R', 'G', 'R', 'S', 'G', 'W', 'S', 'A', 'R', 'T', 'T', 'T', 'A', 'A', 'C', 'L', 'R', 'A', 'S', 'R', 'K', 'S', 'M', 'R', 'A', 'A', 'C', 'S', 'R', 'S', 'A', 'G', 'S', 'R', 'P', 'N', 'R', 'F', 'A', 'P', 'T', 'L', 'M', 'S', 'S', 'C', 'I', 'T', 'S', 'T', 'T', 'G', 'P', 'P', 'A', 'W', 'A', 'G', 'D', 'R', 'S', 'H', 'E'], ['T', 'S', 'P', 'A', 'S', 'I', 'R', 'P', 'P', 'A', 'G', 'P', 'S', 'S', 'R', 'P', 'A', 'M', 'V', 'S', 'S', 'R', '-', '-', 'R', 'P', 'S', 'P', 'P', 'P', 'P', 'R', 'R', 'P', 'P', 'G', 'R', 'P', 'C', 'C', 'S', 'A', 'A', 'P', 'P', 'R', 'P', 'Q', 'A', 'T', 'G', 'G', 'W', 'K', 'T', 'C', 'S', 'G', 'T', 'C', 'T', 'T', 'S', 'T', 'S', 'T', 'R', 'H', 'R', 'G', 'R', 'S', 'G', 'W', 'S', 'A', 'R', 'T', 'T', 'T', 'A', 'A', 'C', 'L', 'R', 'A', 'S', 'R', 'K', 'S', 'M', 'R', 'A', 'A', 'C', 'S', 'R', '-', '-', 'G', 'S', 'R', 'P', 'P', 'R', 'F', 'A', 'P', 'P', 'L', 'M', 'S', 'S', 'C', 'I', 'T', 'S', 'T', 'T', 'G', 'P', 'P', 'P', 'P', 'A', 'G', 'D', 'R', 'S', 'H', 'E']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertEqual(alignment.annotations["Matrix"], "EBLOSUM62") self.assertAlmostEqual(alignment.annotations["Gap_penalty"], 10.0) self.assertAlmostEqual(alignment.annotations["Extend_penalty"], 0.5) self.assertEqual(alignment.annotations["Identity"], 119) self.assertEqual(alignment.annotations["Similarity"], 124) self.assertEqual(alignment.annotations["Gaps"], 7) self.assertAlmostEqual(alignment.annotations["Score"], 609.0) self.assertEqual(alignment.annotations["Longest_Identity"], "95.97%") self.assertEqual(alignment.annotations["Longest_Similarity"], "100.00%") self.assertEqual(alignment.annotations["Shortest_Identity"], "90.84%") self.assertEqual(alignment.annotations["Shortest_Similarity"], "94.66%") self.assertEqual(len(alignment), 2) self.assertEqual(alignment.shape, (2, 131)) self.assertEqual(alignment.sequences[0].id, "IXI_234") self.assertEqual(alignment.sequences[1].id, "IXI_237") self.assertEqual( alignment.sequences[0].seq, "TSPASIRPPAGPSSRPAMVSSRRTRPSPPGPRRPTGRPCCSAAPRRPQATGGWKTCSGTCTTSTSTRHRGRSGWSARTTTAACLRASRKSMRAACSRSAGSRPNRFAPTLMSSCITSTTGPPAWAGDRSHE", ) self.assertEqual( alignment.sequences[1].seq, "TSPASLRPPAGPSSRPAMVSSRRRPSPPGPRRPTCSAAPRRPQATGGYKTCSGTCTTSTSTRHRGRSGYSARTTTAACLRASRKSMRAACSRGSRPNRFAPTLMSSCLTSTTGPPAYAGDRSHE", ) self.assertTrue( np.array_equal( alignment.coordinates, np.array( [[0, 23, 24, 35, 39, 97, 99, 131], [0, 23, 23, 34, 34, 92, 92, 124]] ), ) ) self.assertEqual( alignment[0], "TSPASIRPPAGPSSRPAMVSSRRTRPSPPGPRRPTGRPCCSAAPRRPQATGGWKTCSGTCTTSTSTRHRGRSGWSARTTTAACLRASRKSMRAACSRSAGSRPNRFAPTLMSSCITSTTGPPAWAGDRSHE", ) self.assertEqual( alignment[1], "TSPASLRPPAGPSSRPAMVSSRR-RPSPPGPRRPT----CSAAPRRPQATGGYKTCSGTCTTSTSTRHRGRSGYSARTTTAACLRASRKSMRAACSR--GSRPNRFAPTLMSSCLTSTTGPPAYAGDRSHE", ) self.assertEqual( alignment.column_annotations["emboss_consensus"], "|||||:||||||||||||||||| ||||||||||| |||||||||||||:||||||||||||||||||||:||||||||||||||||||||||| |||||||||||||||:||||||||:|||||||", ) self.assertEqual( str(alignment), """\ IXI_234 0 TSPASIRPPAGPSSRPAMVSSRRTRPSPPGPRRPTGRPCCSAAPRRPQATGGWKTCSGTC 0 |||||.|||||||||||||||||-|||||||||||----|||||||||||||.||||||| IXI_237 0 TSPASLRPPAGPSSRPAMVSSRR-RPSPPGPRRPT----CSAAPRRPQATGGYKTCSGTC IXI_234 60 TTSTSTRHRGRSGWSARTTTAACLRASRKSMRAACSRSAGSRPNRFAPTLMSSCITSTTG 60 |||||||||||||.|||||||||||||||||||||||--|||||||||||||||.||||| IXI_237 55 TTSTSTRHRGRSGYSARTTTAACLRASRKSMRAACSR--GSRPNRFAPTLMSSCLTSTTG IXI_234 120 PPAWAGDRSHE 131 120 |||.||||||| 131 IXI_237 113 PPAYAGDRSHE 124 """, ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['T', 'S', 'P', 'A', 'S', 'I', 'R', 'P', 'P', 'A', 'G', 'P', 'S', 'S', 'R', 'P', 'A', 'M', 'V', 'S', 'S', 'R', 'R', 'T', 'R', 'P', 'S', 'P', 'P', 'G', 'P', 'R', 'R', 'P', 'T', 'G', 'R', 'P', 'C', 'C', 'S', 'A', 'A', 'P', 'R', 'R', 'P', 'Q', 'A', 'T', 'G', 'G', 'W', 'K', 'T', 'C', 'S', 'G', 'T', 'C', 'T', 'T', 'S', 'T', 'S', 'T', 'R', 'H', 'R', 'G', 'R', 'S', 'G', 'W', 'S', 'A', 'R', 'T', 'T', 'T', 'A', 'A', 'C', 'L', 'R', 'A', 'S', 'R', 'K', 'S', 'M', 'R', 'A', 'A', 'C', 'S', 'R', 'S', 'A', 'G', 'S', 'R', 'P', 'N', 'R', 'F', 'A', 'P', 'T', 'L', 'M', 'S', 'S', 'C', 'I', 'T', 'S', 'T', 'T', 'G', 'P', 'P', 'A', 'W', 'A', 'G', 'D', 'R', 'S', 'H', 'E'], ['T', 'S', 'P', 'A', 'S', 'L', 'R', 'P', 'P', 'A', 'G', 'P', 'S', 'S', 'R', 'P', 'A', 'M', 'V', 'S', 'S', 'R', 'R', '-', 'R', 'P', 'S', 'P', 'P', 'G', 'P', 'R', 'R', 'P', 'T', '-', '-', '-', '-', 'C', 'S', 'A', 'A', 'P', 'R', 'R', 'P', 'Q', 'A', 'T', 'G', 'G', 'Y', 'K', 'T', 'C', 'S', 'G', 'T', 'C', 'T', 'T', 'S', 'T', 'S', 'T', 'R', 'H', 'R', 'G', 'R', 'S', 'G', 'Y', 'S', 'A', 'R', 'T', 'T', 'T', 'A', 'A', 'C', 'L', 'R', 'A', 'S', 'R', 'K', 'S', 'M', 'R', 'A', 'A', 'C', 'S', 'R', '-', '-', 'G', 'S', 'R', 'P', 'N', 'R', 'F', 'A', 'P', 'T', 'L', 'M', 'S', 'S', 'C', 'L', 'T', 'S', 'T', 'T', 'G', 'P', 'P', 'A', 'Y', 'A', 'G', 'D', 'R', 'S', 'H', 'E']], dtype='U') # fmt: on ) ) with self.assertRaises(StopIteration): next(alignments) def test_pair_example2(self): path = "Emboss/needle.txt" alignments = Align.parse(path, "emboss") self.assertEqual(alignments.metadata["Program"], "needle") self.assertEqual(alignments.metadata["Rundate"], "Sun 27 Apr 2007 17:20:35") self.assertEqual( alignments.metadata["Command line"], "needle [-asequence] Spo0F.faa [-bsequence] paired_r.faa -sformat2 pearson", ) self.assertEqual(alignments.metadata["Align_format"], "srspair") self.assertEqual(alignments.metadata["Report_file"], "ref_rec .needle") alignment = next(alignments) self.assertEqual(alignment.annotations["Matrix"], "EBLOSUM62") self.assertAlmostEqual(alignment.annotations["Gap_penalty"], 10.0) self.assertAlmostEqual(alignment.annotations["Extend_penalty"], 0.5) self.assertEqual(alignment.annotations["Identity"], 32) self.assertEqual(alignment.annotations["Similarity"], 64) self.assertEqual(alignment.annotations["Gaps"], 17) self.assertAlmostEqual(alignment.annotations["Score"], 112.0) self.assertEqual(len(alignment), 2) self.assertEqual(alignment.shape, (2, 124)) self.assertEqual(alignment.sequences[0].id, "ref_rec") self.assertEqual(alignment.sequences[1].id, "gi|94968718|receiver") self.assertEqual( alignment.sequences[0].seq, "KILIVDDQYGIRILLNEVFNKEGYQTFQAANGLQALDIVTKERPDLVLLDMKIPGMDGIEILKRMKVIDENIRVIIMTAYGELDMIQESKELGALTHFAKPFDIDEIRDAV", ) self.assertEqual( alignment.sequences[1].seq, "VLLADDHALVRRGFRLMLEDDPEIEIVAEAGDGAQAVKLAGELHPRVVVMDCAMPGMSGMDATKQIRTQWPDIAVLMLTMHSEDTWVRLALEAGANGYILKSAIDLDLIQAVRRVANGET", ) self.assertTrue( np.array_equal( alignment.coordinates, np.array( [ [0, 1, 7, 7, 17, 19, 100, 100, 108, 109, 111, 111], [0, 0, 6, 10, 20, 20, 101, 102, 110, 110, 112, 120], ] ), ) ) self.assertEqual( alignment[0], "KILIVDD----QYGIRILLNEVFNKEGYQTFQAANGLQALDIVTKERPDLVLLDMKIPGMDGIEILKRMKVIDENIRVIIMTAYGELDMIQESKELGALTHFAK-PFDIDEIRDAV--------", ) self.assertEqual( alignment[1], "-VLLADDHALVRRGFRLMLED--DPEIEIVAEAGDGAQAVKLAGELHPRVVVMDCAMPGMSGMDATKQIRTQWPDIAVLMLTMHSEDTWVRLALEAGANGYILKSAIDLDLIQ-AVRRVANGET", ) self.assertEqual( alignment.column_annotations["emboss_consensus"], " :|:.|| :.|.|::|.: :.|.....:|.:|.||:.:..:..|.:|::|..:|||.|::..|:::....:|.|:::|.:.|...::.:.|.||..:..| ..|:|.|: || ", ) self.assertEqual( str(alignment), """\ ref_rec 0 KILIVDD----QYGIRILLNEVFNKEGYQTFQAANGLQALDIVTKERPDLVLLDMKIPGM 0 -.|..||----..|.|..|..--..|......|..|.||........|..|..|...||| gi|949687 0 -VLLADDHALVRRGFRLMLED--DPEIEIVAEAGDGAQAVKLAGELHPRVVVMDCAMPGM ref_rec 56 DGIEILKRMKVIDENIRVIIMTAYGELDMIQESKELGALTHFAK-PFDIDEIRDAV---- 60 .|....|........|.|...|...|........|.||.....|-..|.|.|.-||---- gi|949687 57 SGMDATKQIRTQWPDIAVLMLTMHSEDTWVRLALEAGANGYILKSAIDLDLIQ-AVRRVA ref_rec 111 ---- 111 120 ---- 124 gi|949687 116 NGET 120 """, ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['K', 'I', 'L', 'I', 'V', 'D', 'D', '-', '-', '-', '-', 'Q', 'Y', 'G', 'I', 'R', 'I', 'L', 'L', 'N', 'E', 'V', 'F', 'N', 'K', 'E', 'G', 'Y', 'Q', 'T', 'F', 'Q', 'A', 'A', 'N', 'G', 'L', 'Q', 'A', 'L', 'D', 'I', 'V', 'T', 'K', 'E', 'R', 'P', 'D', 'L', 'V', 'L', 'L', 'D', 'M', 'K', 'I', 'P', 'G', 'M', 'D', 'G', 'I', 'E', 'I', 'L', 'K', 'R', 'M', 'K', 'V', 'I', 'D', 'E', 'N', 'I', 'R', 'V', 'I', 'I', 'M', 'T', 'A', 'Y', 'G', 'E', 'L', 'D', 'M', 'I', 'Q', 'E', 'S', 'K', 'E', 'L', 'G', 'A', 'L', 'T', 'H', 'F', 'A', 'K', '-', 'P', 'F', 'D', 'I', 'D', 'E', 'I', 'R', 'D', 'A', 'V', '-', '-', '-', '-', '-', '-', '-', '-'], ['-', 'V', 'L', 'L', 'A', 'D', 'D', 'H', 'A', 'L', 'V', 'R', 'R', 'G', 'F', 'R', 'L', 'M', 'L', 'E', 'D', '-', '-', 'D', 'P', 'E', 'I', 'E', 'I', 'V', 'A', 'E', 'A', 'G', 'D', 'G', 'A', 'Q', 'A', 'V', 'K', 'L', 'A', 'G', 'E', 'L', 'H', 'P', 'R', 'V', 'V', 'V', 'M', 'D', 'C', 'A', 'M', 'P', 'G', 'M', 'S', 'G', 'M', 'D', 'A', 'T', 'K', 'Q', 'I', 'R', 'T', 'Q', 'W', 'P', 'D', 'I', 'A', 'V', 'L', 'M', 'L', 'T', 'M', 'H', 'S', 'E', 'D', 'T', 'W', 'V', 'R', 'L', 'A', 'L', 'E', 'A', 'G', 'A', 'N', 'G', 'Y', 'I', 'L', 'K', 'S', 'A', 'I', 'D', 'L', 'D', 'L', 'I', 'Q', '-', 'A', 'V', 'R', 'R', 'V', 'A', 'N', 'G', 'E', 'T']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertEqual(alignment.annotations["Matrix"], "EBLOSUM62") self.assertAlmostEqual(alignment.annotations["Gap_penalty"], 10.0) self.assertAlmostEqual(alignment.annotations["Extend_penalty"], 0.5) self.assertEqual(alignment.annotations["Identity"], 34) self.assertEqual(alignment.annotations["Similarity"], 58) self.assertEqual(alignment.annotations["Gaps"], 9) self.assertAlmostEqual(alignment.annotations["Score"], 154.0) self.assertEqual(len(alignment), 2) self.assertEqual(alignment.shape, (2, 119)) self.assertEqual(alignment.sequences[0].id, "ref_rec") self.assertEqual(alignment.sequences[1].id, "gi|94968761|receiver") self.assertEqual( alignment.sequences[0].seq, "KILIVDDQYGIRILLNEVFNKEGYQTFQAANGLQALDIVTKERPDLVLLDMKIPGMDGIEILKRMKVIDENIRVIIMTAYGELDMIQESKELGALTHFAKPFDIDEIRDAV", ) self.assertEqual( alignment.sequences[1].seq, "ILIVDDEANTLASLSRAFRLAGHEATVCDNAVRALEIAKSKPFDLILSDVVMPGRDGLTLLEDLKTAGVQAPVVMMSGQAHIEMAVKATRLGALDFLEKPLSTDKLLLTVENALKLKR", ) self.assertTrue( np.array_equal( alignment.coordinates, np.array([[0, 1, 111, 111], [0, 0, 110, 118]]) ) ) self.assertEqual( alignment[0], "KILIVDDQYGIRILLNEVFNKEGYQTFQAANGLQALDIVTKERPDLVLLDMKIPGMDGIEILKRMKVIDENIRVIIMTAYGELDMIQESKELGALTHFAKPFDIDEIRDAV--------", ) self.assertEqual( alignment[1], "-ILIVDDEANTLASLSRAFRLAGHEATVCDNAVRALEIAKSKPFDLILSDVVMPGRDGLTLLEDLKTAGVQAPVVMMSGQAHIEMAVKATRLGALDFLEKPLSTDKLLLTVENALKLKR", ) self.assertEqual( alignment.column_annotations["emboss_consensus"], " ||||||:......|:..|...|::.....|.::||:|...:..||:|.|:.:||.||:.:|:.:|.......|::|:....::|..::..||||....||...|::...| ", ) self.assertEqual( str(alignment), """\ ref_rec 0 KILIVDDQYGIRILLNEVFNKEGYQTFQAANGLQALDIVTKERPDLVLLDMKIPGMDGIE 0 -||||||.......|...|...|.......|...||.|......||.|.|...||.||.. gi|949687 0 -ILIVDDEANTLASLSRAFRLAGHEATVCDNAVRALEIAKSKPFDLILSDVVMPGRDGLT ref_rec 60 ILKRMKVIDENIRVIIMTAYGELDMIQESKELGALTHFAKPFDIDEIRDAV-------- 60 .|...|.......|..|.......|......||||....||...|.....|-------- gi|949687 59 LLEDLKTAGVQAPVVMMSGQAHIEMAVKATRLGALDFLEKPLSTDKLLLTVENALKLKR ref_rec 111 119 gi|949687 118 """, ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['K', 'I', 'L', 'I', 'V', 'D', 'D', 'Q', 'Y', 'G', 'I', 'R', 'I', 'L', 'L', 'N', 'E', 'V', 'F', 'N', 'K', 'E', 'G', 'Y', 'Q', 'T', 'F', 'Q', 'A', 'A', 'N', 'G', 'L', 'Q', 'A', 'L', 'D', 'I', 'V', 'T', 'K', 'E', 'R', 'P', 'D', 'L', 'V', 'L', 'L', 'D', 'M', 'K', 'I', 'P', 'G', 'M', 'D', 'G', 'I', 'E', 'I', 'L', 'K', 'R', 'M', 'K', 'V', 'I', 'D', 'E', 'N', 'I', 'R', 'V', 'I', 'I', 'M', 'T', 'A', 'Y', 'G', 'E', 'L', 'D', 'M', 'I', 'Q', 'E', 'S', 'K', 'E', 'L', 'G', 'A', 'L', 'T', 'H', 'F', 'A', 'K', 'P', 'F', 'D', 'I', 'D', 'E', 'I', 'R', 'D', 'A', 'V', '-', '-', '-', '-', '-', '-', '-', '-'], ['-', 'I', 'L', 'I', 'V', 'D', 'D', 'E', 'A', 'N', 'T', 'L', 'A', 'S', 'L', 'S', 'R', 'A', 'F', 'R', 'L', 'A', 'G', 'H', 'E', 'A', 'T', 'V', 'C', 'D', 'N', 'A', 'V', 'R', 'A', 'L', 'E', 'I', 'A', 'K', 'S', 'K', 'P', 'F', 'D', 'L', 'I', 'L', 'S', 'D', 'V', 'V', 'M', 'P', 'G', 'R', 'D', 'G', 'L', 'T', 'L', 'L', 'E', 'D', 'L', 'K', 'T', 'A', 'G', 'V', 'Q', 'A', 'P', 'V', 'V', 'M', 'M', 'S', 'G', 'Q', 'A', 'H', 'I', 'E', 'M', 'A', 'V', 'K', 'A', 'T', 'R', 'L', 'G', 'A', 'L', 'D', 'F', 'L', 'E', 'K', 'P', 'L', 'S', 'T', 'D', 'K', 'L', 'L', 'L', 'T', 'V', 'E', 'N', 'A', 'L', 'K', 'L', 'K', 'R']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertEqual(alignment.annotations["Matrix"], "EBLOSUM62") self.assertAlmostEqual(alignment.annotations["Gap_penalty"], 10.0) self.assertAlmostEqual(alignment.annotations["Extend_penalty"], 0.5) self.assertEqual(alignment.annotations["Identity"], 29) self.assertEqual(alignment.annotations["Similarity"], 53) self.assertEqual(alignment.annotations["Gaps"], 9) self.assertAlmostEqual(alignment.annotations["Score"], 121.0) self.assertEqual(len(alignment), 2) self.assertEqual(alignment.shape, (2, 120)) self.assertEqual(alignment.sequences[0].id, "ref_rec") self.assertEqual(alignment.sequences[1].id, "gi|94967506|receiver") self.assertEqual( alignment.sequences[0].seq, "KILIVDDQYGIRILLNEVFNKEGYQTFQAANGLQALDIVTKERPDLVLLDMKIPGMDGIEILKRMKVIDENIRVIIMTAYGELDMIQESKELGALTHFAKPFDIDEIRDAV", ) self.assertEqual( alignment.sequences[1].seq, "LHIVVVDDDPGTCVYIESVFAELGHTCKSFVRPEAAEEYILTHPVDLAIVDVYLGSTTGVEVLRRCRVHRPKLYAVIITGQISLEMAARSIAEGAVDYIQKPIDIDALLNIAERALEHKE", ) self.assertTrue( np.array_equal( alignment.coordinates, np.array([[0, 0, 111, 111], [0, 1, 112, 120]]) ) ) self.assertEqual( alignment[0], "-KILIVDDQYGIRILLNEVFNKEGYQTFQAANGLQALDIVTKERPDLVLLDMKIPGMDGIEILKRMKVIDENIRVIIMTAYGELDMIQESKELGALTHFAKPFDIDEIRDAV--------", ) self.assertEqual( alignment[1], "LHIVVVDDDPGTCVYIESVFAELGHTCKSFVRPEAAEEYILTHPVDLAIVDVYLGSTTGVEVLRRCRVHRPKLYAVIITGQISLEMAARSIAEGAVDYIQKPIDIDALLNIAERALEHKE", ) self.assertEqual( alignment.column_annotations["emboss_consensus"], " .|::|||..|..:.:..||.:.|:..........|.:.:.....||.::|:.:....|:|:|:|.:|....:..:|:|....|:|...|...||:.:..||.|||.:.:.. ", ) self.assertEqual( str(alignment), """\ ref_rec 0 -KILIVDDQYGIRILLNEVFNKEGYQTFQAANGLQALDIVTKERPDLVLLDMKIPGMDGI 0 -.|..|||..|.......||...|...........|.........||...|.......|. gi|949675 0 LHIVVVDDDPGTCVYIESVFAELGHTCKSFVRPEAAEEYILTHPVDLAIVDVYLGSTTGV ref_rec 59 EILKRMKVIDENIRVIIMTAYGELDMIQESKELGALTHFAKPFDIDEIRDAV-------- 60 |.|.|..|........|.|....|.|...|...||.....||.|||......-------- gi|949675 60 EVLRRCRVHRPKLYAVIITGQISLEMAARSIAEGAVDYIQKPIDIDALLNIAERALEHKE ref_rec 111 120 gi|949675 120 """, ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['-', 'K', 'I', 'L', 'I', 'V', 'D', 'D', 'Q', 'Y', 'G', 'I', 'R', 'I', 'L', 'L', 'N', 'E', 'V', 'F', 'N', 'K', 'E', 'G', 'Y', 'Q', 'T', 'F', 'Q', 'A', 'A', 'N', 'G', 'L', 'Q', 'A', 'L', 'D', 'I', 'V', 'T', 'K', 'E', 'R', 'P', 'D', 'L', 'V', 'L', 'L', 'D', 'M', 'K', 'I', 'P', 'G', 'M', 'D', 'G', 'I', 'E', 'I', 'L', 'K', 'R', 'M', 'K', 'V', 'I', 'D', 'E', 'N', 'I', 'R', 'V', 'I', 'I', 'M', 'T', 'A', 'Y', 'G', 'E', 'L', 'D', 'M', 'I', 'Q', 'E', 'S', 'K', 'E', 'L', 'G', 'A', 'L', 'T', 'H', 'F', 'A', 'K', 'P', 'F', 'D', 'I', 'D', 'E', 'I', 'R', 'D', 'A', 'V', '-', '-', '-', '-', '-', '-', '-', '-'], ['L', 'H', 'I', 'V', 'V', 'V', 'D', 'D', 'D', 'P', 'G', 'T', 'C', 'V', 'Y', 'I', 'E', 'S', 'V', 'F', 'A', 'E', 'L', 'G', 'H', 'T', 'C', 'K', 'S', 'F', 'V', 'R', 'P', 'E', 'A', 'A', 'E', 'E', 'Y', 'I', 'L', 'T', 'H', 'P', 'V', 'D', 'L', 'A', 'I', 'V', 'D', 'V', 'Y', 'L', 'G', 'S', 'T', 'T', 'G', 'V', 'E', 'V', 'L', 'R', 'R', 'C', 'R', 'V', 'H', 'R', 'P', 'K', 'L', 'Y', 'A', 'V', 'I', 'I', 'T', 'G', 'Q', 'I', 'S', 'L', 'E', 'M', 'A', 'A', 'R', 'S', 'I', 'A', 'E', 'G', 'A', 'V', 'D', 'Y', 'I', 'Q', 'K', 'P', 'I', 'D', 'I', 'D', 'A', 'L', 'L', 'N', 'I', 'A', 'E', 'R', 'A', 'L', 'E', 'H', 'K', 'E']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertEqual(alignment.annotations["Matrix"], "EBLOSUM62") self.assertAlmostEqual(alignment.annotations["Gap_penalty"], 10.0) self.assertAlmostEqual(alignment.annotations["Extend_penalty"], 0.5) self.assertEqual(alignment.annotations["Identity"], 30) self.assertEqual(alignment.annotations["Similarity"], 64) self.assertEqual(alignment.annotations["Gaps"], 9) self.assertAlmostEqual(alignment.annotations["Score"], 126.0) self.assertEqual(len(alignment), 2) self.assertEqual(alignment.shape, (2, 118)) self.assertEqual(alignment.sequences[0].id, "ref_rec") self.assertEqual(alignment.sequences[1].id, "gi|94970045|receiver") self.assertEqual( alignment.sequences[0].seq, "KILIVDDQYGIRILLNEVFNKEGYQTFQAANGLQALDIVTKERPDLVLLDMKIPGMDGIEILKRMKVIDENIRVIIMTAYGELDMIQESKELGALTHFAKPFDIDEIRDAV", ) self.assertEqual( alignment.sequences[1].seq, "VLLVEDEEALRAAAGDFLETRGYKIMTARDGTEALSMASKFAERIDVLITDLVMPGISGRVLAQELVKIHPETKVMYMSGYDDETVMVNGEIDSSSAFLRKPFRMDALSAKIREVL", ) self.assertTrue( np.array_equal( alignment.coordinates, np.array( [ [0, 1, 41, 41, 82, 83, 98, 98, 105, 105, 111], [0, 0, 40, 42, 83, 83, 98, 99, 106, 110, 116], ] ), ) ) self.assertEqual( alignment[0], "KILIVDDQYGIRILLNEVFNKEGYQTFQAANGLQALDIVTK--ERPDLVLLDMKIPGMDGIEILKRMKVIDENIRVIIMTAYGELDMIQESKELGALTHF-AKPFDID----EIRDAV", ) self.assertEqual( alignment[1], "-VLLVEDEEALRAAAGDFLETRGYKIMTARDGTEALSMASKFAERIDVLITDLVMPGISGRVLAQELVKIHPETKVMYMSGYDD-ETVMVNGEIDSSSAFLRKPFRMDALSAKIREVL", ) self.assertEqual( alignment.column_annotations["emboss_consensus"], " :|:|:|:..:|....:.....||:...|.:|.:||.:.:| ||.|:::.|:.:||:.|..:.:.:..|....:|:.|:.|.: :.:..:.|:.:.:.| .|||.:| :||:.:", ) self.assertEqual( str(alignment), """\ ref_rec 0 KILIVDDQYGIRILLNEVFNKEGYQTFQAANGLQALDIVTK--ERPDLVLLDMKIPGMDG 0 -.|.|.|....|..........||....|..|..||....|--||.|....|...||..| gi|949700 0 -VLLVEDEEALRAAAGDFLETRGYKIMTARDGTEALSMASKFAERIDVLITDLVMPGISG ref_rec 58 IEILKRMKVIDENIRVIIMTAYGELDMIQESKELGALTHF-AKPFDID----EIRDAV 60 .........|.....|..|..|..-.......|......|-.|||..|----.||... gi|949700 59 RVLAQELVKIHPETKVMYMSGYDD-ETVMVNGEIDSSSAFLRKPFRMDALSAKIREVL ref_rec 111 118 gi|949700 116 """, ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['K', 'I', 'L', 'I', 'V', 'D', 'D', 'Q', 'Y', 'G', 'I', 'R', 'I', 'L', 'L', 'N', 'E', 'V', 'F', 'N', 'K', 'E', 'G', 'Y', 'Q', 'T', 'F', 'Q', 'A', 'A', 'N', 'G', 'L', 'Q', 'A', 'L', 'D', 'I', 'V', 'T', 'K', '-', '-', 'E', 'R', 'P', 'D', 'L', 'V', 'L', 'L', 'D', 'M', 'K', 'I', 'P', 'G', 'M', 'D', 'G', 'I', 'E', 'I', 'L', 'K', 'R', 'M', 'K', 'V', 'I', 'D', 'E', 'N', 'I', 'R', 'V', 'I', 'I', 'M', 'T', 'A', 'Y', 'G', 'E', 'L', 'D', 'M', 'I', 'Q', 'E', 'S', 'K', 'E', 'L', 'G', 'A', 'L', 'T', 'H', 'F', '-', 'A', 'K', 'P', 'F', 'D', 'I', 'D', '-', '-', '-', '-', 'E', 'I', 'R', 'D', 'A', 'V'], ['-', 'V', 'L', 'L', 'V', 'E', 'D', 'E', 'E', 'A', 'L', 'R', 'A', 'A', 'A', 'G', 'D', 'F', 'L', 'E', 'T', 'R', 'G', 'Y', 'K', 'I', 'M', 'T', 'A', 'R', 'D', 'G', 'T', 'E', 'A', 'L', 'S', 'M', 'A', 'S', 'K', 'F', 'A', 'E', 'R', 'I', 'D', 'V', 'L', 'I', 'T', 'D', 'L', 'V', 'M', 'P', 'G', 'I', 'S', 'G', 'R', 'V', 'L', 'A', 'Q', 'E', 'L', 'V', 'K', 'I', 'H', 'P', 'E', 'T', 'K', 'V', 'M', 'Y', 'M', 'S', 'G', 'Y', 'D', 'D', '-', 'E', 'T', 'V', 'M', 'V', 'N', 'G', 'E', 'I', 'D', 'S', 'S', 'S', 'A', 'F', 'L', 'R', 'K', 'P', 'F', 'R', 'M', 'D', 'A', 'L', 'S', 'A', 'K', 'I', 'R', 'E', 'V', 'L']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertEqual(alignment.annotations["Matrix"], "EBLOSUM62") self.assertAlmostEqual(alignment.annotations["Gap_penalty"], 10.0) self.assertAlmostEqual(alignment.annotations["Extend_penalty"], 0.5) self.assertEqual(alignment.annotations["Identity"], 35) self.assertEqual(alignment.annotations["Similarity"], 70) self.assertEqual(alignment.annotations["Gaps"], 18) self.assertAlmostEqual(alignment.annotations["Score"], 156.5) self.assertEqual(len(alignment), 2) self.assertEqual(alignment.shape, (2, 125)) self.assertEqual(alignment.sequences[0].id, "ref_rec") self.assertEqual(alignment.sequences[1].id, "gi|94970041|receiver") self.assertEqual( alignment.sequences[0].seq, "KILIVDDQYGIRILLNEVFNKEGYQTFQAANGLQALDIVTKERPDLVLLDMKIPGMDGIEILKRMKVIDENIRVIIMTAYGELDMIQESKELGALTHFAKPFDIDEIRDAV", ) self.assertEqual( alignment.sequences[1].seq, "TVLLVEDEEGVRKLVRGILSRQGYHVLEATSGEEALEIVRESTQKIDMLLSDVVLVGMSGRELSERLRIQMPSLKVIYMSGYTDDAIVRHGVLTESAEFLQKPFTSDSLLRKVRAVLQKRQ", ) self.assertTrue( np.array_equal( alignment.coordinates, np.array( [ [0, 39, 39, 88, 92, 99, 99, 111, 111], [0, 39, 41, 90, 90, 97, 101, 113, 121], ] ), ) ) self.assertEqual( alignment[0], "KILIVDDQYGIRILLNEVFNKEGYQTFQAANGLQALDIV--TKERPDLVLLDMKIPGMDGIEILKRMKVIDENIRVIIMTAYGELDMIQESKELGALTHFA----KPFDIDEIRDAV--------", ) self.assertEqual( alignment[1], "TVLLVEDEEGVRKLVRGILSRQGYHVLEATSGEEALEIVRESTQKIDMLLSDVVLVGMSGRELSERLRIQMPSLKVIYMSGYTDDAIVRH----GVLTESAEFLQKPFTSDSLLRKVRAVLQKRQ", ) self.assertEqual( alignment.column_annotations["emboss_consensus"], ".:|:|:|:.|:|.|:..:.:::||...:|.:|.:||:|| :.::.|::|.|:.:.||.|.|:.:|:::...:::||.|:.|.:..:::. |.||..| |||..|.:...| ", ) self.assertEqual( str(alignment), """\ ref_rec 0 KILIVDDQYGIRILLNEVFNKEGYQTFQAANGLQALDIV--TKERPDLVLLDMKIPGMDG 0 ..|.|.|..|.|.|........||....|..|..||.||--.....|..|.|....||.| gi|949700 0 TVLLVEDEEGVRKLVRGILSRQGYHVLEATSGEEALEIVRESTQKIDMLLSDVVLVGMSG ref_rec 58 IEILKRMKVIDENIRVIIMTAYGELDMIQESKELGALTHFA----KPFDIDEIRDAV--- 60 .|...|.........||.|..|........----|.||..|----|||..|.....|--- gi|949700 60 RELSERLRIQMPSLKVIYMSGYTDDAIVRH----GVLTESAEFLQKPFTSDSLLRKVRAV ref_rec 111 ----- 111 120 ----- 125 gi|949700 116 LQKRQ 121 """, ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['K', 'I', 'L', 'I', 'V', 'D', 'D', 'Q', 'Y', 'G', 'I', 'R', 'I', 'L', 'L', 'N', 'E', 'V', 'F', 'N', 'K', 'E', 'G', 'Y', 'Q', 'T', 'F', 'Q', 'A', 'A', 'N', 'G', 'L', 'Q', 'A', 'L', 'D', 'I', 'V', '-', '-', 'T', 'K', 'E', 'R', 'P', 'D', 'L', 'V', 'L', 'L', 'D', 'M', 'K', 'I', 'P', 'G', 'M', 'D', 'G', 'I', 'E', 'I', 'L', 'K', 'R', 'M', 'K', 'V', 'I', 'D', 'E', 'N', 'I', 'R', 'V', 'I', 'I', 'M', 'T', 'A', 'Y', 'G', 'E', 'L', 'D', 'M', 'I', 'Q', 'E', 'S', 'K', 'E', 'L', 'G', 'A', 'L', 'T', 'H', 'F', 'A', '-', '-', '-', '-', 'K', 'P', 'F', 'D', 'I', 'D', 'E', 'I', 'R', 'D', 'A', 'V', '-', '-', '-', '-', '-', '-', '-', '-'], ['T', 'V', 'L', 'L', 'V', 'E', 'D', 'E', 'E', 'G', 'V', 'R', 'K', 'L', 'V', 'R', 'G', 'I', 'L', 'S', 'R', 'Q', 'G', 'Y', 'H', 'V', 'L', 'E', 'A', 'T', 'S', 'G', 'E', 'E', 'A', 'L', 'E', 'I', 'V', 'R', 'E', 'S', 'T', 'Q', 'K', 'I', 'D', 'M', 'L', 'L', 'S', 'D', 'V', 'V', 'L', 'V', 'G', 'M', 'S', 'G', 'R', 'E', 'L', 'S', 'E', 'R', 'L', 'R', 'I', 'Q', 'M', 'P', 'S', 'L', 'K', 'V', 'I', 'Y', 'M', 'S', 'G', 'Y', 'T', 'D', 'D', 'A', 'I', 'V', 'R', 'H', '-', '-', '-', '-', 'G', 'V', 'L', 'T', 'E', 'S', 'A', 'E', 'F', 'L', 'Q', 'K', 'P', 'F', 'T', 'S', 'D', 'S', 'L', 'L', 'R', 'K', 'V', 'R', 'A', 'V', 'L', 'Q', 'K', 'R', 'Q']], dtype='U') # fmt: on ) ) with self.assertRaises(StopIteration): next(alignments) def test_pair_example3(self): path = "Emboss/needle_overhang.txt" alignments = Align.parse(path, "emboss") self.assertEqual(alignments.metadata["Program"], "needle") self.assertEqual(alignments.metadata["Rundate"], "Mon 14 Jul 2008 11:45:42") self.assertEqual( alignments.metadata["Command line"], "needle [-asequence] asis:TGTGGTTAGGTTTGGTTTTATTGGGGGCTTGGTTTGGGCCCACCCCAAATAGGGAGTGGGGGTATGACCTCAGATAGACGAGCTTATTTTAGGGCGGCGACTATAATTATTTCGTTTCCTACAAGGATTAAAGTTTTTTCTTTTACTGTGGGAGGGGGTTTGGTATTAAGAAACGCTAGTCCGGATGTGGCTCTCCATGATACTTATTGTGTAGTAGCTCATTTTCATTATGTTCTTCGAATGGGAGCAGTCATTGGTATTTTTTTGGTTTTTTTTTGAAATTTTTAGGTTATTTAGACCATTTTTTTTTGTTTCGCTAATTAGAATTTTATTAGCCTTTGGTTTTTTTTTATTTTTTGGGGTTAAGACAAGGTGTCGTTGAATTAGTTTAGCAAAATACTGCTTAAGGTAGGCTATAGGATCTACCTTTTATCTTTCTAATCTTTTGTTTTAGTATAATTGGTCTTCGATTCAACAATTTTTAGTCTTCAGTCTTTTTTTTTATTTTGAAAAGGTTTTAACACTCTTGGTTTTGGAGGCTTTGGCTTTCTTCTTACTCTTAGGAGGATGGGCGCTAGAAAGAGTTTTAAGAGGGTGTGAAAGGGGGTTAATAGC [-bsequence] asis:TTATTAATCTTATGGTTTTGCCGTAAAATTTCTTTCTTTATTTTTTATTGTTAGGATTTTGTTGATTTTATTTTTCTCAAGAATTTTTAGGTCAATTAGACCGGCTTATTTTTTTGTCAGTGTTTAAAGTTTTATTAATTTTTGGGGGGGGGGGGAGACGGGGTGTTATCTGAATTAGTTTTTGGGAGTCTCTAGACATCTCATGGGTTGGCCGGGGGCCTGCCGTCTATAGTTCTTATTCCTTTTAAGGGAGTAAGAATTTCGATTCAGCAACTTTAGTTCACAGTCTTTTTTTTTATTAAGAAAGGTTT -filter", ) self.assertEqual(alignments.metadata["Align_format"], "srspair") self.assertEqual(alignments.metadata["Report_file"], "stdout") alignment = next(alignments) self.assertEqual(alignment.annotations["Matrix"], "EDNAFULL") self.assertAlmostEqual(alignment.annotations["Gap_penalty"], 10.0) self.assertAlmostEqual(alignment.annotations["Extend_penalty"], 0.5) self.assertEqual(alignment.annotations["Identity"], 210) self.assertEqual(alignment.annotations["Similarity"], 210) self.assertEqual(alignment.annotations["Gaps"], 408) self.assertAlmostEqual(alignment.annotations["Score"], 561.0) self.assertEqual(len(alignment), 2) self.assertEqual(alignment.shape, (2, 667)) self.assertEqual(alignment.sequences[0].id, "asis") self.assertEqual(alignment.sequences[1].id, "asis") self.assertEqual( alignment.sequences[0].seq, "TGTGGTTAGGTTTGGTTTTATTGGGGGCTTGGTTTGGGCCCACCCCAAATAGGGAGTGGGGGTATGACCTCAGATAGACGAGCTTATTTTAGGGCGGCGACTATAATTATTTCGTTTCCTACAAGGATTAAAGTTTTTTCTTTTACTGTGGGAGGGGGTTTGGTATTAAGAAACGCTAGTCCGGATGTGGCTCTCCATGATACTTATTGTGTAGTAGCTCATTTTCATTATGTTCTTCGAATGGGAGCAGTCATTGGTATTTTTTTGGTTTTTTTTTGAAATTTTTAGGTTATTTAGACCATTTTTTTTTGTTTCGCTAATTAGAATTTTATTAGCCTTTGGTTTTTTTTTATTTTTTGGGGTTAAGACAAGGTGTCGTTGAATTAGTTTAGCAAAATACTGCTTAAGGTAGGCTATAGGATCTACCTTTTATCTTTCTAATCTTTTGTTTTAGTATAATTGGTCTTCGATTCAACAATTTTTAGTCTTCAGTCTTTTTTTTTATTTTGAAAAGGTTTTAACACTCTTGGTTTTGGAGGCTTTGGCTTTCTTCTTACTCTTAGGAGGATGGGCGCTAGAAAGAGTTTTAAGAGGGTGTGAAAGGGGGTTAATAGC", ) self.assertEqual( alignment.sequences[1].seq, "TTATTAATCTTATGGTTTTGCCGTAAAATTTCTTTCTTTATTTTTTATTGTTAGGATTTTGTTGATTTTATTTTTCTCAAGAATTTTTAGGTCAATTAGACCGGCTTATTTTTTTGTCAGTGTTTAAAGTTTTATTAATTTTTGGGGGGGGGGGGAGACGGGGTGTTATCTGAATTAGTTTTTGGGAGTCTCTAGACATCTCATGGGTTGGCCGGGGGCCTGCCGTCTATAGTTCTTATTCCTTTTAAGGGAGTAAGAATTTCGATTCAGCAACTTTAGTTCACAGTCTTTTTTTTTATTAAGAAAGGTTT", ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 162, 169, 201, 210, 210, 220, 222, 236, 240, 244, 253, 277, 277, 278, 279, 300, 300, 310, 310, 314, 320, 334, 351, 357, 357, 379, 379, 390, 403, 405, 407, 418, 418, 442, 442, 447, 447, 448, 452, 455, 455, 460, 465, 478, 479, 509, 510, 518, 615], [ 0, 0, 7, 7, 16, 22, 32, 32, 46, 46, 50, 50, 74, 80, 81, 81, 102, 107, 117, 119, 123, 123, 137, 137, 143, 147, 169, 170, 181, 181, 183, 183, 194, 215, 239, 241, 246, 250, 251, 251, 254, 255, 260, 260, 273, 273, 303, 303, 311, 311]]) # fmt: on ) ) self.assertEqual( alignment[0], "TGTGGTTAGGTTTGGTTTTATTGGGGGCTTGGTTTGGGCCCACCCCAAATAGGGAGTGGGGGTATGACCTCAGATAGACGAGCTTATTTTAGGGCGGCGACTATAATTATTTCGTTTCCTACAAGGATTAAAGTTTTTTCTTTTACTGTGGGAGGGGGTTTGGTATTAAGAAACGCTAGTCCGGATGTGGCTCTCCATGATACTTATTGT------GTAGTAGCTCATTTTCATTATGTTCTTCGAATGGGAGCAGTCATTGGTATTTTTTTGGTTTTTTTTT------GAAATTTTTAGGTTATTTAGACC-----ATTTTTTTTT--GTTTCGCTAATTAGAATTTTATTAGCCTTTGGTTTTTTTTTATTTTT----TGGGGTTAAGACAAGGTGTCGT-TGAATTAGTTTAGCAAAATACTGCTTAAGGTAGGCTATA---------------------GGATCTACCTTTTATCTTTCTAAT--CTTTT----GTTTTAGT-ATAATTGGTCTTCGATTCAACAATTTTTAGTCTTCAGTCTTTTTTTTTATTTTGAAAAGGTTTTAACACTCTTGGTTTTGGAGGCTTTGGCTTTCTTCTTACTCTTAGGAGGATGGGCGCTAGAAAGAGTTTTAAGAGGGTGTGAAAGGGGGTTAATAGC", ) self.assertEqual( alignment[1], "------------------------------------------------------------------------------------------------------------------------------------------------------------------TTATTAA--------------------------------TCTTATGGTTTTGCCGTAAAATTTC--TTTCTTTATTTTTT----ATTG---------TTAGGATTTTGTTGATTTTATTTTTCTCAAG-AATTTTTAGGTCAATTAGACCGGCTTATTTTTTTGTCAGTGT------TTAAAGTTTTATTA-----------------ATTTTTGGGGGGGGGGGGAGACGGGGTGTTATCTGAATTAGTTT-------------TT--GGGAGTCTCTAGACATCTCATGGGTTGGCCGGGGGCCTGCCGTCTATAGTTCTTATTCCTTTTAAGGG----AGTAAGAAT-----TTCGATTCAGCAA-CTTTAGTTCACAGTCTTTTTTTTTATTAAG-AAAGGTTT-------------------------------------------------------------------------------------------------", ) self.assertEqual( alignment.column_annotations["emboss_consensus"], " .|||||| .|||||.|| |||..|..|| ||||.||||.||.| ||.| ||.|.|||||.|||.||||.|||| | |||||||||||.|.||||||| ||||||||.| ||.| |||.|.|||||||| |||||| .||||...||||..|||||..| ||||||||||| || ||.||.||.|| ||..||.||.|.|||..||||.|| ||||| | ||| |.||| |||||||||.||| .||||||...|||||||||||||||||..| |||||||| ", ) self.assertEqual( str(alignment), """\ asis 0 TGTGGTTAGGTTTGGTTTTATTGGGGGCTTGGTTTGGGCCCACCCCAAATAGGGAGTGGG 0 ------------------------------------------------------------ asis 0 ------------------------------------------------------------ asis 60 GGTATGACCTCAGATAGACGAGCTTATTTTAGGGCGGCGACTATAATTATTTCGTTTCCT 60 ------------------------------------------------------------ asis 0 ------------------------------------------------------------ asis 120 ACAAGGATTAAAGTTTTTTCTTTTACTGTGGGAGGGGGTTTGGTATTAAGAAACGCTAGT 120 ------------------------------------------.||||||----------- asis 0 ------------------------------------------TTATTAA----------- asis 180 CCGGATGTGGCTCTCCATGATACTTATTGT------GTAGTAGCTCATTTTCATTATGTT 180 ---------------------.|||||.||------|||..|..||--||||.||||.|| asis 7 ---------------------TCTTATGGTTTTGCCGTAAAATTTC--TTTCTTTATTTT asis 234 CTTCGAATGGGAGCAGTCATTGGTATTTTTTTGGTTTTTTTTT------GAAATTTTTAG 240 .|----||.|---------||.|.|||||.|||.||||.||||------|-||||||||| asis 44 TT----ATTG---------TTAGGATTTTGTTGATTTTATTTTTCTCAAG-AATTTTTAG asis 288 GTTATTTAGACC-----ATTTTTTTTT--GTTTCGCTAATTAGAATTTTATTAGCCTTTG 300 ||.|.|||||||-----||||||||.|--||.|------|||.|.||||||||------- asis 90 GTCAATTAGACCGGCTTATTTTTTTGTCAGTGT------TTAAAGTTTTATTA------- asis 341 GTTTTTTTTTATTTTT----TGGGGTTAAGACAAGGTGTCGT-TGAATTAGTTTAGCAAA 360 ----------||||||----.||||...||||..|||||..|-|||||||||||------ asis 137 ----------ATTTTTGGGGGGGGGGGGAGACGGGGTGTTATCTGAATTAGTTT------ asis 396 ATACTGCTTAAGGTAGGCTATA---------------------GGATCTACCTTTTATCT 420 -------||--||.||.||.||---------------------||..||.||.|.|||.. asis 181 -------TT--GGGAGTCTCTAGACATCTCATGGGTTGGCCGGGGGCCTGCCGTCTATAG asis 435 TTCTAAT--CTTTT----GTTTTAGT-ATAATTGGTCTTCGATTCAACAATTTTTAGTCT 480 ||||.||--|||||----|----|||-|.|||-----|||||||||.|||-.||||||.. asis 232 TTCTTATTCCTTTTAAGGG----AGTAAGAAT-----TTCGATTCAGCAA-CTTTAGTTC asis 488 TCAGTCTTTTTTTTTATTTTGAAAAGGTTTTAACACTCTTGGTTTTGGAGGCTTTGGCTT 540 .|||||||||||||||||..|-||||||||------------------------------ asis 282 ACAGTCTTTTTTTTTATTAAG-AAAGGTTT------------------------------ asis 548 TCTTCTTACTCTTAGGAGGATGGGCGCTAGAAAGAGTTTTAAGAGGGTGTGAAAGGGGGT 600 ------------------------------------------------------------ asis 311 ------------------------------------------------------------ asis 608 TAATAGC 615 660 ------- 667 asis 311 ------- 311 """, ) with self.assertRaises(StopIteration): next(alignments) def test_needle_asis(self): path = "Emboss/needle_asis.txt" alignments = Align.parse(path, "emboss") self.assertEqual(alignments.metadata["Program"], "needle") self.assertEqual(alignments.metadata["Rundate"], "Mon 14 Jul 2008 11:37:15") self.assertEqual( alignments.metadata["Command line"], "needle [-asequence] asis:TATTTTTTGGATTTTTTTCTAGATTTTCTAGGTTATTTAAACCGTTTTTTTTTAATTTAGTGTTTGAGTTTTGACAGGTCTCCACTTTGGGGGCTCCATCGCAAGGAAATTAGAATTCTTATACTTGGTTCTCTTTCCCAGGGACTCCAAGGATCTTTTCATTAGTTTGGATTTTGGTGTTTTCTTTAATTTTGTTAAGAAACAAATCCTTTCTAGAGTTTTTTCTAGCATTATGTTTTTTTTTCTCCTTATCTAAGGGGGTTTGTCGAGGTTTCTTAAATCTTTTTTTCTCTGGGTTTTAAAATTGTTTAAATTTTTTTGACCGAGGGGTTGGGGTGGTTTTCTCATGATAACAGGGGCTGGTGCTTTAGATCCTACCTCTACTGACCCGGGGTCTGCTACTGTGGCTTCTGATGAAGATCCACAGTATGCGCCTACGGAARCTCGGCAGTTTGGTGTTCGAAATCCAGCCCCTCGAATTAATACTCTTGTGCAGGTGGTTGACGAGCGCGGTATCGAATTGCAAAATTTGGGGCGGGACCCCGCTGTTCCGCCTGTTGCTCCGGGGGGGGCAGGTTAATCCTCCAGTCGTCTCCTTTTGGGGGCGTCTTTGACGGGGGTTTAAATCTTTCTTTGGTTGTGGATAGGATTTTTTTTCTAATATCGATCCTACCTGTTTTGGCGGGGCTATTACTTTGTTACTTTTGACCGAAATTTTAATGGAAATTTCTTTGATTCAAATGAATCCCTTAGTTTTCCAACACTTTTTTTTGGTTTTTTTAGGGATAGTCTACGCTGTGGTTAGGTTTGGTTTTATTGGGGGCTTGGTTTGGGCCCACCCCAAATAGGGAGTGGGGGTATGACCTCAGATAGACGAGCTTATTTTAGGGCGGCGACTATAATTATTTCGTTTCCTACAAGGATTAAAGTTTTTTCTTTTACTGTGGGAGGGGGTTTGGTATTAAGAAACGCTAGTCCGGATGTGGCTCTCCATGATACTTATTGTGTAGTAGCTCATTTTCATTATGTTCTTCGAATGGGAGCAGTCATTGGTATTTTTTTGGTTTTTTTTTGAAATTTTTAGGTTATTTAGACCATTTTTTTTTGTTTCGCTAATTAGAATTTTATTAGCCTTTGGTTTTTTTTTATTTTTTGGGGTTAAGACAAGGTGTCGTTGAATTAGTTTAGCAAAATACTGCTTAAGGTAGGCTATAGGATCTACCTTTTATCTTTCTAATCTTTTGTTTTAGTATAATTGGTCTTCGATTCAACAATTTTTAGTCTTCAGTCTTTTTTTTTATTTTGAAAAGGTTTTAACACTCTTGGTTTTGGAGGCTTTGGCTTTCTTCTTACTCTTAGGAGGATGGGCGCTAGAAAGAGTTTTAAGAGGGTGTGAAAGGGGGTTAATAGCAGGATTTGCTTTTTTAACTTATACTGGTTCGTAACGCATTAGCTCAACTCTCTCTTGTAGTTCTAGCAGCCGCCTTTTCTTTGTTGGGGGAGGGTTTAGGAGGAGTCTTTTTTTTCCTAACCCAAGGTGTTTCTTTCTTTTTTTCTTTAAAGTTCTTGACTGTTGGCACTTGTCTCCATAAATTTTCTTTCTTGTAAAGGGCTCCTAAGGCTTCTTGTTTCTGAATTCCTCTTTTCTTTTATTCTGTTTTGAGCTTATTTTTCTTGTTAGCTATTACGTAGGCATAGGGCAAATAATTTTTTTTTCTGCTCTCATTATTCCTTCTCCCTGCTTGTTTCACCCTGTGGGCTCTTTGAGCCCCACTAAGTGAGCGGGGCTCCTGCTTCCGCTCAATTAAATTTTGGTGGGTATTGAGTCTCAGAGGGACTATGATATAGGTTCAGATTGATGGACCTAATCAATCAATTGTATCGCTATACAATCTAGTACCCCTACCAGGGTACCAAGAGAGAGATAACTAGGGTGAATACTACGACTTAGATGTAGTGTTTAAGTTTCTACGGGCTACAGAGAAGCTACCCGCAGGGTAYATATTTGTTCATTACATATTTGTTGACTTTTCTATCTCTGCTTTTACTTTTTTATTTATTTTTAAATCTTTTTAACTTCAGCTGTTTTTCCTTATCTATTTGACGTAGGCATAGGAAAGTTAACGAATTTTGTAATATTTTTAATTATTTTGTATAGTATACAGGGTAGTGGTATGTAATAGGTAAATTCCATAAGTTCATTATAGTTTATCAGTTGAGAGGAATTTAGTATAAGAAGGCCCATTGGGGCTCTTGTCTTATCCAAGAACTGGTAAGATTTAATTCTACCGGGACGGTAGAAATCGGGCAGAGCATGATCTATTTCTTCGGGTATGGCTATAGGGACTAGGTGCTAGGGAGGTATTAGGGCACCGCTCTTTATACAATCTCCATAGATACAACCAGGTCAACTAGGACAACGGAGGACGTTGACAGAGCATAAATAGCGATAGCGTACAAGATAWAATAGGGGCAGTGGTAGCGAAGCGTAGAAGAAAAAATAAGAGTATTGTTTGTAAATAATTCTTTTTTTAGTTTTTAAATATTCTTTTTTTAGGTGGTGTGTGGTTAGGTATGGGGTTAAGGGTGTGGCAAAGAGAAATGTTTATTAAACATTCTTATGGCCGTAGATAGCATATCGATTATACGAGACCTTCGTAAGATCAATCCCCACTAGCATTGCTCATACAGGTTAACTCAATAGGAGGAGCTGGGGTAGAACGTTTCTAGTTCGGGGGTAACCGCAGTTCAATGAAAGTGACGACGTCGGATGGAACAAACTTAATACCACCAGTTGTGCTAACGATTGTTATCTCAATCTATCCCAACAGGCCCCCAGGTAGTGATGAGTGGTGGAATGGTACAGGGTACCAGTGGGTGAAGAGCGTCACGAACCAGGGAATACGGAGTACAGAGTTGAGCGCCCGGGGCTCCGCCCCCGGCTTTTATAGCGCGAGACGTGGTCAGTCGATTCAGCGTTAGGTTTAAACTCCTTTGGCAAAGATTGACTCTAGCGATCCAGAGACCCTGCCTGGCATAAAAGTCTTTATWAACACCAGTAGGTTCAATAAGGTAGTAATCCAATAGAATGGAAAACTCAAGATCTAATCTCTCGAYTTCCTAGTGTCATGGAAATCAGCCAGGTTCTCTTCATCTGCAACAGTAGAAGAAGAAGAGAGACTAGCGAGAGAGTCTTATGGCGGAGACGCTAAGGCTTAAATGTAATGTAGATAACCCCTTACGGAACACTAGAGTGCGACGTAGACTACATAATCCCTCAGGGATATTAGCTCTGCTCGATTAACAATAGCATACTTTGTTACACGGAGTGTATCTAGGGGGAATAATACTAACTTACTTAGCACTATCGCGATGCTACGCATTCGCTCTTTCGCTAAATAAGATACGACGATGAGTGGTTGGTGGAGAGAATAACCGATTCTAACTTGATAATTCGCATGAAATAATTTTTTTATTTTGTTTTTTTTTTGCTCTTAATTTTAGWGGGRGTGTTTATTTTTATTCTAATAAAAAGGATCCGTTGAA [-bsequence] asis:TTATTAATCTTATGGTTTTGCCGTAAAATTTCTTTCTTTATTTTTTATTGTTAGGATTTTGTTGATTTTATTTTTCTCAAGAATTTTTAGGTCAATTAGACCGGCTTATTTTTTTGTCAGTGTTTAAAGTTTTATTAATTTTTGGGGGGGGGGGGAGACGGGGTGTTATCTGAATTAGTTTTTGGGAGTCTCTAGACATCTCATGGGTTGGCCGGGGGCCTGCCGTCTATAGTTCTTATTCCTTTTAAGGGAGTAAGAATTTCGATTCAGCAACTTTAGTTCACAGTCTTTTTTTTTATTAAGAAAGGTTTTAATATTCTTGTGGTTTTGAACCTTTAGGTTTCTTTCTTTACCTTCGAGGGATTGGGCACTAGAATGAGTTTTAAGAGTGTGTGAAAGGGGGCTTGATAGCAGGGGAATGCTTTTTTAACTTATACTGGCTCGTAACGCATCAGTTCAACTCTCTCTTGCAGTTCTAGCAGCCGCCTTTTTTTTGTTGGGGGGGGGTTAAGAGAGTGTTTTTTTTCTAATCCAAGGGTCTTACTTTCTTTCTTTCTTTAAAAATTCTTTGGCTGTCGACACCTTTCTCTCCCGTCAGTCTCATGGTTTCTGGCTCTCTTGGGCTTTTTTTGTTTGTGAATGCCTCTTTTTTTTATTCTGTTTTGAGCTTATTTTTCTTGTTTACTATTACGTAGGTATAGGGCAAATAATTTTTTTTTCGCGTCTCTTGGCATGCCCATTACTCTAGTTTTATTCCCGGGCTTCTTCTCTCACCCTAGAGGGCTCTTTGAGCCCACACTCAAGTGAGCGGGGCTCCCGCTTCCGCTCAATTAAATTTGGTGGGTATTGAGTCTCAGAGGGACTATGATATAGGTTCAGATTGATGGACCTAGTCAATCAATTGTATCGCTATACAATCTAGTACCCCTACCAGGGTACCAGGAGAGAGATAACTAGGGTGAATACTACGACTTAGATGTACTGTTTAAGTTTCTACGGGCTACAGAGAAGCTACCCGCAGGGTATATATTTGCTCATTACATATTTGTTGATTTTTCTATGTCCGCTTTACTTTTTATATTTTTTTAACTTCAGCTGTTTTTCCTTATCTATTTGACGTAGGCATAGGAAAGTTAACGAATTTTGTAATATTTTTAATTATTTTGTATAGTATACAGGGTAGTGGTATGTAATAGGTAAATTCCATAAGTTCATTATAGTCTATCAGTTGAGAGGAATTTAGTATAAGAAAGCCTGTCAGGGCTCTTGCCTTATCCAAGAACTGGTAAGGATTTCTTGACAGAGGGACTCTGTCAAATCGGGCAGAGCATGATCTATTTCTTCGGGTATGGTTATAAGGCTTAGGTGCTTGGAGGGTATTAGGGCACCGCTCTTAATACAGTCTCCATAGGTGTAACCAGGTCAACTAGGACAACGGAGGACGTTGACAAAGCATGGATAGCGATAGCGTAGAAGATAAAATGGGGCAGTGGTAGCGAAGCGTAGAAGAAAAAATAAGAGTATTGTTTGTAAATAATTCTTTTTTTAGTTTTTAAATATTCTTTTTTTAGGTGGTGTGTGGTTAGGTATGGGGTTAGGGGAGTGGCAAAGAGAAGTGTTTATTAAACATTCTTATGGCCGTAGATAGCATATCGATTATACGAGACCTTCGTAAGATCAATCCCCACTAGCATTGCTCATACAGGTTAACTCAATAGGAGGAGCTGGGGTAGAACGTATCTAGTTCGGGGGTAACCGCAGTTCAATGAAAGTGACGACGTCGGATGGAACAAACTTAATACCACCAGTTGTGCTAACGATTGTTATCTCAATCTATCCCAACAGGCCCCCAGGTAGTGATGAGTGGTGGAATGGTACAGGGTACCAGTGGGTGAAGAGCGTCACGAACCAGGGAATACGGAGTACAGAGTTGAGCGCCCGGGGCTCCGCCCCCGGCTTTTATAGCGCGAGACGTGGTCAGTCGATTCAGCGTTAGGTTTTAAACTCCTTTGGCAAAGATTGATTCTAGCGATCCAGAGACCCTGCCTGGCATAAAAGTCTTTATTAGCACCAGTAGGTTCAATAAGGTAGTAGTCCAATAGAATGGAAAACTCGAGATCTAATCTCTCGATTTCCTAGTGTCATGGAAATCAGCCAGGTTCTCTTCATCTGCAACAGTAGAAGAAGAAGAGAGGCTAGCGAGAGAGTCTTATGGCGGAGACGCTAAGGCTTAAATGTAATGTAGATAACCCCTTACGGAACACTTGAGTGCGACGTAGACTACATAATCCCTCAGGGATATTAGCTCTGCTCGATTAACAATAGCATACTTTGTTACACGGAGTGTATCTGGGGGGAATAATACTAACTTACTTAGCACTATCGCGATGCTACGCATTCGCTCTTTCGCTAAATAAGATACGACGATGAGTGGTTGGTGGAGAGAATAACCGATTCTAACTTGATAATTCGCATGAAATAATTTTTTATTTGTTTTTTTTTTTGCTCTTAATTTTAGAGGATGTTTATTTTTATTCTAATAAAAAGGATCCGTTGAA -filter", ) self.assertEqual(alignments.metadata["Align_format"], "srspair") self.assertEqual(alignments.metadata["Report_file"], "stdout") alignment = next(alignments) self.assertEqual(alignment.annotations["Matrix"], "EDNAFULL") self.assertAlmostEqual(alignment.annotations["Gap_penalty"], 10.0) self.assertAlmostEqual(alignment.annotations["Extend_penalty"], 0.5) self.assertEqual(alignment.annotations["Identity"], 2296) self.assertEqual(alignment.annotations["Similarity"], 2301) self.assertEqual(alignment.annotations["Gaps"], 1202) self.assertAlmostEqual(alignment.annotations["Score"], 10155.0) self.assertEqual(len(alignment), 2) self.assertEqual(alignment.shape, (2, 3653)) self.assertEqual(alignment.sequences[0].id, "asis") self.assertEqual(alignment.sequences[1].id, "asis") self.assertEqual( alignment.sequences[0].seq, "TATTTTTTGGATTTTTTTCTAGATTTTCTAGGTTATTTAAACCGTTTTTTTTTAATTTAGTGTTTGAGTTTTGACAGGTCTCCACTTTGGGGGCTCCATCGCAAGGAAATTAGAATTCTTATACTTGGTTCTCTTTCCCAGGGACTCCAAGGATCTTTTCATTAGTTTGGATTTTGGTGTTTTCTTTAATTTTGTTAAGAAACAAATCCTTTCTAGAGTTTTTTCTAGCATTATGTTTTTTTTTCTCCTTATCTAAGGGGGTTTGTCGAGGTTTCTTAAATCTTTTTTTCTCTGGGTTTTAAAATTGTTTAAATTTTTTTGACCGAGGGGTTGGGGTGGTTTTCTCATGATAACAGGGGCTGGTGCTTTAGATCCTACCTCTACTGACCCGGGGTCTGCTACTGTGGCTTCTGATGAAGATCCACAGTATGCGCCTACGGAARCTCGGCAGTTTGGTGTTCGAAATCCAGCCCCTCGAATTAATACTCTTGTGCAGGTGGTTGACGAGCGCGGTATCGAATTGCAAAATTTGGGGCGGGACCCCGCTGTTCCGCCTGTTGCTCCGGGGGGGGCAGGTTAATCCTCCAGTCGTCTCCTTTTGGGGGCGTCTTTGACGGGGGTTTAAATCTTTCTTTGGTTGTGGATAGGATTTTTTTTCTAATATCGATCCTACCTGTTTTGGCGGGGCTATTACTTTGTTACTTTTGACCGAAATTTTAATGGAAATTTCTTTGATTCAAATGAATCCCTTAGTTTTCCAACACTTTTTTTTGGTTTTTTTAGGGATAGTCTACGCTGTGGTTAGGTTTGGTTTTATTGGGGGCTTGGTTTGGGCCCACCCCAAATAGGGAGTGGGGGTATGACCTCAGATAGACGAGCTTATTTTAGGGCGGCGACTATAATTATTTCGTTTCCTACAAGGATTAAAGTTTTTTCTTTTACTGTGGGAGGGGGTTTGGTATTAAGAAACGCTAGTCCGGATGTGGCTCTCCATGATACTTATTGTGTAGTAGCTCATTTTCATTATGTTCTTCGAATGGGAGCAGTCATTGGTATTTTTTTGGTTTTTTTTTGAAATTTTTAGGTTATTTAGACCATTTTTTTTTGTTTCGCTAATTAGAATTTTATTAGCCTTTGGTTTTTTTTTATTTTTTGGGGTTAAGACAAGGTGTCGTTGAATTAGTTTAGCAAAATACTGCTTAAGGTAGGCTATAGGATCTACCTTTTATCTTTCTAATCTTTTGTTTTAGTATAATTGGTCTTCGATTCAACAATTTTTAGTCTTCAGTCTTTTTTTTTATTTTGAAAAGGTTTTAACACTCTTGGTTTTGGAGGCTTTGGCTTTCTTCTTACTCTTAGGAGGATGGGCGCTAGAAAGAGTTTTAAGAGGGTGTGAAAGGGGGTTAATAGCAGGATTTGCTTTTTTAACTTATACTGGTTCGTAACGCATTAGCTCAACTCTCTCTTGTAGTTCTAGCAGCCGCCTTTTCTTTGTTGGGGGAGGGTTTAGGAGGAGTCTTTTTTTTCCTAACCCAAGGTGTTTCTTTCTTTTTTTCTTTAAAGTTCTTGACTGTTGGCACTTGTCTCCATAAATTTTCTTTCTTGTAAAGGGCTCCTAAGGCTTCTTGTTTCTGAATTCCTCTTTTCTTTTATTCTGTTTTGAGCTTATTTTTCTTGTTAGCTATTACGTAGGCATAGGGCAAATAATTTTTTTTTCTGCTCTCATTATTCCTTCTCCCTGCTTGTTTCACCCTGTGGGCTCTTTGAGCCCCACTAAGTGAGCGGGGCTCCTGCTTCCGCTCAATTAAATTTTGGTGGGTATTGAGTCTCAGAGGGACTATGATATAGGTTCAGATTGATGGACCTAATCAATCAATTGTATCGCTATACAATCTAGTACCCCTACCAGGGTACCAAGAGAGAGATAACTAGGGTGAATACTACGACTTAGATGTAGTGTTTAAGTTTCTACGGGCTACAGAGAAGCTACCCGCAGGGTAYATATTTGTTCATTACATATTTGTTGACTTTTCTATCTCTGCTTTTACTTTTTTATTTATTTTTAAATCTTTTTAACTTCAGCTGTTTTTCCTTATCTATTTGACGTAGGCATAGGAAAGTTAACGAATTTTGTAATATTTTTAATTATTTTGTATAGTATACAGGGTAGTGGTATGTAATAGGTAAATTCCATAAGTTCATTATAGTTTATCAGTTGAGAGGAATTTAGTATAAGAAGGCCCATTGGGGCTCTTGTCTTATCCAAGAACTGGTAAGATTTAATTCTACCGGGACGGTAGAAATCGGGCAGAGCATGATCTATTTCTTCGGGTATGGCTATAGGGACTAGGTGCTAGGGAGGTATTAGGGCACCGCTCTTTATACAATCTCCATAGATACAACCAGGTCAACTAGGACAACGGAGGACGTTGACAGAGCATAAATAGCGATAGCGTACAAGATAWAATAGGGGCAGTGGTAGCGAAGCGTAGAAGAAAAAATAAGAGTATTGTTTGTAAATAATTCTTTTTTTAGTTTTTAAATATTCTTTTTTTAGGTGGTGTGTGGTTAGGTATGGGGTTAAGGGTGTGGCAAAGAGAAATGTTTATTAAACATTCTTATGGCCGTAGATAGCATATCGATTATACGAGACCTTCGTAAGATCAATCCCCACTAGCATTGCTCATACAGGTTAACTCAATAGGAGGAGCTGGGGTAGAACGTTTCTAGTTCGGGGGTAACCGCAGTTCAATGAAAGTGACGACGTCGGATGGAACAAACTTAATACCACCAGTTGTGCTAACGATTGTTATCTCAATCTATCCCAACAGGCCCCCAGGTAGTGATGAGTGGTGGAATGGTACAGGGTACCAGTGGGTGAAGAGCGTCACGAACCAGGGAATACGGAGTACAGAGTTGAGCGCCCGGGGCTCCGCCCCCGGCTTTTATAGCGCGAGACGTGGTCAGTCGATTCAGCGTTAGGTTTAAACTCCTTTGGCAAAGATTGACTCTAGCGATCCAGAGACCCTGCCTGGCATAAAAGTCTTTATWAACACCAGTAGGTTCAATAAGGTAGTAATCCAATAGAATGGAAAACTCAAGATCTAATCTCTCGAYTTCCTAGTGTCATGGAAATCAGCCAGGTTCTCTTCATCTGCAACAGTAGAAGAAGAAGAGAGACTAGCGAGAGAGTCTTATGGCGGAGACGCTAAGGCTTAAATGTAATGTAGATAACCCCTTACGGAACACTAGAGTGCGACGTAGACTACATAATCCCTCAGGGATATTAGCTCTGCTCGATTAACAATAGCATACTTTGTTACACGGAGTGTATCTAGGGGGAATAATACTAACTTACTTAGCACTATCGCGATGCTACGCATTCGCTCTTTCGCTAAATAAGATACGACGATGAGTGGTTGGTGGAGAGAATAACCGATTCTAACTTGATAATTCGCATGAAATAATTTTTTTATTTTGTTTTTTTTTTGCTCTTAATTTTAGWGGGRGTGTTTATTTTTATTCTAATAAAAAGGATCCGTTGAA", ) self.assertEqual( alignment.sequences[1].seq, "TTATTAATCTTATGGTTTTGCCGTAAAATTTCTTTCTTTATTTTTTATTGTTAGGATTTTGTTGATTTTATTTTTCTCAAGAATTTTTAGGTCAATTAGACCGGCTTATTTTTTTGTCAGTGTTTAAAGTTTTATTAATTTTTGGGGGGGGGGGGAGACGGGGTGTTATCTGAATTAGTTTTTGGGAGTCTCTAGACATCTCATGGGTTGGCCGGGGGCCTGCCGTCTATAGTTCTTATTCCTTTTAAGGGAGTAAGAATTTCGATTCAGCAACTTTAGTTCACAGTCTTTTTTTTTATTAAGAAAGGTTTTAATATTCTTGTGGTTTTGAACCTTTAGGTTTCTTTCTTTACCTTCGAGGGATTGGGCACTAGAATGAGTTTTAAGAGTGTGTGAAAGGGGGCTTGATAGCAGGGGAATGCTTTTTTAACTTATACTGGCTCGTAACGCATCAGTTCAACTCTCTCTTGCAGTTCTAGCAGCCGCCTTTTTTTTGTTGGGGGGGGGTTAAGAGAGTGTTTTTTTTCTAATCCAAGGGTCTTACTTTCTTTCTTTCTTTAAAAATTCTTTGGCTGTCGACACCTTTCTCTCCCGTCAGTCTCATGGTTTCTGGCTCTCTTGGGCTTTTTTTGTTTGTGAATGCCTCTTTTTTTTATTCTGTTTTGAGCTTATTTTTCTTGTTTACTATTACGTAGGTATAGGGCAAATAATTTTTTTTTCGCGTCTCTTGGCATGCCCATTACTCTAGTTTTATTCCCGGGCTTCTTCTCTCACCCTAGAGGGCTCTTTGAGCCCACACTCAAGTGAGCGGGGCTCCCGCTTCCGCTCAATTAAATTTGGTGGGTATTGAGTCTCAGAGGGACTATGATATAGGTTCAGATTGATGGACCTAGTCAATCAATTGTATCGCTATACAATCTAGTACCCCTACCAGGGTACCAGGAGAGAGATAACTAGGGTGAATACTACGACTTAGATGTACTGTTTAAGTTTCTACGGGCTACAGAGAAGCTACCCGCAGGGTATATATTTGCTCATTACATATTTGTTGATTTTTCTATGTCCGCTTTACTTTTTATATTTTTTTAACTTCAGCTGTTTTTCCTTATCTATTTGACGTAGGCATAGGAAAGTTAACGAATTTTGTAATATTTTTAATTATTTTGTATAGTATACAGGGTAGTGGTATGTAATAGGTAAATTCCATAAGTTCATTATAGTCTATCAGTTGAGAGGAATTTAGTATAAGAAAGCCTGTCAGGGCTCTTGCCTTATCCAAGAACTGGTAAGGATTTCTTGACAGAGGGACTCTGTCAAATCGGGCAGAGCATGATCTATTTCTTCGGGTATGGTTATAAGGCTTAGGTGCTTGGAGGGTATTAGGGCACCGCTCTTAATACAGTCTCCATAGGTGTAACCAGGTCAACTAGGACAACGGAGGACGTTGACAAAGCATGGATAGCGATAGCGTAGAAGATAAAATGGGGCAGTGGTAGCGAAGCGTAGAAGAAAAAATAAGAGTATTGTTTGTAAATAATTCTTTTTTTAGTTTTTAAATATTCTTTTTTTAGGTGGTGTGTGGTTAGGTATGGGGTTAGGGGAGTGGCAAAGAGAAGTGTTTATTAAACATTCTTATGGCCGTAGATAGCATATCGATTATACGAGACCTTCGTAAGATCAATCCCCACTAGCATTGCTCATACAGGTTAACTCAATAGGAGGAGCTGGGGTAGAACGTATCTAGTTCGGGGGTAACCGCAGTTCAATGAAAGTGACGACGTCGGATGGAACAAACTTAATACCACCAGTTGTGCTAACGATTGTTATCTCAATCTATCCCAACAGGCCCCCAGGTAGTGATGAGTGGTGGAATGGTACAGGGTACCAGTGGGTGAAGAGCGTCACGAACCAGGGAATACGGAGTACAGAGTTGAGCGCCCGGGGCTCCGCCCCCGGCTTTTATAGCGCGAGACGTGGTCAGTCGATTCAGCGTTAGGTTTTAAACTCCTTTGGCAAAGATTGATTCTAGCGATCCAGAGACCCTGCCTGGCATAAAAGTCTTTATTAGCACCAGTAGGTTCAATAAGGTAGTAGTCCAATAGAATGGAAAACTCGAGATCTAATCTCTCGATTTCCTAGTGTCATGGAAATCAGCCAGGTTCTCTTCATCTGCAACAGTAGAAGAAGAAGAGAGGCTAGCGAGAGAGTCTTATGGCGGAGACGCTAAGGCTTAAATGTAATGTAGATAACCCCTTACGGAACACTTGAGTGCGACGTAGACTACATAATCCCTCAGGGATATTAGCTCTGCTCGATTAACAATAGCATACTTTGTTACACGGAGTGTATCTGGGGGGAATAATACTAACTTACTTAGCACTATCGCGATGCTACGCATTCGCTCTTTCGCTAAATAAGATACGACGATGAGTGGTTGGTGGAGAGAATAACCGATTCTAACTTGATAATTCGCATGAAATAATTTTTTATTTGTTTTTTTTTTTGCTCTTAATTTTAGAGGATGTTTATTTTTATTCTAATAAAAAGGATCCGTTGAA", ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 958, 965, 997, 1006, 1006, 1016, 1018, 1032, 1036, 1040, 1049, 1073, 1073, 1074, 1075, 1096, 1096, 1106, 1106, 1110, 1116, 1130, 1147, 1153, 1153, 1175, 1175, 1186, 1199, 1201, 1203, 1214, 1214, 1238, 1238, 1243, 1243, 1244, 1248, 1251, 1251, 1256, 1261, 1274, 1275, 1305, 1306, 1323, 1323, 1330, 1331, 1348, 1348, 1353, 1354, 1364, 1364, 1403, 1403, 1414, 1414, 1415, 1417, 1510, 1512, 1526, 1527, 1536, 1536, 1559, 1559, 1566, 1566, 1580, 1580, 1598, 1598, 1603, 1610, 1615, 1615, 1622, 1622, 1646, 1647, 1717, 1718, 1719, 1719, 1723, 1723, 1728, 1728, 1735, 1736, 1738, 1738, 1754, 1754, 1771, 1771, 1775, 1775, 1809, 1810, 2042, 2043, 2053, 2053, 2057, 2069, 2276, 2276, 2279, 2283, 2287, 2287, 2294, 2294, 2298, 2299, 2468, 2469, 2983, 2983, 3467, 3468, 3507, 3509, 3546], [ 0, 0, 7, 7, 16, 22, 32, 32, 46, 46, 50, 50, 74, 80, 81, 81, 102, 107, 117, 119, 123, 123, 137, 137, 143, 147, 169, 170, 181, 181, 183, 183, 194, 215, 239, 241, 246, 250, 251, 251, 254, 255, 260, 260, 273, 273, 303, 303, 320, 322, 329, 329, 346, 348, 353, 353, 363, 364, 403, 404, 415, 418, 419, 419, 512, 512, 526, 526, 535, 536, 559, 560, 567, 568, 582, 584, 602, 606, 611, 611, 616, 617, 624, 626, 650, 650, 720, 720, 721, 724, 728, 737, 742, 749, 756, 756, 758, 761, 777, 778, 795, 796, 800, 801, 835, 835, 1067, 1067, 1077, 1078, 1082, 1082, 1289, 1290, 1293, 1293, 1297, 1301, 1308, 1310, 1314, 1314, 1483, 1483, 1997, 1998, 2482, 2482, 2521, 2521, 2558]]) # fmt: on ) ) self.assertEqual( alignment[0], "TATTTTTTGGATTTTTTTCTAGATTTTCTAGGTTATTTAAACCGTTTTTTTTTAATTTAGTGTTTGAGTTTTGACAGGTCTCCACTTTGGGGGCTCCATCGCAAGGAAATTAGAATTCTTATACTTGGTTCTCTTTCCCAGGGACTCCAAGGATCTTTTCATTAGTTTGGATTTTGGTGTTTTCTTTAATTTTGTTAAGAAACAAATCCTTTCTAGAGTTTTTTCTAGCATTATGTTTTTTTTTCTCCTTATCTAAGGGGGTTTGTCGAGGTTTCTTAAATCTTTTTTTCTCTGGGTTTTAAAATTGTTTAAATTTTTTTGACCGAGGGGTTGGGGTGGTTTTCTCATGATAACAGGGGCTGGTGCTTTAGATCCTACCTCTACTGACCCGGGGTCTGCTACTGTGGCTTCTGATGAAGATCCACAGTATGCGCCTACGGAARCTCGGCAGTTTGGTGTTCGAAATCCAGCCCCTCGAATTAATACTCTTGTGCAGGTGGTTGACGAGCGCGGTATCGAATTGCAAAATTTGGGGCGGGACCCCGCTGTTCCGCCTGTTGCTCCGGGGGGGGCAGGTTAATCCTCCAGTCGTCTCCTTTTGGGGGCGTCTTTGACGGGGGTTTAAATCTTTCTTTGGTTGTGGATAGGATTTTTTTTCTAATATCGATCCTACCTGTTTTGGCGGGGCTATTACTTTGTTACTTTTGACCGAAATTTTAATGGAAATTTCTTTGATTCAAATGAATCCCTTAGTTTTCCAACACTTTTTTTTGGTTTTTTTAGGGATAGTCTACGCTGTGGTTAGGTTTGGTTTTATTGGGGGCTTGGTTTGGGCCCACCCCAAATAGGGAGTGGGGGTATGACCTCAGATAGACGAGCTTATTTTAGGGCGGCGACTATAATTATTTCGTTTCCTACAAGGATTAAAGTTTTTTCTTTTACTGTGGGAGGGGGTTTGGTATTAAGAAACGCTAGTCCGGATGTGGCTCTCCATGATACTTATTGT------GTAGTAGCTCATTTTCATTATGTTCTTCGAATGGGAGCAGTCATTGGTATTTTTTTGGTTTTTTTTT------GAAATTTTTAGGTTATTTAGACC-----ATTTTTTTTT--GTTTCGCTAATTAGAATTTTATTAGCCTTTGGTTTTTTTTTATTTTT----TGGGGTTAAGACAAGGTGTCGT-TGAATTAGTTTAGCAAAATACTGCTTAAGGTAGGCTATA---------------------GGATCTACCTTTTATCTTTCTAAT--CTTTT----GTTTTAGT-ATAATTGGTCTTCGATTCAACAATTTTTAGTCTTCAGTCTTTTTTTTTATTTTGAAAAGGTTTTAACACTCT--TGGTTTTGGAGGCTTTGGCTTTCTT--CTTACTCTTAGGAGGA-TGGGCGCTAGAAAGAGTTTTAAGAGGGTGTGAAAGGGGG-TTAATAGCAGG---ATTTGCTTTTTTAACTTATACTGGTTCGTAACGCATTAGCTCAACTCTCTCTTGTAGTTCTAGCAGCCGCCTTTTCTTTGTTGGGGGAGGGTTTAGGAGGAGTCTTTTTTTTCCTAACCCAA-GGTGTTTCTTTCTTTTTTTCTTT-AAAGTTC-TTGACTGTTGGCAC--TTGTCTCCATAAATTTTC----TTTCTTGTAAAGGGCTC-CTAAGGC--TTCTTGTTTCTGAATTCCTCTTTTCTTTTATTCTGTTTTGAGCTTATTTTTCTTGTTAGCTATTACGTAGGCATAGGGCAAATAATTTTTTTTTCTG---CTCT---------CATTA-------TTCCTTCTCC---CTGCTTGTTTCACCCT-GTGGGCTCTTTGAGCCC-CACT-AAGTGAGCGGGGCTCCTGCTTCCGCTCAATTAAATTTTGGTGGGTATTGAGTCTCAGAGGGACTATGATATAGGTTCAGATTGATGGACCTAATCAATCAATTGTATCGCTATACAATCTAGTACCCCTACCAGGGTACCAAGAGAGAGATAACTAGGGTGAATACTACGACTTAGATGTAGTGTTTAAGTTTCTACGGGCTACAGAGAAGCTACCCGCAGGGTAYATATTTGTTCATTACATATTTGTTGACTTTTCTATCTCTGCTTTTACTTTTT-TATTTATTTTTAAATCTTTTTAACTTCAGCTGTTTTTCCTTATCTATTTGACGTAGGCATAGGAAAGTTAACGAATTTTGTAATATTTTTAATTATTTTGTATAGTATACAGGGTAGTGGTATGTAATAGGTAAATTCCATAAGTTCATTATAGTTTATCAGTTGAGAGGAATTTAGTATAAGAAGGCCCATTGGGGCTCTTGTCTTATCCAAGAACTGGTAA-GATTTAATTCT----ACCGGGA--CGGTAGAAATCGGGCAGAGCATGATCTATTTCTTCGGGTATGGCTATAGGGACTAGGTGCTAGGGAGGTATTAGGGCACCGCTCTTTATACAATCTCCATAGATACAACCAGGTCAACTAGGACAACGGAGGACGTTGACAGAGCATAAATAGCGATAGCGTACAAGATAWAATAGGGGCAGTGGTAGCGAAGCGTAGAAGAAAAAATAAGAGTATTGTTTGTAAATAATTCTTTTTTTAGTTTTTAAATATTCTTTTTTTAGGTGGTGTGTGGTTAGGTATGGGGTTAAGGGTGTGGCAAAGAGAAATGTTTATTAAACATTCTTATGGCCGTAGATAGCATATCGATTATACGAGACCTTCGTAAGATCAATCCCCACTAGCATTGCTCATACAGGTTAACTCAATAGGAGGAGCTGGGGTAGAACGTTTCTAGTTCGGGGGTAACCGCAGTTCAATGAAAGTGACGACGTCGGATGGAACAAACTTAATACCACCAGTTGTGCTAACGATTGTTATCTCAATCTATCCCAACAGGCCCCCAGGTAGTGATGAGTGGTGGAATGGTACAGGGTACCAGTGGGTGAAGAGCGTCACGAACCAGGGAATACGGAGTACAGAGTTGAGCGCCCGGGGCTCCGCCCCCGGCTTTTATAGCGCGAGACGTGGTCAGTCGATTCAGCGTTAGG-TTTAAACTCCTTTGGCAAAGATTGACTCTAGCGATCCAGAGACCCTGCCTGGCATAAAAGTCTTTATWAACACCAGTAGGTTCAATAAGGTAGTAATCCAATAGAATGGAAAACTCAAGATCTAATCTCTCGAYTTCCTAGTGTCATGGAAATCAGCCAGGTTCTCTTCATCTGCAACAGTAGAAGAAGAAGAGAGACTAGCGAGAGAGTCTTATGGCGGAGACGCTAAGGCTTAAATGTAATGTAGATAACCCCTTACGGAACACTAGAGTGCGACGTAGACTACATAATCCCTCAGGGATATTAGCTCTGCTCGATTAACAATAGCATACTTTGTTACACGGAGTGTATCTAGGGGGAATAATACTAACTTACTTAGCACTATCGCGATGCTACGCATTCGCTCTTTCGCTAAATAAGATACGACGATGAGTGGTTGGTGGAGAGAATAACCGATTCTAACTTGATAATTCGCATGAAATAATTTTTTTATTTTGTTTTTTTTTTGCTCTTAATTTTAGWGGGRGTGTTTATTTTTATTCTAATAAAAAGGATCCGTTGAA", ) self.assertEqual( alignment[1], "----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTATTAA--------------------------------TCTTATGGTTTTGCCGTAAAATTTC--TTTCTTTATTTTTT----ATTG---------TTAGGATTTTGTTGATTTTATTTTTCTCAAG-AATTTTTAGGTCAATTAGACCGGCTTATTTTTTTGTCAGTGT------TTAAAGTTTTATTA-----------------ATTTTTGGGGGGGGGGGGAGACGGGGTGTTATCTGAATTAGTTT-------------TT--GGGAGTCTCTAGACATCTCATGGGTTGGCCGGGGGCCTGCCGTCTATAGTTCTTATTCCTTTTAAGGG----AGTAAGAAT-----TTCGATTCAGCAA-CTTTAGTTCACAGTCTTTTTTTTTATTAAG-AAAGGTTTTAATATTCTTGTGGTTTT-GAACCTTTAGGTTTCTTTCTTTAC-CTTCGAGGGATTGGGCACTAGAATGAGTTTTAAGAGTGTGTGAAAGGGGGCTTGATAGCAGGGGAA--TGCTTTTTTAACTTATACTGGCTCGTAACGCATCAGTTCAACTCTCTCTTGCAGTTCTAGCAGCCGCCTTTTTTTTGTTGGGGGGGGGTTAAG--AGAGTGTTTTTTTT-CTAATCCAAGGGTCTTACTTTCTTTCTTTCTTTAAAAATTCTTTGGCTGTCGACACCTTTCTCTCCCGTCAGTCTCATGGTTTCT-------GGCTCTCTTGGGCTTTTTTTGTTTGTGAATGCCTCTTTT-TTTTATTCTGTTTTGAGCTTATTTTTCTTGTTTACTATTACGTAGGTATAGGGCAAATAATTTTTTTTTC-GCGTCTCTTGGCATGCCCATTACTCTAGTTTTATTC-CCGGGCTTCTTCTCTCACCCTAGAGGGCTCTTTGAGCCCACACTCAAGTGAGCGGGGCTCCCGCTTCCGCTCAATTAAA-TTTGGTGGGTATTGAGTCTCAGAGGGACTATGATATAGGTTCAGATTGATGGACCTAGTCAATCAATTGTATCGCTATACAATCTAGTACCCCTACCAGGGTACCAGGAGAGAGATAACTAGGGTGAATACTACGACTTAGATGTACTGTTTAAGTTTCTACGGGCTACAGAGAAGCTACCCGCAGGGTATATATTTGCTCATTACATATTTGTTGATTTTTCTATGTCCGC-TTTACTTTTTATATT------------TTTTTAACTTCAGCTGTTTTTCCTTATCTATTTGACGTAGGCATAGGAAAGTTAACGAATTTTGTAATATTTTTAATTATTTTGTATAGTATACAGGGTAGTGGTATGTAATAGGTAAATTCCATAAGTTCATTATAGTCTATCAGTTGAGAGGAATTTAGTATAAGAAAGCCTGTCAGGGCTCTTGCCTTATCCAAGAACTGGTAAGGAT----TTCTTGACAGAGGGACTCTGT-CAAATCGGGCAGAGCATGATCTATTTCTTCGGGTATGGTTATAAGGCTTAGGTGCTTGGAGGGTATTAGGGCACCGCTCTTAATACAGTCTCCATAGGTGTAACCAGGTCAACTAGGACAACGGAGGACGTTGACAAAGCATGGATAGCGATAGCGTAGAAGATAAAAT-GGGGCAGTGGTAGCGAAGCGTAGAAGAAAAAATAAGAGTATTGTTTGTAAATAATTCTTTTTTTAGTTTTTAAATATTCTTTTTTTAGGTGGTGTGTGGTTAGGTATGGGGTTAGGGGAGTGGCAAAGAGAAGTGTTTATTAAACATTCTTATGGCCGTAGATAGCATATCGATTATACGAGACCTTCGTAAGATCAATCCCCACTAGCATTGCTCATACAGGTTAACTCAATAGGAGGAGCTGGGGTAGAACGTATCTAGTTCGGGGGTAACCGCAGTTCAATGAAAGTGACGACGTCGGATGGAACAAACTTAATACCACCAGTTGTGCTAACGATTGTTATCTCAATCTATCCCAACAGGCCCCCAGGTAGTGATGAGTGGTGGAATGGTACAGGGTACCAGTGGGTGAAGAGCGTCACGAACCAGGGAATACGGAGTACAGAGTTGAGCGCCCGGGGCTCCGCCCCCGGCTTTTATAGCGCGAGACGTGGTCAGTCGATTCAGCGTTAGGTTTTAAACTCCTTTGGCAAAGATTGATTCTAGCGATCCAGAGACCCTGCCTGGCATAAAAGTCTTTATTAGCACCAGTAGGTTCAATAAGGTAGTAGTCCAATAGAATGGAAAACTCGAGATCTAATCTCTCGATTTCCTAGTGTCATGGAAATCAGCCAGGTTCTCTTCATCTGCAACAGTAGAAGAAGAAGAGAGGCTAGCGAGAGAGTCTTATGGCGGAGACGCTAAGGCTTAAATGTAATGTAGATAACCCCTTACGGAACACTTGAGTGCGACGTAGACTACATAATCCCTCAGGGATATTAGCTCTGCTCGATTAACAATAGCATACTTTGTTACACGGAGTGTATCTGGGGGGAATAATACTAACTTACTTAGCACTATCGCGATGCTACGCATTCGCTCTTTCGCTAAATAAGATACGACGATGAGTGGTTGGTGGAGAGAATAACCGATTCTAACTTGATAATTCGCATGAAATAA-TTTTTTATTTGTTTTTTTTTTTGCTCTTAATTTTAGAGG--ATGTTTATTTTTATTCTAATAAAAAGGATCCGTTGAA", ) self.assertEqual( alignment.column_annotations["emboss_consensus"], " .|||||| .|||||.|| |||..|..|| ||||.||||.||.| ||.| ||.|.|||||.|||.||||.|||| | |||||||||||.|.||||||| ||||||||.| ||.| |||.|.|||||||| |||||| .||||...||||..|||||..| ||||||||||| || ||.||.||.|| ||..||.||.|.|||..||||.|| ||||| | ||| |.||| |||||||||.||| .||||||...|||||||||||||||||..| |||||||||||.|.||| ||||||| ||..||||.|.|||||| .|||| |||.|..||| |||||.||||||.||||||||||||.||||||||||||| ||.|||||||| | |||||||||||||||||||||.|||||||||||.||.||||||||||||||.||||||||||||||||||||.|||||||||||.|||||.|| .||||.|||||||| ||||.|||| |||.||.||||||||.||||||| |||.||| |||.||||.|.||| ||.|||||....|.|.|| ||||| ||||| ||..||| ||.||||||.|||||.|||||||| ||||||||||||||||||||||||||||||||..||||||||||||.||||||||||||||||||||||| | |||| ||||| ||..||| || ||.|||.|.||||||| |.||||||||||||||| |||| ||||||||||||||||.||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||.||||||||||||||||||||||||||||||||||||||||||||||||.|||||||||||||||||||||||||||||||||||||||.|||||||||||||||||||||||||||||||||||||||||||.|||||||.||||||||||||||||||.||||||||.||.|| |||||||||| |||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||.|||||||||||||||||||||||||||||.|||..|..|||||||||.||||||||||||||||||| ||| |||| |..|||| |.|| .|||||||||||||||||||||||||||||||||||||.||||.||..||||||||.||..||||||||||||||||||||.|||||.|||||||||.|..|||||||||||||||||||||||||||||||||||.|||||..||||||||||||||.||||||.||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||.|||.|||||||||||||.||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||.|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||.|||||||||||||||||||||||||||||||||||||||||.|.|||||||||||||||||||||||||.||||||||||||||||||||.||||||||||||||||.||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||.||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||.|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||.|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||..||||||||||||||||||||||||.|| .||||||||||||||||||||||||||||||||||||", ) self.assertEqual( str(alignment), """\ asis 0 TATTTTTTGGATTTTTTTCTAGATTTTCTAGGTTATTTAAACCGTTTTTTTTTAATTTAG 0 ------------------------------------------------------------ asis 0 ------------------------------------------------------------ asis 60 TGTTTGAGTTTTGACAGGTCTCCACTTTGGGGGCTCCATCGCAAGGAAATTAGAATTCTT 60 ------------------------------------------------------------ asis 0 ------------------------------------------------------------ asis 120 ATACTTGGTTCTCTTTCCCAGGGACTCCAAGGATCTTTTCATTAGTTTGGATTTTGGTGT 120 ------------------------------------------------------------ asis 0 ------------------------------------------------------------ asis 180 TTTCTTTAATTTTGTTAAGAAACAAATCCTTTCTAGAGTTTTTTCTAGCATTATGTTTTT 180 ------------------------------------------------------------ asis 0 ------------------------------------------------------------ asis 240 TTTTCTCCTTATCTAAGGGGGTTTGTCGAGGTTTCTTAAATCTTTTTTTCTCTGGGTTTT 240 ------------------------------------------------------------ asis 0 ------------------------------------------------------------ asis 300 AAAATTGTTTAAATTTTTTTGACCGAGGGGTTGGGGTGGTTTTCTCATGATAACAGGGGC 300 ------------------------------------------------------------ asis 0 ------------------------------------------------------------ asis 360 TGGTGCTTTAGATCCTACCTCTACTGACCCGGGGTCTGCTACTGTGGCTTCTGATGAAGA 360 ------------------------------------------------------------ asis 0 ------------------------------------------------------------ asis 420 TCCACAGTATGCGCCTACGGAARCTCGGCAGTTTGGTGTTCGAAATCCAGCCCCTCGAAT 420 ------------------------------------------------------------ asis 0 ------------------------------------------------------------ asis 480 TAATACTCTTGTGCAGGTGGTTGACGAGCGCGGTATCGAATTGCAAAATTTGGGGCGGGA 480 ------------------------------------------------------------ asis 0 ------------------------------------------------------------ asis 540 CCCCGCTGTTCCGCCTGTTGCTCCGGGGGGGGCAGGTTAATCCTCCAGTCGTCTCCTTTT 540 ------------------------------------------------------------ asis 0 ------------------------------------------------------------ asis 600 GGGGGCGTCTTTGACGGGGGTTTAAATCTTTCTTTGGTTGTGGATAGGATTTTTTTTCTA 600 ------------------------------------------------------------ asis 0 ------------------------------------------------------------ asis 660 ATATCGATCCTACCTGTTTTGGCGGGGCTATTACTTTGTTACTTTTGACCGAAATTTTAA 660 ------------------------------------------------------------ asis 0 ------------------------------------------------------------ asis 720 TGGAAATTTCTTTGATTCAAATGAATCCCTTAGTTTTCCAACACTTTTTTTTGGTTTTTT 720 ------------------------------------------------------------ asis 0 ------------------------------------------------------------ asis 780 TAGGGATAGTCTACGCTGTGGTTAGGTTTGGTTTTATTGGGGGCTTGGTTTGGGCCCACC 780 ------------------------------------------------------------ asis 0 ------------------------------------------------------------ asis 840 CCAAATAGGGAGTGGGGGTATGACCTCAGATAGACGAGCTTATTTTAGGGCGGCGACTAT 840 ------------------------------------------------------------ asis 0 ------------------------------------------------------------ asis 900 AATTATTTCGTTTCCTACAAGGATTAAAGTTTTTTCTTTTACTGTGGGAGGGGGTTTGGT 900 ----------------------------------------------------------.| asis 0 ----------------------------------------------------------TT asis 960 ATTAAGAAACGCTAGTCCGGATGTGGCTCTCCATGATACTTATTGT------GTAGTAGC 960 |||||--------------------------------.|||||.||------|||..|.. asis 2 ATTAA--------------------------------TCTTATGGTTTTGCCGTAAAATT asis 1014 TCATTTTCATTATGTTCTTCGAATGGGAGCAGTCATTGGTATTTTTTTGGTTTTTTTTT- 1020 ||--||||.||||.||.|----||.|---------||.|.|||||.|||.||||.||||- asis 30 TC--TTTCTTTATTTTTT----ATTG---------TTAGGATTTTGTTGATTTTATTTTT asis 1073 -----GAAATTTTTAGGTTATTTAGACC-----ATTTTTTTTT--GTTTCGCTAATTAGA 1080 -----|-|||||||||||.|.|||||||-----||||||||.|--||.|------|||.| asis 75 CTCAAG-AATTTTTAGGTCAATTAGACCGGCTTATTTTTTTGTCAGTGT------TTAAA asis 1121 ATTTTATTAGCCTTTGGTTTTTTTTTATTTTT----TGGGGTTAAGACAAGGTGTCGT-T 1140 .||||||||-----------------||||||----.||||...||||..|||||..|-| asis 128 GTTTTATTA-----------------ATTTTTGGGGGGGGGGGGAGACGGGGTGTTATCT asis 1176 GAATTAGTTTAGCAAAATACTGCTTAAGGTAGGCTATA---------------------G 1200 ||||||||||-------------||--||.||.||.||---------------------| asis 171 GAATTAGTTT-------------TT--GGGAGTCTCTAGACATCTCATGGGTTGGCCGGG asis 1215 GATCTACCTTTTATCTTTCTAAT--CTTTT----GTTTTAGT-ATAATTGGTCTTCGATT 1260 |..||.||.|.|||..||||.||--|||||----|----|||-|.|||-----||||||| asis 216 GGCCTGCCGTCTATAGTTCTTATTCCTTTTAAGGG----AGTAAGAAT-----TTCGATT asis 1268 CAACAATTTTTAGTCTTCAGTCTTTTTTTTTATTTTGAAAAGGTTTTAACACTCT--TGG 1320 ||.|||-.||||||...|||||||||||||||||..|-|||||||||||.|.|||--||| asis 267 CAGCAA-CTTTAGTTCACAGTCTTTTTTTTTATTAAG-AAAGGTTTTAATATTCTTGTGG asis 1326 TTTTGGAGGCTTTGGCTTTCTT--CTTACTCTTAGGAGGA-TGGGCGCTAGAAAGAGTTT 1380 ||||-||..||||.|.||||||--.||||-|||.|..|||-|||||.||||||.|||||| asis 325 TTTT-GAACCTTTAGGTTTCTTTCTTTAC-CTTCGAGGGATTGGGCACTAGAATGAGTTT asis 1383 TAAGAGGGTGTGAAAGGGGG-TTAATAGCAGG---ATTTGCTTTTTTAACTTATACTGGT 1440 ||||||.|||||||||||||-||.||||||||---|--|||||||||||||||||||||. asis 383 TAAGAGTGTGTGAAAGGGGGCTTGATAGCAGGGGAA--TGCTTTTTTAACTTATACTGGC asis 1439 TCGTAACGCATTAGCTCAACTCTCTCTTGTAGTTCTAGCAGCCGCCTTTTCTTTGTTGGG 1500 |||||||||||.||.||||||||||||||.||||||||||||||||||||.||||||||| asis 441 TCGTAACGCATCAGTTCAACTCTCTCTTGCAGTTCTAGCAGCCGCCTTTTTTTTGTTGGG asis 1499 GGAGGGTTTAGGAGGAGTCTTTTTTTTCCTAACCCAA-GGTGTTTCTTTCTTTTTTTCTT 1560 ||.|||||.||--.||||.||||||||-||||.||||-|||.||.||||||||.|||||| asis 501 GGGGGGTTAAG--AGAGTGTTTTTTTT-CTAATCCAAGGGTCTTACTTTCTTTCTTTCTT asis 1558 T-AAAGTTC-TTGACTGTTGGCAC--TTGTCTCCATAAATTTTC----TTTCTTGTAAAG 1620 |-|||.|||-|||.||||.|.|||--||.|||||....|.|.||----|||||------- asis 558 TAAAAATTCTTTGGCTGTCGACACCTTTCTCTCCCGTCAGTCTCATGGTTTCT------- asis 1610 GGCTC-CTAAGGC--TTCTTGTTTCTGAATTCCTCTTTTCTTTTATTCTGTTTTGAGCTT 1680 |||||-||..|||--||.||||||.|||||.||||||||-|||||||||||||||||||| asis 611 GGCTCTCTTGGGCTTTTTTTGTTTGTGAATGCCTCTTTT-TTTTATTCTGTTTTGAGCTT asis 1667 ATTTTTCTTGTTAGCTATTACGTAGGCATAGGGCAAATAATTTTTTTTTCTG---CTCT- 1740 ||||||||||||..||||||||||||.|||||||||||||||||||||||-|---||||- asis 670 ATTTTTCTTGTTTACTATTACGTAGGTATAGGGCAAATAATTTTTTTTTC-GCGTCTCTT asis 1723 --------CATTA-------TTCCTTCTCC---CTGCTTGTTTCACCCT-GTGGGCTCTT 1800 --------|||||-------||..|||-||---||.|||.|.|||||||-|.|||||||| asis 729 GGCATGCCCATTACTCTAGTTTTATTC-CCGGGCTTCTTCTCTCACCCTAGAGGGCTCTT asis 1764 TGAGCCC-CACT-AAGTGAGCGGGGCTCCTGCTTCCGCTCAATTAAATTTTGGTGGGTAT 1860 |||||||-||||-||||||||||||||||.|||||||||||||||||-|||||||||||| asis 788 TGAGCCCACACTCAAGTGAGCGGGGCTCCCGCTTCCGCTCAATTAAA-TTTGGTGGGTAT asis 1822 TGAGTCTCAGAGGGACTATGATATAGGTTCAGATTGATGGACCTAATCAATCAATTGTAT 1920 |||||||||||||||||||||||||||||||||||||||||||||.|||||||||||||| asis 847 TGAGTCTCAGAGGGACTATGATATAGGTTCAGATTGATGGACCTAGTCAATCAATTGTAT asis 1882 CGCTATACAATCTAGTACCCCTACCAGGGTACCAAGAGAGAGATAACTAGGGTGAATACT 1980 ||||||||||||||||||||||||||||||||||.||||||||||||||||||||||||| asis 907 CGCTATACAATCTAGTACCCCTACCAGGGTACCAGGAGAGAGATAACTAGGGTGAATACT asis 1942 ACGACTTAGATGTAGTGTTTAAGTTTCTACGGGCTACAGAGAAGCTACCCGCAGGGTAYA 2040 ||||||||||||||.|||||||||||||||||||||||||||||||||||||||||||.| asis 967 ACGACTTAGATGTACTGTTTAAGTTTCTACGGGCTACAGAGAAGCTACCCGCAGGGTATA asis 2002 TATTTGTTCATTACATATTTGTTGACTTTTCTATCTCTGCTTTTACTTTTT-TATTTATT 2100 ||||||.||||||||||||||||||.||||||||.||.||-||||||||||-||||---- asis 1027 TATTTGCTCATTACATATTTGTTGATTTTTCTATGTCCGC-TTTACTTTTTATATT---- asis 2061 TTTAAATCTTTTTAACTTCAGCTGTTTTTCCTTATCTATTTGACGTAGGCATAGGAAAGT 2160 --------|||||||||||||||||||||||||||||||||||||||||||||||||||| asis 1082 --------TTTTTAACTTCAGCTGTTTTTCCTTATCTATTTGACGTAGGCATAGGAAAGT asis 2121 TAACGAATTTTGTAATATTTTTAATTATTTTGTATAGTATACAGGGTAGTGGTATGTAAT 2220 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| asis 1134 TAACGAATTTTGTAATATTTTTAATTATTTTGTATAGTATACAGGGTAGTGGTATGTAAT asis 2181 AGGTAAATTCCATAAGTTCATTATAGTTTATCAGTTGAGAGGAATTTAGTATAAGAAGGC 2280 |||||||||||||||||||||||||||.|||||||||||||||||||||||||||||.|| asis 1194 AGGTAAATTCCATAAGTTCATTATAGTCTATCAGTTGAGAGGAATTTAGTATAAGAAAGC asis 2241 CCATTGGGGCTCTTGTCTTATCCAAGAACTGGTAA-GATTTAATTCT----ACCGGGA-- 2340 |..|..|||||||||.|||||||||||||||||||-|||----||||----|..||||-- asis 1254 CTGTCAGGGCTCTTGCCTTATCCAAGAACTGGTAAGGAT----TTCTTGACAGAGGGACT asis 2294 CGGTAGAAATCGGGCAGAGCATGATCTATTTCTTCGGGTATGGCTATAGGGACTAGGTGC 2400 |.||-.|||||||||||||||||||||||||||||||||||||.||||.||..||||||| asis 1310 CTGT-CAAATCGGGCAGAGCATGATCTATTTCTTCGGGTATGGTTATAAGGCTTAGGTGC asis 2354 TAGGGAGGTATTAGGGCACCGCTCTTTATACAATCTCCATAGATACAACCAGGTCAACTA 2460 |.||..||||||||||||||||||||.|||||.|||||||||.|..|||||||||||||| asis 1369 TTGGAGGGTATTAGGGCACCGCTCTTAATACAGTCTCCATAGGTGTAACCAGGTCAACTA asis 2414 GGACAACGGAGGACGTTGACAGAGCATAAATAGCGATAGCGTACAAGATAWAATAGGGGC 2520 |||||||||||||||||||||.|||||..||||||||||||||.||||||.|||-||||| asis 1429 GGACAACGGAGGACGTTGACAAAGCATGGATAGCGATAGCGTAGAAGATAAAAT-GGGGC asis 2474 AGTGGTAGCGAAGCGTAGAAGAAAAAATAAGAGTATTGTTTGTAAATAATTCTTTTTTTA 2580 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| asis 1488 AGTGGTAGCGAAGCGTAGAAGAAAAAATAAGAGTATTGTTTGTAAATAATTCTTTTTTTA asis 2534 GTTTTTAAATATTCTTTTTTTAGGTGGTGTGTGGTTAGGTATGGGGTTAAGGGTGTGGCA 2640 |||||||||||||||||||||||||||||||||||||||||||||||||.|||.|||||| asis 1548 GTTTTTAAATATTCTTTTTTTAGGTGGTGTGTGGTTAGGTATGGGGTTAGGGGAGTGGCA asis 2594 AAGAGAAATGTTTATTAAACATTCTTATGGCCGTAGATAGCATATCGATTATACGAGACC 2700 |||||||.|||||||||||||||||||||||||||||||||||||||||||||||||||| asis 1608 AAGAGAAGTGTTTATTAAACATTCTTATGGCCGTAGATAGCATATCGATTATACGAGACC asis 2654 TTCGTAAGATCAATCCCCACTAGCATTGCTCATACAGGTTAACTCAATAGGAGGAGCTGG 2760 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| asis 1668 TTCGTAAGATCAATCCCCACTAGCATTGCTCATACAGGTTAACTCAATAGGAGGAGCTGG asis 2714 GGTAGAACGTTTCTAGTTCGGGGGTAACCGCAGTTCAATGAAAGTGACGACGTCGGATGG 2820 ||||||||||.||||||||||||||||||||||||||||||||||||||||||||||||| asis 1728 GGTAGAACGTATCTAGTTCGGGGGTAACCGCAGTTCAATGAAAGTGACGACGTCGGATGG asis 2774 AACAAACTTAATACCACCAGTTGTGCTAACGATTGTTATCTCAATCTATCCCAACAGGCC 2880 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| asis 1788 AACAAACTTAATACCACCAGTTGTGCTAACGATTGTTATCTCAATCTATCCCAACAGGCC asis 2834 CCCAGGTAGTGATGAGTGGTGGAATGGTACAGGGTACCAGTGGGTGAAGAGCGTCACGAA 2940 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| asis 1848 CCCAGGTAGTGATGAGTGGTGGAATGGTACAGGGTACCAGTGGGTGAAGAGCGTCACGAA asis 2894 CCAGGGAATACGGAGTACAGAGTTGAGCGCCCGGGGCTCCGCCCCCGGCTTTTATAGCGC 3000 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| asis 1908 CCAGGGAATACGGAGTACAGAGTTGAGCGCCCGGGGCTCCGCCCCCGGCTTTTATAGCGC asis 2954 GAGACGTGGTCAGTCGATTCAGCGTTAGG-TTTAAACTCCTTTGGCAAAGATTGACTCTA 3060 |||||||||||||||||||||||||||||-|||||||||||||||||||||||||.|||| asis 1968 GAGACGTGGTCAGTCGATTCAGCGTTAGGTTTTAAACTCCTTTGGCAAAGATTGATTCTA asis 3013 GCGATCCAGAGACCCTGCCTGGCATAAAAGTCTTTATWAACACCAGTAGGTTCAATAAGG 3120 |||||||||||||||||||||||||||||||||||||.|.|||||||||||||||||||| asis 2028 GCGATCCAGAGACCCTGCCTGGCATAAAAGTCTTTATTAGCACCAGTAGGTTCAATAAGG asis 3073 TAGTAATCCAATAGAATGGAAAACTCAAGATCTAATCTCTCGAYTTCCTAGTGTCATGGA 3180 |||||.||||||||||||||||||||.||||||||||||||||.|||||||||||||||| asis 2088 TAGTAGTCCAATAGAATGGAAAACTCGAGATCTAATCTCTCGATTTCCTAGTGTCATGGA asis 3133 AATCAGCCAGGTTCTCTTCATCTGCAACAGTAGAAGAAGAAGAGAGACTAGCGAGAGAGT 3240 ||||||||||||||||||||||||||||||||||||||||||||||.||||||||||||| asis 2148 AATCAGCCAGGTTCTCTTCATCTGCAACAGTAGAAGAAGAAGAGAGGCTAGCGAGAGAGT asis 3193 CTTATGGCGGAGACGCTAAGGCTTAAATGTAATGTAGATAACCCCTTACGGAACACTAGA 3300 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||.|| asis 2208 CTTATGGCGGAGACGCTAAGGCTTAAATGTAATGTAGATAACCCCTTACGGAACACTTGA asis 3253 GTGCGACGTAGACTACATAATCCCTCAGGGATATTAGCTCTGCTCGATTAACAATAGCAT 3360 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| asis 2268 GTGCGACGTAGACTACATAATCCCTCAGGGATATTAGCTCTGCTCGATTAACAATAGCAT asis 3313 ACTTTGTTACACGGAGTGTATCTAGGGGGAATAATACTAACTTACTTAGCACTATCGCGA 3420 |||||||||||||||||||||||.|||||||||||||||||||||||||||||||||||| asis 2328 ACTTTGTTACACGGAGTGTATCTGGGGGGAATAATACTAACTTACTTAGCACTATCGCGA asis 3373 TGCTACGCATTCGCTCTTTCGCTAAATAAGATACGACGATGAGTGGTTGGTGGAGAGAAT 3480 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| asis 2388 TGCTACGCATTCGCTCTTTCGCTAAATAAGATACGACGATGAGTGGTTGGTGGAGAGAAT asis 3433 AACCGATTCTAACTTGATAATTCGCATGAAATAATTTTTTTATTTTGTTTTTTTTTTGCT 3540 ||||||||||||||||||||||||||||||||||-||||||||||..||||||||||||| asis 2448 AACCGATTCTAACTTGATAATTCGCATGAAATAA-TTTTTTATTTGTTTTTTTTTTTGCT asis 3493 CTTAATTTTAGWGGGRGTGTTTATTTTTATTCTAATAAAAAGGATCCGTTGAA 3546 3600 |||||||||||.||--.|||||||||||||||||||||||||||||||||||| 3653 asis 2507 CTTAATTTTAGAGG--ATGTTTATTTTTATTCTAATAAAAAGGATCCGTTGAA 2558 """, ) with self.assertRaises(StopIteration): next(alignments) def test_water_reverse1(self): # water -asequence seqA.fa -bsequence seqB.fa -gapopen 10 -gapextend 0.5 -sreverse1 -outfile water_reverse1.txt path = "Emboss/water_reverse1.txt" alignments = Align.parse(path, "emboss") self.assertEqual(alignments.metadata["Program"], "water") self.assertEqual(alignments.metadata["Rundate"], "Sat 22 Oct 2022 23:47:41") self.assertEqual( alignments.metadata["Command line"], "water -asequence seqA.fa -bsequence seqB.fa -gapopen 0.001 -gapextend 0.001 -sreverse1 -outfile water_reverse1.txt", ) self.assertEqual(alignments.metadata["Align_format"], "srspair") self.assertEqual(alignments.metadata["Report_file"], "water_reverse1.txt") alignment = next(alignments) self.assertEqual(alignment.annotations["Matrix"], "EDNAFULL") self.assertAlmostEqual(alignment.annotations["Gap_penalty"], 0.001) self.assertAlmostEqual(alignment.annotations["Extend_penalty"], 0.001) self.assertEqual(alignment.annotations["Identity"], 32) self.assertEqual(alignment.annotations["Similarity"], 32) self.assertEqual(alignment.annotations["Gaps"], 89) self.assertAlmostEqual(alignment.annotations["Score"], 159.911) self.assertEqual(len(alignment), 2) self.assertEqual(alignment.shape, (2, 121)) self.assertEqual(alignment.sequences[0].id, "seqA") self.assertEqual(alignment.sequences[1].id, "seqB") self.assertEqual( alignment.sequences[0].seq, "GGGGGGGGGGGGGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCC", ) self.assertEqual( alignment.sequences[1].seq, "GGGGGGGGGGGGGGGGGGGCCCCCCCCCCCCC", ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[121, 102, 13, 0], [ 0, 19, 19, 32]]) # fmt: on ) ) self.assertEqual( alignment[0], "GGGGGGGGGGGGGGGGGGGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCCCCCCCCCCCCC", ) self.assertEqual( alignment[1], "GGGGGGGGGGGGGGGGGGG-----------------------------------------------------------------------------------------CCCCCCCCCCCCC", ) self.assertEqual( alignment.column_annotations["emboss_consensus"], "||||||||||||||||||| |||||||||||||", ) self.assertEqual( str(alignment), """\ seqA 121 GGGGGGGGGGGGGGGGGGGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 0 |||||||||||||||||||----------------------------------------- seqB 0 GGGGGGGGGGGGGGGGGGG----------------------------------------- seqA 61 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCCCCCCCCCCCC 60 ------------------------------------------------|||||||||||| seqB 19 ------------------------------------------------CCCCCCCCCCCC seqA 1 C 0 120 | 121 seqB 31 C 32 """, ) with self.assertRaises(StopIteration): next(alignments) def test_water_reverse2(self): # water -asequence seqA.fa -bsequence seqB.fa -gapopen 10 -gapextend 0.5 -sreverse2 -outfile water_reverse2.txt path = "Emboss/water_reverse2.txt" alignments = Align.parse(path, "emboss") self.assertEqual(alignments.metadata["Program"], "water") self.assertEqual(alignments.metadata["Rundate"], "Sun 23 Oct 2022 00:06:18") self.assertEqual( alignments.metadata["Command line"], "water -asequence seqA.fa -bsequence seqB.fa -gapopen 0.001 -gapextend 0.001 -sreverse2 -outfile water_reverse2.txt", ) self.assertEqual(alignments.metadata["Align_format"], "srspair") self.assertEqual(alignments.metadata["Report_file"], "water_reverse2.txt") alignment = next(alignments) self.assertEqual(alignment.annotations["Matrix"], "EDNAFULL") self.assertAlmostEqual(alignment.annotations["Gap_penalty"], 0.001) self.assertAlmostEqual(alignment.annotations["Extend_penalty"], 0.001) self.assertEqual(alignment.annotations["Identity"], 32) self.assertEqual(alignment.annotations["Similarity"], 32) self.assertEqual(alignment.annotations["Gaps"], 89) self.assertAlmostEqual(alignment.annotations["Score"], 159.911) self.assertEqual(len(alignment), 2) self.assertEqual(alignment.shape, (2, 121)) self.assertEqual(alignment.sequences[0].id, "seqA") self.assertEqual(alignment.sequences[1].id, "seqB") self.assertEqual( alignment.sequences[0].seq, "GGGGGGGGGGGGGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCC", ) self.assertEqual( alignment.sequences[1].seq, "GGGGGGGGGGGGGGGGGGGCCCCCCCCCCCCC", ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 13, 102, 121], [32, 19, 19, 0]]) # fmt: on ) ) self.assertEqual( alignment[0], "GGGGGGGGGGGGGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCC", ) self.assertEqual( alignment[1], "GGGGGGGGGGGGG-----------------------------------------------------------------------------------------CCCCCCCCCCCCCCCCCCC", ) self.assertEqual( alignment.column_annotations["emboss_consensus"], "||||||||||||| |||||||||||||||||||", ) self.assertEqual( str(alignment), """\ seqA 0 GGGGGGGGGGGGGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 0 |||||||||||||----------------------------------------------- seqB 32 GGGGGGGGGGGGG----------------------------------------------- seqA 60 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCC 60 ------------------------------------------|||||||||||||||||| seqB 19 ------------------------------------------CCCCCCCCCCCCCCCCCC seqA 120 C 121 120 | 121 seqB 1 C 0 """, ) with self.assertRaises(StopIteration): next(alignments) def test_water_reverse3(self): # water -asequence seqA.fa -bsequence seqB.fa -gapopen 10 -gapextend 0.5 -sreverse1 -outfile water_reverse3.txt path = "Emboss/water_reverse3.txt" alignments = Align.parse(path, "emboss") self.assertEqual(alignments.metadata["Program"], "water") self.assertEqual(alignments.metadata["Rundate"], "Sat 22 Oct 2022 22:56:03") self.assertEqual( alignments.metadata["Command line"], "water -asequence seqA.fa -bsequence seqB.fa -gapopen 1 -gapextend 0.5 -sreverse1 -outfile water_reverse3.txt", ) self.assertEqual(alignments.metadata["Align_format"], "srspair") self.assertEqual(alignments.metadata["Report_file"], "water_reverse3.txt") alignment = next(alignments) self.assertEqual(alignment.annotations["Matrix"], "EDNAFULL") self.assertAlmostEqual(alignment.annotations["Gap_penalty"], 1.0) self.assertAlmostEqual(alignment.annotations["Extend_penalty"], 0.5) self.assertEqual(alignment.annotations["Identity"], 16) self.assertEqual(alignment.annotations["Similarity"], 16) self.assertEqual(alignment.annotations["Gaps"], 3) self.assertAlmostEqual(alignment.annotations["Score"], 77.5) self.assertEqual(len(alignment), 2) self.assertEqual(alignment.shape, (2, 19)) self.assertEqual(alignment.sequences[0].id, "seqA") self.assertEqual(alignment.sequences[1].id, "seqB") self.assertEqual( repr(alignment.sequences[0].seq), "Seq({2: 'GGGCCCGGTTTAAAAAAA'}, length=20)", ) self.assertEqual( repr(alignment.sequences[1].seq), "Seq({2: 'TTTTTTTACCCGGGCCC'}, length=19)", ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[20, 13, 11, 10, 10, 2], [ 2, 9, 9, 10, 11, 19]]) # fmt: on ) ) self.assertEqual(alignment[0], "TTTTTTTAAA-CCGGGCCC") self.assertEqual(alignment[1], "TTTTTTT--ACCCGGGCCC") self.assertEqual( alignment.column_annotations["emboss_consensus"], "||||||| | ||||||||", ) self.assertEqual( str(alignment), """\ seqA 20 TTTTTTTAAA-CCGGGCCC 2 0 |||||||--|-|||||||| 19 seqB 2 TTTTTTT--ACCCGGGCCC 19 """, ) with self.assertRaises(StopIteration): next(alignments) def test_water_reverse4(self): # water -asequence seqA.fa -bsequence seqB.fa -gapopen 10 -gapextend 0.5 -sreverse2 -outfile water_reverse4.txt path = "Emboss/water_reverse4.txt" alignments = Align.parse(path, "emboss") self.assertEqual(alignments.metadata["Program"], "water") self.assertEqual(alignments.metadata["Rundate"], "Sat 22 Oct 2022 22:56:15") self.assertEqual( alignments.metadata["Command line"], "water -asequence seqA.fa -bsequence seqB.fa -gapopen 1 -gapextend 0.5 -sreverse2 -outfile water_reverse4.txt", ) self.assertEqual(alignments.metadata["Align_format"], "srspair") self.assertEqual(alignments.metadata["Report_file"], "water_reverse4.txt") alignment = next(alignments) self.assertEqual(alignment.annotations["Matrix"], "EDNAFULL") self.assertAlmostEqual(alignment.annotations["Gap_penalty"], 1.0) self.assertAlmostEqual(alignment.annotations["Extend_penalty"], 0.5) self.assertEqual(alignment.annotations["Identity"], 16) self.assertEqual(alignment.annotations["Similarity"], 16) self.assertEqual(alignment.annotations["Gaps"], 3) self.assertAlmostEqual(alignment.annotations["Score"], 77.5) self.assertEqual(len(alignment), 2) self.assertEqual(alignment.shape, (2, 19)) self.assertEqual(alignment.sequences[0].id, "seqA") self.assertEqual(alignment.sequences[1].id, "seqB") self.assertEqual( repr(alignment.sequences[0].seq), "Seq({2: 'GGGCCCGGTTTAAAAAAA'}, length=20)", ) self.assertEqual( repr(alignment.sequences[1].seq), "Seq({2: 'TTTTTTTACCCGGGCCC'}, length=19)", ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 2, 10, 12, 12, 20], [19, 11, 11, 10, 2]]) # fmt: on ) ) self.assertEqual(alignment[0], "GGGCCCGGTT-TAAAAAAA") self.assertEqual(alignment[1], "GGGCCCGG--GTAAAAAAA") self.assertEqual( alignment.column_annotations["emboss_consensus"], "|||||||| ||||||||", ) self.assertEqual( str(alignment), """\ seqA 2 GGGCCCGGTT-TAAAAAAA 20 0 ||||||||---|||||||| 19 seqB 19 GGGCCCGG--GTAAAAAAA 2 """, ) with self.assertRaises(StopIteration): next(alignments) def test_pair_aln_full_blank_line(self): path = "Emboss/emboss_pair_aln_full_blank_line.txt" alignments = Align.parse(path, "emboss") self.assertEqual(alignments.metadata["Program"], "stretcher") self.assertEqual(alignments.metadata["Rundate"], "Tue 15 May 2018 17:01:31") self.assertEqual( alignments.metadata["Command line"], "stretcher -auto -stdout -asequence emboss_stretcher-I20180515-170128-0371-22292969-p1m.aupfile -bsequence emboss_stretcher-I20180515-170128-0371-22292969-p1m.bupfile -datafile EDNAFULL -gapopen 16 -gapextend 4 -aformat3 pair -snucleotide1 -snucleotide2", ) self.assertEqual(alignments.metadata["Align_format"], "pair") self.assertEqual(alignments.metadata["Report_file"], "stdout") alignment = next(alignments) self.assertEqual(alignment.annotations["Matrix"], "EDNAFULL") self.assertAlmostEqual(alignment.annotations["Gap_penalty"], 16) self.assertAlmostEqual(alignment.annotations["Extend_penalty"], 4) self.assertEqual(alignment.annotations["Identity"], 441) self.assertEqual(alignment.annotations["Similarity"], 441) self.assertEqual(alignment.annotations["Gaps"], 847) self.assertAlmostEqual(alignment.annotations["Score"], -2623) self.assertEqual(len(alignment), 2) self.assertEqual(alignment.shape, (2, 1450)) self.assertEqual( alignment.sequences[0].id, "hg38_chrX_131691529_131830643_47210_48660" ) self.assertEqual( alignment.sequences[1].id, "mm10_chrX_50555743_50635321_27140_27743" ) self.assertEqual( alignment.sequences[0].seq, "GGCAGGTGCATAGCTTGAGCCTAGGAGTTCAAGTCCAGCCCTGACAATGTAGAGAGACCCCGTCTCTTCAAAAAATACAAAAAATAGCCAGGCATGGTGACCTACAATGGAAGCCCTAGCTACGTAGGAGGCGGAAATGGGAGGATCACCTCAGCCCAGGGAGGCTGATGTTGCAGTGAGCCATGATCATGCCTCTACACTCCACCCTGGGCAACAGAGTAAGATGCTGTCTAAAATATATATATATGCATATCTGTGTGTATATATATATATATATATGTGTGTGTGTGTGTGTGTATATACATATGTGTGTGTATATACATATATGTGTATATATATATGTGTGTATATATACATATACATATTCAGCATCACCTTATATTCTTTGAATATATCTACATCAATACATACTTTTGAGTGCTTGAAATTTTTTATATTTTACTCTAGAAGAACTGTAAGAAATTATAAAGTAGAAAACTTGTGGTAGGTCAAACATAGTAAGAAGAAATAATCACTTTTTAAAGGTCTGTGCTAGGTACTATGATCTGTTCCCTATATATACATAATATGGACTTTTATAAACTAATGTTCAAATTCCCCTGTAGTATAACTTCTTGTTGTTGTTTATTTTTTTTTTTTTGTATTTTTCATTTTAGATATGGGGTTTCACTCTGTTGACCAGGCTGATCTCGAACCACTGGTCTCAAGCGATCCTCCCATCTTGGACTCCCAAAGTGCTAGGATTACAGGCACGAGGCACCTTGACTGGCCACCATGTACTATAGCTGTTAAAACAAGTTTGTTTCACTGATAACTGGAGTACTTTTCAAATATAATTAATAATTCATGGAAATAATGATAGCTTTAAAAGTATTGGCACTTTTAAAAACTGAGTTTGTAAACTTCATATAACATAAAATTAACCATTAAAATGTATTAATTTCAATGGCATTTAGGACACTCACAATGCAGTGCAAGCATTACCACTATGTAGTGGCAAATCATTTTCACTACCACAAAAGAAAATCCTGGACCCATTAGTTAGTCATTCCCCATTCCACTCTCTGCCCAGCCCCTGGCAAACACTCATCTGATTTCCCTCACTACTGATCATCACAACAAGTGGCCTTGTTCATCTTGTTGTGGGAACCAGGAGACCAGAGAGACCAATGGGTGGAACAGGAGGATTTTACTAGGTGGTCACCGACTCAGCAGATTAACATCCAAAGGCTGAGCCCCAAACCAAGAGAGGGCTTGACTTTTATACATATATCTGAAAAGGGCCCAAAACCTGTAAGGCCGGTAAGCAAGCTTACAGCAGAACAAAGGCAGTTTATCAAACAGTGACAGGTTTTACAGTTCAGGCATGTCTTGTGACCTTTGCCATAACTGCACAGCTGGAAAACAGGAACTTACAAAATCCTTACAAGCTTGCAGAAACAGTTACAAA", ) self.assertEqual( alignment.sequences[1].seq, "GTTCAAGGCCATCCGGGATTAAAGGTGTGGTAGAACTCTTCTGATGGAGACAATATAAGGACATTGGAAGAAGGGAGTCTTGCCCTTGCTCCTTCGCCTACTTGCTGTGTAAGACTGAGTAACTCCTAGACCCTTGGACTTCCATTTCAGCCACTACTGAACCATTGTTGGGAATTGGGCTGCAGACTGTAAGTCATCAATAAATTCCTTTACTATATAGAGACTATCCATAAATTCTGTGACTCTAGAGAACCCTGACAATACAACTGGGAAGCACGGACATCCTCTTTGAGATATAATTATCAACTGGCAAGTGTTTGTTTATTGATATTTTACTTAAGACAAAGTTAAACCTACTCCTGTCCTCTGGGCATGGTAGCATGGACTTATTCTGGAACTACCAGAGGAAAAGACAGAAGCCTACTGGAAAGGCCCAGGCCATCCTGCCTCTTGTAGTTCACTAGGACCAGGGCTCAGCATAGTCCTTGGCTTCTAAATCTGCTACCATATCTTTATCATGTAAAACTGACACAAAATTAAACATATCAAAATTTTATGAAAACCATTAAGTATCTGGAAAAGAAAAAAATCAACAGTTATAAA", ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[ 0, 1, 27, 45, 49, 54, 61, 68, 79, 91, 93, 101, 105, 113, 133, 145, 157, 163, 168, 174, 180, 199, 224, 236, 253, 259, 370, 377, 378, 391, 408, 420, 440, 466, 469, 479, 483, 497, 509, 518, 537, 543, 576, 585, 595, 598, 606, 616, 647, 659, 668, 673, 676, 682, 693, 701, 753, 760, 767, 778, 825, 839, 844, 847, 854, 858, 861, 863, 868, 877, 881, 885, 895, 898, 899, 927, 939, 944, 946, 957, 962, 964, 972, 983, 985, 988, 989, 997, 1008, 1019, 1021, 1036, 1042, 1044, 1064, 1080, 1087, 1091, 1106, 1109, 1133, 1144, 1189, 1197, 1210, 1215, 1228, 1236, 1247, 1263, 1269, 1279, 1285, 1297, 1299, 1305, 1308, 1327, 1329, 1331, 1334, 1341, 1357, 1368, 1376, 1381, 1386, 1391, 1395, 1407, 1414, 1422, 1438, 1450], [ 0, 1, 1, 19, 19, 24, 24, 31, 31, 43, 43, 51, 51, 59, 59, 71, 71, 77, 77, 83, 83, 102, 102, 114, 114, 120, 120, 127, 127, 140, 140, 152, 152, 178, 178, 188, 188, 202, 202, 211, 211, 217, 217, 226, 226, 229, 229, 239, 239, 251, 251, 256, 256, 262, 262, 270, 270, 277, 277, 288, 288, 302, 302, 305, 305, 309, 309, 311, 311, 320, 320, 324, 324, 327, 327, 355, 355, 360, 360, 371, 371, 373, 373, 384, 384, 387, 387, 395, 395, 406, 406, 421, 421, 423, 423, 439, 439, 443, 443, 446, 446, 457, 457, 465, 465, 470, 470, 478, 478, 494, 494, 504, 504, 516, 516, 522, 522, 541, 541, 543, 543, 550, 550, 561, 561, 566, 566, 571, 571, 583, 583, 591, 591, 603]]) # fmt: on ) ) self.assertEqual( alignment[0], "GGCAGGTGCATAGCTTGAGCCTAGGAGTTCAAGTCCAGCCCTGACAATGTAGAGAGACCCCGTCTCTTCAAAAAATACAAAAAATAGCCAGGCATGGTGACCTACAATGGAAGCCCTAGCTACGTAGGAGGCGGAAATGGGAGGATCACCTCAGCCCAGGGAGGCTGATGTTGCAGTGAGCCATGATCATGCCTCTACACTCCACCCTGGGCAACAGAGTAAGATGCTGTCTAAAATATATATATATGCATATCTGTGTGTATATATATATATATATATGTGTGTGTGTGTGTGTGTATATACATATGTGTGTGTATATACATATATGTGTATATATATATGTGTGTATATATACATATACATATTCAGCATCACCTTATATTCTTTGAATATATCTACATCAATACATACTTTTGAGTGCTTGAAATTTTTTATATTTTACTCTAGAAGAACTGTAAGAAATTATAAAGTAGAAAACTTGTGGTAGGTCAAACATAGTAAGAAGAAATAATCACTTTTTAAAGGTCTGTGCTAGGTACTATGATCTGTTCCCTATATATACATAATATGGACTTTTATAAACTAATGTTCAAATTCCCCTGTAGTATAACTTCTTGTTGTTGTTTATTTTTTTTTTTTTGTATTTTTCATTTTAGATATGGGGTTTCACTCTGTTGACCAGGCTGATCTCGAACCACTGGTCTCAAGCGATCCTCCCATCTTGGACTCCCAAAGTGCTAGGATTACAGGCACGAGGCACCTTGACTGGCCACCATGTACTATAGCTGTTAAAACAAGTTTGTTTCACTGATAACTGGAGTACTTTTCAAATATAATTAATAATTCATGGAAATAATGATAGCTTTAAAAGTATTGGCACTTTTAAAAACTGAGTTTGTAAACTTCATATAACATAAAATTAACCATTAAAATGTATTAATTTCAATGGCATTTAGGACACTCACAATGCAGTGCAAGCATTACCACTATGTAGTGGCAAATCATTTTCACTACCACAAAAGAAAATCCTGGACCCATTAGTTAGTCATTCCCCATTCCACTCTCTGCCCAGCCCCTGGCAAACACTCATCTGATTTCCCTCACTACTGATCATCACAACAAGTGGCCTTGTTCATCTTGTTGTGGGAACCAGGAGACCAGAGAGACCAATGGGTGGAACAGGAGGATTTTACTAGGTGGTCACCGACTCAGCAGATTAACATCCAAAGGCTGAGCCCCAAACCAAGAGAGGGCTTGACTTTTATACATATATCTGAAAAGGGCCCAAAACCTGTAAGGCCGGTAAGCAAGCTTACAGCAGAACAAAGGCAGTTTATCAAACAGTGACAGGTTTTACAGTTCAGGCATGTCTTGTGACCTTTGCCATAACTGCACAGCTGGAAAACAGGAACTTACAAAATCCTTACAAGCTTGCAGAAACAGTTACAAA", ) self.assertEqual( alignment[1], "G--------------------------TTCAAGGCCATCCGGGAT----TAAAG-------GTGTGGT-----------AGAACTCTTCTG--ATGGAGAC----AATATAAG--------------------GACATTGGAAGA------------AGGGAG-----TCTTGC------CCTTGCTCCTTCGCCTACT-------------------------TGCTGTGTAAGA-----------------CTGAGT---------------------------------------------------------------------------------------------------------------AACTCCT-AGACCCTTGGACT-----------------TCCATTTCAGCC--------------------ACTACTGAACCATTGTTGGGAATTGG---GCTGCAGACT----GTAAGTCATCAATA------------AATTCCTTT-------------------ACTATA---------------------------------TAGAGACTA----------TCC--------ATAAATTCTG-------------------------------TGACTCTAGAGA---------ACCCT---GACAAT-----------ACAACTGG----------------------------------------------------GAAGCAC-------GGACATCCTCT-----------------------------------------------TTGAGATATAATTA-----TCA-------ACTG---GC-----AAGTGTTTG----TTTA----------TTG-ATATTTTACTTAAGACAAAGTTAAACCT------------ACTCC--TGTCCTCTGGG-----CA--------TGGTAGCATGG--ACT-TATTCTGG-----------AACTACCAGAG--GAAAAGACAGAAGCC------TA--------------------CTGGAAAGGCCCAGGC-------CATC---------------CTG------------------------CCTCTTGTAGT---------------------------------------------TCACTAGG-------------ACCAG-------------GGCTCAGC-----------ATAGTCCTTGGCTTCT------AAATCTGCTA------CCATATCTTTAT--CATGTA---AAACTGACACAAAATTAAA--CA---TATCAAA----------------ATTTTATGAAA--------ACCAT-----TAAGT----ATCTGGAAAAGA-------AAAAAATC----------------AACAGTTATAAA", ) self.assertEqual( alignment.column_annotations["emboss_consensus"], "| ||||||.|||.||..||. ||.|| ||.|..| |.||.|...|.| ||||.||| |||..||| ||.||.|||.|| |||||| |.|||| ||.||.||.|.|..||||. ||||||.|||.| |||.|| |.|.||| |.|..|||.||.| |.|.|||.||.. |||...|||..|.|||..|.||||.. |..|.|.||| |||.||||...||| |||..|||| |||||. ||.|.|||| ||| ||||.||||. |.|.|.||||.| ||.|| |||.|. ||.||||| ||.|||| ||.||.|.|.| ||.|.||||||||| ||| |.|| || ||||.||.| |||| ||| |.|.||.|..|||.|.|||.||||.|.| |.|.| ||.|.|.|.|| || ||..|||||.. ||| |.|..||| .|||||||.|. |||||..|.|.|.|| || |||...||.|||.||| |||| ||| |.||||||.|| |.|||||| |.||| ||||.||| |.||..||||.|||.| |.|||||..| |.|.|.||.||. |..||| ||.||.|||..|.|..||| || ||||||| |.||.|.|.|. |||.| |||.| |.||||||||.| |.|||||| ||||||||.|||", ) self.assertEqual( str(alignment), """\ hg38_chrX 0 GGCAGGTGCATAGCTTGAGCCTAGGAGTTCAAGTCCAGCCCTGACAATGTAGAGAGACCC 0 |--------------------------||||||.|||.||..||.----||.||------ mm10_chrX 0 G--------------------------TTCAAGGCCATCCGGGAT----TAAAG------ hg38_chrX 60 CGTCTCTTCAAAAAATACAAAAAATAGCCAGGCATGGTGACCTACAATGGAAGCCCTAGC 60 -||.|..|-----------|.||.|...|.|--||||.|||----|||..|||------- mm10_chrX 24 -GTGTGGT-----------AGAACTCTTCTG--ATGGAGAC----AATATAAG------- hg38_chrX 120 TACGTAGGAGGCGGAAATGGGAGGATCACCTCAGCCCAGGGAGGCTGATGTTGCAGTGAG 120 -------------||.||.|||.||------------||||||-----|.||||------ mm10_chrX 59 -------------GACATTGGAAGA------------AGGGAG-----TCTTGC------ hg38_chrX 180 CCATGATCATGCCTCTACACTCCACCCTGGGCAACAGAGTAAGATGCTGTCTAAAATATA 180 ||.||.||.|.|..||||.-------------------------||||||.|||.|---- mm10_chrX 83 CCTTGCTCCTTCGCCTACT-------------------------TGCTGTGTAAGA---- hg38_chrX 240 TATATATGCATATCTGTGTGTATATATATATATATATATGTGTGTGTGTGTGTGTGTATA 240 -------------|||.||----------------------------------------- mm10_chrX 114 -------------CTGAGT----------------------------------------- hg38_chrX 300 TACATATGTGTGTGTATATACATATATGTGTATATATATATGTGTGTATATATACATATA 300 ------------------------------------------------------------ mm10_chrX 120 ------------------------------------------------------------ hg38_chrX 360 CATATTCAGCATCACCTTATATTCTTTGAATATATCTACATCAATACATACTTTTGAGTG 360 ----------|.|.|||-|.|..|||.||.|-----------------|.|.|||.||.. mm10_chrX 120 ----------AACTCCT-AGACCCTTGGACT-----------------TCCATTTCAGCC hg38_chrX 420 CTTGAAATTTTTTATATTTTACTCTAGAAGAACTGTAAGAAATTATAAAGTAGAAAACTT 420 --------------------|||...|||..|.|||..|.||||..---|..|.|.|||- mm10_chrX 152 --------------------ACTACTGAACCATTGTTGGGAATTGG---GCTGCAGACT- hg38_chrX 480 GTGGTAGGTCAAACATAGTAAGAAGAAATAATCACTTTTTAAAGGTCTGTGCTAGGTACT 480 ---|||.||||...|||------------|||..||||-------------------||| mm10_chrX 188 ---GTAAGTCATCAATA------------AATTCCTTT-------------------ACT hg38_chrX 540 ATGATCTGTTCCCTATATATACATAATATGGACTTTTATAAACTAATGTTCAAATTCCCC 540 ||.---------------------------------||.|.||||----------|||-- mm10_chrX 214 ATA---------------------------------TAGAGACTA----------TCC-- hg38_chrX 600 TGTAGTATAACTTCTTGTTGTTGTTTATTTTTTTTTTTTTGTATTTTTCATTTTAGATAT 600 ------||||.||||.-------------------------------|.|.|.||||.|- mm10_chrX 229 ------ATAAATTCTG-------------------------------TGACTCTAGAGA- hg38_chrX 660 GGGGTTTCACTCTGTTGACCAGGCTGATCTCGAACCACTGGTCTCAAGCGATCCTCCCAT 660 --------||.||---|||.|.-----------||.|||||------------------- mm10_chrX 251 --------ACCCT---GACAAT-----------ACAACTGG------------------- hg38_chrX 720 CTTGGACTCCCAAAGTGCTAGGATTACAGGCACGAGGCACCTTGACTGGCCACCATGTAC 720 ---------------------------------||.||||-------||.||.|.|.|-- mm10_chrX 270 ---------------------------------GAAGCAC-------GGACATCCTCT-- hg38_chrX 780 TATAGCTGTTAAAACAAGTTTGTTTCACTGATAACTGGAGTACTTTTCAAATATAATTAA 780 ---------------------------------------------||.|.|||||||||- mm10_chrX 288 ---------------------------------------------TTGAGATATAATTA- hg38_chrX 840 TAATTCATGGAAATAATGATAGCTTTAAAAGTATTGGCACTTTTAAAAACTGAGTTTGTA 840 ----|||-------|.||---||-----||||.||.|----||||----------|||-| mm10_chrX 302 ----TCA-------ACTG---GC-----AAGTGTTTG----TTTA----------TTG-A hg38_chrX 900 AACTTCATATAACATAAAATTAACCATTAAAATGTATTAATTTCAATGGCATTTAGGACA 900 .|.||.|..|||.|.|||.||||.|.|------------|.|.|--||.|.|.|.||--- mm10_chrX 328 TATTTTACTTAAGACAAAGTTAAACCT------------ACTCC--TGTCCTCTGGG--- hg38_chrX 960 CTCACAATGCAGTGCAAGCATTACCACTATGTAGTGGCAAATCATTTTCACTACCACAAA 960 --||--------||..|||||..--|||-|.|..|||-----------.|||||||.|.- mm10_chrX 371 --CA--------TGGTAGCATGG--ACT-TATTCTGG-----------AACTACCAGAG- hg38_chrX 1020 AGAAAATCCTGGACCCATTAGTTAGTCATTCCCCATTCCACTCTCTGCCCAGCCCCTGGC 1020 -|||||..|.|.|.||------||--------------------|||...||.|||.||| mm10_chrX 406 -GAAAAGACAGAAGCC------TA--------------------CTGGAAAGGCCCAGGC hg38_chrX 1080 AAACACTCATCTGATTTCCCTCACTACTGATCATCACAACAAGTGGCCTTGTTCATCTTG 1080 -------||||---------------|||------------------------|.||||| mm10_chrX 439 -------CATC---------------CTG------------------------CCTCTTG hg38_chrX 1140 TTGTGGGAACCAGGAGACCAGAGAGACCAATGGGTGGAACAGGAGGATTTTACTAGGTGG 1140 |.||---------------------------------------------|.||||||--- mm10_chrX 453 TAGT---------------------------------------------TCACTAGG--- hg38_chrX 1200 TCACCGACTCAGCAGATTAACATCCAAAGGCTGAGCCCCAAACCAAGAGAGGGCTTGACT 1200 ----------|.|||-------------||||.|||-----------|.||..||||.|| mm10_chrX 465 ----------ACCAG-------------GGCTCAGC-----------ATAGTCCTTGGCT hg38_chrX 1260 TTTATACATATATCTGAAAAGGGCCCAAAACCTGTAAGGCCGGTAAGCAAGCTTACAGCA 1260 |.|------|.|||||..|------|.|.|.||.||.--|..|||---||.||.|||..| mm10_chrX 491 TCT------AAATCTGCTA------CCATATCTTTAT--CATGTA---AAACTGACACAA hg38_chrX 1320 GAACAAAGGCAGTTTATCAAACAGTGACAGGTTTTACAGTTCAGGCATGTCTTGTGACCT 1320 .|..|||--||---|||||||----------------|.||.|.|.|.--------|||. mm10_chrX 534 AATTAAA--CA---TATCAAA----------------ATTTTATGAAA--------ACCA hg38_chrX 1380 TTGCCATAACTGCACAGCTGGAAAACAGGAACTTACAAAATCCTTACAAGCTTGCAGAAA 1380 |-----|||.|----|.||||||||.|-------|.||||||----------------|| mm10_chrX 565 T-----TAAGT----ATCTGGAAAAGA-------AAAAAATC----------------AA hg38_chrX 1440 CAGTTACAAA 1450 1440 ||||||.||| 1450 mm10_chrX 593 CAGTTATAAA 603 """, ) with self.assertRaises(StopIteration): next(alignments) if __name__ == "__main__": runner = unittest.TextTestRunner(verbosity=2) unittest.main(testRunner=runner)