# Copyright 2022 by Michiel de Hoon. All rights reserved. # This code is part of the Biopython distribution and governed by its # license. Please see the LICENSE file that should have been included # as part of this package. """Tests for Align.bigmaf module.""" import tempfile import unittest from io import StringIO import numpy as np from Bio import Align class TestAlign_declaration(unittest.TestCase): def test_declaration(self): with open("MAF/bigMaf.as") as stream: declaration = stream.read() self.assertEqual(str(Align.bigmaf.declaration), declaration) class TestAlign_ucsc_test(unittest.TestCase): path = "MAF/ucsc_test.bb" def test_reading(self): """Test reading ucsc_test.bb.""" # BigMaf file ucsc_test.bb was created using the commands # tail -n +2 ucsc_test.maf | mafToBigMaf hg16 stdin stdout | sort -k1,1 -k2,2n > ucsc_test.txt # bedToBigBed -type=bed3+1 -as=bigMaf.as -tab ucsc_test.txt hg16.chrom.sizes ucsc_test.bb alignments = Align.parse(self.path, "bigmaf") self.check_alignments(alignments) alignments = iter(alignments) self.check_alignments(alignments) with Align.parse(self.path, "bigmaf") as alignments: self.check_alignments(alignments) with self.assertRaises(AttributeError): alignments._stream with Align.parse(self.path, "bigmaf") as alignments: pass with self.assertRaises(AttributeError): alignments._stream def test_writing(self): """Test writing ucsc_test.bb.""" alignments = Align.parse(self.path, "bigmaf") with tempfile.TemporaryFile() as output: Align.write(alignments, output, "bigmaf") output.flush() output.seek(0) alignments = Align.parse(output, "bigmaf") self.check_alignments(alignments) def check_alignments(self, alignments): self.assertEqual( str(alignments.declaration), """\ table bedMaf "Bed3 with MAF block" ( string chrom; "Reference sequence chromosome or scaffold" uint chromStart; "Start position in chromosome" uint chromEnd; "End position in chromosome" lstring mafBlock; "MAF block" ) """, ) self.assertEqual(alignments.reference, "hg16") self.assertEqual(len(alignments.targets), 1) self.assertEqual(alignments.targets[0].id, "hg16.chr7") self.assertEqual(len(alignments.targets[0]), 158545518) self.assertEqual(len(alignments), 3) alignment = next(alignments) self.assertAlmostEqual(alignment.score, 23262) self.assertEqual(len(alignment.sequences), 5) self.assertEqual(alignment.sequences[0].id, "hg16.chr7") self.assertEqual(len(alignment.sequences[0]), 158545518) self.assertEqual( alignment.sequences[0].seq[27578828 : 27578828 + 38], "AAAGGGAATGTTAACCAAATGAATTGTCTCTTACGGTG", ) self.assertEqual(alignment[0], "AAA-GGGAATGTTAACCAAATGA---ATTGTCTCTTACGGTG") self.assertEqual(alignment.sequences[1].id, "panTro1.chr6") self.assertEqual(len(alignment.sequences[1]), 161576975) self.assertEqual( alignment.sequences[1].seq[28741140 : 28741140 + 38], "AAAGGGAATGTTAACCAAATGAATTGTCTCTTACGGTG", ) self.assertEqual(alignment[1], "AAA-GGGAATGTTAACCAAATGA---ATTGTCTCTTACGGTG") self.assertEqual(alignment.sequences[2].id, "baboon") self.assertEqual(len(alignment.sequences[2]), 4622798) self.assertEqual( alignment.sequences[2].seq[116834 : 116834 + 38], "AAAGGGAATGTTAACCAAATGAGTTGTCTCTTATGGTG", ) self.assertEqual(alignment[2], "AAA-GGGAATGTTAACCAAATGA---GTTGTCTCTTATGGTG") self.assertEqual(alignment.sequences[3].id, "mm4.chr6") self.assertEqual(len(alignment.sequences[3]), 151104725) self.assertEqual( alignment.sequences[3].seq[53215344 : 53215344 + 38], "AATGGGAATGTTAAGCAAACGAATTGTCTCTCAGTGTG", ) self.assertEqual(alignment[3], "-AATGGGAATGTTAAGCAAACGA---ATTGTCTCTCAGTGTG") self.assertEqual(alignment.sequences[4].id, "rn3.chr4") self.assertEqual(len(alignment.sequences[4]), 187371129) self.assertEqual( alignment.sequences[4].seq[81344243 : 81344243 + 40], "AAGGGGATGCTAAGCCAATGAGTTGTTGTCTCTCAATGTG", ) self.assertEqual(alignment[4], "-AA-GGGGATGCTAAGCCAATGAGTTGTTGTCTCTCAATGTG") self.assertEqual( str(alignment), """\ hg16.chr7 27578828 AAA-GGGAATGTTAACCAAATGA---ATTGTCTCTTACGGTG 27578866 panTro1.c 28741140 AAA-GGGAATGTTAACCAAATGA---ATTGTCTCTTACGGTG 28741178 baboon 116834 AAA-GGGAATGTTAACCAAATGA---GTTGTCTCTTATGGTG 116872 mm4.chr6 53215344 -AATGGGAATGTTAAGCAAACGA---ATTGTCTCTCAGTGTG 53215382 rn3.chr4 81344243 -AA-GGGGATGCTAAGCCAATGAGTTGTTGTCTCTCAATGTG 81344283 """, ) self.assertTrue( np.array_equal( alignment.coordinates, np.array( [ # fmt: off [27578828, 27578829, 27578831, 27578831, 27578850, 27578850, 27578866], [28741140, 28741141, 28741143, 28741143, 28741162, 28741162, 28741178], [ 116834, 116835, 116837, 116837, 116856, 116856, 116872], [53215344, 53215344, 53215346, 53215347, 53215366, 53215366, 53215382], [81344243, 81344243, 81344245, 81344245, 81344264, 81344267, 81344283], # fmt: on ] ), ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['A', 'A', 'A', '-', 'G', 'G', 'G', 'A', 'A', 'T', 'G', 'T', 'T', 'A', 'A', 'C', 'C', 'A', 'A', 'A', 'T', 'G', 'A', '-', '-', '-', 'A', 'T', 'T', 'G', 'T', 'C', 'T', 'C', 'T', 'T', 'A', 'C', 'G', 'G', 'T', 'G'], ['A', 'A', 'A', '-', 'G', 'G', 'G', 'A', 'A', 'T', 'G', 'T', 'T', 'A', 'A', 'C', 'C', 'A', 'A', 'A', 'T', 'G', 'A', '-', '-', '-', 'A', 'T', 'T', 'G', 'T', 'C', 'T', 'C', 'T', 'T', 'A', 'C', 'G', 'G', 'T', 'G'], ['A', 'A', 'A', '-', 'G', 'G', 'G', 'A', 'A', 'T', 'G', 'T', 'T', 'A', 'A', 'C', 'C', 'A', 'A', 'A', 'T', 'G', 'A', '-', '-', '-', 'G', 'T', 'T', 'G', 'T', 'C', 'T', 'C', 'T', 'T', 'A', 'T', 'G', 'G', 'T', 'G'], ['-', 'A', 'A', 'T', 'G', 'G', 'G', 'A', 'A', 'T', 'G', 'T', 'T', 'A', 'A', 'G', 'C', 'A', 'A', 'A', 'C', 'G', 'A', '-', '-', '-', 'A', 'T', 'T', 'G', 'T', 'C', 'T', 'C', 'T', 'C', 'A', 'G', 'T', 'G', 'T', 'G'], ['-', 'A', 'A', '-', 'G', 'G', 'G', 'G', 'A', 'T', 'G', 'C', 'T', 'A', 'A', 'G', 'C', 'C', 'A', 'A', 'T', 'G', 'A', 'G', 'T', 'T', 'G', 'T', 'T', 'G', 'T', 'C', 'T', 'C', 'T', 'C', 'A', 'A', 'T', 'G', 'T', 'G']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.score, 5062.0) self.assertEqual(len(alignment.sequences), 5) self.assertEqual(alignment.sequences[0].id, "hg16.chr7") self.assertEqual(len(alignment.sequences[0]), 158545518) self.assertEqual(alignment.sequences[0].seq[27699739 : 27699739 + 6], "TAAAGA") self.assertEqual(alignment[0], "TAAAGA") self.assertEqual(alignment.sequences[1].id, "panTro1.chr6") self.assertEqual(len(alignment.sequences[1]), 161576975) self.assertEqual(alignment.sequences[1].seq[28862317 : 28862317 + 6], "TAAAGA") self.assertEqual(alignment[1], "TAAAGA") self.assertEqual(alignment.sequences[2].id, "baboon") self.assertEqual(len(alignment.sequences[2]), 4622798) self.assertEqual(alignment.sequences[2].seq[241163 : 241163 + 6], "TAAAGA") self.assertEqual(alignment[2], "TAAAGA") self.assertEqual(alignment.sequences[3].id, "mm4.chr6") self.assertEqual(len(alignment.sequences[3]), 151104725) self.assertEqual(alignment.sequences[3].seq[53303881 : 53303881 + 6], "TAAAGA") self.assertEqual(alignment[3], "TAAAGA") self.assertEqual(alignment.sequences[4].id, "rn3.chr4") self.assertEqual(len(alignment.sequences[4]), 187371129) self.assertEqual(alignment.sequences[4].seq[81444246 : 81444246 + 6], "taagga") self.assertEqual(alignment[4], "taagga") self.assertEqual( str(alignment), """\ hg16.chr7 27699739 TAAAGA 27699745 panTro1.c 28862317 TAAAGA 28862323 baboon 241163 TAAAGA 241169 mm4.chr6 53303881 TAAAGA 53303887 rn3.chr4 81444246 taagga 81444252 """, ) self.assertTrue( np.array_equal( alignment.coordinates, np.array( [ # fmt: off [27699739, 27699745], [28862317, 28862323], [ 241163, 241169], [53303881, 53303887], [81444246, 81444252], # fmt: on ] ), ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['T', 'A', 'A', 'A', 'G', 'A'], ['T', 'A', 'A', 'A', 'G', 'A'], ['T', 'A', 'A', 'A', 'G', 'A'], ['T', 'A', 'A', 'A', 'G', 'A'], ['t', 'a', 'a', 'g', 'g', 'a']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.score, 6636.0) self.assertEqual(len(alignment.sequences), 4) self.assertEqual(alignment.sequences[0].id, "hg16.chr7") self.assertEqual(len(alignment.sequences[0]), 158545518) self.assertEqual( alignment.sequences[0].seq[27707221 : 27707221 + 13], "gcagctgaaaaca" ) self.assertEqual(alignment[0], "gcagctgaaaaca") self.assertEqual(alignment.sequences[1].id, "panTro1.chr6") self.assertEqual(len(alignment.sequences[1]), 161576975) self.assertEqual( alignment.sequences[1].seq[28869787 : 28869787 + 13], "gcagctgaaaaca" ) self.assertEqual(alignment[1], "gcagctgaaaaca") self.assertEqual(alignment.sequences[2].id, "baboon") self.assertEqual(len(alignment.sequences[2]), 4622798) self.assertEqual( alignment.sequences[2].seq[249182 : 249182 + 13], "gcagctgaaaaca" ) self.assertEqual(alignment[2], "gcagctgaaaaca") self.assertEqual(alignment.sequences[3].id, "mm4.chr6") self.assertEqual(len(alignment.sequences[3]), 151104725) self.assertEqual( alignment.sequences[3].seq[53310102 : 53310102 + 13], "ACAGCTGAAAATA" ) self.assertEqual(alignment[3], "ACAGCTGAAAATA") self.assertEqual( str(alignment), """\ hg16.chr7 27707221 gcagctgaaaaca 27707234 panTro1.c 28869787 gcagctgaaaaca 28869800 baboon 249182 gcagctgaaaaca 249195 mm4.chr6 53310102 ACAGCTGAAAATA 53310115 """, ) self.assertTrue( np.array_equal( alignment.coordinates, np.array( [ # fmt: off [27707221, 27707234], [28869787, 28869800], [ 249182, 249195], [53310102, 53310115], # fmt: on ] ), ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['g', 'c', 'a', 'g', 'c', 't', 'g', 'a', 'a', 'a', 'a', 'c', 'a'], ['g', 'c', 'a', 'g', 'c', 't', 'g', 'a', 'a', 'a', 'a', 'c', 'a'], ['g', 'c', 'a', 'g', 'c', 't', 'g', 'a', 'a', 'a', 'a', 'c', 'a'], ['A', 'C', 'A', 'G', 'C', 'T', 'G', 'A', 'A', 'A', 'A', 'T', 'A']], dtype='U') # fmt: on ) ) self.assertRaises(StopIteration, next, alignments) class TestAlign_bundle_without_target(unittest.TestCase): path = "MAF/bundle_without_target.bb" def test_reading(self): """Test parsing bundle_without_target.bb.""" # BigMaf file bundle_without_target.bb was created using the commands # mafToBigMaf mm8 bundle_without_target.maf stdout | sort -k1,1 -k2,2n > bundle_without_target.txt # bedToBigBed -type=bed3+1 -as=bigMaf.as -tab bundle_without_target.txt mm8.chrom.sizes bundle_without_target.bb alignments = Align.parse(self.path, "bigmaf") self.check_alignments(alignments) alignments = iter(alignments) self.check_alignments(alignments) with Align.parse(self.path, "bigmaf") as alignments: self.check_alignments(alignments) with self.assertRaises(AttributeError): alignments._stream with Align.parse(self.path, "bigmaf") as alignments: pass with self.assertRaises(AttributeError): alignments._stream def test_writing(self): """Test writing bundle_without_target.bb.""" alignments = Align.parse(self.path, "bigmaf") with tempfile.TemporaryFile() as output: Align.write(alignments, output, "bigmaf") output.flush() output.seek(0) alignments = Align.parse(output, "bigmaf") self.check_alignments(alignments) def check_alignments(self, alignments): self.assertEqual( str(alignments.declaration), """\ table bedMaf "Bed3 with MAF block" ( string chrom; "Reference sequence chromosome or scaffold" uint chromStart; "Start position in chromosome" uint chromEnd; "End position in chromosome" lstring mafBlock; "MAF block" ) """, ) self.assertEqual(alignments.reference, "mm8") self.assertEqual(len(alignments.targets), 1) self.assertEqual(alignments.targets[0].id, "mm8.chr10") self.assertEqual(len(alignments.targets[0]), 129959148) self.assertEqual(len(alignments), 1) alignment = next(alignments) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['T', 'C', 'A', 'T', 'A', 'G', 'G', 'T', 'A', 'T', 'T', 'T', 'A', 'T', 'T', 'T', 'T', 'T', 'A', 'A', 'A', 'T', 'A', 'T', 'G', 'G', 'T', 'T', 'T', 'G', 'C', 'T', 'T', 'T', 'A', 'T', 'G', 'G', 'C', 'T', 'A', 'G', 'A', 'A', 'C', 'A', 'C', 'A', 'C', 'C', 'G', 'A', 'T', 'T', 'A', 'C', 'T', 'T', 'A', 'A', 'A', 'A', 'T', 'A', 'G', 'G', 'A', 'T', 'T', 'A', 'A', 'C', 'C', '-', '-', 'C', 'C', 'C', 'A', 'T', 'A', 'C', 'A', 'C', 'T', 'T', 'T', 'A', 'A', 'A', 'A', 'A', 'T', 'G', 'A', 'T', 'T', 'A', 'A', 'A', 'C', 'A', 'A', 'C', 'A', 'T', 'T', 'T', 'C', 'T', 'G', 'C', 'T', 'G', 'C', 'T', 'C', 'G', 'C', 'T', 'C', 'A', 'C', 'A', 'T', 'T', 'C', 'T', 'T', 'C', 'A', 'T', 'A', 'G', 'A', 'A', 'G', 'A', 'T', 'G', 'A', 'C', 'A', 'T', 'A', 'A', 'T', 'G', 'T', 'A', 'T', 'T', 'T', 'T', 'C', 'C', 'T', 'T', 'T', 'T', 'G', 'G', 'T', 'T'], ['T', 'C', 'A', 'C', 'A', 'G', 'A', 'T', 'A', 'T', 'T', 'T', 'A', 'C', 'T', 'A', 'T', 'T', 'A', 'A', 'A', 'T', 'A', 'T', 'G', 'G', 'T', 'T', 'T', 'G', 'T', 'T', 'A', 'T', 'A', 'T', 'G', 'G', 'T', 'T', 'A', 'C', 'G', 'G', 'T', 'T', 'C', 'A', 'T', 'A', 'G', 'G', 'T', 'T', 'A', 'C', 'T', 'T', 'G', 'G', 'A', 'A', 'T', 'T', 'G', 'G', 'A', 'T', 'T', 'A', 'A', 'C', 'C', 'T', 'T', 'C', 'T', 'T', 'A', 'T', 'T', 'C', 'A', 'T', 'T', 'G', 'C', 'A', 'G', 'A', 'A', 'T', 'T', 'G', 'G', 'T', 'T', 'A', 'C', 'A', 'C', 'T', 'G', 'T', 'G', 'T', 'T', 'C', 'T', 'T', 'G', 'A', 'C', 'C', 'T', 'T', 'T', 'G', 'C', 'T', 'T', 'G', 'T', 'T', 'T', 'T', 'C', 'T', 'C', 'C', 'A', 'T', 'G', 'G', 'A', 'A', 'A', 'C', 'T', 'G', 'A', 'T', 'G', 'T', 'C', 'A', 'A', 'A', 'T', 'A', 'C', 'T', 'T', 'T', 'C', 'C', 'C', 'T', 'T', 'T', 'G', 'G', 'T', 'T']], dtype='U') # fmt: on ) ) self.assertRaises(StopIteration, next, alignments) self.assertAlmostEqual(alignment.score, 6441) self.assertEqual(len(alignment.sequences), 2) self.assertEqual(alignment.sequences[0].id, "mm8.chr10") self.assertEqual(alignment.sequences[1].id, "oryCun1.scaffold_133159") self.assertEqual(len(alignment.sequences[0].seq), 129993255) self.assertEqual(len(alignment.sequences[1].seq), 13221) self.assertEqual( alignment.sequences[0].seq[3009319 : 3009319 + 162], "TCATAGGTATTTATTTTTAAATATGGTTTGCTTTATGGCTAGAACACACCGATTACTTAAAATAGGATTAACCCCCATACACTTTAAAAATGATTAAACAACATTTCTGCTGCTCGCTCACATTCTTCATAGAAGATGACATAATGTATTTTCCTTTTGGTT", ) self.assertEqual( alignment.sequences[1].seq[11087 : 11087 + 164], "TCACAGATATTTACTATTAAATATGGTTTGTTATATGGTTACGGTTCATAGGTTACTTGGAATTGGATTAACCTTCTTATTCATTGCAGAATTGGTTACACTGTGTTCTTGACCTTTGCTTGTTTTCTCCATGGAAACTGATGTCAAATACTTTCCCTTTGGTT", ) self.assertEqual( alignment[0], "TCATAGGTATTTATTTTTAAATATGGTTTGCTTTATGGCTAGAACACACCGATTACTTAAAATAGGATTAACC--CCCATACACTTTAAAAATGATTAAACAACATTTCTGCTGCTCGCTCACATTCTTCATAGAAGATGACATAATGTATTTTCCTTTTGGTT", ) self.assertEqual( alignment[1], "TCACAGATATTTACTATTAAATATGGTTTGTTATATGGTTACGGTTCATAGGTTACTTGGAATTGGATTAACCTTCTTATTCATTGCAGAATTGGTTACACTGTGTTCTTGACCTTTGCTTGTTTTCTCCATGGAAACTGATGTCAAATACTTTCCCTTTGGTT", ) self.assertEqual( alignment.sequences[1].annotations["quality"], "99569899999998999999999999999999999999999999999999999999999999999999999757878999975999999999999999979999999999997899999999999997997999999869999996999988997997999999", ) self.assertEqual(alignment.sequences[1].annotations["leftStatus"], "N") self.assertEqual(alignment.sequences[1].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[1].annotations["rightStatus"], "N") self.assertEqual(alignment.sequences[1].annotations["rightCount"], 0) self.assertEqual( str(alignment), """\ mm8.chr10 3009319 TCATAGGTATTTATTTTTAAATATGGTTTGCTTTATGGCTAGAACACACCGATTACTTAA 0 |||.||.||||||.|.||||||||||||||.|.|||||.||.....||..|.||||||.. oryCun1.s 11087 TCACAGATATTTACTATTAAATATGGTTTGTTATATGGTTACGGTTCATAGGTTACTTGG mm8.chr10 3009379 AATAGGATTAACC--CCCATACACTTTAAAAATGATTAAACAACATTTCTGCTGCTCGCT 60 |||.|||||||||--|..||.||.|..|.||.||.|||.||....||..||....|.||| oryCun1.s 11147 AATTGGATTAACCTTCTTATTCATTGCAGAATTGGTTACACTGTGTTCTTGACCTTTGCT mm8.chr10 3009437 CACATTCTTCATAGAAGATGACATAATGTATTTTCCTTTTGGTT 3009481 120 ....||||.|||.|||..|||..|.|..||.|||||.||||||| 164 oryCun1.s 11207 TGTTTTCTCCATGGAAACTGATGTCAAATACTTTCCCTTTGGTT 11251 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[3009319, 3009392, 3009392, 3009481], [ 11087, 11160, 11162, 11251], ]) # fmt: on ) ) class TestAlign_ucsc_mm9_chr10(unittest.TestCase): path = "MAF/ucsc_mm9_chr10.bb" def test_reading(self): """Test parsing file ucsc_mm9_chr10.bb.""" # BigMaf file ucsc_mm9_chr10.bb was created using the commands # mafToBigMaf mm9 ucsc_mm9_chr10.maf stdout | sort -k1,1 -k2,2n > ucsc_mm9_chr10.txt # bedToBigBed -type=bed3+1 -as=bigMaf.as -tab ucsc_mm9_chr10.txt mm9.chrom.sizes ucsc_mm9_chr10.bb alignments = Align.parse(self.path, "bigmaf") self.check_alignments(alignments) def test_writing(self): """Test writing file ucsc_mm9_chr10.bb.""" alignments = Align.parse(self.path, "bigmaf") with tempfile.TemporaryFile() as output: Align.write(alignments, output, "bigmaf") output.flush() output.seek(0) alignments = Align.parse(output, "bigmaf") self.check_alignments(alignments) def check_alignments(self, alignments): self.assertEqual( str(alignments.declaration), """\ table bedMaf "Bed3 with MAF block" ( string chrom; "Reference sequence chromosome or scaffold" uint chromStart; "Start position in chromosome" uint chromEnd; "End position in chromosome" lstring mafBlock; "MAF block" ) """, ) self.assertEqual(alignments.reference, "mm9") self.assertEqual(len(alignments.targets), 1) self.assertEqual(alignments.targets[0].id, "mm9.chr10") self.assertEqual(len(alignments.targets[0]), 129993255) self.assertEqual(len(alignments), 48) alignment = next(alignments) self.assertAlmostEqual(alignment.score, 6441) self.assertEqual(alignment.sequences[0].id, "mm9.chr10") self.assertEqual(len(alignment.sequences[0].seq), 129993255) self.assertEqual( alignment.sequences[0].seq[3009319 : 3009319 + 162], "TCATAGGTATTTATTTTTAAATATGGTTTGCTTTATGGCTAGAACACACCGATTACTTAAAATAGGATTAACCCCCATACACTTTAAAAATGATTAAACAACATTTCTGCTGCTCGCTCACATTCTTCATAGAAGATGACATAATGTATTTTCCTTTTGGTT", ) self.assertEqual( alignment[0], "TCATAGGTATTTATTTTTAAATATGGTTTGCTTTATGGCTAGAACACACCGATTACTTAAAATAGGATTAACC--CCCATACACTTTAAAAATGATTAAACAACATTTCTGCTGCTCGCTCACATTCTTCATAGAAGATGACATAATGTATTTTCCTTTTGGTT", ) self.assertEqual(alignment.sequences[1].id, "oryCun1.scaffold_133159") self.assertEqual(len(alignment.sequences[1].seq), 13221) self.assertEqual( alignment.sequences[1].seq[11087 : 11087 + 164], "TCACAGATATTTACTATTAAATATGGTTTGTTATATGGTTACGGTTCATAGGTTACTTGGAATTGGATTAACCTTCTTATTCATTGCAGAATTGGTTACACTGTGTTCTTGACCTTTGCTTGTTTTCTCCATGGAAACTGATGTCAAATACTTTCCCTTTGGTT", ) self.assertEqual( alignment[1], "TCACAGATATTTACTATTAAATATGGTTTGTTATATGGTTACGGTTCATAGGTTACTTGGAATTGGATTAACCTTCTTATTCATTGCAGAATTGGTTACACTGTGTTCTTGACCTTTGCTTGTTTTCTCCATGGAAACTGATGTCAAATACTTTCCCTTTGGTT", ) self.assertEqual( alignment.sequences[1].annotations["quality"], "99569899999998999999999999999999999999999999999999999999999999999999999757878999975999999999999999979999999999997899999999999997997999999869999996999988997997999999", ) self.assertEqual(alignment.sequences[1].annotations["leftStatus"], "N") self.assertEqual(alignment.sequences[1].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[1].annotations["rightStatus"], "N") self.assertEqual(alignment.sequences[1].annotations["rightCount"], 0) self.assertEqual(len(alignment.sequences), 2) self.assertNotIn("empty", alignment.annotations) self.assertEqual( str(alignment), """\ mm9.chr10 3009319 TCATAGGTATTTATTTTTAAATATGGTTTGCTTTATGGCTAGAACACACCGATTACTTAA 0 |||.||.||||||.|.||||||||||||||.|.|||||.||.....||..|.||||||.. oryCun1.s 11087 TCACAGATATTTACTATTAAATATGGTTTGTTATATGGTTACGGTTCATAGGTTACTTGG mm9.chr10 3009379 AATAGGATTAACC--CCCATACACTTTAAAAATGATTAAACAACATTTCTGCTGCTCGCT 60 |||.|||||||||--|..||.||.|..|.||.||.|||.||....||..||....|.||| oryCun1.s 11147 AATTGGATTAACCTTCTTATTCATTGCAGAATTGGTTACACTGTGTTCTTGACCTTTGCT mm9.chr10 3009437 CACATTCTTCATAGAAGATGACATAATGTATTTTCCTTTTGGTT 3009481 120 ....||||.|||.|||..|||..|.|..||.|||||.||||||| 164 oryCun1.s 11207 TGTTTTCTCCATGGAAACTGATGTCAAATACTTTCCCTTTGGTT 11251 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[3009319, 3009392, 3009392, 3009481], [ 11087, 11160, 11162, 11251], ]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['T', 'C', 'A', 'T', 'A', 'G', 'G', 'T', 'A', 'T', 'T', 'T', 'A', 'T', 'T', 'T', 'T', 'T', 'A', 'A', 'A', 'T', 'A', 'T', 'G', 'G', 'T', 'T', 'T', 'G', 'C', 'T', 'T', 'T', 'A', 'T', 'G', 'G', 'C', 'T', 'A', 'G', 'A', 'A', 'C', 'A', 'C', 'A', 'C', 'C', 'G', 'A', 'T', 'T', 'A', 'C', 'T', 'T', 'A', 'A', 'A', 'A', 'T', 'A', 'G', 'G', 'A', 'T', 'T', 'A', 'A', 'C', 'C', '-', '-', 'C', 'C', 'C', 'A', 'T', 'A', 'C', 'A', 'C', 'T', 'T', 'T', 'A', 'A', 'A', 'A', 'A', 'T', 'G', 'A', 'T', 'T', 'A', 'A', 'A', 'C', 'A', 'A', 'C', 'A', 'T', 'T', 'T', 'C', 'T', 'G', 'C', 'T', 'G', 'C', 'T', 'C', 'G', 'C', 'T', 'C', 'A', 'C', 'A', 'T', 'T', 'C', 'T', 'T', 'C', 'A', 'T', 'A', 'G', 'A', 'A', 'G', 'A', 'T', 'G', 'A', 'C', 'A', 'T', 'A', 'A', 'T', 'G', 'T', 'A', 'T', 'T', 'T', 'T', 'C', 'C', 'T', 'T', 'T', 'T', 'G', 'G', 'T', 'T'], ['T', 'C', 'A', 'C', 'A', 'G', 'A', 'T', 'A', 'T', 'T', 'T', 'A', 'C', 'T', 'A', 'T', 'T', 'A', 'A', 'A', 'T', 'A', 'T', 'G', 'G', 'T', 'T', 'T', 'G', 'T', 'T', 'A', 'T', 'A', 'T', 'G', 'G', 'T', 'T', 'A', 'C', 'G', 'G', 'T', 'T', 'C', 'A', 'T', 'A', 'G', 'G', 'T', 'T', 'A', 'C', 'T', 'T', 'G', 'G', 'A', 'A', 'T', 'T', 'G', 'G', 'A', 'T', 'T', 'A', 'A', 'C', 'C', 'T', 'T', 'C', 'T', 'T', 'A', 'T', 'T', 'C', 'A', 'T', 'T', 'G', 'C', 'A', 'G', 'A', 'A', 'T', 'T', 'G', 'G', 'T', 'T', 'A', 'C', 'A', 'C', 'T', 'G', 'T', 'G', 'T', 'T', 'C', 'T', 'T', 'G', 'A', 'C', 'C', 'T', 'T', 'T', 'G', 'C', 'T', 'T', 'G', 'T', 'T', 'T', 'T', 'C', 'T', 'C', 'C', 'A', 'T', 'G', 'G', 'A', 'A', 'A', 'C', 'T', 'G', 'A', 'T', 'G', 'T', 'C', 'A', 'A', 'A', 'T', 'A', 'C', 'T', 'T', 'T', 'C', 'C', 'C', 'T', 'T', 'T', 'G', 'G', 'T', 'T']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.score, 103072) self.assertEqual(alignment.sequences[0].id, "mm9.chr10") self.assertEqual(len(alignment.sequences[0].seq), 129993255) self.assertEqual( alignment.sequences[0].seq[3012076 : 3012076 + 365], "AGTCTTTCCAATGGGACCTGTGAGTCCTAACTATGCCAGCACTCCCAACAGCAAGACACTAAGTTCACTCATCCTTGGTGGATGGGATTTTGCTCCTGGAGTGTCACCAAATTAAATAACCAGTGAGCAGAGTTGTGACGAGCATCAGGCTCTGGATTTAGGTGAGAGACCTTAGTGTATGTCTCCTGTAGGTCGCAGCTCCCTATGGATGAGTCAAGTGAAGGTCCTGAGACAACAAGTCCTCGGCTATGTGGGGGTGAGGGATGCAGCTGGAACCTCAGGGATCTCTGTAAGCAGTGGCATAAATGCTTGGCGGGAGAGAGCATGTTAGAGCTCACACGACATAGGAAGCCACTGAGACACTG", ) self.assertEqual( alignment[0], "AGTCTTTCCAATGGGACCTGTGAGTCCTAACTATGCCAGC-----ACTCCCAACAGCAAGACACTAAGTT---------CACTCATCCTTGGTGGATGGGATTTTGCTCCTGGAGTGTCAC-----CAAATTAAATAACCAGTGAGCAGAGTTG--TGACGAGCATCAGGCTCTGGATTTAGGTGAGAGACCTTAGTGTATGTCTCCTGTAGGTCGCAGCTCCCTATGGAT--------------------------GAGTCAAGTGAAGGTCCTGAGACAA-------------------CAAGTCCTC----GGCTATGTGGGGGTGAGGG-------------ATGC----AG--------CTGGAACCTCAGGGA-TCTCTGT-AAGCAGTGGCATAAATGCTTGGCGG--GAGAGAGCATGTTAGAGCTCACACGACATAGGAAGCCACTGA--GACACTG", ) self.assertEqual(alignment.sequences[1].id, "ponAbe2.chr6") self.assertEqual(len(alignment.sequences[1].seq), 174210431) self.assertEqual( alignment.sequences[1].seq[158049785 : 158049785 + 443], "GAACACAAGTCCATGGCCTTTTCAACCACGTTAGGCGTTGGAGGCCACGTCAGCCCCCACAGATCCACTCTACAACTTTAGAAAGAATTTGTTAGGCACCAGTGGCTTGCTTCAGAGTTCTAGTTCCTACGCTGTCAGGGAGTCTACAGCAGCCCTATCCACAACTTACCTCCAGGATTTTGCTTAATTTCTGTGGAAAGCGATCTCAACTTCCCAGTTCACACACAGATGCAACCAGCATGAGACATTCCTAGAAATCAACAACCTTTGGTGACTGGTCTATCTCATGCTATTCTAAATACTGCTTGCTCACTTCATAAGTACGACATTCCAAGAGCACAAGGCTATCTGGTAAGGATGAGTATGGAGATAAATATTAACATCTTTTTACTGTGATGATTTGGCTGGAATAATTAAAACTTATATTTCCACTTATGAAGACT", ) self.assertEqual( alignment[1], "AGTCTTCATAAGTGGAAATATAAGTTTTAATTATTCCAGCCAAATCATCACAGTAAAAAGATGTTAATATTTATCTCCATACTCATCCTTACCAGATAGCCTTGTGCTCTTGGAATGTCGTACTTATGAAGTGAGCAAGCAGTATTTAGAATAGCATGAGATAGACCAGTCACCAA----AGGTTGTTGATTTCTAGGAATGTCTCATGCTGGTTGCATCTGTGTGTGAACTGGGAAGTTGAGATCGCTTTCCACAGAAATTAAGCAAAATCCTGGAGGTAAGTTGTGGA-----------TAGGGCTGCTGTAGACTCCCTGACAGCGTAGGAACT--------AGAACTCTGAAGCAAGCCACTGGTGCCTAACAAATTCTTTCTAAAGTTGTAGAGTGGATCTGTGGGGGCTGACGTGGCCTCCAACGCCTAACGTGGTTGAAAAGGCCATGGACTTGTGTTC", ) self.assertEqual(alignment.sequences[1].annotations["leftStatus"], "N") self.assertEqual(alignment.sequences[1].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[1].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[1].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[2].id, "panTro2.chr6") self.assertEqual(len(alignment.sequences[2].seq), 173908612) self.assertEqual( alignment.sequences[2].seq[157529165 : 157529165 + 443], "GAACACAAGTCCATGGCCTTTTCAACCATGTTAGGCGTTGGAGGCCACGTCAGCCCCCACAGATCCACTCTACAACTTTATAAAGAATTTGTTAGGCACCAGTGGCTTGCTTCAGAGTTCTAGTTCCTATGCTGTCAGGGAGTCTACAGCATCCCTATCCACAACTTACCTCCAGGATTTTGCTTAATTTCTGTGGAAAGCGATCTCAACTTCCCAGTTCACACACAGATGCAACCAGCATGAGACATTCCTAGAAATCAACAACCTTTGGTGACTGGTCTATCTCATGCTATTCTACATACTGCTTGCTCACTTCACAAATACGACATTCCAAGAGCACAAGGCTATCTGGTAAGGATGAGTATGGAGATAAATATTAACATCTTTTTACTGTGATGATTTAGCTGGAATAATTAAAACTTATATTTCCACTTATGAAGACT", ) self.assertEqual( alignment[2], "AGTCTTCATAAGTGGAAATATAAGTTTTAATTATTCCAGCTAAATCATCACAGTAAAAAGATGTTAATATTTATCTCCATACTCATCCTTACCAGATAGCCTTGTGCTCTTGGAATGTCGTATTTGTGAAGTGAGCAAGCAGTATGTAGAATAGCATGAGATAGACCAGTCACCAA----AGGTTGTTGATTTCTAGGAATGTCTCATGCTGGTTGCATCTGTGTGTGAACTGGGAAGTTGAGATCGCTTTCCACAGAAATTAAGCAAAATCCTGGAGGTAAGTTGTGGA-----------TAGGGATGCTGTAGACTCCCTGACAGCATAGGAACTAGAACTCTGAAGC----AAGCCA----CTGGTGCCTAACAAATTCTTTATAAAGTTGTAGAGTGGATCTGTGGGGGCTGACGTGGCCTCCAACGCCTAACATGGTTGAAAAGGCCATGGACTTGTGTTC", ) self.assertEqual( alignment.sequences[2].annotations["quality"], "99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999", ) self.assertEqual(alignment.sequences[2].annotations["leftStatus"], "N") self.assertEqual(alignment.sequences[2].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[2].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[2].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[3].id, "hg18.chr6") self.assertEqual(len(alignment.sequences[3].seq), 170899992) self.assertEqual( alignment.sequences[3].seq[155039093 : 155039093 + 443], "GAACACAAGTCCATGGCCTTTTCAACCATGTTAGGCGTTGGAGGCCACGTCAGCCCCCATGGATCCACTCTACAACTTTATAAAGAATTTGTTAGGCACCAGTGGCTTGCTTCAGAGTTCTAGTTCCTATGCTGTCAGGGAGTCTACAGCATCCCTATCCACAACTTACCTCCAGGATTTTGCTTAATTTCTGTGGAAAGCGATCTCAACTTCCCAGTTCACACACAGATGCAACCAGCATGAGACATTCCTAGAAATCAACAACCTTTGGTGACTGGTCTATCTCATGCTATTCTACATACTGCTTGCTCACTTCACAAATACGACATTCCAAGAGCACAAGGCTATCTGGTAAGGATGAGTATGGAGATAAATATTAACATCTTTTTACTGTGATGATTTAGCTGGAATAATTAAAACTTATATTTCCACTTATGAAGACT", ) self.assertEqual( alignment[3], "AGTCTTCATAAGTGGAAATATAAGTTTTAATTATTCCAGCTAAATCATCACAGTAAAAAGATGTTAATATTTATCTCCATACTCATCCTTACCAGATAGCCTTGTGCTCTTGGAATGTCGTATTTGTGAAGTGAGCAAGCAGTATGTAGAATAGCATGAGATAGACCAGTCACCAA----AGGTTGTTGATTTCTAGGAATGTCTCATGCTGGTTGCATCTGTGTGTGAACTGGGAAGTTGAGATCGCTTTCCACAGAAATTAAGCAAAATCCTGGAGGTAAGTTGTGGATAGGGATGCTGTAGACTCCCT---GACAGCATAGGAAC-TAGAACTCTGAAGC---AAGC----CA--------CTGGTGCCTAACAAATTCTTTATAAAGTTGTAGAGTGGATCCATGGGGGCTGACGTGGCCTCCAACGCCTAACATGGTTGAAAAGGCCATGGACTTGTGTTC", ) self.assertEqual(alignment.sequences[3].annotations["leftStatus"], "N") self.assertEqual(alignment.sequences[3].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[3].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[3].annotations["rightCount"], 0) self.assertEqual(len(alignment.sequences), 4) self.assertNotIn("empty", alignment.annotations) self.assertEqual( str(alignment), """\ mm9.chr10 3012076 AGTCTTTCCAATGGGACCTGTGAGTCCTAACTATGCCAGC-----ACTCCCAACAGCAAG ponAbe2.c 158050228 AGTCTTCATAAGTGGAAATATAAGTTTTAATTATTCCAGCCAAATCATCACAGTAAAAAG panTro2.c 157529608 AGTCTTCATAAGTGGAAATATAAGTTTTAATTATTCCAGCTAAATCATCACAGTAAAAAG hg18.chr6 155039536 AGTCTTCATAAGTGGAAATATAAGTTTTAATTATTCCAGCTAAATCATCACAGTAAAAAG mm9.chr10 3012131 ACACTAAGTT---------CACTCATCCTTGGTGGATGGGATTTTGCTCCTGGAGTGTCA ponAbe2.c 158050168 ATGTTAATATTTATCTCCATACTCATCCTTACCAGATAGCCTTGTGCTCTTGGAATGTCG panTro2.c 157529548 ATGTTAATATTTATCTCCATACTCATCCTTACCAGATAGCCTTGTGCTCTTGGAATGTCG hg18.chr6 155039476 ATGTTAATATTTATCTCCATACTCATCCTTACCAGATAGCCTTGTGCTCTTGGAATGTCG mm9.chr10 3012182 C-----CAAATTAAATAACCAGTGAGCAGAGTTG--TGACGAGCATCAGGCTCTGGATTT ponAbe2.c 158050108 TACTTATGAAGTGAGCAAGCAGTATTTAGAATAGCATGAGATAGACCAGTCACCAA---- panTro2.c 157529488 TATTTGTGAAGTGAGCAAGCAGTATGTAGAATAGCATGAGATAGACCAGTCACCAA---- hg18.chr6 155039416 TATTTGTGAAGTGAGCAAGCAGTATGTAGAATAGCATGAGATAGACCAGTCACCAA---- mm9.chr10 3012235 AGGTGAGAGACCTTAGTGTATGTCTCCTGTAGGTCGCAGCTCCCTATGGAT--------- ponAbe2.c 158050052 AGGTTGTTGATTTCTAGGAATGTCTCATGCTGGTTGCATCTGTGTGTGAACTGGGAAGTT panTro2.c 157529432 AGGTTGTTGATTTCTAGGAATGTCTCATGCTGGTTGCATCTGTGTGTGAACTGGGAAGTT hg18.chr6 155039360 AGGTTGTTGATTTCTAGGAATGTCTCATGCTGGTTGCATCTGTGTGTGAACTGGGAAGTT mm9.chr10 3012286 -----------------GAGTCAAGTGAAGGTCCTGAGACAA------------------ ponAbe2.c 158049992 GAGATCGCTTTCCACAGAAATTAAGCAAAATCCTGGAGGTAAGTTGTGGA---------- panTro2.c 157529372 GAGATCGCTTTCCACAGAAATTAAGCAAAATCCTGGAGGTAAGTTGTGGA---------- hg18.chr6 155039300 GAGATCGCTTTCCACAGAAATTAAGCAAAATCCTGGAGGTAAGTTGTGGATAGGGATGCT mm9.chr10 3012311 -CAAGTCCTC----GGCTATGTGGGGGTGAGGG-------------ATGC----AG---- ponAbe2.c 158049942 -TAGGGCTGCTGTAGACTCCCTGACAGCGTAGGAACT--------AGAACTCTGAAGCAA panTro2.c 157529322 -TAGGGATGCTGTAGACTCCCTGACAGCATAGGAACTAGAACTCTGAAGC----AAGCCA hg18.chr6 155039240 GTAGACTCCCT---GACAGCATAGGAAC-TAGAACTCTGAAGC---AAGC----CA---- mm9.chr10 3012345 ----CTGGAACCTCAGGGA-TCTCTGT-AAGCAGTGGCATAAATGCTTGGCGG--GAGAG ponAbe2.c 158049891 GCCACTGGTGCCTAACAAATTCTTTCTAAAGTTGTAGAGTGGATCTGTGGGGGCTGACGT panTro2.c 157529267 ----CTGGTGCCTAACAAATTCTTTATAAAGTTGTAGAGTGGATCTGTGGGGGCTGACGT hg18.chr6 155039195 ----CTGGTGCCTAACAAATTCTTTATAAAGTTGTAGAGTGGATCCATGGGGGCTGACGT mm9.chr10 3012397 AGCATGTTAGAGCTCACACGACATAGGAAGCCACTGA--GACACTG 3012441 ponAbe2.c 158049831 GGCCTCCAACGCCTAACGTGGTTGAAAAGGCCATGGACTTGTGTTC 158049785 panTro2.c 157529211 GGCCTCCAACGCCTAACATGGTTGAAAAGGCCATGGACTTGTGTTC 157529165 hg18.chr6 155039139 GGCCTCCAACGCCTAACATGGTTGAAAAGGCCATGGACTTGTGTTC 155039093 """, ) self.assertTrue( np.array_equal( alignment.coordinates, np.array( # fmt: off [[ 3012076, 3012116, 3012116, 3012141, 3012141, 3012183, 3012183, 3012211, 3012211, 3012231, 3012235, 3012286, 3012286, 3012311, 3012311, 3012311, 3012320, 3012320, 3012320, 3012334, 3012335, 3012339, 3012339, 3012339, 3012339, 3012339, 3012343, 3012343, 3012345, 3012345, 3012345, 3012360, 3012360, 3012367, 3012367, 3012392, 3012392, 3012434, 3012434, 3012441], [158050228, 158050188, 158050183, 158050158, 158050149, 158050107, 158050102, 158050074, 158050072, 158050052, 158050052, 158050001, 158049975, 158049950, 158049942, 158049942, 158049933, 158049932, 158049929, 158049915, 158049914, 158049910, 158049906, 158049906, 158049906, 158049905, 158049901, 158049897, 158049895, 158049891, 158049887, 158049872, 158049871, 158049864, 158049863, 158049838, 158049836, 158049794, 158049792, 158049785], [157529608, 157529568, 157529563, 157529538, 157529529, 157529487, 157529482, 157529454, 157529452, 157529432, 157529432, 157529381, 157529355, 157529330, 157529322, 157529322, 157529313, 157529312, 157529309, 157529295, 157529294, 157529290, 157529286, 157529280, 157529278, 157529277, 157529273, 157529273, 157529271, 157529267, 157529267, 157529252, 157529251, 157529244, 157529243, 157529218, 157529216, 157529174, 157529172, 157529165], [155039536, 155039496, 155039491, 155039466, 155039457, 155039415, 155039410, 155039382, 155039380, 155039360, 155039360, 155039309, 155039283, 155039258, 155039250, 155039239, 155039230, 155039229, 155039229, 155039215, 155039215, 155039211, 155039207, 155039201, 155039201, 155039201, 155039197, 155039197, 155039195, 155039195, 155039195, 155039180, 155039179, 155039172, 155039171, 155039146, 155039144, 155039102, 155039100, 155039093], ] # fmt: on ), ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.score, 49128) self.assertEqual(alignment.sequences[0].id, "mm9.chr10") self.assertEqual(len(alignment.sequences[0].seq), 129993255) self.assertEqual( alignment.sequences[0].seq[3012441 : 3012441 + 125], "TGGGTCCCCTTGGCACATCCAGATCTCCCCAGTTAACCTGTCCTGCTTAGACCACTTACCTGAATTGAATTGGGAGGAGAGAAAGAAGCCAGTTTCCCAGAGAGGGAAAAGGAAAAGCTCGACAC", ) self.assertEqual( alignment[0], "TGGGTCCCCTTGGCACATCCAGATCTCCCCAGTTAACCTGTCCTGCTTAGACCACTTACCTGAATTG--AATTGGGAGGAGAGAAAGAAGCCAGTTTCCCAGAGAGGGAAAAGGAAAAGCTCGACAC", ) self.assertEqual(alignment.sequences[1].id, "hg18.chr6") self.assertEqual(len(alignment.sequences[1].seq), 170899992) self.assertEqual( alignment.sequences[1].seq[155038979 : 155038979 + 114], "GCTTCCAGCATTTTCCATTGGCCCTCAGCAAGGTGCTCCCCAAGATCAGCGGTCAAGAGAGGTGGTCAATACACACCAGGTTACGTGAGGACTTGGTTATTCTAGAGGAACCCA", ) self.assertEqual( alignment[1], "TGGGTTCCTCTAGAATAACCAAG--TCCTCACGTAACCTGGTGTGTATTGACCACCTCTCTTGACCGCTGATCTTGGGGAG----------CACCTTGCT-GAGGGCCAATGGAAAATGCTGGAAGC", ) self.assertEqual(alignment.sequences[1].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[1].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[1].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[1].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[2].id, "panTro2.chr6") self.assertEqual(len(alignment.sequences[2].seq), 173908612) self.assertEqual( alignment.sequences[2].seq[157529051 : 157529051 + 114], "GCTTCCAGCATTTTCCATTGGCCCTCAGCAAGGTGCTCCCCAAGATCAGCGGTCAAGAGAGGTGGTCAATACACACCAGGTTACGTGAGGACTTGGTTATTCTAGAGGAACCCA", ) self.assertEqual( alignment[2], "TGGGTTCCTCTAGAATAACCAAG--TCCTCACGTAACCTGGTGTGTATTGACCACCTCTCTTGACCGCTGATCTTGGGGAG----------CACCTTGCT-GAGGGCCAATGGAAAATGCTGGAAGC", ) self.assertEqual( alignment.sequences[2].annotations["quality"], "999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999", ) self.assertEqual(alignment.sequences[2].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[2].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[2].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[2].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[3].id, "ponAbe2.chr6") self.assertEqual(len(alignment.sequences[3].seq), 174210431) self.assertEqual( alignment.sequences[3].seq[158049671 : 158049671 + 114], "GCTTCCAGCATTTTCCATTGGCCCTCAGCAAGGTGCTCCCCAAGATCAACAGTCAAGACAGGTGGTCAATATAGACCAGGTTACGTGAGGACTTGGTTATTCTAGAGGAACCCA", ) self.assertEqual( alignment[3], "TGGGTTCCTCTAGAATAACCAAG--TCCTCACGTAACCTGGTCTATATTGACCACCTGTCTTGACTGTTGATCTTGGGGAG----------CACCTTGCT-GAGGGCCAATGGAAAATGCTGGAAGC", ) self.assertEqual(alignment.sequences[3].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[3].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[3].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[3].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[4].id, "otoGar1.scaffold_334.1-359464") self.assertEqual(len(alignment.sequences[4].seq), 359464) self.assertEqual( alignment.sequences[4].seq[178838 : 178838 + 101], "GCTTCCCGTGTTTGCTGTTGCCCCTCAGCAAAGGGCTCCCCAAGTTTGGTGGTCAGTGTAAACCCGGGTGAGTGAGGACTTGGCCAGGTCAGGGGGGCCCA", ) self.assertEqual( alignment[4], "TGGGCCCCCCTGACCTGGCCAAG--TCCTCACTCACCCGGGTTTACACTGACCACC-------------AAACTTGGGGAG----------CCCTTTGCT-GAGGGGCAACAGCAAACACGGGAAGC", ) self.assertEqual( alignment.sequences[4].annotations["quality"], "99999999999999999999999999999999999999999999999999999999999999999999999999999999979999999999999999999", ) self.assertEqual(alignment.sequences[4].annotations["leftStatus"], "N") self.assertEqual(alignment.sequences[4].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[4].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[4].annotations["rightCount"], 0) self.assertEqual(len(alignment.sequences), 5) self.assertNotIn("empty", alignment.annotations) self.assertEqual( str(alignment), """\ mm9.chr10 3012441 TGGGTCCCCTTGGCACATCCAGATCTCCCCAGTTAACCTGTCCTGCTTAGACCACTTACC hg18.chr6 155039093 TGGGTTCCTCTAGAATAACCAAG--TCCTCACGTAACCTGGTGTGTATTGACCACCTCTC panTro2.c 157529165 TGGGTTCCTCTAGAATAACCAAG--TCCTCACGTAACCTGGTGTGTATTGACCACCTCTC ponAbe2.c 158049785 TGGGTTCCTCTAGAATAACCAAG--TCCTCACGTAACCTGGTCTATATTGACCACCTGTC otoGar1.s 178939 TGGGCCCCCCTGACCTGGCCAAG--TCCTCACTCACCCGGGTTTACACTGACCACC---- mm9.chr10 3012501 TGAATTG--AATTGGGAGGAGAGAAAGAAGCCAGTTTCCCAGAGAGGGAAAAGGAAAAGC hg18.chr6 155039035 TTGACCGCTGATCTTGGGGAG----------CACCTTGCT-GAGGGCCAATGGAAAATGC panTro2.c 157529107 TTGACCGCTGATCTTGGGGAG----------CACCTTGCT-GAGGGCCAATGGAAAATGC ponAbe2.c 158049727 TTGACTGTTGATCTTGGGGAG----------CACCTTGCT-GAGGGCCAATGGAAAATGC otoGar1.s 178885 ---------AAACTTGGGGAG----------CCCTTTGCT-GAGGGGCAACAGCAAACAC mm9.chr10 3012559 TCGACAC 3012566 hg18.chr6 155038986 TGGAAGC 155038979 panTro2.c 157529058 TGGAAGC 157529051 ponAbe2.c 158049678 TGGAAGC 158049671 otoGar1.s 178845 GGGAAGC 178838 """, ) self.assertTrue( np.array_equal( alignment.coordinates, np.array( # fmt: off [[ 3012441, 3012464, 3012466, 3012497, 3012508, 3012508, 3012520, 3012530, 3012539, 3012540, 3012566], [155039093, 155039070, 155039070, 155039039, 155039028, 155039026, 155039014, 155039014, 155039005, 155039005, 155038979], [157529165, 157529142, 157529142, 157529111, 157529100, 157529098, 157529086, 157529086, 157529077, 157529077, 157529051], [158049785, 158049762, 158049762, 158049731, 158049720, 158049718, 158049706, 158049706, 158049697, 158049697, 158049671], [ 178939, 178916, 178916, 178885, 178885, 178885, 178873, 178873, 178864, 178864, 178838], ] # fmt: on ), ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['T', 'G', 'G', 'G', 'T', 'C', 'C', 'C', 'C', 'T', 'T', 'G', 'G', 'C', 'A', 'C', 'A', 'T', 'C', 'C', 'A', 'G', 'A', 'T', 'C', 'T', 'C', 'C', 'C', 'C', 'A', 'G', 'T', 'T', 'A', 'A', 'C', 'C', 'T', 'G', 'T', 'C', 'C', 'T', 'G', 'C', 'T', 'T', 'A', 'G', 'A', 'C', 'C', 'A', 'C', 'T', 'T', 'A', 'C', 'C', 'T', 'G', 'A', 'A', 'T', 'T', 'G', '-', '-', 'A', 'A', 'T', 'T', 'G', 'G', 'G', 'A', 'G', 'G', 'A', 'G', 'A', 'G', 'A', 'A', 'A', 'G', 'A', 'A', 'G', 'C', 'C', 'A', 'G', 'T', 'T', 'T', 'C', 'C', 'C', 'A', 'G', 'A', 'G', 'A', 'G', 'G', 'G', 'A', 'A', 'A', 'A', 'G', 'G', 'A', 'A', 'A', 'A', 'G', 'C', 'T', 'C', 'G', 'A', 'C', 'A', 'C'], ['T', 'G', 'G', 'G', 'T', 'T', 'C', 'C', 'T', 'C', 'T', 'A', 'G', 'A', 'A', 'T', 'A', 'A', 'C', 'C', 'A', 'A', 'G', '-', '-', 'T', 'C', 'C', 'T', 'C', 'A', 'C', 'G', 'T', 'A', 'A', 'C', 'C', 'T', 'G', 'G', 'T', 'G', 'T', 'G', 'T', 'A', 'T', 'T', 'G', 'A', 'C', 'C', 'A', 'C', 'C', 'T', 'C', 'T', 'C', 'T', 'T', 'G', 'A', 'C', 'C', 'G', 'C', 'T', 'G', 'A', 'T', 'C', 'T', 'T', 'G', 'G', 'G', 'G', 'A', 'G', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'C', 'A', 'C', 'C', 'T', 'T', 'G', 'C', 'T', '-', 'G', 'A', 'G', 'G', 'G', 'C', 'C', 'A', 'A', 'T', 'G', 'G', 'A', 'A', 'A', 'A', 'T', 'G', 'C', 'T', 'G', 'G', 'A', 'A', 'G', 'C'], ['T', 'G', 'G', 'G', 'T', 'T', 'C', 'C', 'T', 'C', 'T', 'A', 'G', 'A', 'A', 'T', 'A', 'A', 'C', 'C', 'A', 'A', 'G', '-', '-', 'T', 'C', 'C', 'T', 'C', 'A', 'C', 'G', 'T', 'A', 'A', 'C', 'C', 'T', 'G', 'G', 'T', 'G', 'T', 'G', 'T', 'A', 'T', 'T', 'G', 'A', 'C', 'C', 'A', 'C', 'C', 'T', 'C', 'T', 'C', 'T', 'T', 'G', 'A', 'C', 'C', 'G', 'C', 'T', 'G', 'A', 'T', 'C', 'T', 'T', 'G', 'G', 'G', 'G', 'A', 'G', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'C', 'A', 'C', 'C', 'T', 'T', 'G', 'C', 'T', '-', 'G', 'A', 'G', 'G', 'G', 'C', 'C', 'A', 'A', 'T', 'G', 'G', 'A', 'A', 'A', 'A', 'T', 'G', 'C', 'T', 'G', 'G', 'A', 'A', 'G', 'C'], ['T', 'G', 'G', 'G', 'T', 'T', 'C', 'C', 'T', 'C', 'T', 'A', 'G', 'A', 'A', 'T', 'A', 'A', 'C', 'C', 'A', 'A', 'G', '-', '-', 'T', 'C', 'C', 'T', 'C', 'A', 'C', 'G', 'T', 'A', 'A', 'C', 'C', 'T', 'G', 'G', 'T', 'C', 'T', 'A', 'T', 'A', 'T', 'T', 'G', 'A', 'C', 'C', 'A', 'C', 'C', 'T', 'G', 'T', 'C', 'T', 'T', 'G', 'A', 'C', 'T', 'G', 'T', 'T', 'G', 'A', 'T', 'C', 'T', 'T', 'G', 'G', 'G', 'G', 'A', 'G', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'C', 'A', 'C', 'C', 'T', 'T', 'G', 'C', 'T', '-', 'G', 'A', 'G', 'G', 'G', 'C', 'C', 'A', 'A', 'T', 'G', 'G', 'A', 'A', 'A', 'A', 'T', 'G', 'C', 'T', 'G', 'G', 'A', 'A', 'G', 'C'], ['T', 'G', 'G', 'G', 'C', 'C', 'C', 'C', 'C', 'C', 'T', 'G', 'A', 'C', 'C', 'T', 'G', 'G', 'C', 'C', 'A', 'A', 'G', '-', '-', 'T', 'C', 'C', 'T', 'C', 'A', 'C', 'T', 'C', 'A', 'C', 'C', 'C', 'G', 'G', 'G', 'T', 'T', 'T', 'A', 'C', 'A', 'C', 'T', 'G', 'A', 'C', 'C', 'A', 'C', 'C', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'A', 'A', 'A', 'C', 'T', 'T', 'G', 'G', 'G', 'G', 'A', 'G', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'C', 'C', 'C', 'T', 'T', 'T', 'G', 'C', 'T', '-', 'G', 'A', 'G', 'G', 'G', 'G', 'C', 'A', 'A', 'C', 'A', 'G', 'C', 'A', 'A', 'A', 'C', 'A', 'C', 'G', 'G', 'G', 'A', 'A', 'G', 'C']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.score, 117109) self.assertEqual(alignment.sequences[0].id, "mm9.chr10") self.assertEqual(len(alignment.sequences[0].seq), 129993255) self.assertEqual( alignment.sequences[0].seq[3012566 : 3012566 + 262], "TGTGGGCTCCTCACTTTCCTGTCTCAGGTGTGTCTGTGAGTTTCGGTGAGTGTCGTACAGGAAAGAGGGTGAAAACTCAGTCTGAGCTGTCATTCTTGCCAGCTATGTTGCTTTCCTGTCCTCTTTAGCTTATCTCAGGCAACCTATCTTATTTTGTTTGCTTTCAGAAGGCAAGCGAtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtatgtgtgtgtgcgtgCGCGCGCGCGAGCACATGTGCATGCATGCGCACTCGTG", ) self.assertEqual( alignment[0], "--TGTGGGCTCCTCACTTTCCTG-TCTCAGGTGTGTCTGTGAGTTTCGGTGAGTGTCGTACAGGAAAGAGGGTGAAAACTCAGTCTGAGCTGTCATTCTTGCCAGCTATGTTGCTTTCCTGTCCTCTTTAGC-------TTATCTCAGGCAACCTATCTTATTTTGTT-TGCTTTC--AGAAGGCAAG---CGAtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtatgtgtgtgtgcgtgCGCGCGCGCGAGCACATGTGCATGCATGCGCACTCGTG", ) self.assertEqual(alignment.sequences[1].id, "hg18.chr6") self.assertEqual(len(alignment.sequences[1].seq), 170899992) self.assertEqual( alignment.sequences[1].seq[155038780 : 155038780 + 199], "CCAAAACTCATACACAACTCATCTTCTGGGAAAACAGAATAAGTAAGATGTGTTGCTAGAAATAAGGTAGTGAAGGAAAAAAATAAGAGGATTGATTGACAGGAATGAAAACTCAGACTGGATTTTGAGGCTGTTTCTGGATGGCTTCCACCAAAAACCATAGACCCATCTAAGATCAGGGATACAAGGAGGGCTCATG", ) self.assertEqual( alignment[1], "CATGAGCCCTCCTTGTATCCCTGATCTTAGATGGGTCTATGGTTTTTGGTGGAAGCCATCCAG-AAACAGCCTCAAAATCCAGTCTGAGTTTTCATTCCTGTCAATCAATCCTCTTATTTTTTTCCTTCACTACC----TTATTTCTAGCAACACATCTTAC-TTATTCTGTTTTCCCAGAAGA-------TGAGTTGTGTATGAGTTTTGG------------------------------------------------------------------", ) self.assertEqual(alignment.sequences[1].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[1].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[1].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[1].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[2].id, "panTro2.chr6") self.assertEqual(len(alignment.sequences[2].seq), 173908612) self.assertEqual( alignment.sequences[2].seq[157528852 : 157528852 + 199], "CCAAAACTCATACACAACTCATCTTCTGGGAAAACAAAATAAGTAAGATGTGTTGCTAGAAATAAGGTAGTGAAGGAAAAAAATAAGAGGATTGATTGACAGGAATGAAAACTCAGACTGGATTTTGAGGCTGTTTCTGGATGGCTTCCACCAAAAACCATAGACCCATCTAAGATCAGGGATACAAGGAGGGCTCATG", ) self.assertEqual( alignment[2], "CATGAGCCCTCCTTGTATCCCTGATCTTAGATGGGTCTATGGTTTTTGGTGGAAGCCATCCAG-AAACAGCCTCAAAATCCAGTCTGAGTTTTCATTCCTGTCAATCAATCCTCTTATTTTTTTCCTTCACTACC----TTATTTCTAGCAACACATCTTAC-TTATTTTGTTTTCCCAGAAGA-------TGAGTTGTGTATGAGTTTTGG------------------------------------------------------------------", ) self.assertEqual( alignment.sequences[2].annotations["quality"], "9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999", ) self.assertEqual(alignment.sequences[2].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[2].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[2].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[2].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[3].id, "ponAbe2.chr6") self.assertEqual(len(alignment.sequences[3].seq), 174210431) self.assertEqual( alignment.sequences[3].seq[158049472 : 158049472 + 199], "CCAAAACTCATACACAACTCATCTTCTGGGAAAACAAAATAAGTAAGATATGTTGCTAGAAATAAGGTAATGAAGGAAAAAAACAAGAGGATTGATTGACAGGAATGACAACTCAGACTGGATTTTGAGGCTGTTTCTGGATGGCTTCCACCAAAAACCATAGACCCATCTAAGATCAGGGATACAAGGAGGGCTCATG", ) self.assertEqual( alignment[3], "CATGAGCCCTCCTTGTATCCCTGATCTTAGATGGGTCTATGGTTTTTGGTGGAAGCCATCCAG-AAACAGCCTCAAAATCCAGTCTGAGTTGTCATTCCTGTCAATCAATCCTCTTGTTTTTTTCCTTCATTACC----TTATTTCTAGCAACATATCTTAC-TTATTTTGTTTTCCCAGAAGA-------TGAGTTGTGTATGAGTTTTGG------------------------------------------------------------------", ) self.assertEqual(alignment.sequences[3].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[3].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[3].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[3].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[4].id, "otoGar1.scaffold_334.1-359464") self.assertEqual(len(alignment.sequences[4].seq), 359464) self.assertEqual( alignment.sequences[4].seq[178634 : 178634 + 204], "TCAAAACTCATACACAAGTCACCACTTGTCTTCTGGGAAAACAAAACAAAGTAAGCTATGTCACCTGAAATAACAAGGCAACCTAAAAATAAGGGACTGATTGCCAGCAATGACCACAGAGACTGGGTTTTCAGGTGGTTTTCTGGACAGCTTTCCCCAGAAACCAGGGCTACGCCTAAGACAGAGACACGATGAGTGCATGTG", ) self.assertEqual( alignment[4], "CACATGCACTCATCGTGTCTCTG-TCTTAGGCGTAGCCCTGGTTTCTGGGGAAAGCTGTCCAGAAAACCACCTGAAAACCCAGTCTCTGTGGTCATTGCTGGCAATCAGTCC-CTTATTTTTAGGTTGCCTTG------TTATTTCAGGTGACATAGCTTACTTTGTTTTGTTTTCCCAGAAGACAAGTGGTGACTTGTGTATGAGTTTTGA------------------------------------------------------------------", ) self.assertEqual( alignment.sequences[4].annotations["quality"], "999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999", ) self.assertEqual(alignment.sequences[4].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[4].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[4].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[4].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[5].id, "cavPor2.scaffold_290371") self.assertEqual(len(alignment.sequences[5].seq), 39932) self.assertEqual( alignment.sequences[5].seq[39417 : 39417 + 205], "CTCAAACtcacacaaaattcatttatcttccaggaaaacagaacaaaataagatATGTTTTGCAATAACGAGGTCACTATGGGGTAAAAACAAGAGGATTGGCAGGAGGGAATAACAATTTAGACTAGGTTTTGAAGTTCTTTTCTGGATGGCTTTCACCAAAAACCACAGCCACACCTCGGATCAGGATCGCAAGGGATACGCA", ) self.assertEqual( alignment[5], "--TGCGTATCCCTTGCGATCCTGATCCGAGGTGTGGCTGTGGTTTTTGGTGAAAGCCATCCAGAAAAGAACTTCAAAACCTAGTCTAAATTGTTATTCCCTCCTGCCAATCCTCTTGTTTTTACCCCATAGTGACCTCGTTATTGCAA--AACATatcttattttgttctgttttcctggaagataaa---tgaattttgtgtgaGTTTGAG------------------------------------------------------------------", ) self.assertEqual( alignment.sequences[5].annotations["quality"], "9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999799999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999", ) self.assertEqual(alignment.sequences[5].annotations["leftStatus"], "N") self.assertEqual(alignment.sequences[5].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[5].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[5].annotations["rightCount"], 0) self.assertEqual(len(alignment.sequences), 6) self.assertNotIn("empty", alignment.annotations) self.assertEqual( str(alignment), """\ mm9.chr10 3012566 --TGTGGGCTCCTCACTTTCCTG-TCTCAGGTGTGTCTGTGAGTTTCGGTGAGTGTCGTA hg18.chr6 155038979 CATGAGCCCTCCTTGTATCCCTGATCTTAGATGGGTCTATGGTTTTTGGTGGAAGCCATC panTro2.c 157529051 CATGAGCCCTCCTTGTATCCCTGATCTTAGATGGGTCTATGGTTTTTGGTGGAAGCCATC ponAbe2.c 158049671 CATGAGCCCTCCTTGTATCCCTGATCTTAGATGGGTCTATGGTTTTTGGTGGAAGCCATC otoGar1.s 178838 CACATGCACTCATCGTGTCTCTG-TCTTAGGCGTAGCCCTGGTTTCTGGGGAAAGCTGTC cavPor2.s 39622 --TGCGTATCCCTTGCGATCCTGATCCGAGGTGTGGCTGTGGTTTTTGGTGAAAGCCATC mm9.chr10 3012623 CAGGAAAGAGGGTGAAAACTCAGTCTGAGCTGTCATTCTTGCCAGCTATGTTGCTTTCCT hg18.chr6 155038919 CAG-AAACAGCCTCAAAATCCAGTCTGAGTTTTCATTCCTGTCAATCAATCCTCTTATTT panTro2.c 157528991 CAG-AAACAGCCTCAAAATCCAGTCTGAGTTTTCATTCCTGTCAATCAATCCTCTTATTT ponAbe2.c 158049611 CAG-AAACAGCCTCAAAATCCAGTCTGAGTTGTCATTCCTGTCAATCAATCCTCTTGTTT otoGar1.s 178779 CAGAAAACCACCTGAAAACCCAGTCTCTGTGGTCATTGCTGGCAATCAGTCC-CTTATTT cavPor2.s 39564 CAGAAAAGAACTTCAAAACCTAGTCTAAATTGTTATTCCCTCCTGCCAATCCTCTTGTTT mm9.chr10 3012683 GTCCTCTTTAGC-------TTATCTCAGGCAACCTATCTTATTTTGTT-TGCTTTC--AG hg18.chr6 155038860 TTTTCCTTCACTACC----TTATTTCTAGCAACACATCTTAC-TTATTCTGTTTTCCCAG panTro2.c 157528932 TTTTCCTTCACTACC----TTATTTCTAGCAACACATCTTAC-TTATTTTGTTTTCCCAG ponAbe2.c 158049552 TTTTCCTTCATTACC----TTATTTCTAGCAACATATCTTAC-TTATTTTGTTTTCCCAG otoGar1.s 178720 TTAGGTTGCCTTG------TTATTTCAGGTGACATAGCTTACTTTGTTTTGTTTTCCCAG cavPor2.s 39504 TTACCCCATAGTGACCTCGTTATTGCAA--AACATatcttattttgttctgttttcctgg mm9.chr10 3012733 AAGGCAAG---CGAtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtatgtgtgtgtgcgtg hg18.chr6 155038805 AAGA-------TGAGTTGTGTATGAGTTTTGG---------------------------- panTro2.c 157528877 AAGA-------TGAGTTGTGTATGAGTTTTGG---------------------------- ponAbe2.c 158049497 AAGA-------TGAGTTGTGTATGAGTTTTGG---------------------------- otoGar1.s 178666 AAGACAAGTGGTGACTTGTGTATGAGTTTTGA---------------------------- cavPor2.s 39446 aagataaa---tgaattttgtgtgaGTTTGAG---------------------------- mm9.chr10 3012790 CGCGCGCGCGAGCACATGTGCATGCATGCGCACTCGTG 3012828 hg18.chr6 155038780 -------------------------------------- 155038780 panTro2.c 157528852 -------------------------------------- 157528852 ponAbe2.c 158049472 -------------------------------------- 158049472 otoGar1.s 178634 -------------------------------------- 178634 cavPor2.s 39417 -------------------------------------- 39417 """, ) self.assertTrue( np.array_equal( alignment.coordinates, np.array( # fmt: off [[ 3012566, 3012566, 3012587, 3012587, 3012626, 3012627, 3012675, 3012676, 3012695, 3012695, 3012695, 3012695, 3012704, 3012706, 3012718, 3012719, 3012724, 3012724, 3012731, 3012731, 3012737, 3012741, 3012741, 3012762, 3012828], [155038979, 155038977, 155038956, 155038955, 155038916, 155038916, 155038868, 155038867, 155038848, 155038847, 155038845, 155038845, 155038836, 155038834, 155038822, 155038822, 155038817, 155038816, 155038809, 155038807, 155038801, 155038801, 155038801, 155038780, 155038780], [157529051, 157529049, 157529028, 157529027, 157528988, 157528988, 157528940, 157528939, 157528920, 157528919, 157528917, 157528917, 157528908, 157528906, 157528894, 157528894, 157528889, 157528888, 157528881, 157528879, 157528873, 157528873, 157528873, 157528852, 157528852], [158049671, 158049669, 158049648, 158049647, 158049608, 158049608, 158049560, 158049559, 158049540, 158049539, 158049537, 158049537, 158049528, 158049526, 158049514, 158049514, 158049509, 158049508, 158049501, 158049499, 158049493, 158049493, 158049493, 158049472, 158049472], [ 178838, 178836, 178815, 178815, 178776, 178775, 178727, 178727, 178708, 178707, 178707, 178707, 178698, 178696, 178684, 178683, 178678, 178677, 178670, 178668, 178662, 178658, 178655, 178634, 178634], [ 39622, 39622, 39601, 39600, 39561, 39560, 39512, 39511, 39492, 39491, 39489, 39485, 39476, 39476, 39464, 39463, 39458, 39457, 39450, 39448, 39442, 39438, 39438, 39417, 39417], ] # fmt: on ), ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.score, 128047) self.assertEqual(alignment.sequences[0].id, "mm9.chr10") self.assertEqual(len(alignment.sequences[0].seq), 129993255) self.assertEqual( alignment.sequences[0].seq[3012828 : 3012828 + 168], "TTTGCATAGACTCTCTTGGCAACAAAATAACGTTATATTTAAACATCCATTAAAATAATGCACTTAGCACAGCCTGCCCTGAGGGATGAACACTATTGTTAAAGAACTATTCCGCTAAGGCAGCAACCTCTGGATCTTCAGCATTCTGGCGCCATCTGCTGGTCATAT", ) self.assertEqual( alignment[0], "TTTGCATAGACTCTCTTGGCAACAAAATAACGTTATATTTAAACATCCATTAAAATAATGCACTTAGCACAGCCTGCCCTGAGGGAT----GAACACT--ATTGTTAA-AGAACTATTCCGCTAAGGCAGCAACCTCTGGATCTTCAGCATTCTGGCGCCATCTGCTGGTCATAT", ) self.assertEqual(alignment.sequences[1].id, "cavPor2.scaffold_290371") self.assertEqual(len(alignment.sequences[1].seq), 39932) self.assertEqual( alignment.sequences[1].seq[39251 : 39251 + 166], "ATATGACCAGCAGATGGCACTAGAATCCCACGGAACCTGAAGTTGCCTCCTGCTAAACAGCTTTGCTGACAATAAAGGTCTCAGAGCTACTAGAGCGAACCATGATAACCTCATTATTTTCataaatgcttaaatataagACTATTTAGCTGTCAAGACATCCCAC", ) self.assertEqual( alignment[1], "-----GTGGGATGTCTTGACAGCTAAATAGTcttatatttaagcatttatGAAAATAATGAGGTTATCATGGTTCGCTCTAGTAGCTCTGAGACCTTT--ATTGTCAGCAAAGCTGTTTAGC--AGGAGGCAACTTCAGGTTCCGTGGGATTCTAGTGCCATCTGCTGGTCATAT", ) self.assertEqual( alignment.sequences[1].annotations["quality"], "9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999", ) self.assertEqual(alignment.sequences[1].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[1].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[1].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[1].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[2].id, "otoGar1.scaffold_334.1-359464") self.assertEqual(len(alignment.sequences[2].seq), 359464) self.assertEqual( alignment.sequences[2].seq[178473 : 178473 + 161], "CTGTGACCAGCAGATGGCGCTAAAATCCCACAGATCCTGAGGCTGCTGCTCCGCAAAACCGCTTCCCTGACAGTAGCCTCTCACTTCTAAGGGGCTGAGCTAAGTTTATCATTTCAACAAATGTTTAAATAGAACACTATTTGCCTGTCACGAATGTCCAC", ) self.assertEqual( alignment[2], "-----GTGGACATTCGTGACAGGCAAATAGTGTTCTATTTAAACATTTGTTGAAATGATAAACTTAGCTCAGCC--CCTT---AGAAGTG-AGAGGCT--ACTGTCAGGGAAGCGGTTTTGCG-GAGCAGCAGCCTCAGGATCTGTGGGATTTTAGCGCCATCTGCTGGTCACAG", ) self.assertEqual( alignment.sequences[2].annotations["quality"], "99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999989996999999999999999999999999999999999999999999999999", ) self.assertEqual(alignment.sequences[2].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[2].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[2].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[2].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[3].id, "ponAbe2.chr6") self.assertEqual(len(alignment.sequences[3].seq), 174210431) self.assertEqual( alignment.sequences[3].seq[158049311 : 158049311 + 161], "ATGTGACCAGCAGATGGCATTAGAGTCCCACAGATCCTGAGATTGAGCCTTAGCTAAACAACTTCACTAGGCATACCACATCTGTCAAGGCAGGTTATGCTAAGCTTATTATTTTCATAAATGTTTAAATATAACGCTATTTGGTTGTCAGGATAGTCCAC", ) self.assertEqual( alignment[3], "-----GTGGACTATCCTGACAACCAAATAGCGTTATATTTAAACATTTATGAAAATAATAAGCTTAGCATAACCTGCCTTGACAGATGTG-GTATGC-------CTAGTGAAGTTGTTTAGCT-AAGGCTCAATCTCAGGATCTGTGGGACTCTAATGCCATCTGCTGGTCACAT", ) self.assertEqual(alignment.sequences[3].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[3].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[3].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[3].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[4].id, "panTro2.chr6") self.assertEqual(len(alignment.sequences[4].seq), 173908612) self.assertEqual( alignment.sequences[4].seq[157528691 : 157528691 + 161], "GTGTGACCAGCAGATGGCATTAGAGTCCCACAGATCCTGAGATTGAGCCATAGCTAAGCAACTTCACTAGGCATACCACATCTGTCAAGGCAGGTTATGCTAAGCTTATTATTTTCATAAACGTTTAAATATAACGCTATTTGGTTGTCAAGATAGTCCGC", ) self.assertEqual( alignment[4], "-----GCGGACTATCTTGACAACCAAATAGCGTTATATTTAAACGTTTATGAAAATAATAAGCTTAGCATAACCTGCCTTGACAGATGTG-GTATGC-------CTAGTGAAGTTGCTTAGCT-ATGGCTCAATCTCAGGATCTGTGGGACTCTAATGCCATCTGCTGGTCACAC", ) self.assertEqual( alignment.sequences[4].annotations["quality"], "99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999", ) self.assertEqual(alignment.sequences[4].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[4].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[4].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[4].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[5].id, "hg18.chr6") self.assertEqual(len(alignment.sequences[5].seq), 170899992) self.assertEqual( alignment.sequences[5].seq[155038619 : 155038619 + 161], "GTGTGACCAGCAGATGGCATTAGAGTCCCACAGATCCTGAGATTGAGCCATAGCTAAGCAACTTCACTAGGCATACCACATCTGTCAAGGCAGGTTATGCTAAGCTTATTATTTTCACAAACGTTTAAATATAACGCTATTTGGTTGTCAAGATAGTCCAC", ) self.assertEqual( alignment[5], "-----GTGGACTATCTTGACAACCAAATAGCGTTATATTTAAACGTTTGTGAAAATAATAAGCTTAGCATAACCTGCCTTGACAGATGTG-GTATGC-------CTAGTGAAGTTGCTTAGCT-ATGGCTCAATCTCAGGATCTGTGGGACTCTAATGCCATCTGCTGGTCACAC", ) self.assertEqual(alignment.sequences[5].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[5].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[5].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[5].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[6].id, "echTel1.scaffold_288249") self.assertEqual(len(alignment.sequences[6].seq), 100002) self.assertEqual( alignment.sequences[6].seq[87492 : 87492 + 169], "TTGGGGTGGATGCTCTTGGCAGTCACACAGTGCTCTATTTTAGGATTTACTAGAACAATGAGTTTGTCATAACTGCCTCCTCCCAAGTGGGAAGCTGAAGCACCAAGTACTGACTCAGCAGTCCCTGACCTCACATCCATGGAAATCTAGTGACATCTGCTGGACACAT", ) self.assertEqual( alignment[6], "TTGGGGTGGATGCTCTTGGCAGTCACACAGTGCTCTATTTTAGGATTTACTAGAACAATGAGTTTGTCATAACT-GCCTCCTCCCAAGTG-GGAAGCTGAAGCACCAA-GTACTGACTCAGC--AGTCCCTGACCTCA-CATCCATGGAAATCTAGTGACATCTGCTGGACACAT", ) self.assertEqual( alignment.sequences[6].annotations["quality"], "9998999999897966589999999999967689989799789997987889999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999", ) self.assertEqual(alignment.sequences[6].annotations["leftStatus"], "N") self.assertEqual(alignment.sequences[6].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[6].annotations["rightStatus"], "I") self.assertEqual(alignment.sequences[6].annotations["rightCount"], 7564) self.assertEqual(len(alignment.sequences), 7) self.assertNotIn("empty", alignment.annotations) self.assertEqual( str(alignment), """\ mm9.chr10 3012828 TTTGCATAGACTCTCTTGGCAACAAAATAACGTTATATTTAAACATCCATTAAAATAATG cavPor2.s 39417 -----GTGGGATGTCTTGACAGCTAAATAGTcttatatttaagcatttatGAAAATAATG otoGar1.s 178634 -----GTGGACATTCGTGACAGGCAAATAGTGTTCTATTTAAACATTTGTTGAAATGATA ponAbe2.c 158049472 -----GTGGACTATCCTGACAACCAAATAGCGTTATATTTAAACATTTATGAAAATAATA panTro2.c 157528852 -----GCGGACTATCTTGACAACCAAATAGCGTTATATTTAAACGTTTATGAAAATAATA hg18.chr6 155038780 -----GTGGACTATCTTGACAACCAAATAGCGTTATATTTAAACGTTTGTGAAAATAATA echTel1.s 87492 TTGGGGTGGATGCTCTTGGCAGTCACACAGTGCTCTATTTTAGGATTTACTAGAACAATG mm9.chr10 3012888 CACTTAGCACAGCCTGCCCTGAGGGAT----GAACACT--ATTGTTAA-AGAACTATTCC cavPor2.s 39362 AGGTTATCATGGTTCGCTCTAGTAGCTCTGAGACCTTT--ATTGTCAGCAAAGCTGTTTA otoGar1.s 178579 AACTTAGCTCAGCC--CCTT---AGAAGTG-AGAGGCT--ACTGTCAGGGAAGCGGTTTT ponAbe2.c 158049417 AGCTTAGCATAACCTGCCTTGACAGATGTG-GTATGC-------CTAGTGAAGTTGTTTA panTro2.c 157528797 AGCTTAGCATAACCTGCCTTGACAGATGTG-GTATGC-------CTAGTGAAGTTGCTTA hg18.chr6 155038725 AGCTTAGCATAACCTGCCTTGACAGATGTG-GTATGC-------CTAGTGAAGTTGCTTA echTel1.s 87552 AGTTTGTCATAACT-GCCTCCTCCCAAGTG-GGAAGCTGAAGCACCAA-GTACTGACTCA mm9.chr10 3012941 GCTAAGGCAGCAACCTCTGGATCTTCAGCATTCTGGCGCCATCTGCTGGTCATAT cavPor2.s 39304 GC--AGGAGGCAACTTCAGGTTCCGTGGGATTCTAGTGCCATCTGCTGGTCATAT otoGar1.s 178527 GCG-GAGCAGCAGCCTCAGGATCTGTGGGATTTTAGCGCCATCTGCTGGTCACAG ponAbe2.c 158049365 GCT-AAGGCTCAATCTCAGGATCTGTGGGACTCTAATGCCATCTGCTGGTCACAT panTro2.c 157528745 GCT-ATGGCTCAATCTCAGGATCTGTGGGACTCTAATGCCATCTGCTGGTCACAC hg18.chr6 155038673 GCT-ATGGCTCAATCTCAGGATCTGTGGGACTCTAATGCCATCTGCTGGTCACAC echTel1.s 87609 GC--AGTCCCTGACCTCA-CATCCATGGAAATCTAGTGACATCTGCTGGACACAT mm9.chr10 3012996 cavPor2.s 39251 otoGar1.s 178473 ponAbe2.c 158049311 panTro2.c 157528691 hg18.chr6 155038619 echTel1.s 87661 """, ) self.assertTrue( np.array_equal( alignment.coordinates, np.array( # fmt: off [[ 3012828, 3012833, 3012902, 3012903, 3012904, 3012908, 3012911, 3012915, 3012915, 3012915, 3012921, 3012922, 3012922, 3012926, 3012930, 3012930, 3012943, 3012944, 3012945, 3012959, 3012960, 3012996], [ 39417, 39417, 39348, 39347, 39346, 39342, 39339, 39335, 39332, 39331, 39325, 39324, 39324, 39320, 39316, 39315, 39302, 39302, 39302, 39288, 39287, 39251], [ 178634, 178634, 178565, 178565, 178565, 178561, 178561, 178557, 178554, 178554, 178548, 178547, 178547, 178543, 178539, 178538, 178525, 178524, 178524, 178510, 178509, 178473], [158049472, 158049472, 158049403, 158049402, 158049401, 158049397, 158049394, 158049390, 158049387, 158049387, 158049381, 158049381, 158049381, 158049381, 158049377, 158049376, 158049363, 158049362, 158049362, 158049348, 158049347, 158049311], [157528852, 157528852, 157528783, 157528782, 157528781, 157528777, 157528774, 157528770, 157528767, 157528767, 157528761, 157528761, 157528761, 157528761, 157528757, 157528756, 157528743, 157528742, 157528742, 157528728, 157528727, 157528691], [155038780, 155038780, 155038711, 155038710, 155038709, 155038705, 155038702, 155038698, 155038695, 155038695, 155038689, 155038689, 155038689, 155038689, 155038685, 155038684, 155038671, 155038670, 155038670, 155038656, 155038655, 155038619], [ 87492, 87497, 87566, 87566, 87567, 87571, 87574, 87578, 87581, 87581, 87587, 87588, 87590, 87594, 87598, 87598, 87611, 87611, 87611, 87625, 87625, 87661], ] # fmt: on ), ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.score, 98097) self.assertEqual(alignment.sequences[0].id, "mm9.chr10") self.assertEqual(len(alignment.sequences[0].seq), 129993255) self.assertEqual( alignment.sequences[0].seq[3012996 : 3012996 + 222], "AGATGTCTGCTGTGGAGACCTGGCCAACTTTGCTTTCTTCAAAAAGGCAACAGAAGGTAATCAGTTGAATGCCCACCATTAGGAAGGCGACCTCTAGTGCACAAACCTTGACATTTTCCCTTTTAATGGAATTTAACAGAAGTTCAGGATGTTCTTTGGGTAATTTACAATTAGGGGGCAAAAATCAAAAGTATTTCGAGCATATCAAAACTGTTAGCTATG", ) self.assertEqual( alignment[0], "AGATGTCTGCTGTGGAGA-------CCTGGCCAACTTTG----CTT--TCTTC-----AAAAAGGCAACAGAAGGTAATCAGTTGAATGCCCACCA-----TTAGGAAGGCGACCTCTAGTGCACAAACCTTGAC-ATTTTCCCTTTTAATGGAA-TTTAACAGAAGTTCAGGATGTTCTTTGGGTAATTTACAATT---A----GGGGGCAAAAATCAAAAGTATTTCGAGCATATCAAAACTGTTAGCTATG", ) self.assertEqual(alignment.sequences[1].id, "cavPor2.scaffold_290371") self.assertEqual(len(alignment.sequences[1].seq), 39932) self.assertEqual( alignment.sequences[1].seq[39074 : 39074 + 177], "AAATGcctctgcttttccttttctagctgtAAATTGTTTAAATGGAATTCTGAACCTGACAGAGTcgaagaaaaaaattgcaaagctTTTCCGCTAGAGGTCACTCTCCCCACTATGTGGTGTGGTCGGCTTTAGCGCGGAAGACTGGAGTTAGCCAGCCCGTGGCTGCAGACGTCA", ) self.assertEqual( alignment[1], "TGACGTCTGCAGCCACGG-------GCTGGCTAACTCCA--GTCTT--CCGCG-----CTAAAGCCGAC--------------------CACACCACATAGTGGGGAGAGTGACCTCTAGCGGAAAagctttgca-atttttttcttc----gAC-TCTGTCAG--GTTCAGAATTCCATTTAAACAATTTacagct---a----gaaaaggaaaagcagaggCATTT--------------------------", ) self.assertEqual( alignment.sequences[1].annotations["quality"], "999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999997999999999995699999999999336991774687", ) self.assertEqual(alignment.sequences[1].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[1].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[1].annotations["rightStatus"], "N") self.assertEqual(alignment.sequences[1].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[2].id, "hg18.chr6") self.assertEqual(len(alignment.sequences[2].seq), 170899992) self.assertEqual( alignment.sequences[2].seq[155038435 : 155038435 + 184], "ATACTCTTACCTCCCCCCACCATTACAAATTGTCTAAATGGCATTCTAAGCCTTTATGAATTCAATTAAAAAGAAAAATGCCAAGGCCTGCTCGCTAGAGGTCGCTCTCCTAACTATGGGGTCCTGTTAGTCTTATAGAGTAAGACAGCAGAGTAGGCCAAGAAAGTGATGGCAGCAGCCATCA", ) self.assertEqual( alignment[2], "TGATGGCTGCTGCCATCA---CTTTCTTGGCCTACTCTGCTGTCTT--ACTCT-----ATAAGACTAAC--------------------AGGACCCCATAGTTAGGAGAGCGACCTCTAGCGAGCAGGCCTTGGC-ATTTTTCTTTTTAATTGAA-TTCATAAA-GGCTTAGAATGCCATTTAGACAATTTGTAATG---GTGGGGGGAGGTAAGAGTAT----------------------------------", ) self.assertEqual(alignment.sequences[2].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[2].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[2].annotations["rightStatus"], "I") self.assertEqual(alignment.sequences[2].annotations["rightCount"], 14) self.assertEqual(alignment.sequences[3].id, "panTro2.chr6") self.assertEqual(len(alignment.sequences[3].seq), 173908612) self.assertEqual( alignment.sequences[3].seq[157528507 : 157528507 + 184], "ATACTCTTACCTCCCCCCACCATTACAAATTGTCTAAATGGCATTCTAAGCCTTTATGAATTTAATTAAAAAGAAAAATTCCAAGGCCTGCTCGCTAGAGGTCGCTCTCCTAACCATGGGGTCCTGTTAGTCTTATAGAATAAGACAGCAGAGTAGGCCAAGAAAGTGATGGCAGCAGCCATCA", ) self.assertEqual( alignment[3], "TGATGGCTGCTGCCATCA---CTTTCTTGGCCTACTCTGCTGTCTT--ATTCT-----ATAAGACTAAC--------------------AGGACCCCATGGTTAGGAGAGCGACCTCTAGCGAGCAGGCCTTGGA-ATTTTTCTTTTTAATTAAA-TTCATAAA-GGCTTAGAATGCCATTTAGACAATTTGTAATG---GTGGGGGGAGGTAAGAGTAT----------------------------------", ) self.assertEqual( alignment.sequences[3].annotations["quality"], "9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999", ) self.assertEqual(alignment.sequences[3].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[3].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[3].annotations["rightStatus"], "I") self.assertEqual(alignment.sequences[3].annotations["rightCount"], 14) self.assertEqual(alignment.sequences[4].id, "ponAbe2.chr6") self.assertEqual(len(alignment.sequences[4].seq), 174210431) self.assertEqual( alignment.sequences[4].seq[158049094 : 158049094 + 217], "CATCATTGACAGGTTTGAATACATTCAATATTTATACTCTTACCTCCCCCCACCATTACAAATTGTCTAAATGGCATTCTAAGCCTTTATGAATTCAATTAAAAAGAAAAATTCCAAGGCCTGCTCGCTAGAGGTCGCTCTCCTAACTATGGGGTCCTGTTAGTCTTATAGAGTAAGACGGCCTAGTAGGCCAAGAAAGTGATGGCAGCAGCCATCA", ) self.assertEqual( alignment[4], "TGATGGCTGCTGCCATCA---CTTTCTTGGCCTACTAGGCCGTCTT--ACTCT-----ATAAGACTAAC--------------------AGGACCCCATAGTTAGGAGAGCGACCTCTAGCGAGCAGGCCTTGGA-ATTTTTCTTTTTAATTGAA-TTCATAAA-GGCTTAGAATGCCATTTAGACAATTTGTAATG---GTGGGGGGAGGTAAGAGTATAAATATTGAATGTAT-TCAAACCTGTCAATGATG", ) self.assertEqual(alignment.sequences[4].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[4].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[4].annotations["rightStatus"], "I") self.assertEqual(alignment.sequences[4].annotations["rightCount"], 2) self.assertEqual(alignment.sequences[5].id, "otoGar1.scaffold_334.1-359464") self.assertEqual(len(alignment.sequences[5].seq), 359464) self.assertEqual( alignment.sequences[5].seq[178247 : 178247 + 226], "TAACAAGGCTGAATGCCAGCAATATTTGCACTCTCAGGTCCCCACACATACACTATGAATTGTCTAACTTGCATTTTGAGCCGTTGTAAAATTCAATTAAAAAGAAAAAAATCCAAGGCTTGTTCACCAGAGGTCGCTCTAGTAACTGCAGGGTCCGATTTTTCTTTTGTTGCAGAATTTAAGACGGTGGAGTTGGCAGGGAAAGCGGTGGTGGCGGCGGCCGTCC", ) self.assertEqual( alignment[5], "GGACGGCCGCCGCCACCACCGCTTTCCCTGCCAACTCCACCGTCTTAAATTCTGCAACAAAAGAAAAAT--------------------CGGACCCTGCAGTTACTAGAGCGACCTCTGGTGAACAAGCCTTGGATTTTTTTCTTTTTAATTGAATTTTACAAC-GGCTCAAAATGCAAGTTAGACAATTCATAGTGTATGTGTGGGGACCTGAGAGTGCAAATATTGCTGGCAT-TCAGCCTTGTTA------", ) self.assertEqual( alignment.sequences[5].annotations["quality"], "9999989999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999699999999999999999999999999999999999999", ) self.assertEqual(alignment.sequences[5].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[5].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[5].annotations["rightStatus"], "I") self.assertEqual(alignment.sequences[5].annotations["rightCount"], 2931) self.assertEqual(alignment.sequences[6].id, "tupBel1.scaffold_114895.1-498454") self.assertEqual(len(alignment.sequences[6].seq), 498454) self.assertEqual( alignment.sequences[6].seq[331078 : 331078 + 159], "TAATTATAAGTTGTCTAAATGGCATTTGAACCTTTATAAATTCTGTTTTAAAGAAAAATTCCAAGGTTTGCTCACTAGAGGTCTCCTCTCCCGGAGGATCCAGTTTGTCTTTCGTTGAGAGAGCTGAGTGGTCCAAGAAAGTGACAGCTGTAGCCATCA", ) self.assertEqual( alignment[6], "TGATGGCTACAGCTGTCA---CTTTCTTGGACCACTCAGCTCTCTC--AAC-------GAAAGACAAAC--------------------TGGATCCTCCGG---GAGAGGAGACCTCTAGTGAGCAAACCTTGGA-ATTTTTCTTTAAAACAGAA-TTTATAAA-GGTTCA-AATGCCATTTAGACAACTTATAATT---A-----------------------------------------------------", ) self.assertEqual( alignment.sequences[6].annotations["quality"], "234233433332122232158211222021213444332433213323732111754365002326236241111233524253535324593652222413766453735782535545832457354545484445655854554657999679999", ) self.assertEqual(alignment.sequences[6].annotations["leftStatus"], "N") self.assertEqual(alignment.sequences[6].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[6].annotations["rightStatus"], "I") self.assertEqual(alignment.sequences[6].annotations["rightCount"], 4145) empty = alignment.annotations["empty"][0] (record, segment, status) = empty self.assertEqual(record.id, "echTel1.scaffold_288249") self.assertEqual(len(record.seq), 100002) self.assertEqual(segment, (87661, 95225)) self.assertEqual(status, "I") self.assertEqual(len(alignment.sequences), 7) self.assertEqual(len(alignment.annotations["empty"]), 1) self.assertEqual( str(alignment), """\ mm9.chr10 3012996 AGATGTCTGCTGTGGAGA-------CCTGGCCAACTTTG----CTT--TCTTC-----AA cavPor2.s 39251 TGACGTCTGCAGCCACGG-------GCTGGCTAACTCCA--GTCTT--CCGCG-----CT hg18.chr6 155038619 TGATGGCTGCTGCCATCA---CTTTCTTGGCCTACTCTGCTGTCTT--ACTCT-----AT panTro2.c 157528691 TGATGGCTGCTGCCATCA---CTTTCTTGGCCTACTCTGCTGTCTT--ATTCT-----AT ponAbe2.c 158049311 TGATGGCTGCTGCCATCA---CTTTCTTGGCCTACTAGGCCGTCTT--ACTCT-----AT otoGar1.s 178473 GGACGGCCGCCGCCACCACCGCTTTCCCTGCCAACTCCACCGTCTTAAATTCTGCAACAA tupBel1.s 331237 TGATGGCTACAGCTGTCA---CTTTCTTGGACCACTCAGCTCTCTC--AAC-------GA mm9.chr10 3013038 AAAGGCAACAGAAGGTAATCAGTTGAATGCCCACCA-----TTAGGAAGGCGACCTCTAG cavPor2.s 39207 AAAGCCGAC--------------------CACACCACATAGTGGGGAGAGTGACCTCTAG hg18.chr6 155038569 AAGACTAAC--------------------AGGACCCCATAGTTAGGAGAGCGACCTCTAG panTro2.c 157528641 AAGACTAAC--------------------AGGACCCCATGGTTAGGAGAGCGACCTCTAG ponAbe2.c 158049261 AAGACTAAC--------------------AGGACCCCATAGTTAGGAGAGCGACCTCTAG otoGar1.s 178413 AAGAAAAAT--------------------CGGACCCTGCAGTTACTAGAGCGACCTCTGG tupBel1.s 331189 AAGACAAAC--------------------TGGATCCTCCGG---GAGAGGAGACCTCTAG mm9.chr10 3013093 TGCACAAACCTTGAC-ATTTTCCCTTTTAATGGAA-TTTAACAGAAGTTCAGGATGTTCT cavPor2.s 39167 CGGAAAagctttgca-atttttttcttc----gAC-TCTGTCAG--GTTCAGAATTCCAT hg18.chr6 155038529 CGAGCAGGCCTTGGC-ATTTTTCTTTTTAATTGAA-TTCATAAA-GGCTTAGAATGCCAT panTro2.c 157528601 CGAGCAGGCCTTGGA-ATTTTTCTTTTTAATTAAA-TTCATAAA-GGCTTAGAATGCCAT ponAbe2.c 158049221 CGAGCAGGCCTTGGA-ATTTTTCTTTTTAATTGAA-TTCATAAA-GGCTTAGAATGCCAT otoGar1.s 178373 TGAACAAGCCTTGGATTTTTTTCTTTTTAATTGAATTTTACAAC-GGCTCAAAATGCAAG tupBel1.s 331152 TGAGCAAACCTTGGA-ATTTTTCTTTAAAACAGAA-TTTATAAA-GGTTCA-AATGCCAT mm9.chr10 3013151 TTGGGTAATTTACAATT---A----GGGGGCAAAAATCAAAAGTATTTCGAGCATATCAA cavPor2.s 39115 TTAAACAATTTacagct---a----gaaaaggaaaagcagaggCATTT------------ hg18.chr6 155038472 TTAGACAATTTGTAATG---GTGGGGGGAGGTAAGAGTAT-------------------- panTro2.c 157528544 TTAGACAATTTGTAATG---GTGGGGGGAGGTAAGAGTAT-------------------- ponAbe2.c 158049164 TTAGACAATTTGTAATG---GTGGGGGGAGGTAAGAGTATAAATATTGAATGTAT-TCAA otoGar1.s 178314 TTAGACAATTCATAGTGTATGTGTGGGGACCTGAGAGTGCAAATATTGCTGGCAT-TCAG tupBel1.s 331096 TTAGACAACTTATAATT---A--------------------------------------- mm9.chr10 3013204 AACTGTTAGCTATG 3013218 cavPor2.s 39074 -------------- 39074 hg18.chr6 155038435 -------------- 155038435 panTro2.c 157528507 -------------- 157528507 ponAbe2.c 158049108 ACCTGTCAATGATG 158049094 otoGar1.s 178255 CCTTGTTA------ 178247 tupBel1.s 331078 -------------- 331078 """, ) self.assertTrue( np.array_equal( alignment.coordinates, np.array( # fmt: off [[ 3012996, 3013014, 3013014, 3013014, 3013028, 3013028, 3013028, 3013031, 3013031, 3013034, 3013036, 3013036, 3013047, 3013067, 3013074, 3013074, 3013077, 3013108, 3013108, 3013120, 3013124, 3013127, 3013127, 3013135, 3013136, 3013137, 3013142, 3013143, 3013168, 3013168, 3013169, 3013169, 3013184, 3013192, 3013199, 3013200, 3013212, 3013218], [ 39251, 39233, 39233, 39233, 39219, 39219, 39217, 39214, 39214, 39211, 39209, 39209, 39198, 39198, 39191, 39186, 39183, 39152, 39152, 39140, 39140, 39137, 39137, 39129, 39129, 39129, 39124, 39123, 39098, 39098, 39097, 39097, 39082, 39074, 39074, 39074, 39074, 39074], [155038619, 155038601, 155038601, 155038597, 155038583, 155038581, 155038579, 155038576, 155038576, 155038573, 155038571, 155038571, 155038560, 155038560, 155038553, 155038548, 155038545, 155038514, 155038514, 155038502, 155038498, 155038495, 155038495, 155038487, 155038487, 155038486, 155038481, 155038480, 155038455, 155038455, 155038454, 155038450, 155038435, 155038435, 155038435, 155038435, 155038435, 155038435], [157528691, 157528673, 157528673, 157528669, 157528655, 157528653, 157528651, 157528648, 157528648, 157528645, 157528643, 157528643, 157528632, 157528632, 157528625, 157528620, 157528617, 157528586, 157528586, 157528574, 157528570, 157528567, 157528567, 157528559, 157528559, 157528558, 157528553, 157528552, 157528527, 157528527, 157528526, 157528522, 157528507, 157528507, 157528507, 157528507, 157528507, 157528507], [158049311, 158049293, 158049293, 158049289, 158049275, 158049273, 158049271, 158049268, 158049268, 158049265, 158049263, 158049263, 158049252, 158049252, 158049245, 158049240, 158049237, 158049206, 158049206, 158049194, 158049190, 158049187, 158049187, 158049179, 158049179, 158049178, 158049173, 158049172, 158049147, 158049147, 158049146, 158049142, 158049127, 158049119, 158049112, 158049112, 158049100, 158049094], [ 178473, 178455, 178452, 178448, 178434, 178432, 178430, 178427, 178425, 178422, 178420, 178415, 178404, 178404, 178397, 178392, 178389, 178358, 178357, 178345, 178341, 178338, 178337, 178329, 178329, 178328, 178323, 178322, 178297, 178294, 178293, 178289, 178274, 178266, 178259, 178259, 178247, 178247], [ 331237, 331219, 331219, 331215, 331201, 331199, 331197, 331194, 331194, 331191, 331191, 331191, 331180, 331180, 331173, 331168, 331168, 331137, 331137, 331125, 331121, 331118, 331118, 331110, 331110, 331109, 331104, 331104, 331079, 331079, 331078, 331078, 331078, 331078, 331078, 331078, 331078, 331078], ] # fmt: on ), ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.score, 0) self.assertEqual(alignment.sequences[0].id, "mm9.chr10") self.assertEqual(len(alignment.sequences[0].seq), 129993255) self.assertEqual( alignment.sequences[0].seq[3013218 : 3013218 + 219], "agccaggcgtggtggcacacacctttactcccagcatttggggggcagaggcaggtggatctgtgagtttgaggccagcctggtctacagagggagtctcaggacagccagagctacacagaaataacctgcctagaaaaacaaaacaaaacaaaacatcaaaactcaaaacaaaTAAAAAAAATAAAAAACCCAACCTAAACCAAATAACAAAACACT", ) self.assertEqual( alignment[0], "agccaggcgtggtggcacacacctttactcccagcatttggggggcagaggcaggtggatctgtgagtttgaggccagcctggtctacagagggagtctcaggacagccagagctacacagaaataacctgcctagaaaaacaaaacaaaacaaaacatcaaaactcaaaacaaaTAAAAAAAATAAAAAACCCAACCTAAACCAAATAACAAAACACT", ) empty = alignment.annotations["empty"][0] (record, segment, status) = empty self.assertEqual(record.id, "tupBel1.scaffold_114895.1-498454") self.assertEqual(len(record.seq), 498454) self.assertEqual(segment, (331078, 326933)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][1] (record, segment, status) = empty self.assertEqual(record.id, "echTel1.scaffold_288249") self.assertEqual(len(record.seq), 100002) self.assertEqual(segment, (87661, 95225)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][2] (record, segment, status) = empty self.assertEqual(record.id, "otoGar1.scaffold_334.1-359464") self.assertEqual(len(record.seq), 359464) self.assertEqual(segment, (178247, 175316)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][3] (record, segment, status) = empty self.assertEqual(record.id, "hg18.chr6") self.assertEqual(len(record.seq), 170899992) self.assertEqual(segment, (155038435, 155038421)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][4] (record, segment, status) = empty self.assertEqual(record.id, "panTro2.chr6") self.assertEqual(len(record.seq), 173908612) self.assertEqual(segment, (157528507, 157528493)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][5] (record, segment, status) = empty self.assertEqual(record.id, "ponAbe2.chr6") self.assertEqual(len(record.seq), 174210431) self.assertEqual(segment, (158049094, 158049092)) self.assertEqual(status, "I") self.assertEqual(len(alignment.sequences), 1) self.assertEqual(len(alignment.annotations["empty"]), 6) self.assertEqual( str(alignment), """\ mm9.chr10 3013218 agccaggcgtggtggcacacacctttactcccagcatttggggggcagaggcaggtggat mm9.chr10 3013278 ctgtgagtttgaggccagcctggtctacagagggagtctcaggacagccagagctacaca mm9.chr10 3013338 gaaataacctgcctagaaaaacaaaacaaaacaaaacatcaaaactcaaaacaaaTAAAA mm9.chr10 3013398 AAAATAAAAAACCCAACCTAAACCAAATAACAAAACACT 3013437 """, ) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[3013218, 3013437]])) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['a', 'g', 'c', 'c', 'a', 'g', 'g', 'c', 'g', 't', 'g', 'g', 't', 'g', 'g', 'c', 'a', 'c', 'a', 'c', 'a', 'c', 'c', 't', 't', 't', 'a', 'c', 't', 'c', 'c', 'c', 'a', 'g', 'c', 'a', 't', 't', 't', 'g', 'g', 'g', 'g', 'g', 'g', 'c', 'a', 'g', 'a', 'g', 'g', 'c', 'a', 'g', 'g', 't', 'g', 'g', 'a', 't', 'c', 't', 'g', 't', 'g', 'a', 'g', 't', 't', 't', 'g', 'a', 'g', 'g', 'c', 'c', 'a', 'g', 'c', 'c', 't', 'g', 'g', 't', 'c', 't', 'a', 'c', 'a', 'g', 'a', 'g', 'g', 'g', 'a', 'g', 't', 'c', 't', 'c', 'a', 'g', 'g', 'a', 'c', 'a', 'g', 'c', 'c', 'a', 'g', 'a', 'g', 'c', 't', 'a', 'c', 'a', 'c', 'a', 'g', 'a', 'a', 'a', 't', 'a', 'a', 'c', 'c', 't', 'g', 'c', 'c', 't', 'a', 'g', 'a', 'a', 'a', 'a', 'a', 'c', 'a', 'a', 'a', 'a', 'c', 'a', 'a', 'a', 'a', 'c', 'a', 'a', 'a', 'a', 'c', 'a', 't', 'c', 'a', 'a', 'a', 'a', 'c', 't', 'c', 'a', 'a', 'a', 'a', 'c', 'a', 'a', 'a', 'T', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A', 'T', 'A', 'A', 'A', 'A', 'A', 'A', 'C', 'C', 'C', 'A', 'A', 'C', 'C', 'T', 'A', 'A', 'A', 'C', 'C', 'A', 'A', 'A', 'T', 'A', 'A', 'C', 'A', 'A', 'A', 'A', 'C', 'A', 'C', 'T']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.score, 40604) self.assertEqual(alignment.sequences[0].id, "mm9.chr10") self.assertEqual(len(alignment.sequences[0].seq), 129993255) self.assertEqual( alignment.sequences[0].seq[3013437 : 3013437 + 166], "TCCAAAATGGTTAGCTATGCCCAACTCCTTTCACTCCAAGAAAATATCCTAACCATGTAAGAGAGCTAGCCTGTTGGTGGCAGCCAAGCCTGATGGTGGCAGACTAGATTGATGGTGCCAGACTACTTTATGGCTGTATCATTTTCCATTCATGTGTTGTGTTATA", ) self.assertEqual( alignment[0], "TCCAAAATGGTTAGCTATGCCCAACTCCTTTCACTCCAAGAAAATATCCTAACCATGTAAGAGAGCTAGCCTGTTGGTGGCAGCCAAGCCTGATGGTGGCAGACTAGATTGATGGTGCCAGACTACTTTATGGCTGTATCATTTTCCATTCATGTGTTGTGTTATA", ) self.assertEqual(alignment.sequences[1].id, "panTro2.chr6") self.assertEqual(len(alignment.sequences[1].seq), 173908612) self.assertEqual( alignment.sequences[1].seq[157528363 : 157528363 + 130], "TATCAAACAGCCCATGAATGCAAAACGATACACCCATAAAATAGGATGTAATCGCCAAAATCTAATTCTATTGCATCTAGAAGATCTTTATCCACAGTGAAAAGAGTTGAACATCATTGACAGGTTTGAA", ) self.assertEqual( alignment[1], "TTCAAACCTGTCAATGATGTTCAACTCTTTTCACTGTGGATAAAGATCTTCTAGATGCAATAGAATTAGATT------------------------------------TTGGCGATTACATCCTATTTTATGGGTGTATCGTTTTGCATTCATGGGCTGTTTGATA", ) self.assertEqual( alignment.sequences[1].annotations["quality"], "9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999099999999999999999999", ) self.assertEqual(alignment.sequences[1].annotations["leftStatus"], "I") self.assertEqual(alignment.sequences[1].annotations["leftCount"], 14) self.assertEqual(alignment.sequences[1].annotations["rightStatus"], "I") self.assertEqual(alignment.sequences[1].annotations["rightCount"], 9106) self.assertEqual(alignment.sequences[2].id, "hg18.chr6") self.assertEqual(len(alignment.sequences[2].seq), 170899992) self.assertEqual( alignment.sequences[2].seq[155038291 : 155038291 + 130], "TATCAAACAGCCCATGAATGCAAAACGATACACCCATAAAATAGGATGTAATCGCCAAAATCTAATTCTATTGCATCTAGAAGATCTTTATCCACAGTGAAAAGAGTTGAACATCATTGACAGGTTTGAA", ) self.assertEqual( alignment[2], "TTCAAACCTGTCAATGATGTTCAACTCTTTTCACTGTGGATAAAGATCTTCTAGATGCAATAGAATTAGATT------------------------------------TTGGCGATTACATCCTATTTTATGGGTGTATCGTTTTGCATTCATGGGCTGTTTGATA", ) self.assertEqual(alignment.sequences[2].annotations["leftStatus"], "I") self.assertEqual(alignment.sequences[2].annotations["leftCount"], 14) self.assertEqual(alignment.sequences[2].annotations["rightStatus"], "I") self.assertEqual(alignment.sequences[2].annotations["rightCount"], 9085) self.assertEqual(alignment.sequences[3].id, "ponAbe2.chr6") self.assertEqual(len(alignment.sequences[3].seq), 174210431) self.assertEqual( alignment.sequences[3].seq[158048983 : 158048983 + 109], "TATCAAACAGCCCATGAATGCAAAACGATACACCCATAAAATAGGATGTAATCGCCAAAATCTAATTCTATTGCATCTAGAAGATCTTTATCCACAGTGAAAAGAGTTG", ) self.assertEqual( alignment[3], "---------------------CAACTCTTTTCACTGTGGATAAAGATCTTCTAGATGCAATAGAATTAGATT------------------------------------TTGGCGATTACATCCTATTTTATGGGTGTATCGTTTTGCATTCATGGGCTGTTTGATA", ) self.assertEqual(alignment.sequences[3].annotations["leftStatus"], "I") self.assertEqual(alignment.sequences[3].annotations["leftCount"], 2) self.assertEqual(alignment.sequences[3].annotations["rightStatus"], "I") self.assertEqual(alignment.sequences[3].annotations["rightCount"], 8044) empty = alignment.annotations["empty"][0] (record, segment, status) = empty self.assertEqual(record.id, "tupBel1.scaffold_114895.1-498454") self.assertEqual(len(record.seq), 498454) self.assertEqual(segment, (331078, 326933)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][1] (record, segment, status) = empty self.assertEqual(record.id, "echTel1.scaffold_288249") self.assertEqual(len(record.seq), 100002) self.assertEqual(segment, (87661, 95225)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][2] (record, segment, status) = empty self.assertEqual(record.id, "otoGar1.scaffold_334.1-359464") self.assertEqual(len(record.seq), 359464) self.assertEqual(segment, (178247, 175316)) self.assertEqual(status, "I") self.assertEqual(len(alignment.sequences), 4) self.assertEqual(len(alignment.annotations["empty"]), 3) self.assertEqual( str(alignment), """\ mm9.chr10 3013437 TCCAAAATGGTTAGCTATGCCCAACTCCTTTCACTCCAAGAAAATATCCTAACCATGTAA panTro2.c 157528493 TTCAAACCTGTCAATGATGTTCAACTCTTTTCACTGTGGATAAAGATCTTCTAGATGCAA hg18.chr6 155038421 TTCAAACCTGTCAATGATGTTCAACTCTTTTCACTGTGGATAAAGATCTTCTAGATGCAA ponAbe2.c 158049092 ---------------------CAACTCTTTTCACTGTGGATAAAGATCTTCTAGATGCAA mm9.chr10 3013497 GAGAGCTAGCCTGTTGGTGGCAGCCAAGCCTGATGGTGGCAGACTAGATTGATGGTGCCA panTro2.c 157528433 TAGAATTAGATT------------------------------------TTGGCGATTACA hg18.chr6 155038361 TAGAATTAGATT------------------------------------TTGGCGATTACA ponAbe2.c 158049053 TAGAATTAGATT------------------------------------TTGGCGATTACA mm9.chr10 3013557 GACTACTTTATGGCTGTATCATTTTCCATTCATGTGTTGTGTTATA 3013603 panTro2.c 157528409 TCCTATTTTATGGGTGTATCGTTTTGCATTCATGGGCTGTTTGATA 157528363 hg18.chr6 155038337 TCCTATTTTATGGGTGTATCGTTTTGCATTCATGGGCTGTTTGATA 155038291 ponAbe2.c 158049029 TCCTATTTTATGGGTGTATCGTTTTGCATTCATGGGCTGTTTGATA 158048983 """, ) self.assertTrue( np.array_equal( alignment.coordinates, np.array( # fmt: off [[ 3013437, 3013458, 3013509, 3013545, 3013603], [157528493, 157528472, 157528421, 157528421, 157528363], [155038421, 155038400, 155038349, 155038349, 155038291], [158049092, 158049092, 158049041, 158049041, 158048983], ] # fmt: on ), ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['T', 'C', 'C', 'A', 'A', 'A', 'A', 'T', 'G', 'G', 'T', 'T', 'A', 'G', 'C', 'T', 'A', 'T', 'G', 'C', 'C', 'C', 'A', 'A', 'C', 'T', 'C', 'C', 'T', 'T', 'T', 'C', 'A', 'C', 'T', 'C', 'C', 'A', 'A', 'G', 'A', 'A', 'A', 'A', 'T', 'A', 'T', 'C', 'C', 'T', 'A', 'A', 'C', 'C', 'A', 'T', 'G', 'T', 'A', 'A', 'G', 'A', 'G', 'A', 'G', 'C', 'T', 'A', 'G', 'C', 'C', 'T', 'G', 'T', 'T', 'G', 'G', 'T', 'G', 'G', 'C', 'A', 'G', 'C', 'C', 'A', 'A', 'G', 'C', 'C', 'T', 'G', 'A', 'T', 'G', 'G', 'T', 'G', 'G', 'C', 'A', 'G', 'A', 'C', 'T', 'A', 'G', 'A', 'T', 'T', 'G', 'A', 'T', 'G', 'G', 'T', 'G', 'C', 'C', 'A', 'G', 'A', 'C', 'T', 'A', 'C', 'T', 'T', 'T', 'A', 'T', 'G', 'G', 'C', 'T', 'G', 'T', 'A', 'T', 'C', 'A', 'T', 'T', 'T', 'T', 'C', 'C', 'A', 'T', 'T', 'C', 'A', 'T', 'G', 'T', 'G', 'T', 'T', 'G', 'T', 'G', 'T', 'T', 'A', 'T', 'A'], ['T', 'T', 'C', 'A', 'A', 'A', 'C', 'C', 'T', 'G', 'T', 'C', 'A', 'A', 'T', 'G', 'A', 'T', 'G', 'T', 'T', 'C', 'A', 'A', 'C', 'T', 'C', 'T', 'T', 'T', 'T', 'C', 'A', 'C', 'T', 'G', 'T', 'G', 'G', 'A', 'T', 'A', 'A', 'A', 'G', 'A', 'T', 'C', 'T', 'T', 'C', 'T', 'A', 'G', 'A', 'T', 'G', 'C', 'A', 'A', 'T', 'A', 'G', 'A', 'A', 'T', 'T', 'A', 'G', 'A', 'T', 'T', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'T', 'T', 'G', 'G', 'C', 'G', 'A', 'T', 'T', 'A', 'C', 'A', 'T', 'C', 'C', 'T', 'A', 'T', 'T', 'T', 'T', 'A', 'T', 'G', 'G', 'G', 'T', 'G', 'T', 'A', 'T', 'C', 'G', 'T', 'T', 'T', 'T', 'G', 'C', 'A', 'T', 'T', 'C', 'A', 'T', 'G', 'G', 'G', 'C', 'T', 'G', 'T', 'T', 'T', 'G', 'A', 'T', 'A'], ['T', 'T', 'C', 'A', 'A', 'A', 'C', 'C', 'T', 'G', 'T', 'C', 'A', 'A', 'T', 'G', 'A', 'T', 'G', 'T', 'T', 'C', 'A', 'A', 'C', 'T', 'C', 'T', 'T', 'T', 'T', 'C', 'A', 'C', 'T', 'G', 'T', 'G', 'G', 'A', 'T', 'A', 'A', 'A', 'G', 'A', 'T', 'C', 'T', 'T', 'C', 'T', 'A', 'G', 'A', 'T', 'G', 'C', 'A', 'A', 'T', 'A', 'G', 'A', 'A', 'T', 'T', 'A', 'G', 'A', 'T', 'T', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'T', 'T', 'G', 'G', 'C', 'G', 'A', 'T', 'T', 'A', 'C', 'A', 'T', 'C', 'C', 'T', 'A', 'T', 'T', 'T', 'T', 'A', 'T', 'G', 'G', 'G', 'T', 'G', 'T', 'A', 'T', 'C', 'G', 'T', 'T', 'T', 'T', 'G', 'C', 'A', 'T', 'T', 'C', 'A', 'T', 'G', 'G', 'G', 'C', 'T', 'G', 'T', 'T', 'T', 'G', 'A', 'T', 'A'], ['-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'C', 'A', 'A', 'C', 'T', 'C', 'T', 'T', 'T', 'T', 'C', 'A', 'C', 'T', 'G', 'T', 'G', 'G', 'A', 'T', 'A', 'A', 'A', 'G', 'A', 'T', 'C', 'T', 'T', 'C', 'T', 'A', 'G', 'A', 'T', 'G', 'C', 'A', 'A', 'T', 'A', 'G', 'A', 'A', 'T', 'T', 'A', 'G', 'A', 'T', 'T', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'T', 'T', 'G', 'G', 'C', 'G', 'A', 'T', 'T', 'A', 'C', 'A', 'T', 'C', 'C', 'T', 'A', 'T', 'T', 'T', 'T', 'A', 'T', 'G', 'G', 'G', 'T', 'G', 'T', 'A', 'T', 'C', 'G', 'T', 'T', 'T', 'T', 'G', 'C', 'A', 'T', 'T', 'C', 'A', 'T', 'G', 'G', 'G', 'C', 'T', 'G', 'T', 'T', 'T', 'G', 'A', 'T', 'A']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.score, 0) self.assertEqual(alignment.sequences[0].id, "mm9.chr10") self.assertEqual(len(alignment.sequences[0].seq), 129993255) self.assertEqual( alignment.sequences[0].seq[3013603 : 3013603 + 1041], "CCTTCTTAAGAACACTAGACTCAggactggggagatggctcagcagttaagaatcggtgctgttaagagtgggagacaagtttggttcccagctcccacattggtcagctcacagccacccgtaactctaagatggtacacacctttaatcccaggagacagaggcaatcagatctgagttcaagattcagcctgagacagagcatgttccaaattcaggcatggtgggtcatacctttaatatgggacataccttctgctggaggcctacctaaggacaacggagaaaggaagtattcgttcttctcctgcttgcacttacttgccagcgcatctactggaacccacttcttcaggattccagcttatacaggagaccagctgaaatatccagcctctcgggactgaacaagtactagagtctcagacttcccattcacagctgcccattgttggttggttgtactacagactgtaagtcattgtaataatttcccttaatatatagagacattatataagttctgtgactctagagaaccctgactagtacaCGTGGCTAACTAGAAAGctctggtatgtgcttacttaatgctgaggttttaggcatggccacggtgctctgcttcttatgtgggtgctgggaatgcagactcaggtcctcatgtgtatgcagcaaacacttcatacactcagctgcttccctaacccTATGCTTGTGTCTTATTACTAACTTGTGAAAAGCTTTGAGTTTATTTTCTATGTTTTCAACCACTTTCTTGAGTATGCTCAGCTCGTGGCTTTAAACTGGATTTCCCCCTAATATGTAATGACTATAAGTATTCCTTAAATAGGACACACTTTTGTTATACTTTTTGTTATCatataaaatatttcaaaaaaatttttttGCTATTTTTATCTTTGAGCCATTGGTCATTTTGACGTGTATCTCTTGATTTTTATAGATGGTAATATTTTATGTATTGCTAGCCAATCTCGTTTTCTTGTTTGCTTGCTTGTTTGTTTTGGTCAATGCAG", ) self.assertEqual( alignment[0], "CCTTCTTAAGAACACTAGACTCAggactggggagatggctcagcagttaagaatcggtgctgttaagagtgggagacaagtttggttcccagctcccacattggtcagctcacagccacccgtaactctaagatggtacacacctttaatcccaggagacagaggcaatcagatctgagttcaagattcagcctgagacagagcatgttccaaattcaggcatggtgggtcatacctttaatatgggacataccttctgctggaggcctacctaaggacaacggagaaaggaagtattcgttcttctcctgcttgcacttacttgccagcgcatctactggaacccacttcttcaggattccagcttatacaggagaccagctgaaatatccagcctctcgggactgaacaagtactagagtctcagacttcccattcacagctgcccattgttggttggttgtactacagactgtaagtcattgtaataatttcccttaatatatagagacattatataagttctgtgactctagagaaccctgactagtacaCGTGGCTAACTAGAAAGctctggtatgtgcttacttaatgctgaggttttaggcatggccacggtgctctgcttcttatgtgggtgctgggaatgcagactcaggtcctcatgtgtatgcagcaaacacttcatacactcagctgcttccctaacccTATGCTTGTGTCTTATTACTAACTTGTGAAAAGCTTTGAGTTTATTTTCTATGTTTTCAACCACTTTCTTGAGTATGCTCAGCTCGTGGCTTTAAACTGGATTTCCCCCTAATATGTAATGACTATAAGTATTCCTTAAATAGGACACACTTTTGTTATACTTTTTGTTATCatataaaatatttcaaaaaaatttttttGCTATTTTTATCTTTGAGCCATTGGTCATTTTGACGTGTATCTCTTGATTTTTATAGATGGTAATATTTTATGTATTGCTAGCCAATCTCGTTTTCTTGTTTGCTTGCTTGTTTGTTTTGGTCAATGCAG", ) empty = alignment.annotations["empty"][0] (record, segment, status) = empty self.assertEqual(record.id, "tupBel1.scaffold_114895.1-498454") self.assertEqual(len(record.seq), 498454) self.assertEqual(segment, (331078, 326933)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][1] (record, segment, status) = empty self.assertEqual(record.id, "echTel1.scaffold_288249") self.assertEqual(len(record.seq), 100002) self.assertEqual(segment, (87661, 95225)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][2] (record, segment, status) = empty self.assertEqual(record.id, "otoGar1.scaffold_334.1-359464") self.assertEqual(len(record.seq), 359464) self.assertEqual(segment, (178247, 175316)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][3] (record, segment, status) = empty self.assertEqual(record.id, "hg18.chr6") self.assertEqual(len(record.seq), 170899992) self.assertEqual(segment, (155038291, 155029206)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][4] (record, segment, status) = empty self.assertEqual(record.id, "panTro2.chr6") self.assertEqual(len(record.seq), 173908612) self.assertEqual(segment, (157528363, 157519257)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][5] (record, segment, status) = empty self.assertEqual(record.id, "ponAbe2.chr6") self.assertEqual(len(record.seq), 174210431) self.assertEqual(segment, (158048983, 158040939)) self.assertEqual(status, "I") self.assertEqual(len(alignment.sequences), 1) self.assertEqual(len(alignment.annotations["empty"]), 6) self.assertEqual( str(alignment), """\ mm9.chr10 3013603 CCTTCTTAAGAACACTAGACTCAggactggggagatggctcagcagttaagaatcggtgc mm9.chr10 3013663 tgttaagagtgggagacaagtttggttcccagctcccacattggtcagctcacagccacc mm9.chr10 3013723 cgtaactctaagatggtacacacctttaatcccaggagacagaggcaatcagatctgagt mm9.chr10 3013783 tcaagattcagcctgagacagagcatgttccaaattcaggcatggtgggtcataccttta mm9.chr10 3013843 atatgggacataccttctgctggaggcctacctaaggacaacggagaaaggaagtattcg mm9.chr10 3013903 ttcttctcctgcttgcacttacttgccagcgcatctactggaacccacttcttcaggatt mm9.chr10 3013963 ccagcttatacaggagaccagctgaaatatccagcctctcgggactgaacaagtactaga mm9.chr10 3014023 gtctcagacttcccattcacagctgcccattgttggttggttgtactacagactgtaagt mm9.chr10 3014083 cattgtaataatttcccttaatatatagagacattatataagttctgtgactctagagaa mm9.chr10 3014143 ccctgactagtacaCGTGGCTAACTAGAAAGctctggtatgtgcttacttaatgctgagg mm9.chr10 3014203 ttttaggcatggccacggtgctctgcttcttatgtgggtgctgggaatgcagactcaggt mm9.chr10 3014263 cctcatgtgtatgcagcaaacacttcatacactcagctgcttccctaacccTATGCTTGT mm9.chr10 3014323 GTCTTATTACTAACTTGTGAAAAGCTTTGAGTTTATTTTCTATGTTTTCAACCACTTTCT mm9.chr10 3014383 TGAGTATGCTCAGCTCGTGGCTTTAAACTGGATTTCCCCCTAATATGTAATGACTATAAG mm9.chr10 3014443 TATTCCTTAAATAGGACACACTTTTGTTATACTTTTTGTTATCatataaaatatttcaaa mm9.chr10 3014503 aaaatttttttGCTATTTTTATCTTTGAGCCATTGGTCATTTTGACGTGTATCTCTTGAT mm9.chr10 3014563 TTTTATAGATGGTAATATTTTATGTATTGCTAGCCAATCTCGTTTTCTTGTTTGCTTGCT mm9.chr10 3014623 TGTTTGTTTTGGTCAATGCAG 3014644 """, ) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[3013603, 3014644]])) ) alignment = next(alignments) self.assertAlmostEqual(alignment.score, 19159) self.assertEqual(alignment.sequences[0].id, "mm9.chr10") self.assertEqual(len(alignment.sequences[0].seq), 129993255) self.assertEqual( alignment.sequences[0].seq[3014644 : 3014644 + 45], "CCTGTACCCTTTGGTGAGAATTTTTGTTTCAGTGTTAAAAGTTTG", ) self.assertEqual( alignment[0], "CCTGTACC---CTTTGGTGAGAATTTTTGTTTCAGTGTTAAAAGTTTG" ) self.assertEqual(alignment.sequences[1].id, "hg18.chr6") self.assertEqual(len(alignment.sequences[1].seq), 170899992) self.assertEqual( alignment.sequences[1].seq[155029160 : 155029160 + 46], "AAAAGTTTAGGATTAAAACAAAATTCTCATAAAAGAAAGGTATAGG", ) self.assertEqual( alignment[1], "CCTATACCTTTCTTTTATGAGAA-TTTTGTTTTAATCCTAAAC-TTTT" ) self.assertEqual(alignment.sequences[1].annotations["leftStatus"], "I") self.assertEqual(alignment.sequences[1].annotations["leftCount"], 9085) self.assertEqual(alignment.sequences[1].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[1].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[2].id, "panTro2.chr6") self.assertEqual(len(alignment.sequences[2].seq), 173908612) self.assertEqual( alignment.sequences[2].seq[157519211 : 157519211 + 46], "AAAAGTTTAGGATTAAAACAAAATTCTCATAAAAGAAAGGTATAGG", ) self.assertEqual( alignment[2], "CCTATACCTTTCTTTTATGAGAA-TTTTGTTTTAATCCTAAAC-TTTT" ) self.assertEqual( alignment.sequences[2].annotations["quality"], "9999999999999999999999999999999999999999999999", ) self.assertEqual(alignment.sequences[2].annotations["leftStatus"], "I") self.assertEqual(alignment.sequences[2].annotations["leftCount"], 9106) self.assertEqual(alignment.sequences[2].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[2].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[3].id, "calJac1.Contig6394") self.assertEqual(len(alignment.sequences[3].seq), 133105) self.assertEqual( alignment.sequences[3].seq[6182 : 6182 + 46], "CCTATACCTTTCTTTCATGAGAATTTTGTTTGAATCCTAAACTTTT", ) self.assertEqual( alignment[3], "CCTATACCTTTCTTTCATGAGAA-TTTTGTTTGAATCCTAAAC-TTTT" ) self.assertEqual(alignment.sequences[3].annotations["leftStatus"], "N") self.assertEqual(alignment.sequences[3].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[3].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[3].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[4].id, "loxAfr1.scaffold_75566") self.assertEqual(len(alignment.sequences[4].seq), 10574) self.assertEqual( alignment.sequences[4].seq[9373 : 9373 + 34], "GGAAGTTTTGAATTAAAGCATAATTCTAACCAAA", ) self.assertEqual( alignment[4], "------------TTTGGTTAGAA-TTATGCTTTAATTCAAAAC-TTCC" ) self.assertEqual( alignment.sequences[4].annotations["quality"], "9999969989999999999999998699989997", ) self.assertEqual(alignment.sequences[4].annotations["leftStatus"], "N") self.assertEqual(alignment.sequences[4].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[4].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[4].annotations["rightCount"], 0) empty = alignment.annotations["empty"][0] (record, segment, status) = empty self.assertEqual(record.id, "tupBel1.scaffold_114895.1-498454") self.assertEqual(len(record.seq), 498454) self.assertEqual(segment, (331078, 326933)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][1] (record, segment, status) = empty self.assertEqual(record.id, "echTel1.scaffold_288249") self.assertEqual(len(record.seq), 100002) self.assertEqual(segment, (87661, 95225)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][2] (record, segment, status) = empty self.assertEqual(record.id, "otoGar1.scaffold_334.1-359464") self.assertEqual(len(record.seq), 359464) self.assertEqual(segment, (178247, 175316)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][3] (record, segment, status) = empty self.assertEqual(record.id, "ponAbe2.chr6") self.assertEqual(len(record.seq), 174210431) self.assertEqual(segment, (158048983, 158040939)) self.assertEqual(status, "I") self.assertEqual(len(alignment.sequences), 5) self.assertEqual(len(alignment.annotations["empty"]), 4) self.assertEqual( str(alignment), """\ mm9.chr10 3014644 CCTGTACC---CTTTGGTGAGAATTTTTGTTTCAGTGTTAAAAGTTTG 3014689 hg18.chr6 155029206 CCTATACCTTTCTTTTATGAGAA-TTTTGTTTTAATCCTAAAC-TTTT 155029160 panTro2.c 157519257 CCTATACCTTTCTTTTATGAGAA-TTTTGTTTTAATCCTAAAC-TTTT 157519211 calJac1.C 6182 CCTATACCTTTCTTTCATGAGAA-TTTTGTTTGAATCCTAAAC-TTTT 6228 loxAfr1.s 9407 ------------TTTGGTTAGAA-TTATGCTTTAATTCAAAAC-TTCC 9373 """, ) self.assertTrue( np.array_equal( alignment.coordinates, np.array( # fmt: off [[ 3014644, 3014652, 3014652, 3014653, 3014664, 3014665, 3014684, 3014685, 3014689], [155029206, 155029198, 155029195, 155029194, 155029183, 155029183, 155029164, 155029164, 155029160], [157519257, 157519249, 157519246, 157519245, 157519234, 157519234, 157519215, 157519215, 157519211], [ 6182, 6190, 6193, 6194, 6205, 6205, 6224, 6224, 6228], [ 9407, 9407, 9407, 9407, 9396, 9396, 9377, 9377, 9373], ] # fmt: on ), ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['C', 'C', 'T', 'G', 'T', 'A', 'C', 'C', '-', '-', '-', 'C', 'T', 'T', 'T', 'G', 'G', 'T', 'G', 'A', 'G', 'A', 'A', 'T', 'T', 'T', 'T', 'T', 'G', 'T', 'T', 'T', 'C', 'A', 'G', 'T', 'G', 'T', 'T', 'A', 'A', 'A', 'A', 'G', 'T', 'T', 'T', 'G'], ['C', 'C', 'T', 'A', 'T', 'A', 'C', 'C', 'T', 'T', 'T', 'C', 'T', 'T', 'T', 'T', 'A', 'T', 'G', 'A', 'G', 'A', 'A', '-', 'T', 'T', 'T', 'T', 'G', 'T', 'T', 'T', 'T', 'A', 'A', 'T', 'C', 'C', 'T', 'A', 'A', 'A', 'C', '-', 'T', 'T', 'T', 'T'], ['C', 'C', 'T', 'A', 'T', 'A', 'C', 'C', 'T', 'T', 'T', 'C', 'T', 'T', 'T', 'T', 'A', 'T', 'G', 'A', 'G', 'A', 'A', '-', 'T', 'T', 'T', 'T', 'G', 'T', 'T', 'T', 'T', 'A', 'A', 'T', 'C', 'C', 'T', 'A', 'A', 'A', 'C', '-', 'T', 'T', 'T', 'T'], ['C', 'C', 'T', 'A', 'T', 'A', 'C', 'C', 'T', 'T', 'T', 'C', 'T', 'T', 'T', 'C', 'A', 'T', 'G', 'A', 'G', 'A', 'A', '-', 'T', 'T', 'T', 'T', 'G', 'T', 'T', 'T', 'G', 'A', 'A', 'T', 'C', 'C', 'T', 'A', 'A', 'A', 'C', '-', 'T', 'T', 'T', 'T'], ['-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'T', 'T', 'T', 'G', 'G', 'T', 'T', 'A', 'G', 'A', 'A', '-', 'T', 'T', 'A', 'T', 'G', 'C', 'T', 'T', 'T', 'A', 'A', 'T', 'T', 'C', 'A', 'A', 'A', 'A', 'C', '-', 'T', 'T', 'C', 'C']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.score, 40840) self.assertEqual(alignment.sequences[0].id, "mm9.chr10") self.assertEqual(len(alignment.sequences[0].seq), 129993255) self.assertEqual( alignment.sequences[0].seq[3014689 : 3014689 + 53], "GGGAGCATAAAACTCTAAATCTGCTAAATGTCTTGTCCCTTTGGAAAGAGTTG", ) self.assertEqual( alignment[0], "GGGAGCATAAAACTCTAAATCTGCTAAATGTCTTGTCCCT-TTGGAAAGAGTTG" ) self.assertEqual(alignment.sequences[1].id, "hg18.chr6") self.assertEqual(len(alignment.sequences[1].seq), 170899992) self.assertEqual( alignment.sequences[1].seq[155029107 : 155029107 + 53], "CCACTATTTCCCAAAAGATTAGATATTTCACAGATTAAATGGTTTATGATCCC", ) self.assertEqual( alignment[1], "GGGATCATAAACCATTTAATCTGTGAAATATCTAATCTTT-TGGGAAATAGTGG" ) self.assertEqual(alignment.sequences[1].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[1].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[1].annotations["rightStatus"], "I") self.assertEqual(alignment.sequences[1].annotations["rightCount"], 401) self.assertEqual(alignment.sequences[2].id, "panTro2.chr6") self.assertEqual(len(alignment.sequences[2].seq), 173908612) self.assertEqual( alignment.sequences[2].seq[157519158 : 157519158 + 53], "CCACTATTTCCCAAAAGATTAGATATTTCACAGATTAAATGGTTTATGATCCC", ) self.assertEqual( alignment[2], "GGGATCATAAACCATTTAATCTGTGAAATATCTAATCTTT-TGGGAAATAGTGG" ) self.assertEqual( alignment.sequences[2].annotations["quality"], "99999999999999999999999999999999999999999999999999999", ) self.assertEqual(alignment.sequences[2].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[2].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[2].annotations["rightStatus"], "I") self.assertEqual(alignment.sequences[2].annotations["rightCount"], 400) self.assertEqual(alignment.sequences[3].id, "calJac1.Contig6394") self.assertEqual(len(alignment.sequences[3].seq), 133105) self.assertEqual( alignment.sequences[3].seq[6228 : 6228 + 53], "GGGATCATAAGCCATTTAATCTGTGAAATGTGAAATCTTTTGGGAAACAGTGG", ) self.assertEqual( alignment[3], "GGGATCATAAGCCATTTAATCTGTGAAATGTGAAATCTTT-TGGGAAACAGTGG" ) self.assertEqual(alignment.sequences[3].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[3].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[3].annotations["rightStatus"], "I") self.assertEqual(alignment.sequences[3].annotations["rightCount"], 2) self.assertEqual(alignment.sequences[4].id, "otoGar1.scaffold_334.1-359464") self.assertEqual(len(alignment.sequences[4].seq), 359464) self.assertEqual( alignment.sequences[4].seq[175264 : 175264 + 52], "CAGCTATTGCCCAAGTGATTTGATATTTCATAGATTAAAAGTTTATGCTTCC", ) self.assertEqual( alignment[4], "GGAAGCATAAACT-TTTAATCTATGAAATATCAAATCACT-TGGGCAATAGCTG" ) self.assertEqual( alignment.sequences[4].annotations["quality"], "7455455669566996656997698955556899975999984787795599", ) self.assertEqual(alignment.sequences[4].annotations["leftStatus"], "I") self.assertEqual(alignment.sequences[4].annotations["leftCount"], 2931) self.assertEqual(alignment.sequences[4].annotations["rightStatus"], "I") self.assertEqual(alignment.sequences[4].annotations["rightCount"], 2) self.assertEqual(alignment.sequences[5].id, "loxAfr1.scaffold_75566") self.assertEqual(len(alignment.sequences[5].seq), 10574) self.assertEqual( alignment.sequences[5].seq[9319 : 9319 + 54], "CAGCTTTTTCCCCTGAAGATTTGGCATTTCGCAGACTAAATGGTTTATACTCCC", ) self.assertEqual( alignment[5], "GGGAGTATAAACCATTTAGTCTGCGAAATGCCAAATCTTCAGGGGAAAAAGCTG" ) self.assertEqual( alignment.sequences[5].annotations["quality"], "899989799999979999999999999999797999999999999999999999", ) self.assertEqual(alignment.sequences[5].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[5].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[5].annotations["rightStatus"], "I") self.assertEqual(alignment.sequences[5].annotations["rightCount"], 2) empty = alignment.annotations["empty"][0] (record, segment, status) = empty self.assertEqual(record.id, "tupBel1.scaffold_114895.1-498454") self.assertEqual(len(record.seq), 498454) self.assertEqual(segment, (331078, 326933)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][1] (record, segment, status) = empty self.assertEqual(record.id, "echTel1.scaffold_288249") self.assertEqual(len(record.seq), 100002) self.assertEqual(segment, (87661, 95225)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][2] (record, segment, status) = empty self.assertEqual(record.id, "ponAbe2.chr6") self.assertEqual(len(record.seq), 174210431) self.assertEqual(segment, (158048983, 158040939)) self.assertEqual(status, "I") self.assertEqual(len(alignment.sequences), 6) self.assertEqual(len(alignment.annotations["empty"]), 3) self.assertEqual( str(alignment), """\ mm9.chr10 3014689 GGGAGCATAAAACTCTAAATCTGCTAAATGTCTTGTCCCT-TTGGAAAGAGTTG hg18.chr6 155029160 GGGATCATAAACCATTTAATCTGTGAAATATCTAATCTTT-TGGGAAATAGTGG panTro2.c 157519211 GGGATCATAAACCATTTAATCTGTGAAATATCTAATCTTT-TGGGAAATAGTGG calJac1.C 6228 GGGATCATAAGCCATTTAATCTGTGAAATGTGAAATCTTT-TGGGAAACAGTGG otoGar1.s 175316 GGAAGCATAAACT-TTTAATCTATGAAATATCAAATCACT-TGGGCAATAGCTG loxAfr1.s 9373 GGGAGTATAAACCATTTAGTCTGCGAAATGCCAAATCTTCAGGGGAAAAAGCTG mm9.chr10 3014742 hg18.chr6 155029107 panTro2.c 157519158 calJac1.C 6281 otoGar1.s 175264 loxAfr1.s 9319 """, ) self.assertTrue( np.array_equal( alignment.coordinates, np.array( # fmt: off [[ 3014689, 3014702, 3014703, 3014729, 3014729, 3014742], [155029160, 155029147, 155029146, 155029120, 155029120, 155029107], [157519211, 157519198, 157519197, 157519171, 157519171, 157519158], [ 6228, 6241, 6242, 6268, 6268, 6281], [ 175316, 175303, 175303, 175277, 175277, 175264], [ 9373, 9360, 9359, 9333, 9332, 9319], ] # fmt: on ), ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['G', 'G', 'G', 'A', 'G', 'C', 'A', 'T', 'A', 'A', 'A', 'A', 'C', 'T', 'C', 'T', 'A', 'A', 'A', 'T', 'C', 'T', 'G', 'C', 'T', 'A', 'A', 'A', 'T', 'G', 'T', 'C', 'T', 'T', 'G', 'T', 'C', 'C', 'C', 'T', '-', 'T', 'T', 'G', 'G', 'A', 'A', 'A', 'G', 'A', 'G', 'T', 'T', 'G'], ['G', 'G', 'G', 'A', 'T', 'C', 'A', 'T', 'A', 'A', 'A', 'C', 'C', 'A', 'T', 'T', 'T', 'A', 'A', 'T', 'C', 'T', 'G', 'T', 'G', 'A', 'A', 'A', 'T', 'A', 'T', 'C', 'T', 'A', 'A', 'T', 'C', 'T', 'T', 'T', '-', 'T', 'G', 'G', 'G', 'A', 'A', 'A', 'T', 'A', 'G', 'T', 'G', 'G'], ['G', 'G', 'G', 'A', 'T', 'C', 'A', 'T', 'A', 'A', 'A', 'C', 'C', 'A', 'T', 'T', 'T', 'A', 'A', 'T', 'C', 'T', 'G', 'T', 'G', 'A', 'A', 'A', 'T', 'A', 'T', 'C', 'T', 'A', 'A', 'T', 'C', 'T', 'T', 'T', '-', 'T', 'G', 'G', 'G', 'A', 'A', 'A', 'T', 'A', 'G', 'T', 'G', 'G'], ['G', 'G', 'G', 'A', 'T', 'C', 'A', 'T', 'A', 'A', 'G', 'C', 'C', 'A', 'T', 'T', 'T', 'A', 'A', 'T', 'C', 'T', 'G', 'T', 'G', 'A', 'A', 'A', 'T', 'G', 'T', 'G', 'A', 'A', 'A', 'T', 'C', 'T', 'T', 'T', '-', 'T', 'G', 'G', 'G', 'A', 'A', 'A', 'C', 'A', 'G', 'T', 'G', 'G'], ['G', 'G', 'A', 'A', 'G', 'C', 'A', 'T', 'A', 'A', 'A', 'C', 'T', '-', 'T', 'T', 'T', 'A', 'A', 'T', 'C', 'T', 'A', 'T', 'G', 'A', 'A', 'A', 'T', 'A', 'T', 'C', 'A', 'A', 'A', 'T', 'C', 'A', 'C', 'T', '-', 'T', 'G', 'G', 'G', 'C', 'A', 'A', 'T', 'A', 'G', 'C', 'T', 'G'], ['G', 'G', 'G', 'A', 'G', 'T', 'A', 'T', 'A', 'A', 'A', 'C', 'C', 'A', 'T', 'T', 'T', 'A', 'G', 'T', 'C', 'T', 'G', 'C', 'G', 'A', 'A', 'A', 'T', 'G', 'C', 'C', 'A', 'A', 'A', 'T', 'C', 'T', 'T', 'C', 'A', 'G', 'G', 'G', 'G', 'A', 'A', 'A', 'A', 'A', 'G', 'C', 'T', 'G']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.score, 411) self.assertEqual(alignment.sequences[0].id, "mm9.chr10") self.assertEqual(len(alignment.sequences[0].seq), 129993255) self.assertEqual( alignment.sequences[0].seq[3014742 : 3014742 + 36], "AAGTTCCCTCCATAATTCCTTCCTCCCACCCCCACA", ) self.assertEqual(alignment[0], "AAGTTCCCTCCATAATTCCTTCCTCCCACCCCCACA") self.assertEqual(alignment.sequences[1].id, "calJac1.Contig6394") self.assertEqual(len(alignment.sequences[1].seq), 133105) self.assertEqual( alignment.sequences[1].seq[6283 : 6283 + 28], "AAATGTATGATCTCCCCATCCTGCCCTG" ) self.assertEqual(alignment[1], "AAATGTA-----TGATCTCCCCATCCTGCCCTG---") self.assertEqual(alignment.sequences[1].annotations["leftStatus"], "I") self.assertEqual(alignment.sequences[1].annotations["leftCount"], 2) self.assertEqual(alignment.sequences[1].annotations["rightStatus"], "I") self.assertEqual(alignment.sequences[1].annotations["rightCount"], 54) self.assertEqual(alignment.sequences[2].id, "otoGar1.scaffold_334.1-359464") self.assertEqual(len(alignment.sequences[2].seq), 359464) self.assertEqual( alignment.sequences[2].seq[175231 : 175231 + 31], "TGCACGGAGGGGGTGAGGGCATCAGAAATCT", ) self.assertEqual(alignment[2], "AGATTTC-----TGATGCCCTCACCCCCTCCGTGCA") self.assertEqual( alignment.sequences[2].annotations["quality"], "9996999965974999999999999999999", ) self.assertEqual(alignment.sequences[2].annotations["leftStatus"], "I") self.assertEqual(alignment.sequences[2].annotations["leftCount"], 2) self.assertEqual(alignment.sequences[2].annotations["rightStatus"], "I") self.assertEqual(alignment.sequences[2].annotations["rightCount"], 24) self.assertEqual(alignment.sequences[3].id, "loxAfr1.scaffold_75566") self.assertEqual(len(alignment.sequences[3].seq), 10574) self.assertEqual( alignment.sequences[3].seq[9290 : 9290 + 27], "TGTGGGGGTGGGGGGTGGCATAAGCCT" ) self.assertEqual(alignment[3], "AGGCTTA-----TG----CCACCCCCCACCCCCACA") self.assertEqual( alignment.sequences[3].annotations["quality"], "999999999997999999999999999" ) self.assertEqual(alignment.sequences[3].annotations["leftStatus"], "I") self.assertEqual(alignment.sequences[3].annotations["leftCount"], 2) self.assertEqual(alignment.sequences[3].annotations["rightStatus"], "I") self.assertEqual(alignment.sequences[3].annotations["rightCount"], 25) empty = alignment.annotations["empty"][0] (record, segment, status) = empty self.assertEqual(record.id, "tupBel1.scaffold_114895.1-498454") self.assertEqual(len(record.seq), 498454) self.assertEqual(segment, (331078, 326933)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][1] (record, segment, status) = empty self.assertEqual(record.id, "echTel1.scaffold_288249") self.assertEqual(len(record.seq), 100002) self.assertEqual(segment, (87661, 95225)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][2] (record, segment, status) = empty self.assertEqual(record.id, "hg18.chr6") self.assertEqual(len(record.seq), 170899992) self.assertEqual(segment, (155029107, 155028706)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][3] (record, segment, status) = empty self.assertEqual(record.id, "panTro2.chr6") self.assertEqual(len(record.seq), 173908612) self.assertEqual(segment, (157519158, 157518758)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][4] (record, segment, status) = empty self.assertEqual(record.id, "ponAbe2.chr6") self.assertEqual(len(record.seq), 174210431) self.assertEqual(segment, (158048983, 158040939)) self.assertEqual(status, "I") self.assertEqual(len(alignment.sequences), 4) self.assertEqual(len(alignment.annotations["empty"]), 5) self.assertEqual( str(alignment), """\ mm9.chr10 3014742 AAGTTCCCTCCATAATTCCTTCCTCCCACCCCCACA 3014778 calJac1.C 6283 AAATGTA-----TGATCTCCCCATCCTGCCCTG--- 6311 otoGar1.s 175262 AGATTTC-----TGATGCCCTCACCCCCTCCGTGCA 175231 loxAfr1.s 9317 AGGCTTA-----TG----CCACCCCCCACCCCCACA 9290 """, ) self.assertTrue( np.array_equal( alignment.coordinates, np.array( # fmt: off [[3014742, 3014749, 3014754, 3014756, 3014760, 3014775, 3014778], [ 6283, 6290, 6290, 6292, 6296, 6311, 6311], [ 175262, 175255, 175255, 175253, 175249, 175234, 175231], [ 9317, 9310, 9310, 9308, 9308, 9293, 9290], ] # fmt: on ), ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['A', 'A', 'G', 'T', 'T', 'C', 'C', 'C', 'T', 'C', 'C', 'A', 'T', 'A', 'A', 'T', 'T', 'C', 'C', 'T', 'T', 'C', 'C', 'T', 'C', 'C', 'C', 'A', 'C', 'C', 'C', 'C', 'C', 'A', 'C', 'A'], ['A', 'A', 'A', 'T', 'G', 'T', 'A', '-', '-', '-', '-', '-', 'T', 'G', 'A', 'T', 'C', 'T', 'C', 'C', 'C', 'C', 'A', 'T', 'C', 'C', 'T', 'G', 'C', 'C', 'C', 'T', 'G', '-', '-', '-'], ['A', 'G', 'A', 'T', 'T', 'T', 'C', '-', '-', '-', '-', '-', 'T', 'G', 'A', 'T', 'G', 'C', 'C', 'C', 'T', 'C', 'A', 'C', 'C', 'C', 'C', 'C', 'T', 'C', 'C', 'G', 'T', 'G', 'C', 'A'], ['A', 'G', 'G', 'C', 'T', 'T', 'A', '-', '-', '-', '-', '-', 'T', 'G', '-', '-', '-', '-', 'C', 'C', 'A', 'C', 'C', 'C', 'C', 'C', 'C', 'A', 'C', 'C', 'C', 'C', 'C', 'A', 'C', 'A']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.score, 0) self.assertEqual(alignment.sequences[0].id, "mm9.chr10") self.assertEqual(len(alignment.sequences[0].seq), 129993255) self.assertEqual( alignment.sequences[0].seq[3014778 : 3014778 + 17], "TCCCATGTCCACCCTGA" ) self.assertEqual(alignment[0], "TCCCATGTCCACCCTGA") empty = alignment.annotations["empty"][0] (record, segment, status) = empty self.assertEqual(record.id, "loxAfr1.scaffold_75566") self.assertEqual(len(record.seq), 10574) self.assertEqual(segment, (9290, 9265)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][1] (record, segment, status) = empty self.assertEqual(record.id, "calJac1.Contig6394") self.assertEqual(len(record.seq), 133105) self.assertEqual(segment, (6311, 6365)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][2] (record, segment, status) = empty self.assertEqual(record.id, "tupBel1.scaffold_114895.1-498454") self.assertEqual(len(record.seq), 498454) self.assertEqual(segment, (331078, 326933)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][3] (record, segment, status) = empty self.assertEqual(record.id, "echTel1.scaffold_288249") self.assertEqual(len(record.seq), 100002) self.assertEqual(segment, (87661, 95225)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][4] (record, segment, status) = empty self.assertEqual(record.id, "otoGar1.scaffold_334.1-359464") self.assertEqual(len(record.seq), 359464) self.assertEqual(segment, (175231, 175207)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][5] (record, segment, status) = empty self.assertEqual(record.id, "hg18.chr6") self.assertEqual(len(record.seq), 170899992) self.assertEqual(segment, (155029107, 155028706)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][6] (record, segment, status) = empty self.assertEqual(record.id, "panTro2.chr6") self.assertEqual(len(record.seq), 173908612) self.assertEqual(segment, (157519158, 157518758)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][7] (record, segment, status) = empty self.assertEqual(record.id, "ponAbe2.chr6") self.assertEqual(len(record.seq), 174210431) self.assertEqual(segment, (158048983, 158040939)) self.assertEqual(status, "I") self.assertEqual(len(alignment.sequences), 1) self.assertEqual(len(alignment.annotations["empty"]), 8) self.assertEqual( str(alignment), """\ mm9.chr10 3014778 TCCCATGTCCACCCTGA 3014795 """, ) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[3014778, 3014795]])) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['T', 'C', 'C', 'C', 'A', 'T', 'G', 'T', 'C', 'C', 'A', 'C', 'C', 'C', 'T', 'G', 'A']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.score, -12243) self.assertEqual(alignment.sequences[0].id, "mm9.chr10") self.assertEqual(len(alignment.sequences[0].seq), 129993255) self.assertEqual( alignment.sequences[0].seq[3014795 : 3014795 + 47], "GTTTCAGGGGCAGCTCGCTGTTAGCAGCTAAGGCATGGTGTCTCTCA", ) self.assertEqual( alignment[0], "GTTTCAGGGGCAGCTCGCTG----------------TTAGCAG-CTAAGGCATGGTGTCTCTCA", ) self.assertEqual(alignment.sequences[1].id, "otoGar1.scaffold_334.1-359464") self.assertEqual(len(alignment.sequences[1].seq), 359464) self.assertEqual( alignment.sequences[1].seq[175147 : 175147 + 60], "AGAAATACACCCCACCTAAACCATCTAAACCAAATATCCATGACTGCAACTTGTTCCCGA", ) self.assertEqual( alignment[1], "---TCGGGAACAAGTTGCAGTCATGGATAT-TTGGTTTAGATGGTTTAGGTGGGGTGTATTTCT", ) self.assertEqual( alignment.sequences[1].annotations["quality"], "899999999999999999999999999999999999999999999999999999999999", ) self.assertEqual(alignment.sequences[1].annotations["leftStatus"], "I") self.assertEqual(alignment.sequences[1].annotations["leftCount"], 24) self.assertEqual(alignment.sequences[1].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[1].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[2].id, "calJac1.Contig6394") self.assertEqual(len(alignment.sequences[2].seq), 133105) self.assertEqual( alignment.sequences[2].seq[6365 : 6365 + 39], "GCCATGAATATTTTAGACATGCAGGTGTGGCGTGTTTCT", ) self.assertEqual( alignment[2], "-------------------GCCATGAATAT-----TTTAGAC-ATGCAGGTGTGGCGTGTTTCT", ) self.assertEqual(alignment.sequences[2].annotations["leftStatus"], "I") self.assertEqual(alignment.sequences[2].annotations["leftCount"], 54) self.assertEqual(alignment.sequences[2].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[2].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[3].id, "hg18.chr6") self.assertEqual(len(alignment.sequences[3].seq), 170899992) self.assertEqual( alignment.sequences[3].seq[155028686 : 155028686 + 20], "AGAAACATGCCACACCTGCt", ) self.assertEqual( alignment[3], "--------------------------------------------aGCAGGTGTGGCATGTTTCT", ) self.assertEqual(alignment.sequences[3].annotations["leftStatus"], "I") self.assertEqual(alignment.sequences[3].annotations["leftCount"], 401) self.assertEqual(alignment.sequences[3].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[3].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[4].id, "panTro2.chr6") self.assertEqual(len(alignment.sequences[4].seq), 173908612) self.assertEqual( alignment.sequences[4].seq[157518738 : 157518738 + 20], "AGAAACATGCCACACCTGCt", ) self.assertEqual( alignment[4], "--------------------------------------------aGCAGGTGTGGCATGTTTCT", ) self.assertEqual( alignment.sequences[4].annotations["quality"], "99999999999999999999" ) self.assertEqual(alignment.sequences[4].annotations["leftStatus"], "I") self.assertEqual(alignment.sequences[4].annotations["leftCount"], 400) self.assertEqual(alignment.sequences[4].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[4].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[5].id, "ponAbe2.chr6") self.assertEqual(len(alignment.sequences[5].seq), 174210431) self.assertEqual( alignment.sequences[5].seq[158040919 : 158040919 + 20], "AGAAACATGCCACACCTGCt", ) self.assertEqual( alignment[5], "--------------------------------------------aGCAGGTGTGGCATGTTTCT", ) self.assertEqual(alignment.sequences[5].annotations["leftStatus"], "I") self.assertEqual(alignment.sequences[5].annotations["leftCount"], 8044) self.assertEqual(alignment.sequences[5].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[5].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[6].id, "tupBel1.scaffold_114895.1-498454") self.assertEqual(len(alignment.sequences[6].seq), 498454) self.assertEqual( alignment.sequences[6].seq[326906 : 326906 + 27], "AGCGATGCGCCACACCCACATTTCTAA", ) self.assertEqual( alignment[6], "------------------------------------TTAGAAA-TGTGGGTGTGGCGCATCGCT", ) self.assertEqual( alignment.sequences[6].annotations["quality"], "999999999999989998899999699" ) self.assertEqual(alignment.sequences[6].annotations["leftStatus"], "I") self.assertEqual(alignment.sequences[6].annotations["leftCount"], 4145) self.assertEqual(alignment.sequences[6].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[6].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[7].id, "cavPor2.scaffold_216473") self.assertEqual(len(alignment.sequences[7].seq), 10026) self.assertEqual( alignment.sequences[7].seq[2184 : 2184 + 26], "GAACCATGCCACACCTAAATTTCTAA" ) self.assertEqual( alignment[7], "------------------------------------TTAGAAA-TTTAGGTGTGGCATGGTTC-", ) self.assertEqual( alignment.sequences[7].annotations["quality"], "42558311324566557465575854" ) self.assertEqual(alignment.sequences[7].annotations["leftStatus"], "N") self.assertEqual(alignment.sequences[7].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[7].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[7].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[8].id, "loxAfr1.scaffold_75566") self.assertEqual(len(alignment.sequences[8].seq), 10574) self.assertEqual( alignment.sequences[8].seq[9203 : 9203 + 62], "aGAGATACAGCAAACCTCAATTTCTGAAACAACGTATTGATGTCCTAAACTTGCTCTCAAAC", ) self.assertEqual( alignment[8], "GTT-TGAGAGCAAGTTTAGGACATCAATACGTTGTTTCAGAAA-TTGAGGTTTGCTGTATCTCt", ) self.assertEqual( alignment.sequences[8].annotations["quality"], "99999999999999999999999999999999999999999999999999999999999999", ) self.assertEqual(alignment.sequences[8].annotations["leftStatus"], "I") self.assertEqual(alignment.sequences[8].annotations["leftCount"], 25) self.assertEqual(alignment.sequences[8].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[8].annotations["rightCount"], 0) empty = alignment.annotations["empty"][0] (record, segment, status) = empty self.assertEqual(record.id, "echTel1.scaffold_288249") self.assertEqual(len(record.seq), 100002) self.assertEqual(segment, (87661, 95225)) self.assertEqual(status, "I") self.assertEqual(len(alignment.sequences), 9) self.assertEqual(len(alignment.annotations["empty"]), 1) self.assertEqual( str(alignment), """\ mm9.chr10 3014795 GTTTCAGGGGCAGCTCGCTG----------------TTAGCAG-CTAAGGCATGGTGTCT otoGar1.s 175207 ---TCGGGAACAAGTTGCAGTCATGGATAT-TTGGTTTAGATGGTTTAGGTGGGGTGTAT calJac1.C 6365 -------------------GCCATGAATAT-----TTTAGAC-ATGCAGGTGTGGCGTGT hg18.chr6 155028706 --------------------------------------------aGCAGGTGTGGCATGT panTro2.c 157518758 --------------------------------------------aGCAGGTGTGGCATGT ponAbe2.c 158040939 --------------------------------------------aGCAGGTGTGGCATGT tupBel1.s 326933 ------------------------------------TTAGAAA-TGTGGGTGTGGCGCAT cavPor2.s 2210 ------------------------------------TTAGAAA-TTTAGGTGTGGCATGG loxAfr1.s 9265 GTT-TGAGAGCAAGTTTAGGACATCAATACGTTGTTTCAGAAA-TTGAGGTTTGCTGTAT mm9.chr10 3014838 CTCA 3014842 otoGar1.s 175151 TTCT 175147 calJac1.C 6400 TTCT 6404 hg18.chr6 155028690 TTCT 155028686 panTro2.c 157518742 TTCT 157518738 ponAbe2.c 158040923 TTCT 158040919 tupBel1.s 326910 CGCT 326906 cavPor2.s 2187 TTC- 2184 loxAfr1.s 9207 CTCt 9203 """, ) self.assertTrue( np.array_equal( alignment.coordinates, np.array( # fmt: off [[ 3014795, 3014798, 3014799, 3014814, 3014815, 3014815, 3014815, 3014815, 3014815, 3014821, 3014822, 3014822, 3014841, 3014842], [ 175207, 175207, 175206, 175191, 175190, 175180, 175180, 175176, 175175, 175169, 175168, 175167, 175148, 175147], [ 6365, 6365, 6365, 6365, 6366, 6376, 6376, 6376, 6377, 6383, 6383, 6384, 6403, 6404], [155028706, 155028706, 155028706, 155028706, 155028706, 155028706, 155028706, 155028706, 155028706, 155028706, 155028706, 155028706, 155028687, 155028686], [157518758, 157518758, 157518758, 157518758, 157518758, 157518758, 157518758, 157518758, 157518758, 157518758, 157518758, 157518758, 157518739, 157518738], [158040939, 158040939, 158040939, 158040939, 158040939, 158040939, 158040939, 158040939, 158040939, 158040939, 158040939, 158040939, 158040920, 158040919], [ 326933, 326933, 326933, 326933, 326933, 326933, 326933, 326933, 326933, 326927, 326926, 326926, 326907, 326906], [ 2210, 2210, 2210, 2210, 2210, 2210, 2210, 2210, 2210, 2204, 2203, 2203, 2184, 2184], [ 9265, 9262, 9262, 9247, 9246, 9236, 9235, 9231, 9230, 9224, 9223, 9223, 9204, 9203], ] # fmt: on ), ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['G', 'T', 'T', 'T', 'C', 'A', 'G', 'G', 'G', 'G', 'C', 'A', 'G', 'C', 'T', 'C', 'G', 'C', 'T', 'G', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'T', 'T', 'A', 'G', 'C', 'A', 'G', '-', 'C', 'T', 'A', 'A', 'G', 'G', 'C', 'A', 'T', 'G', 'G', 'T', 'G', 'T', 'C', 'T', 'C', 'T', 'C', 'A'], ['-', '-', '-', 'T', 'C', 'G', 'G', 'G', 'A', 'A', 'C', 'A', 'A', 'G', 'T', 'T', 'G', 'C', 'A', 'G', 'T', 'C', 'A', 'T', 'G', 'G', 'A', 'T', 'A', 'T', '-', 'T', 'T', 'G', 'G', 'T', 'T', 'T', 'A', 'G', 'A', 'T', 'G', 'G', 'T', 'T', 'T', 'A', 'G', 'G', 'T', 'G', 'G', 'G', 'G', 'T', 'G', 'T', 'A', 'T', 'T', 'T', 'C', 'T'], ['-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'G', 'C', 'C', 'A', 'T', 'G', 'A', 'A', 'T', 'A', 'T', '-', '-', '-', '-', '-', 'T', 'T', 'T', 'A', 'G', 'A', 'C', '-', 'A', 'T', 'G', 'C', 'A', 'G', 'G', 'T', 'G', 'T', 'G', 'G', 'C', 'G', 'T', 'G', 'T', 'T', 'T', 'C', 'T'], ['-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'a', 'G', 'C', 'A', 'G', 'G', 'T', 'G', 'T', 'G', 'G', 'C', 'A', 'T', 'G', 'T', 'T', 'T', 'C', 'T'], ['-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'a', 'G', 'C', 'A', 'G', 'G', 'T', 'G', 'T', 'G', 'G', 'C', 'A', 'T', 'G', 'T', 'T', 'T', 'C', 'T'], ['-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'a', 'G', 'C', 'A', 'G', 'G', 'T', 'G', 'T', 'G', 'G', 'C', 'A', 'T', 'G', 'T', 'T', 'T', 'C', 'T'], ['-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'T', 'T', 'A', 'G', 'A', 'A', 'A', '-', 'T', 'G', 'T', 'G', 'G', 'G', 'T', 'G', 'T', 'G', 'G', 'C', 'G', 'C', 'A', 'T', 'C', 'G', 'C', 'T'], ['-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'T', 'T', 'A', 'G', 'A', 'A', 'A', '-', 'T', 'T', 'T', 'A', 'G', 'G', 'T', 'G', 'T', 'G', 'G', 'C', 'A', 'T', 'G', 'G', 'T', 'T', 'C', '-'], ['G', 'T', 'T', '-', 'T', 'G', 'A', 'G', 'A', 'G', 'C', 'A', 'A', 'G', 'T', 'T', 'T', 'A', 'G', 'G', 'A', 'C', 'A', 'T', 'C', 'A', 'A', 'T', 'A', 'C', 'G', 'T', 'T', 'G', 'T', 'T', 'T', 'C', 'A', 'G', 'A', 'A', 'A', '-', 'T', 'T', 'G', 'A', 'G', 'G', 'T', 'T', 'T', 'G', 'C', 'T', 'G', 'T', 'A', 'T', 'C', 'T', 'C', 't']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.score, 320596) self.assertEqual(alignment.sequences[0].id, "mm9.chr10") self.assertEqual(len(alignment.sequences[0].seq), 129993255) self.assertEqual( alignment.sequences[0].seq[3014842 : 3014842 + 186], "CTTGGGATGCTTTATAGTGGAAATGGAAAGCAATTTATTTAGATCTTAAATCATTTTGAAGGTTAATAAAATGACCATATTAATATTCCCATGAACAAAGCCTTCATTTTTAAAATATTGCATCCTATAATACACATAAATCTTGTTCTCGtttttatttttttatttatttatttttttttcttt", ) self.assertEqual( alignment[0], "C--TTGGGA---------TGCTTTATAGTGGAAATGGAAAGCA----A-TTTATTTAGATCTTAAATCATTTT-GAAGGTTAATAAAATGACCATATTAATATTCCCATGAACAAAGCCTTCATTT----TTAAAATATTGCATCCTATAATACACATAA-ATCTTGT-----TCTCGtttttatttttt----tatt-tat-----------------------ttattttttttt------------cttt", ) self.assertEqual(alignment.sequences[1].id, "loxAfr1.scaffold_75566") self.assertEqual(len(alignment.sequences[1].seq), 10574) self.assertEqual( alignment.sequences[1].seq[8958 : 8958 + 245], "AGATTTGGCCAAAGTCAATGAAAAAAGAGAGAGAGAGTGAACTTGCTAAGACACCTGCTTAAAAAGGGAATGAGATTTTGAAAAGATGCTGTGTGTGGTATAAAACCCAATTTTTTTTTTTAAATGAGGGTATTGTTCACAGGAATATTAAAGTGAAAATTTCATTATACTTCAAAGGGATTTATGGCCAAAAGAAACAGTGTGACTTTCACTTCAGCtttaaaaaaaaaaaaaaatcaaaaata", ) self.assertEqual( alignment[1], "tatttttgatttttttttttttttaaaGCTGAAGTGAAAGTCACACTG-TTTCTTTTGGCCATAAATCCCTTT-GAAGTATAATGAAATTTTCACTTTAATATTCCTGTGAACAATACCCTCATTT-AAAAAAAAAAATTGGGTTTTATACCACACACAGCATCTTTTCAAAATCTCATTCCC-TTTTTAAGCAGGTG-TCT---TAGCAAGTTCACTCTCTCTCTCTTTTTTCATTGACTTTGGCCAAATCT", ) self.assertEqual( alignment.sequences[1].annotations["quality"], "99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999", ) self.assertEqual(alignment.sequences[1].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[1].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[1].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[1].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[2].id, "cavPor2.scaffold_216473") self.assertEqual(len(alignment.sequences[2].seq), 10026) self.assertEqual( alignment.sequences[2].seq[1986 : 1986 + 198], "agagaaagagagactaaTAAACCTGCCAGAAGAAGGAAATGAGATGTTGGAAATATGCTGTATGTGGTACAAAATCCAAACTTTTTTAAATGAGGGCATTGTTAGTAGGAATATTAATGTGATCATTTTATTATACTTCAAAAGGATTTAAGTCCTAAAGAAACAGGGTGCCTTTCATTCCAACTGTGAATATCCAAA", ) self.assertEqual( alignment[2], "---TTTGGA---------TA-TTCACAGTTGGAATGAAAGGCACCCTG-TTTCTTTAGGACTTAAATCCTTTT-GAAGTATAATAAAATGATCACATTAATATTCCTACTAACAATGCCCTCATTT----AAAAAAGTTTGGATTTTGTACCACATACAGCATATTTCCAACATCTCATTTCCTTCTTCTGGCAGGTT-TAt-----------------------tagtctctcttt------------ctct", ) self.assertEqual( alignment.sequences[2].annotations["quality"], "610137772001955312362668764253688587789879568878689568989568988778987788768588885664786777656586678636299978766899797899369899566878676899958889788869976598977898999989967788999979899987999997779899", ) self.assertEqual(alignment.sequences[2].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[2].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[2].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[2].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[3].id, "tupBel1.scaffold_114895.1-498454") self.assertEqual(len(alignment.sequences[3].seq), 498454) self.assertEqual( alignment.sequences[3].seq[326691 : 326691 + 215], "AAGTCAATAGACAAAAAGGGAACTTGCTAATAAACCTGCCAAAAAAGGAAATGAGATTTTGGAAATATGCTGTACGTGGTATAAAATCCCAGATTTTGTAAAATGAGGGCATTGTTCACAGGAATAGTAAAGTGATCATTTTATTATACTTCAAAAGGATTTAAGACCTACAGACACAGTGTGCTTTTTATTTCAGCTGTAAAAAATCCAAAAGG", ) self.assertEqual( alignment[3], "CCTTTTGGA---------TTTTTTACAGCTGAAATAAAAAGCACACTG-TGTCTGTAGGTCTTAAATCCTTTT-GAAGTATAATAAAATGATCACTTTACTATTCCTGTGAACAATGCCCTCATTT---TACAAAATCTGGGATTTTATACCACGTACAGCATATTTCCAAAATCTCATTTCC-TTTTTTGGCAGGTT-TAT---TAGCAAGTTCCCT-------TTTTGTCTATTG------------ACTT", ) self.assertEqual( alignment.sequences[3].annotations["quality"], "98999999989999999899999999999999999999999999999999999999999999999999989999999999999999999999999998999999999999999999988999999999739999999989999999999999999799999999999999999999769984999999999999999999999999999999999", ) self.assertEqual(alignment.sequences[3].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[3].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[3].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[3].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[4].id, "ponAbe2.chr6") self.assertEqual(len(alignment.sequences[4].seq), 174210431) self.assertEqual( alignment.sequences[4].seq[158040700 : 158040700 + 219], "AAGTAAATAAGAGAGAGAGATAACTTGCTATAAATAAACCTGCCAAGAAAGGAAATGAGATTTCAGAAATATGCTGCATGTGGTATAAAATCCAGGATTTTTTTAAAAGAGGACATTGCTCACAGGAGTATTAAAGTGATCGTTTTATTATACTTCAAAAGTATTTAAGACCTAAAGAAACAGTGTGCCTTCCATTTCAGCTATAAAAAGTCCAAAAGG", ) self.assertEqual( alignment[4], "CCTTTTGGA---------CTTTTTATAGCTGAAATGGAAGGCACACTG-TTTCTTTAGGTCTTAAATACTTTT-GAAGTATAATAAAACGATCACTTTAATACTCCTGTGAGCAATGTCCTCTTTT---AAAAAAATCCTGGATTTTATACCACATGCAGCATATTTCTGAAATCTCATTTCC-TTTCTTGGCAGGTT-TATTTATAGCAAGTTATCTC------TCTCTCTTATTT------------ACTT", ) self.assertEqual(alignment.sequences[4].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[4].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[4].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[4].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[5].id, "panTro2.chr6") self.assertEqual(len(alignment.sequences[5].seq), 173908612) self.assertEqual( alignment.sequences[5].seq[157518570 : 157518570 + 168], "AAATGGGATTTCAGAAATATGCTGCATGTGGTATAAAATCCAGGATTTTTTTAAAAAGAGGGCATTGTTCACAGGAGTATTAAAGTGATCATTTTTTTATACTTCAAAAGTATTTAAGACCTAAAGAAATATTGTGCCTTCCATTTCAGCTATAAAAAGTCCAAAAGG", ) self.assertEqual( alignment[5], "CCTTTTGGA---------CTTTTTATAGCTGAAATGGAAGGCACAATA-TTTCTTTAGGTCTTAAATACTTTT-GAAGTATAAAAAAATGATCACTTTAATACTCCTGTGAACAATGCCCTCTTTTT--AAAAAAATCCTGGATTTTATACCACATGCAGCATATTTCTGAAATCCCATTT------------------------------------------------------------------------", ) self.assertEqual( alignment.sequences[5].annotations["quality"], "999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999", ) self.assertEqual(alignment.sequences[5].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[5].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[5].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[5].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[6].id, "hg18.chr6") self.assertEqual(len(alignment.sequences[6].seq), 170899992) self.assertEqual( alignment.sequences[6].seq[155028517 : 155028517 + 169], "AAATGAGATTTCAGAAATATGCTGCATGTGGTATAAAATCCAGGATTTTTTTTAAAAAGAGGGCATTGTTCACAGGAGTATTAAAGTGATCATTTTTTTATACTTCAAAAGTATTTAAGACCTAAAGAAATATTGTGCCTTCCATTTCAGCTATAAAAAGTCCAAAAGG", ) self.assertEqual( alignment[6], "CCTTTTGGA---------CTTTTTATAGCTGAAATGGAAGGCACAATA-TTTCTTTAGGTCTTAAATACTTTT-GAAGTATAAAAAAATGATCACTTTAATACTCCTGTGAACAATGCCCTCTTTTT-AAAAAAAATCCTGGATTTTATACCACATGCAGCATATTTCTGAAATCTCATTT------------------------------------------------------------------------", ) self.assertEqual(alignment.sequences[6].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[6].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[6].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[6].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[7].id, "calJac1.Contig6394") self.assertEqual(len(alignment.sequences[7].seq), 133105) self.assertEqual( alignment.sequences[7].seq[6404 : 6404 + 223], "TCTTTTGTATTTTTTTATAGCTGAAAAGGAAGGCACACTGTCTCTTTAGGTCTTAAATACGTTTGAAGCATAATAAAATGATCACTTTCATACTCCTGTGAATAATGCCCTCCTTTTAAAAAGAAATCTTGGATTTTATATCACACGCAGCATATTTCTGAAATCTCATTTCCTTTCCTGGCAGGTTTATTAATAGCAAGTTCTCTCTCTTATTTATTTATTT", ) self.assertEqual( alignment[7], "TCTTTTGTA--------TTTTTTTATAGCTGAAAAGGAAGGCACACTG-TCTCTTTAGGTCTTAAATACGTTT-GAAGCATAATAAAATGATCACTTTCATACTCCTGTGAATAATGCCCTCCTTTTAAAAAGAAATCTTGGATTTTATATCACACGCAGCATATTTCTGAAATCTCATTTCC-TTTCCTGGCAGGTT-TATTAATAGCAAGTTCTCTC------TCTTATTTATTT------------ATTT", ) self.assertEqual(alignment.sequences[7].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[7].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[7].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[7].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[8].id, "otoGar1.scaffold_334.1-359464") self.assertEqual(len(alignment.sequences[8].seq), 359464) self.assertEqual( alignment.sequences[8].seq[174925 : 174925 + 222], "GAGAAAAAGAAGAAGAAAGCCGGAGAGAACTTGCTAACAAACCCGCCAAAAAGGAAATGAGATTTTGGAAATATGCTGGATCTGGTATAAAATCCAAGATTTTTTTAAATGAGGGCATTGTTCACAGGAACAGTAAAGTAATCGTTTTATTATACTTCAAAAGGATTTAAGTCCTAAAAAAACAGTGTGCCTTTCATTTCACCCATAAAAAAGCCCAAAATA", ) self.assertEqual( alignment[8], "TATTTTGGG--------CTTTTTTATGGGTGAAATGAAAGGCACACTG-TTTTTTTAGGACTTAAATCCTTTT-GAAGTATAATAAAACGATTACTTTACTGTTCCTGTGAACAATGCCCTCATTT---AAAAAAATCTTGGATTTTATACCAGATCCAGCATATTTCCAAAATCTCATTT-C-CTTTTTGGCGGGTT-TGT---TAGCAAGTTCTCTCCGGCTTTCTTCTTCTTTT------------TCTC", ) self.assertEqual( alignment.sequences[8].annotations["quality"], "999999999999999999999999999999999799999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999", ) self.assertEqual(alignment.sequences[8].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[8].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[8].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[8].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[9].id, "ornAna1.chr2") self.assertEqual(len(alignment.sequences[9].seq), 54797317) self.assertEqual( alignment.sequences[9].seq[40046122 : 40046122 + 201], "AAAGAGAGAACGGTTAATACAATGCACCCAAAAAGGAACTAAGATTTTGGAAATGGGCTGTATGTCGTTAAAATACAAAGATATTTTAATGAGGGCTTTGTTAGCGGGGAAATGAAGATCATAATTACAATACACTTTTAAAAAGGCTTAAGATAGAAAGAAAACAATGAGCCTTTCACTTTTGCAGTAACATTTCCAAGG", ) self.assertEqual( alignment[9], "--CCTTGGA---------AATGTTACTGCAAAAGTGAAAGGCTCATTGTTTTCTTTCTATCTTAAGCCTTTTTAAAAGTGTATTGTAATTATGATCTTCATTTCCCCGCTAACAAAGCCCTCATTA----AAATATCTTTGTATTTTA-ACGACATACAGCCCATTTCCAAAATCTTAGTTCC-TTTTTGGGTGCATTGTAT---TAAC----------------CGTTCTCTCTTT----------------", ) self.assertEqual(alignment.sequences[9].annotations["leftStatus"], "N") self.assertEqual(alignment.sequences[9].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[9].annotations["rightStatus"], "I") self.assertEqual(alignment.sequences[9].annotations["rightCount"], 5690) empty = alignment.annotations["empty"][0] (record, segment, status) = empty self.assertEqual(record.id, "echTel1.scaffold_288249") self.assertEqual(len(record.seq), 100002) self.assertEqual(segment, (87661, 95225)) self.assertEqual(status, "I") self.assertEqual(len(alignment.sequences), 10) self.assertEqual(len(alignment.annotations["empty"]), 1) self.assertEqual( str(alignment), """\ mm9.chr10 3014842 C--TTGGGA---------TGCTTTATAGTGGAAATGGAAAGCA----A-TTTATTTAGAT loxAfr1.s 9203 tatttttgatttttttttttttttaaaGCTGAAGTGAAAGTCACACTG-TTTCTTTTGGC cavPor2.s 2184 ---TTTGGA---------TA-TTCACAGTTGGAATGAAAGGCACCCTG-TTTCTTTAGGA tupBel1.s 326906 CCTTTTGGA---------TTTTTTACAGCTGAAATAAAAAGCACACTG-TGTCTGTAGGT ponAbe2.c 158040919 CCTTTTGGA---------CTTTTTATAGCTGAAATGGAAGGCACACTG-TTTCTTTAGGT panTro2.c 157518738 CCTTTTGGA---------CTTTTTATAGCTGAAATGGAAGGCACAATA-TTTCTTTAGGT hg18.chr6 155028686 CCTTTTGGA---------CTTTTTATAGCTGAAATGGAAGGCACAATA-TTTCTTTAGGT calJac1.C 6404 TCTTTTGTA--------TTTTTTTATAGCTGAAAAGGAAGGCACACTG-TCTCTTTAGGT otoGar1.s 175147 TATTTTGGG--------CTTTTTTATGGGTGAAATGAAAGGCACACTG-TTTTTTTAGGA ornAna1.c 40046323 --CCTTGGA---------AATGTTACTGCAAAAGTGAAAGGCTCATTGTTTTCTTTCTAT mm9.chr10 3014886 CTTAAATCATTTT-GAAGGTTAATAAAATGACCATATTAATATTCCCATGAACAAAGCCT loxAfr1.s 9144 CATAAATCCCTTT-GAAGTATAATGAAATTTTCACTTTAATATTCCTGTGAACAATACCC cavPor2.s 2138 CTTAAATCCTTTT-GAAGTATAATAAAATGATCACATTAATATTCCTACTAACAATGCCC tupBel1.s 326856 CTTAAATCCTTTT-GAAGTATAATAAAATGATCACTTTACTATTCCTGTGAACAATGCCC ponAbe2.c 158040869 CTTAAATACTTTT-GAAGTATAATAAAACGATCACTTTAATACTCCTGTGAGCAATGTCC panTro2.c 157518688 CTTAAATACTTTT-GAAGTATAAAAAAATGATCACTTTAATACTCCTGTGAACAATGCCC hg18.chr6 155028636 CTTAAATACTTTT-GAAGTATAAAAAAATGATCACTTTAATACTCCTGTGAACAATGCCC calJac1.C 6455 CTTAAATACGTTT-GAAGCATAATAAAATGATCACTTTCATACTCCTGTGAATAATGCCC otoGar1.s 175096 CTTAAATCCTTTT-GAAGTATAATAAAACGATTACTTTACTGTTCCTGTGAACAATGCCC ornAna1.c 40046274 CTTAAGCCTTTTTAAAAGTGTATTGTAATTATGATCTTCATTTCCCCGCTAACAAAGCCC mm9.chr10 3014945 TCATTT----TTAAAATATTGCATCCTATAATACACATAA-ATCTTGT-----TCTCGtt loxAfr1.s 9085 TCATTT-AAAAAAAAAAATTGGGTTTTATACCACACACAGCATCTTTTCAAAATCTCATT cavPor2.s 2079 TCATTT----AAAAAAGTTTGGATTTTGTACCACATACAGCATATTTCCAACATCTCATT tupBel1.s 326797 TCATTT---TACAAAATCTGGGATTTTATACCACGTACAGCATATTTCCAAAATCTCATT ponAbe2.c 158040810 TCTTTT---AAAAAAATCCTGGATTTTATACCACATGCAGCATATTTCTGAAATCTCATT panTro2.c 157518629 TCTTTTT--AAAAAAATCCTGGATTTTATACCACATGCAGCATATTTCTGAAATCCCATT hg18.chr6 155028577 TCTTTTT-AAAAAAAATCCTGGATTTTATACCACATGCAGCATATTTCTGAAATCTCATT calJac1.C 6514 TCCTTTTAAAAAGAAATCTTGGATTTTATATCACACGCAGCATATTTCTGAAATCTCATT otoGar1.s 175037 TCATTT---AAAAAAATCTTGGATTTTATACCAGATCCAGCATATTTCCAAAATCTCATT ornAna1.c 40046214 TCATTA----AAATATCTTTGTATTTTA-ACGACATACAGCCCATTTCCAAAATCTTAGT mm9.chr10 3014995 tttatttttt----tatt-tat-----------------------ttattttttttt--- loxAfr1.s 9026 CCC-TTTTTAAGCAGGTG-TCT---TAGCAAGTTCACTCTCTCTCTCTTTTTTCATTGAC cavPor2.s 2023 TCCTTCTTCTGGCAGGTT-TAt-----------------------tagtctctcttt--- tupBel1.s 326740 TCC-TTTTTTGGCAGGTT-TAT---TAGCAAGTTCCCT-------TTTTGTCTATTG--- ponAbe2.c 158040753 TCC-TTTCTTGGCAGGTT-TATTTATAGCAAGTTATCTC------TCTCTCTTATTT--- panTro2.c 157518571 T----------------------------------------------------------- hg18.chr6 155028518 T----------------------------------------------------------- calJac1.C 6574 TCC-TTTCCTGGCAGGTT-TATTAATAGCAAGTTCTCTC------TCTTATTTATTT--- otoGar1.s 174980 T-C-CTTTTTGGCGGGTT-TGT---TAGCAAGTTCTCTCCGGCTTTCTTCTTCTTTT--- ornAna1.c 40046159 TCC-TTTTTGGGTGCATTGTAT---TAAC----------------CGTTCTCTCTTT--- mm9.chr10 3015024 ---------cttt 3015028 loxAfr1.s 8971 TTTGGCCAAATCT 8958 cavPor2.s 1990 ---------ctct 1986 tupBel1.s 326695 ---------ACTT 326691 ponAbe2.c 158040704 ---------ACTT 158040700 panTro2.c 157518570 ------------- 157518570 hg18.chr6 155028517 ------------- 155028517 calJac1.C 6623 ---------ATTT 6627 otoGar1.s 174929 ---------TCTC 174925 ornAna1.c 40046122 ------------- 40046122 """, ) self.assertTrue( np.array_equal( alignment.coordinates, np.array( # fmt: off [[ 3014842, 3014843, 3014843, 3014843, 3014849, 3014849, 3014849, 3014851, 3014852, 3014874, 3014874, 3014875, 3014875, 3014899, 3014899, 3014951, 3014951, 3014951, 3014951, 3014951, 3014969, 3014970, 3014981, 3014981, 3014988, 3014988, 3014996, 3014997, 3014998, 3014999, 3015005, 3015005, 3015009, 3015009, 3015012, 3015012, 3015012, 3015012, 3015012, 3015012, 3015024, 3015024, 3015028], [ 9203, 9202, 9201, 9200, 9194, 9186, 9185, 9183, 9182, 9160, 9156, 9155, 9155, 9131, 9131, 9079, 9079, 9078, 9077, 9076, 9058, 9057, 9046, 9045, 9038, 9033, 9025, 9024, 9023, 9023, 9017, 9013, 9009, 9009, 9006, 9006, 9002, 8993, 8992, 8986, 8974, 8962, 8958], [ 2184, 2184, 2184, 2184, 2178, 2178, 2178, 2176, 2176, 2154, 2150, 2149, 2149, 2125, 2125, 2073, 2073, 2073, 2073, 2073, 2055, 2054, 2043, 2042, 2035, 2030, 2022, 2021, 2020, 2019, 2013, 2009, 2005, 2005, 2002, 2002, 2002, 2002, 2002, 2002, 1990, 1990, 1986], [ 326906, 326905, 326904, 326903, 326897, 326897, 326897, 326895, 326894, 326872, 326868, 326867, 326867, 326843, 326843, 326791, 326791, 326791, 326791, 326790, 326772, 326771, 326760, 326759, 326752, 326747, 326739, 326738, 326737, 326737, 326731, 326727, 326723, 326723, 326720, 326720, 326716, 326707, 326707, 326707, 326695, 326695, 326691], [158040919, 158040918, 158040917, 158040916, 158040910, 158040910, 158040910, 158040908, 158040907, 158040885, 158040881, 158040880, 158040880, 158040856, 158040856, 158040804, 158040804, 158040804, 158040804, 158040803, 158040785, 158040784, 158040773, 158040772, 158040765, 158040760, 158040752, 158040751, 158040750, 158040750, 158040744, 158040740, 158040736, 158040736, 158040733, 158040730, 158040726, 158040717, 158040716, 158040716, 158040704, 158040704, 158040700], [157518738, 157518737, 157518736, 157518735, 157518729, 157518729, 157518729, 157518727, 157518726, 157518704, 157518700, 157518699, 157518699, 157518675, 157518675, 157518623, 157518622, 157518622, 157518622, 157518621, 157518603, 157518602, 157518591, 157518590, 157518583, 157518578, 157518570, 157518570, 157518570, 157518570, 157518570, 157518570, 157518570, 157518570, 157518570, 157518570, 157518570, 157518570, 157518570, 157518570, 157518570, 157518570, 157518570], [155028686, 155028685, 155028684, 155028683, 155028677, 155028677, 155028677, 155028675, 155028674, 155028652, 155028648, 155028647, 155028647, 155028623, 155028623, 155028571, 155028570, 155028570, 155028569, 155028568, 155028550, 155028549, 155028538, 155028537, 155028530, 155028525, 155028517, 155028517, 155028517, 155028517, 155028517, 155028517, 155028517, 155028517, 155028517, 155028517, 155028517, 155028517, 155028517, 155028517, 155028517, 155028517, 155028517], [ 6404, 6405, 6406, 6407, 6413, 6413, 6414, 6416, 6417, 6439, 6443, 6444, 6444, 6468, 6468, 6520, 6521, 6522, 6523, 6524, 6542, 6543, 6554, 6555, 6562, 6567, 6575, 6576, 6577, 6577, 6583, 6587, 6591, 6591, 6594, 6597, 6601, 6610, 6611, 6611, 6623, 6623, 6627], [ 175147, 175146, 175145, 175144, 175138, 175138, 175137, 175135, 175134, 175112, 175108, 175107, 175107, 175083, 175083, 175031, 175031, 175031, 175031, 175030, 175012, 175011, 175000, 174999, 174992, 174987, 174979, 174979, 174978, 174978, 174972, 174968, 174964, 174964, 174961, 174961, 174957, 174948, 174947, 174941, 174929, 174929, 174925], [ 40046323, 40046323, 40046323, 40046322, 40046316, 40046316, 40046316, 40046314, 40046313, 40046291, 40046287, 40046286, 40046285, 40046261, 40046260, 40046208, 40046208, 40046208, 40046208, 40046208, 40046190, 40046190, 40046179, 40046178, 40046171, 40046166, 40046158, 40046157, 40046156, 40046156, 40046150, 40046146, 40046142, 40046141, 40046138, 40046138, 40046134, 40046134, 40046134, 40046134, 40046122, 40046122, 40046122], ] # fmt: on ), ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.score, -36127) self.assertEqual(alignment.sequences[0].id, "mm9.chr10") self.assertEqual(len(alignment.sequences[0].seq), 129993255) self.assertEqual( alignment.sequences[0].seq[3015028 : 3015028 + 58], "ccattttttattaggtatttagctcatttacatttccaatgctataccaaaagtcccc", ) self.assertEqual( alignment[0], "ccatttt----------ttattaggtatttagctcatttacatttccaatgctatac----caaaagtcccc", ) self.assertEqual(alignment.sequences[1].id, "loxAfr1.scaffold_75566") self.assertEqual(len(alignment.sequences[1].seq), 10574) self.assertEqual( alignment.sequences[1].seq[8925 : 8925 + 33], "GAGAACTTTTGTAAGGAATGGAGGTAGAAGTGA", ) self.assertEqual( alignment[1], "TCACTTCTA---------------------------------------CCTCCATTCCTTACAAAAGTTCTC", ) self.assertEqual( alignment.sequences[1].annotations["quality"], "999999999999999999999999999999999", ) self.assertEqual(alignment.sequences[1].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[1].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[1].annotations["rightStatus"], "N") self.assertEqual(alignment.sequences[1].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[2].id, "cavPor2.scaffold_216473") self.assertEqual(len(alignment.sequences[2].seq), 10026) self.assertEqual(alignment.sequences[2].seq[1978 : 1978 + 8], "agacacag") self.assertEqual( alignment[2], "ctgtgtc----------t------------------------------------------------------", ) self.assertEqual(alignment.sequences[2].annotations["quality"], "67889899") self.assertEqual(alignment.sequences[2].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[2].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[2].annotations["rightStatus"], "I") self.assertEqual(alignment.sequences[2].annotations["rightCount"], 1372) self.assertEqual(alignment.sequences[3].id, "tupBel1.scaffold_114895.1-498454") self.assertEqual(len(alignment.sequences[3].seq), 498454) self.assertEqual(alignment.sequences[3].seq[326690 : 326690 + 1], "A") self.assertEqual( alignment[3], "T-----------------------------------------------------------------------", ) self.assertEqual(alignment.sequences[3].annotations["quality"], "9") self.assertEqual(alignment.sequences[3].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[3].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[3].annotations["rightStatus"], "I") self.assertEqual(alignment.sequences[3].annotations["rightCount"], 2374) self.assertEqual(alignment.sequences[4].id, "ponAbe2.chr6") self.assertEqual(len(alignment.sequences[4].seq), 174210431) self.assertEqual( alignment.sequences[4].seq[158040688 : 158040688 + 12], "GAAAAGGCAAAA" ) self.assertEqual( alignment[4], "TTTTGCCTTTTC------------------------------------------------------------", ) self.assertEqual(alignment.sequences[4].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[4].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[4].annotations["rightStatus"], "I") self.assertEqual(alignment.sequences[4].annotations["rightCount"], 75) self.assertEqual(alignment.sequences[5].id, "calJac1.Contig6394") self.assertEqual(len(alignment.sequences[5].seq), 133105) self.assertEqual( alignment.sequences[5].seq[6627 : 6627 + 22], "TGCTTTTTCTCAAATCTCCACT" ) self.assertEqual( alignment[5], "TGCTTTTTCTCAAATCTCCACT--------------------------------------------------", ) self.assertEqual(alignment.sequences[5].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[5].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[5].annotations["rightStatus"], "I") self.assertEqual(alignment.sequences[5].annotations["rightCount"], 3479) self.assertEqual(alignment.sequences[6].id, "otoGar1.scaffold_334.1-359464") self.assertEqual(len(alignment.sequences[6].seq), 359464) self.assertEqual( alignment.sequences[6].seq[174889 : 174889 + 36], "TGGAAGTGAATATTTGGCAAAAGTCAATAGAAAAAA", ) self.assertEqual( alignment[6], "TTTTTTCTATT------------GACTTTTGCCAAATATTCACTTCCA------------------------", ) self.assertEqual( alignment.sequences[6].annotations["quality"], "999999999999999999999999999999999999", ) self.assertEqual(alignment.sequences[6].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[6].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[6].annotations["rightStatus"], "I") self.assertEqual(alignment.sequences[6].annotations["rightCount"], 137) empty = alignment.annotations["empty"][0] (record, segment, status) = empty self.assertEqual(record.id, "ornAna1.chr2") self.assertEqual(len(record.seq), 54797317) self.assertEqual(segment, (40046122, 40040432)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][1] (record, segment, status) = empty self.assertEqual(record.id, "echTel1.scaffold_288249") self.assertEqual(len(record.seq), 100002) self.assertEqual(segment, (87661, 95225)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][2] (record, segment, status) = empty self.assertEqual(record.id, "hg18.chr6") self.assertEqual(len(record.seq), 170899992) self.assertEqual(segment, (155028517, 155028517)) self.assertEqual(status, "C") empty = alignment.annotations["empty"][3] (record, segment, status) = empty self.assertEqual(record.id, "panTro2.chr6") self.assertEqual(len(record.seq), 173908612) self.assertEqual(segment, (157518570, 157518570)) self.assertEqual(status, "C") self.assertEqual(len(alignment.sequences), 7) self.assertEqual(len(alignment.annotations["empty"]), 4) self.assertEqual( str(alignment), """\ mm9.chr10 3015028 ccatttt----------ttattaggtatttagctcatttacatttccaatgctatac--- loxAfr1.s 8958 TCACTTCTA---------------------------------------CCTCCATTCCTT cavPor2.s 1986 ctgtgtc----------t------------------------------------------ tupBel1.s 326691 T----------------------------------------------------------- ponAbe2.c 158040700 TTTTGCCTTTTC------------------------------------------------ calJac1.C 6627 TGCTTTTTCTCAAATCTCCACT-------------------------------------- otoGar1.s 174925 TTTTTTCTATT------------GACTTTTGCCAAATATTCACTTCCA------------ mm9.chr10 3015075 -caaaagtcccc 3015086 loxAfr1.s 8937 ACAAAAGTTCTC 8925 cavPor2.s 1978 ------------ 1978 tupBel1.s 326690 ------------ 326690 ponAbe2.c 158040688 ------------ 158040688 calJac1.C 6649 ------------ 6649 otoGar1.s 174889 ------------ 174889 """, ) self.assertTrue( np.array_equal( alignment.coordinates, np.array( # fmt: off [[ 3015028, 3015029, 3015035, 3015035, 3015035, 3015035, 3015035, 3015036, 3015040, 3015041, 3015066, 3015075, 3015075, 3015086], [ 8958, 8957, 8951, 8949, 8949, 8949, 8949, 8949, 8949, 8949, 8949, 8940, 8936, 8925], [ 1986, 1985, 1979, 1979, 1979, 1979, 1979, 1978, 1978, 1978, 1978, 1978, 1978, 1978], [ 326691, 326690, 326690, 326690, 326690, 326690, 326690, 326690, 326690, 326690, 326690, 326690, 326690, 326690], [158040700, 158040699, 158040693, 158040691, 158040689, 158040688, 158040688, 158040688, 158040688, 158040688, 158040688, 158040688, 158040688, 158040688], [ 6627, 6628, 6634, 6636, 6638, 6639, 6644, 6645, 6649, 6649, 6649, 6649, 6649, 6649], [ 174925, 174924, 174918, 174916, 174914, 174914, 174914, 174914, 174914, 174914, 174889, 174889, 174889, 174889], ] # fmt: on ), ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['c', 'c', 'a', 't', 't', 't', 't', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 't', 't', 'a', 't', 't', 'a', 'g', 'g', 't', 'a', 't', 't', 't', 'a', 'g', 'c', 't', 'c', 'a', 't', 't', 't', 'a', 'c', 'a', 't', 't', 't', 'c', 'c', 'a', 'a', 't', 'g', 'c', 't', 'a', 't', 'a', 'c', '-', '-', '-', '-', 'c', 'a', 'a', 'a', 'a', 'g', 't', 'c', 'c', 'c', 'c'], ['T', 'C', 'A', 'C', 'T', 'T', 'C', 'T', 'A', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'C', 'C', 'T', 'C', 'C', 'A', 'T', 'T', 'C', 'C', 'T', 'T', 'A', 'C', 'A', 'A', 'A', 'A', 'G', 'T', 'T', 'C', 'T', 'C'], ['c', 't', 'g', 't', 'g', 't', 'c', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 't', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-'], ['T', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-'], ['T', 'T', 'T', 'T', 'G', 'C', 'C', 'T', 'T', 'T', 'T', 'C', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-'], ['T', 'G', 'C', 'T', 'T', 'T', 'T', 'T', 'C', 'T', 'C', 'A', 'A', 'A', 'T', 'C', 'T', 'C', 'C', 'A', 'C', 'T', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-'], ['T', 'T', 'T', 'T', 'T', 'T', 'C', 'T', 'A', 'T', 'T', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'G', 'A', 'C', 'T', 'T', 'T', 'T', 'G', 'C', 'C', 'A', 'A', 'A', 'T', 'A', 'T', 'T', 'C', 'A', 'C', 'T', 'T', 'C', 'C', 'A', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.score, 0) self.assertEqual(alignment.sequences[0].id, "mm9.chr10") self.assertEqual(len(alignment.sequences[0].seq), 129993255) self.assertEqual( alignment.sequences[0].seq[3015086 : 3015086 + 2572], "catacccacccacccccactcccctacccgcccactccccctttttggccctggcgttcccctgttctggggcatataaagtttgtgtgtccaatgggcctctctttccagtgatggccgactaggccatcttttgatacatatgcagctagagtcaagagctccggggtactggttagttcataatgttgatccacctatagggttgcagatccctttagctccttgggtactttctctagctcccccattgggagccctgtgatccatccattagctgactgtgggcatccacttctgtgtttgctaggccccggcatagtctcacaagagacagctacatctgggtcctttcgataagatcttgctagtgtatgcaatggtgtcagcgtttggatgctgattatggggtagatccctggataaggcagtctctacatggtccatcctttcatctcagctccaaactttgtctctgtaactccttccaagggtgttttgttcccacttctaaggaggggcatagtgtccacacttcagtcttcatttttcttgagtttcatgtgtttaggaaattgtatcttatatcttgggtatcctaggttttgggctaatatccacttatcagtgagtacatattgtgtgagttcctttgtgaatgtgttacctcactcaggatgatgccctccaggtccatccatttggctaggaatttcataaattaattctttttaatagctgagtagtactccattgtgtagatgtaccacattttctgtatccattcctctgttgaggggcatctgggttctttccagcttctggctattataaataaggctgctatgaacatagtggagcatgtgtccttcttaccagttggggcatcttttggatatatgcccaggagaggtattgctggatcctccggtagtactatgtccaattttctgaggaaccgccagacggatttccagagtggttgtacaagcctgcaatcccaccaacaatggaggagtgttcctctttctccacatcctcgccagcatctgctgtcacctgaatttttgatcttagccattctgactggtgtgaggtggaatctcagggttgttttgatttgcatttctctgatgattaaggatgttgaacatgttttcaggtgcttctctgccattcggtattcctcaggtgagaattctttgttcagttctgagccccattttttaatggggttatttgattttctgaagtccaccttcttgagttctttatatatgttggatattagtcccctatctgatttaggataggtaaagatcctttcccaatctgttggtggtctctttgtgttattgacggtgtcttttgccttgcagaaactttggagtttcattaggtcccatttgtcaattctcgatcttacagcacaagccattgctgttctgttcaggaatttttcccctgtgcccatatcttcaaggcttttccccactttctcctctataagtttcagtgtctctggttttatgtggagttctttgatccatttagatttgaccttagtacaaggagataagtatggatcgattcgcattcttctacatgataacaaccagttgtgccagcaccaattgttgaaaatgctgtctttcttccactggatggttttagctcccttgtcgaagatcaagtgaccataggtgtgtgggttcatttctgggtcttcaattctattccattggtctacttgtctgtctctataccagtaccatgcagtttttaccacaattgctctgtagtaaagctttaggtcaggcatggtgattccaccagaggttcttttatccttgagaagagtttttgctatcctaggttttttgttattccagatgaatttgcaaattgctccttctaattcgttgaagaattgagttggaattgtgatggggattgcattgaatctgtagattgcttttggcaagatagccatttttacaatgttgatcctgccaatccatgagcatgggagagctttccatcttctgagatcttctttaatttctttcttcagagacttgaagtttttatcatacagatctttcacttccttagttagagtcacgccgagatattttatattatttgtgactattgagaagggtgttgtttccctaatttctttctcagcctgtttattctttgtgtagagaaaggccattgacttgtttgagttaattttatatccagctacttcaccgaagctgtttatcaggtttaggagttctctggtggaatttttagggtcacttatatatactatcatatcatctgcaaaaagtgatattttgacttcctcctttccaatttgtatccccttgatctccttttgttgtcgaattgctctggctaatacttcaagtactatgttgaaaaggtagggagaaagtgggcagccttgtctagtccctgattttagtgagattgcttccagcttctctccatttactttgatgttggctactggtttgctgtagattgcttttatcatgtttaggtatgggTGTTCTCG", ) self.assertEqual( alignment[0], "catacccacccacccccactcccctacccgcccactccccctttttggccctggcgttcccctgttctggggcatataaagtttgtgtgtccaatgggcctctctttccagtgatggccgactaggccatcttttgatacatatgcagctagagtcaagagctccggggtactggttagttcataatgttgatccacctatagggttgcagatccctttagctccttgggtactttctctagctcccccattgggagccctgtgatccatccattagctgactgtgggcatccacttctgtgtttgctaggccccggcatagtctcacaagagacagctacatctgggtcctttcgataagatcttgctagtgtatgcaatggtgtcagcgtttggatgctgattatggggtagatccctggataaggcagtctctacatggtccatcctttcatctcagctccaaactttgtctctgtaactccttccaagggtgttttgttcccacttctaaggaggggcatagtgtccacacttcagtcttcatttttcttgagtttcatgtgtttaggaaattgtatcttatatcttgggtatcctaggttttgggctaatatccacttatcagtgagtacatattgtgtgagttcctttgtgaatgtgttacctcactcaggatgatgccctccaggtccatccatttggctaggaatttcataaattaattctttttaatagctgagtagtactccattgtgtagatgtaccacattttctgtatccattcctctgttgaggggcatctgggttctttccagcttctggctattataaataaggctgctatgaacatagtggagcatgtgtccttcttaccagttggggcatcttttggatatatgcccaggagaggtattgctggatcctccggtagtactatgtccaattttctgaggaaccgccagacggatttccagagtggttgtacaagcctgcaatcccaccaacaatggaggagtgttcctctttctccacatcctcgccagcatctgctgtcacctgaatttttgatcttagccattctgactggtgtgaggtggaatctcagggttgttttgatttgcatttctctgatgattaaggatgttgaacatgttttcaggtgcttctctgccattcggtattcctcaggtgagaattctttgttcagttctgagccccattttttaatggggttatttgattttctgaagtccaccttcttgagttctttatatatgttggatattagtcccctatctgatttaggataggtaaagatcctttcccaatctgttggtggtctctttgtgttattgacggtgtcttttgccttgcagaaactttggagtttcattaggtcccatttgtcaattctcgatcttacagcacaagccattgctgttctgttcaggaatttttcccctgtgcccatatcttcaaggcttttccccactttctcctctataagtttcagtgtctctggttttatgtggagttctttgatccatttagatttgaccttagtacaaggagataagtatggatcgattcgcattcttctacatgataacaaccagttgtgccagcaccaattgttgaaaatgctgtctttcttccactggatggttttagctcccttgtcgaagatcaagtgaccataggtgtgtgggttcatttctgggtcttcaattctattccattggtctacttgtctgtctctataccagtaccatgcagtttttaccacaattgctctgtagtaaagctttaggtcaggcatggtgattccaccagaggttcttttatccttgagaagagtttttgctatcctaggttttttgttattccagatgaatttgcaaattgctccttctaattcgttgaagaattgagttggaattgtgatggggattgcattgaatctgtagattgcttttggcaagatagccatttttacaatgttgatcctgccaatccatgagcatgggagagctttccatcttctgagatcttctttaatttctttcttcagagacttgaagtttttatcatacagatctttcacttccttagttagagtcacgccgagatattttatattatttgtgactattgagaagggtgttgtttccctaatttctttctcagcctgtttattctttgtgtagagaaaggccattgacttgtttgagttaattttatatccagctacttcaccgaagctgtttatcaggtttaggagttctctggtggaatttttagggtcacttatatatactatcatatcatctgcaaaaagtgatattttgacttcctcctttccaatttgtatccccttgatctccttttgttgtcgaattgctctggctaatacttcaagtactatgttgaaaaggtagggagaaagtgggcagccttgtctagtccctgattttagtgagattgcttccagcttctctccatttactttgatgttggctactggtttgctgtagattgcttttatcatgtttaggtatgggTGTTCTCG", ) empty = alignment.annotations["empty"][0] (record, segment, status) = empty self.assertEqual(record.id, "ornAna1.chr2") self.assertEqual(len(record.seq), 54797317) self.assertEqual(segment, (40046122, 40040432)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][1] (record, segment, status) = empty self.assertEqual(record.id, "calJac1.Contig6394") self.assertEqual(len(record.seq), 133105) self.assertEqual(segment, (6649, 10128)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][2] (record, segment, status) = empty self.assertEqual(record.id, "tupBel1.scaffold_114895.1-498454") self.assertEqual(len(record.seq), 498454) self.assertEqual(segment, (326690, 324316)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][3] (record, segment, status) = empty self.assertEqual(record.id, "echTel1.scaffold_288249") self.assertEqual(len(record.seq), 100002) self.assertEqual(segment, (87661, 95225)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][4] (record, segment, status) = empty self.assertEqual(record.id, "cavPor2.scaffold_216473") self.assertEqual(len(record.seq), 10026) self.assertEqual(segment, (1978, 606)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][5] (record, segment, status) = empty self.assertEqual(record.id, "otoGar1.scaffold_334.1-359464") self.assertEqual(len(record.seq), 359464) self.assertEqual(segment, (174889, 174752)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][6] (record, segment, status) = empty self.assertEqual(record.id, "hg18.chr6") self.assertEqual(len(record.seq), 170899992) self.assertEqual(segment, (155028517, 155028517)) self.assertEqual(status, "C") empty = alignment.annotations["empty"][7] (record, segment, status) = empty self.assertEqual(record.id, "panTro2.chr6") self.assertEqual(len(record.seq), 173908612) self.assertEqual(segment, (157518570, 157518570)) self.assertEqual(status, "C") empty = alignment.annotations["empty"][8] (record, segment, status) = empty self.assertEqual(record.id, "ponAbe2.chr6") self.assertEqual(len(record.seq), 174210431) self.assertEqual(segment, (158040688, 158040613)) self.assertEqual(status, "I") self.assertEqual(len(alignment.sequences), 1) self.assertEqual(len(alignment.annotations["empty"]), 9) self.assertEqual( str(alignment), """\ mm9.chr10 3015086 catacccacccacccccactcccctacccgcccactccccctttttggccctggcgttcc mm9.chr10 3015146 cctgttctggggcatataaagtttgtgtgtccaatgggcctctctttccagtgatggccg mm9.chr10 3015206 actaggccatcttttgatacatatgcagctagagtcaagagctccggggtactggttagt mm9.chr10 3015266 tcataatgttgatccacctatagggttgcagatccctttagctccttgggtactttctct mm9.chr10 3015326 agctcccccattgggagccctgtgatccatccattagctgactgtgggcatccacttctg mm9.chr10 3015386 tgtttgctaggccccggcatagtctcacaagagacagctacatctgggtcctttcgataa mm9.chr10 3015446 gatcttgctagtgtatgcaatggtgtcagcgtttggatgctgattatggggtagatccct mm9.chr10 3015506 ggataaggcagtctctacatggtccatcctttcatctcagctccaaactttgtctctgta mm9.chr10 3015566 actccttccaagggtgttttgttcccacttctaaggaggggcatagtgtccacacttcag mm9.chr10 3015626 tcttcatttttcttgagtttcatgtgtttaggaaattgtatcttatatcttgggtatcct mm9.chr10 3015686 aggttttgggctaatatccacttatcagtgagtacatattgtgtgagttcctttgtgaat mm9.chr10 3015746 gtgttacctcactcaggatgatgccctccaggtccatccatttggctaggaatttcataa mm9.chr10 3015806 attaattctttttaatagctgagtagtactccattgtgtagatgtaccacattttctgta mm9.chr10 3015866 tccattcctctgttgaggggcatctgggttctttccagcttctggctattataaataagg mm9.chr10 3015926 ctgctatgaacatagtggagcatgtgtccttcttaccagttggggcatcttttggatata mm9.chr10 3015986 tgcccaggagaggtattgctggatcctccggtagtactatgtccaattttctgaggaacc mm9.chr10 3016046 gccagacggatttccagagtggttgtacaagcctgcaatcccaccaacaatggaggagtg mm9.chr10 3016106 ttcctctttctccacatcctcgccagcatctgctgtcacctgaatttttgatcttagcca mm9.chr10 3016166 ttctgactggtgtgaggtggaatctcagggttgttttgatttgcatttctctgatgatta mm9.chr10 3016226 aggatgttgaacatgttttcaggtgcttctctgccattcggtattcctcaggtgagaatt mm9.chr10 3016286 ctttgttcagttctgagccccattttttaatggggttatttgattttctgaagtccacct mm9.chr10 3016346 tcttgagttctttatatatgttggatattagtcccctatctgatttaggataggtaaaga mm9.chr10 3016406 tcctttcccaatctgttggtggtctctttgtgttattgacggtgtcttttgccttgcaga mm9.chr10 3016466 aactttggagtttcattaggtcccatttgtcaattctcgatcttacagcacaagccattg mm9.chr10 3016526 ctgttctgttcaggaatttttcccctgtgcccatatcttcaaggcttttccccactttct mm9.chr10 3016586 cctctataagtttcagtgtctctggttttatgtggagttctttgatccatttagatttga mm9.chr10 3016646 ccttagtacaaggagataagtatggatcgattcgcattcttctacatgataacaaccagt mm9.chr10 3016706 tgtgccagcaccaattgttgaaaatgctgtctttcttccactggatggttttagctccct mm9.chr10 3016766 tgtcgaagatcaagtgaccataggtgtgtgggttcatttctgggtcttcaattctattcc mm9.chr10 3016826 attggtctacttgtctgtctctataccagtaccatgcagtttttaccacaattgctctgt mm9.chr10 3016886 agtaaagctttaggtcaggcatggtgattccaccagaggttcttttatccttgagaagag mm9.chr10 3016946 tttttgctatcctaggttttttgttattccagatgaatttgcaaattgctccttctaatt mm9.chr10 3017006 cgttgaagaattgagttggaattgtgatggggattgcattgaatctgtagattgcttttg mm9.chr10 3017066 gcaagatagccatttttacaatgttgatcctgccaatccatgagcatgggagagctttcc mm9.chr10 3017126 atcttctgagatcttctttaatttctttcttcagagacttgaagtttttatcatacagat mm9.chr10 3017186 ctttcacttccttagttagagtcacgccgagatattttatattatttgtgactattgaga mm9.chr10 3017246 agggtgttgtttccctaatttctttctcagcctgtttattctttgtgtagagaaaggcca mm9.chr10 3017306 ttgacttgtttgagttaattttatatccagctacttcaccgaagctgtttatcaggttta mm9.chr10 3017366 ggagttctctggtggaatttttagggtcacttatatatactatcatatcatctgcaaaaa mm9.chr10 3017426 gtgatattttgacttcctcctttccaatttgtatccccttgatctccttttgttgtcgaa mm9.chr10 3017486 ttgctctggctaatacttcaagtactatgttgaaaaggtagggagaaagtgggcagcctt mm9.chr10 3017546 gtctagtccctgattttagtgagattgcttccagcttctctccatttactttgatgttgg mm9.chr10 3017606 ctactggtttgctgtagattgcttttatcatgtttaggtatgggTGTTCTCG 3017658 """, ) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[3015086, 3017658]])) ) alignment = next(alignments) self.assertAlmostEqual(alignment.score, 12170) self.assertEqual(alignment.sequences[0].id, "mm9.chr10") self.assertEqual(len(alignment.sequences[0].seq), 129993255) self.assertEqual( alignment.sequences[0].seq[3017658 : 3017658 + 85], "TTTTTATTTGCAGGTTTCTTTACAGTTCTCTTTCATTCTTCTCCTCTTTTCTTCTGTTGACCTTTATCAGATTTCTGCTTTAACC", ) self.assertEqual( alignment[0], "TTTTTATTTGCAGGTTTCTTTAC----AGTTCTCTTTCATTCTTCTCCTCTTTTCTTCTGTTGACCTTTATCAGATTTCTGCTTTAACC", ) self.assertEqual(alignment.sequences[1].id, "hg18.chr6") self.assertEqual(len(alignment.sequences[1].seq), 170899992) self.assertEqual( alignment.sequences[1].seq[155028434 : 155028434 + 83], "GGTGGAAGTGGAGATTTGGGAAAAGGCAAAAAAATAAATAAGAGAGAGAGATAACTTGCTATAAATAACCCTGCCAAGAAAGG", ) self.assertEqual( alignment[1], "CCTTTCTTGGCAGGGTTATTTATAGCAAGTTATCTCTCTCTCTTA------TTTATTTTTTTGCCTTTTCCCAAATCTCCACTTCCACC", ) self.assertEqual(alignment.sequences[1].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[1].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[1].annotations["rightStatus"], "I") self.assertEqual(alignment.sequences[1].annotations["rightCount"], 53) self.assertEqual(alignment.sequences[2].id, "panTro2.chr6") self.assertEqual(len(alignment.sequences[2].seq), 173908612) self.assertEqual( alignment.sequences[2].seq[157518487 : 157518487 + 83], "GGTGGAAGTGGAGATTTGGGAAAAGGCAAAAAAATAAATAAGAGAGAGAGATAACTTGCTATAAATAACCCTGCCAAGAAAGG", ) self.assertEqual( alignment[2], "CCTTTCTTGGCAGGGTTATTTATAGCAAGTTATCTCTCTCTCTTA------TTTATTTTTTTGCCTTTTCCCAAATCTCCACTTCCACC", ) self.assertEqual( alignment.sequences[2].annotations["quality"], "99999999999999999999999999999999999999999999999999999999999999999999999999999999999", ) self.assertEqual(alignment.sequences[2].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[2].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[2].annotations["rightStatus"], "I") self.assertEqual(alignment.sequences[2].annotations["rightCount"], 53) empty = alignment.annotations["empty"][0] (record, segment, status) = empty self.assertEqual(record.id, "ornAna1.chr2") self.assertEqual(len(record.seq), 54797317) self.assertEqual(segment, (40046122, 40040432)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][1] (record, segment, status) = empty self.assertEqual(record.id, "calJac1.Contig6394") self.assertEqual(len(record.seq), 133105) self.assertEqual(segment, (6649, 10128)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][2] (record, segment, status) = empty self.assertEqual(record.id, "tupBel1.scaffold_114895.1-498454") self.assertEqual(len(record.seq), 498454) self.assertEqual(segment, (326690, 324316)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][3] (record, segment, status) = empty self.assertEqual(record.id, "echTel1.scaffold_288249") self.assertEqual(len(record.seq), 100002) self.assertEqual(segment, (87661, 95225)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][4] (record, segment, status) = empty self.assertEqual(record.id, "cavPor2.scaffold_216473") self.assertEqual(len(record.seq), 10026) self.assertEqual(segment, (1978, 606)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][5] (record, segment, status) = empty self.assertEqual(record.id, "otoGar1.scaffold_334.1-359464") self.assertEqual(len(record.seq), 359464) self.assertEqual(segment, (174889, 174752)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][6] (record, segment, status) = empty self.assertEqual(record.id, "ponAbe2.chr6") self.assertEqual(len(record.seq), 174210431) self.assertEqual(segment, (158040688, 158040613)) self.assertEqual(status, "I") self.assertEqual(len(alignment.sequences), 3) self.assertEqual(len(alignment.annotations["empty"]), 7) self.assertEqual( str(alignment), """\ mm9.chr10 3017658 TTTTTATTTGCAGGTTTCTTTAC----AGTTCTCTTTCATTCTTCTCCTCTTTTCTTCTG hg18.chr6 155028517 CCTTTCTTGGCAGGGTTATTTATAGCAAGTTATCTCTCTCTCTTA------TTTATTTTT panTro2.c 157518570 CCTTTCTTGGCAGGGTTATTTATAGCAAGTTATCTCTCTCTCTTA------TTTATTTTT mm9.chr10 3017714 TTGACCTTTATCAGATTTCTGCTTTAACC 3017743 hg18.chr6 155028463 TTGCCTTTTCCCAAATCTCCACTTCCACC 155028434 panTro2.c 157518516 TTGCCTTTTCCCAAATCTCCACTTCCACC 157518487 """, ) self.assertTrue( np.array_equal( alignment.coordinates, np.array( # fmt: off [[ 3017658, 3017681, 3017681, 3017699, 3017705, 3017743], [155028517, 155028494, 155028490, 155028472, 155028472, 155028434], [157518570, 157518547, 157518543, 157518525, 157518525, 157518487], ] # fmt: on ), ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['T', 'T', 'T', 'T', 'T', 'A', 'T', 'T', 'T', 'G', 'C', 'A', 'G', 'G', 'T', 'T', 'T', 'C', 'T', 'T', 'T', 'A', 'C', '-', '-', '-', '-', 'A', 'G', 'T', 'T', 'C', 'T', 'C', 'T', 'T', 'T', 'C', 'A', 'T', 'T', 'C', 'T', 'T', 'C', 'T', 'C', 'C', 'T', 'C', 'T', 'T', 'T', 'T', 'C', 'T', 'T', 'C', 'T', 'G', 'T', 'T', 'G', 'A', 'C', 'C', 'T', 'T', 'T', 'A', 'T', 'C', 'A', 'G', 'A', 'T', 'T', 'T', 'C', 'T', 'G', 'C', 'T', 'T', 'T', 'A', 'A', 'C', 'C'], ['C', 'C', 'T', 'T', 'T', 'C', 'T', 'T', 'G', 'G', 'C', 'A', 'G', 'G', 'G', 'T', 'T', 'A', 'T', 'T', 'T', 'A', 'T', 'A', 'G', 'C', 'A', 'A', 'G', 'T', 'T', 'A', 'T', 'C', 'T', 'C', 'T', 'C', 'T', 'C', 'T', 'C', 'T', 'T', 'A', '-', '-', '-', '-', '-', '-', 'T', 'T', 'T', 'A', 'T', 'T', 'T', 'T', 'T', 'T', 'T', 'G', 'C', 'C', 'T', 'T', 'T', 'T', 'C', 'C', 'C', 'A', 'A', 'A', 'T', 'C', 'T', 'C', 'C', 'A', 'C', 'T', 'T', 'C', 'C', 'A', 'C', 'C'], ['C', 'C', 'T', 'T', 'T', 'C', 'T', 'T', 'G', 'G', 'C', 'A', 'G', 'G', 'G', 'T', 'T', 'A', 'T', 'T', 'T', 'A', 'T', 'A', 'G', 'C', 'A', 'A', 'G', 'T', 'T', 'A', 'T', 'C', 'T', 'C', 'T', 'C', 'T', 'C', 'T', 'C', 'T', 'T', 'A', '-', '-', '-', '-', '-', '-', 'T', 'T', 'T', 'A', 'T', 'T', 'T', 'T', 'T', 'T', 'T', 'G', 'C', 'C', 'T', 'T', 'T', 'T', 'C', 'C', 'C', 'A', 'A', 'A', 'T', 'C', 'T', 'C', 'C', 'A', 'C', 'T', 'T', 'C', 'C', 'A', 'C', 'C']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.score, 0) self.assertEqual(alignment.sequences[0].id, "mm9.chr10") self.assertEqual(len(alignment.sequences[0].seq), 129993255) self.assertEqual( alignment.sequences[0].seq[3017743 : 3017743 + 418], "ACCACAGACCTTCTGTTTAGTCCAAAGGACGCAAATTATGTATCCACTTtagtaggaggctgacccgcagcctacatgaaccaggtatttctggaaggcaggctggggttgaaagagaaattagatggtgagaaaagaataatgaggccaagacaaatttttctcttatcaaggcccaagagagtttactaagagactatgcttaaaagggggaaggcccatcccccccccccctcgcgccagtctatccttggtgctttgtcaccatgccatcagcacttggtcggcaggtagcagaatctcagggcagttgacacttcaaaagaaaccagccaagtcagaaagctgcactgcaggagacctgcactcagtggtgacaaggtctgtaccagcctgcttcaggctgggggaggctaca", ) self.assertEqual( alignment[0], "ACCACAGACCTTCTGTTTAGTCCAAAGGACGCAAATTATGTATCCACTTtagtaggaggctgacccgcagcctacatgaaccaggtatttctggaaggcaggctggggttgaaagagaaattagatggtgagaaaagaataatgaggccaagacaaatttttctcttatcaaggcccaagagagtttactaagagactatgcttaaaagggggaaggcccatcccccccccccctcgcgccagtctatccttggtgctttgtcaccatgccatcagcacttggtcggcaggtagcagaatctcagggcagttgacacttcaaaagaaaccagccaagtcagaaagctgcactgcaggagacctgcactcagtggtgacaaggtctgtaccagcctgcttcaggctgggggaggctaca", ) empty = alignment.annotations["empty"][0] (record, segment, status) = empty self.assertEqual(record.id, "ornAna1.chr2") self.assertEqual(len(record.seq), 54797317) self.assertEqual(segment, (40046122, 40040432)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][1] (record, segment, status) = empty self.assertEqual(record.id, "calJac1.Contig6394") self.assertEqual(len(record.seq), 133105) self.assertEqual(segment, (6649, 10128)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][2] (record, segment, status) = empty self.assertEqual(record.id, "tupBel1.scaffold_114895.1-498454") self.assertEqual(len(record.seq), 498454) self.assertEqual(segment, (326690, 324316)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][3] (record, segment, status) = empty self.assertEqual(record.id, "echTel1.scaffold_288249") self.assertEqual(len(record.seq), 100002) self.assertEqual(segment, (87661, 95225)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][4] (record, segment, status) = empty self.assertEqual(record.id, "cavPor2.scaffold_216473") self.assertEqual(len(record.seq), 10026) self.assertEqual(segment, (1978, 606)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][5] (record, segment, status) = empty self.assertEqual(record.id, "otoGar1.scaffold_334.1-359464") self.assertEqual(len(record.seq), 359464) self.assertEqual(segment, (174889, 174752)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][6] (record, segment, status) = empty self.assertEqual(record.id, "hg18.chr6") self.assertEqual(len(record.seq), 170899992) self.assertEqual(segment, (155028434, 155028381)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][7] (record, segment, status) = empty self.assertEqual(record.id, "panTro2.chr6") self.assertEqual(len(record.seq), 173908612) self.assertEqual(segment, (157518487, 157518434)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][8] (record, segment, status) = empty self.assertEqual(record.id, "ponAbe2.chr6") self.assertEqual(len(record.seq), 174210431) self.assertEqual(segment, (158040688, 158040613)) self.assertEqual(status, "I") self.assertEqual(len(alignment.sequences), 1) self.assertEqual(len(alignment.annotations["empty"]), 9) self.assertEqual( str(alignment), """\ mm9.chr10 3017743 ACCACAGACCTTCTGTTTAGTCCAAAGGACGCAAATTATGTATCCACTTtagtaggaggc mm9.chr10 3017803 tgacccgcagcctacatgaaccaggtatttctggaaggcaggctggggttgaaagagaaa mm9.chr10 3017863 ttagatggtgagaaaagaataatgaggccaagacaaatttttctcttatcaaggcccaag mm9.chr10 3017923 agagtttactaagagactatgcttaaaagggggaaggcccatcccccccccccctcgcgc mm9.chr10 3017983 cagtctatccttggtgctttgtcaccatgccatcagcacttggtcggcaggtagcagaat mm9.chr10 3018043 ctcagggcagttgacacttcaaaagaaaccagccaagtcagaaagctgcactgcaggaga mm9.chr10 3018103 cctgcactcagtggtgacaaggtctgtaccagcctgcttcaggctgggggaggctaca mm9.chr10 3018161 """, ) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[3017743, 3018161]])) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['A', 'C', 'C', 'A', 'C', 'A', 'G', 'A', 'C', 'C', 'T', 'T', 'C', 'T', 'G', 'T', 'T', 'T', 'A', 'G', 'T', 'C', 'C', 'A', 'A', 'A', 'G', 'G', 'A', 'C', 'G', 'C', 'A', 'A', 'A', 'T', 'T', 'A', 'T', 'G', 'T', 'A', 'T', 'C', 'C', 'A', 'C', 'T', 'T', 't', 'a', 'g', 't', 'a', 'g', 'g', 'a', 'g', 'g', 'c', 't', 'g', 'a', 'c', 'c', 'c', 'g', 'c', 'a', 'g', 'c', 'c', 't', 'a', 'c', 'a', 't', 'g', 'a', 'a', 'c', 'c', 'a', 'g', 'g', 't', 'a', 't', 't', 't', 'c', 't', 'g', 'g', 'a', 'a', 'g', 'g', 'c', 'a', 'g', 'g', 'c', 't', 'g', 'g', 'g', 'g', 't', 't', 'g', 'a', 'a', 'a', 'g', 'a', 'g', 'a', 'a', 'a', 't', 't', 'a', 'g', 'a', 't', 'g', 'g', 't', 'g', 'a', 'g', 'a', 'a', 'a', 'a', 'g', 'a', 'a', 't', 'a', 'a', 't', 'g', 'a', 'g', 'g', 'c', 'c', 'a', 'a', 'g', 'a', 'c', 'a', 'a', 'a', 't', 't', 't', 't', 't', 'c', 't', 'c', 't', 't', 'a', 't', 'c', 'a', 'a', 'g', 'g', 'c', 'c', 'c', 'a', 'a', 'g', 'a', 'g', 'a', 'g', 't', 't', 't', 'a', 'c', 't', 'a', 'a', 'g', 'a', 'g', 'a', 'c', 't', 'a', 't', 'g', 'c', 't', 't', 'a', 'a', 'a', 'a', 'g', 'g', 'g', 'g', 'g', 'a', 'a', 'g', 'g', 'c', 'c', 'c', 'a', 't', 'c', 'c', 'c', 'c', 'c', 'c', 'c', 'c', 'c', 'c', 'c', 'c', 't', 'c', 'g', 'c', 'g', 'c', 'c', 'a', 'g', 't', 'c', 't', 'a', 't', 'c', 'c', 't', 't', 'g', 'g', 't', 'g', 'c', 't', 't', 't', 'g', 't', 'c', 'a', 'c', 'c', 'a', 't', 'g', 'c', 'c', 'a', 't', 'c', 'a', 'g', 'c', 'a', 'c', 't', 't', 'g', 'g', 't', 'c', 'g', 'g', 'c', 'a', 'g', 'g', 't', 'a', 'g', 'c', 'a', 'g', 'a', 'a', 't', 'c', 't', 'c', 'a', 'g', 'g', 'g', 'c', 'a', 'g', 't', 't', 'g', 'a', 'c', 'a', 'c', 't', 't', 'c', 'a', 'a', 'a', 'a', 'g', 'a', 'a', 'a', 'c', 'c', 'a', 'g', 'c', 'c', 'a', 'a', 'g', 't', 'c', 'a', 'g', 'a', 'a', 'a', 'g', 'c', 't', 'g', 'c', 'a', 'c', 't', 'g', 'c', 'a', 'g', 'g', 'a', 'g', 'a', 'c', 'c', 't', 'g', 'c', 'a', 'c', 't', 'c', 'a', 'g', 't', 'g', 'g', 't', 'g', 'a', 'c', 'a', 'a', 'g', 'g', 't', 'c', 't', 'g', 't', 'a', 'c', 'c', 'a', 'g', 'c', 'c', 't', 'g', 'c', 't', 't', 'c', 'a', 'g', 'g', 'c', 't', 'g', 'g', 'g', 'g', 'g', 'a', 'g', 'g', 'c', 't', 'a', 'c', 'a']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.score, 22499) self.assertEqual(alignment.sequences[0].id, "mm9.chr10") self.assertEqual(len(alignment.sequences[0].seq), 129993255) self.assertEqual( alignment.sequences[0].seq[3018161 : 3018161 + 69], "ATCCACAAAAGAGACAAAGAAGAAAACCAAAAGAAAAGATTGTAGCTTAAAACAATTCCATTTTATTGA", ) self.assertEqual( alignment[0], "ATCCACAAAAGAGAC-----AAAGAAGAAAACCAAAAGAAAAGATTGTAGCTTAAAACAATTCCATTTTATTGA", ) self.assertEqual(alignment.sequences[1].id, "panTro2.chr6") self.assertEqual(len(alignment.sequences[1].seq), 173908612) self.assertEqual( alignment.sequences[1].seq[157518369 : 157518369 + 65], "TCAATAAAATAAAATTGTTTTATGGTACAAACTTTTCTTATGGTTAATTGTTTTCCTTTGTAGGT", ) self.assertEqual( alignment[1], "ACCTACAAAGG---------AAAACAATTAACCATAAGAAAAGTTTGTACCATAAAACAATTTTATTTTATTGA", ) self.assertEqual( alignment.sequences[1].annotations["quality"], "99999999999999999999999999999999999999999999999999999999999999999", ) self.assertEqual(alignment.sequences[1].annotations["leftStatus"], "I") self.assertEqual(alignment.sequences[1].annotations["leftCount"], 53) self.assertEqual(alignment.sequences[1].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[1].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[2].id, "hg18.chr6") self.assertEqual(len(alignment.sequences[2].seq), 170899992) self.assertEqual( alignment.sequences[2].seq[155028316 : 155028316 + 65], "TCAATAAAATAAAATTGTTTTATGGTACAAACTTTTCTTGTGGTTAATTGTTTTCCTTTGTAGGT", ) self.assertEqual( alignment[2], "ACCTACAAAGG---------AAAACAATTAACCACAAGAAAAGTTTGTACCATAAAACAATTTTATTTTATTGA", ) self.assertEqual(alignment.sequences[2].annotations["leftStatus"], "I") self.assertEqual(alignment.sequences[2].annotations["leftCount"], 53) self.assertEqual(alignment.sequences[2].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[2].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[3].id, "ponAbe2.chr6") self.assertEqual(len(alignment.sequences[3].seq), 174210431) self.assertEqual( alignment.sequences[3].seq[158040552 : 158040552 + 61], "TCAATAAAATAAAATTGTTTTATGGTACAAACTTTTCTTATGGTTAATTGTTTTCCTTTGT", ) self.assertEqual( alignment[3], "-------------ACAAAGGAAAACAATTAACCATAAGAAAAGTTTGTACCATAAAACAATTTTATTTTATTGA", ) self.assertEqual(alignment.sequences[3].annotations["leftStatus"], "I") self.assertEqual(alignment.sequences[3].annotations["leftCount"], 75) self.assertEqual(alignment.sequences[3].annotations["rightStatus"], "I") self.assertEqual(alignment.sequences[3].annotations["rightCount"], 97) empty = alignment.annotations["empty"][0] (record, segment, status) = empty self.assertEqual(record.id, "ornAna1.chr2") self.assertEqual(len(record.seq), 54797317) self.assertEqual(segment, (40046122, 40040432)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][1] (record, segment, status) = empty self.assertEqual(record.id, "calJac1.Contig6394") self.assertEqual(len(record.seq), 133105) self.assertEqual(segment, (6649, 10128)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][2] (record, segment, status) = empty self.assertEqual(record.id, "tupBel1.scaffold_114895.1-498454") self.assertEqual(len(record.seq), 498454) self.assertEqual(segment, (326690, 324316)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][3] (record, segment, status) = empty self.assertEqual(record.id, "echTel1.scaffold_288249") self.assertEqual(len(record.seq), 100002) self.assertEqual(segment, (87661, 95225)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][4] (record, segment, status) = empty self.assertEqual(record.id, "cavPor2.scaffold_216473") self.assertEqual(len(record.seq), 10026) self.assertEqual(segment, (1978, 606)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][5] (record, segment, status) = empty self.assertEqual(record.id, "otoGar1.scaffold_334.1-359464") self.assertEqual(len(record.seq), 359464) self.assertEqual(segment, (174889, 174752)) self.assertEqual(status, "I") self.assertEqual(len(alignment.sequences), 4) self.assertEqual(len(alignment.annotations["empty"]), 6) self.assertEqual( str(alignment), """\ mm9.chr10 3018161 ATCCACAAAAGAGAC-----AAAGAAGAAAACCAAAAGAAAAGATTGTAGCTTAAAACAA panTro2.c 157518434 ACCTACAAAGG---------AAAACAATTAACCATAAGAAAAGTTTGTACCATAAAACAA hg18.chr6 155028381 ACCTACAAAGG---------AAAACAATTAACCACAAGAAAAGTTTGTACCATAAAACAA ponAbe2.c 158040613 -------------ACAAAGGAAAACAATTAACCATAAGAAAAGTTTGTACCATAAAACAA mm9.chr10 3018216 TTCCATTTTATTGA 3018230 panTro2.c 157518383 TTTTATTTTATTGA 157518369 hg18.chr6 155028330 TTTTATTTTATTGA 155028316 ponAbe2.c 158040566 TTTTATTTTATTGA 158040552 """, ) self.assertTrue( np.array_equal( alignment.coordinates, np.array( # fmt: off [[ 3018161, 3018172, 3018174, 3018176, 3018176, 3018230], [157518434, 157518423, 157518423, 157518423, 157518423, 157518369], [155028381, 155028370, 155028370, 155028370, 155028370, 155028316], [158040613, 158040613, 158040613, 158040611, 158040606, 158040552], ] # fmt: on ), ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['A', 'T', 'C', 'C', 'A', 'C', 'A', 'A', 'A', 'A', 'G', 'A', 'G', 'A', 'C', '-', '-', '-', '-', '-', 'A', 'A', 'A', 'G', 'A', 'A', 'G', 'A', 'A', 'A', 'A', 'C', 'C', 'A', 'A', 'A', 'A', 'G', 'A', 'A', 'A', 'A', 'G', 'A', 'T', 'T', 'G', 'T', 'A', 'G', 'C', 'T', 'T', 'A', 'A', 'A', 'A', 'C', 'A', 'A', 'T', 'T', 'C', 'C', 'A', 'T', 'T', 'T', 'T', 'A', 'T', 'T', 'G', 'A'], ['A', 'C', 'C', 'T', 'A', 'C', 'A', 'A', 'A', 'G', 'G', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'A', 'A', 'A', 'A', 'C', 'A', 'A', 'T', 'T', 'A', 'A', 'C', 'C', 'A', 'T', 'A', 'A', 'G', 'A', 'A', 'A', 'A', 'G', 'T', 'T', 'T', 'G', 'T', 'A', 'C', 'C', 'A', 'T', 'A', 'A', 'A', 'A', 'C', 'A', 'A', 'T', 'T', 'T', 'T', 'A', 'T', 'T', 'T', 'T', 'A', 'T', 'T', 'G', 'A'], ['A', 'C', 'C', 'T', 'A', 'C', 'A', 'A', 'A', 'G', 'G', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'A', 'A', 'A', 'A', 'C', 'A', 'A', 'T', 'T', 'A', 'A', 'C', 'C', 'A', 'C', 'A', 'A', 'G', 'A', 'A', 'A', 'A', 'G', 'T', 'T', 'T', 'G', 'T', 'A', 'C', 'C', 'A', 'T', 'A', 'A', 'A', 'A', 'C', 'A', 'A', 'T', 'T', 'T', 'T', 'A', 'T', 'T', 'T', 'T', 'A', 'T', 'T', 'G', 'A'], ['-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'A', 'C', 'A', 'A', 'A', 'G', 'G', 'A', 'A', 'A', 'A', 'C', 'A', 'A', 'T', 'T', 'A', 'A', 'C', 'C', 'A', 'T', 'A', 'A', 'G', 'A', 'A', 'A', 'A', 'G', 'T', 'T', 'T', 'G', 'T', 'A', 'C', 'C', 'A', 'T', 'A', 'A', 'A', 'A', 'C', 'A', 'A', 'T', 'T', 'T', 'T', 'A', 'T', 'T', 'T', 'T', 'A', 'T', 'T', 'G', 'A']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.score, 4781) self.assertEqual(alignment.sequences[0].id, "mm9.chr10") self.assertEqual(len(alignment.sequences[0].seq), 129993255) self.assertEqual( alignment.sequences[0].seq[3018230 : 3018230 + 129], "AGGACAAAATAATACAGAtttttttttttttttttttttGCAGTACTGGAAATGGAATGAATGTCCCTCACAATCACTATCAAGGTCCCTATCAAGGCAATCACTCTGTCACCGAGCTACAGCCCCAGC", ) self.assertEqual( alignment[0], "AGGA-CAAAATAATACAGAtttttttttttttttttttttGCAGTACTGGAAATGGAATGAATGTCCCTCACAATCACTATCAAGGTCCCTATCAAGGCAATCACTCTGTCACCGAGCTA-CAGCCCCAGC", ) self.assertEqual(alignment.sequences[1].id, "hg18.chr6") self.assertEqual(len(alignment.sequences[1].seq), 170899992) self.assertEqual( alignment.sequences[1].seq[155028221 : 155028221 + 95], "CATATACCTAATAAATCTATATATGTGTAAATTCTTTTTCATAATGACTATCAGAACATTGGGAGCCAGGTTCTGATATATATTGATTGGATTAT", ) self.assertEqual( alignment[1], "ATAATCCAATCAATATATAT---------------------CAGAACCTGGCTCCCAATG-----TTCTGATAGTCATTATGAA----------AAAGAATTTACACATATATAGATTTATTAGGTATATG", ) self.assertEqual(alignment.sequences[1].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[1].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[1].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[1].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[2].id, "panTro2.chr6") self.assertEqual(len(alignment.sequences[2].seq), 173908612) self.assertEqual( alignment.sequences[2].seq[157518274 : 157518274 + 95], "catatacctaataaatctatatatgtgtaaatTCTTTTTCACAATGACTATCAGAACATTGGGAGCCAGGTTCTGATATATATTGATTGGATTAT", ) self.assertEqual( alignment[2], "ATAATCCAATCAATATATAT---------------------CAGAACCTGGCTCCCAATG-----TTCTGATAGTCATTGTGAA----------AAAGAatttacacatatatagatttattaggtatatg", ) self.assertEqual( alignment.sequences[2].annotations["quality"], "99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999", ) self.assertEqual(alignment.sequences[2].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[2].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[2].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[2].annotations["rightCount"], 0) empty = alignment.annotations["empty"][0] (record, segment, status) = empty self.assertEqual(record.id, "ornAna1.chr2") self.assertEqual(len(record.seq), 54797317) self.assertEqual(segment, (40046122, 40040432)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][1] (record, segment, status) = empty self.assertEqual(record.id, "calJac1.Contig6394") self.assertEqual(len(record.seq), 133105) self.assertEqual(segment, (6649, 10128)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][2] (record, segment, status) = empty self.assertEqual(record.id, "tupBel1.scaffold_114895.1-498454") self.assertEqual(len(record.seq), 498454) self.assertEqual(segment, (326690, 324316)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][3] (record, segment, status) = empty self.assertEqual(record.id, "echTel1.scaffold_288249") self.assertEqual(len(record.seq), 100002) self.assertEqual(segment, (87661, 95225)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][4] (record, segment, status) = empty self.assertEqual(record.id, "cavPor2.scaffold_216473") self.assertEqual(len(record.seq), 10026) self.assertEqual(segment, (1978, 606)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][5] (record, segment, status) = empty self.assertEqual(record.id, "otoGar1.scaffold_334.1-359464") self.assertEqual(len(record.seq), 359464) self.assertEqual(segment, (174889, 174752)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][6] (record, segment, status) = empty self.assertEqual(record.id, "ponAbe2.chr6") self.assertEqual(len(record.seq), 174210431) self.assertEqual(segment, (158040552, 158040455)) self.assertEqual(status, "I") self.assertEqual(len(alignment.sequences), 3) self.assertEqual(len(alignment.annotations["empty"]), 7) self.assertEqual( str(alignment), """\ mm9.chr10 3018230 AGGA-CAAAATAATACAGAtttttttttttttttttttttGCAGTACTGGAAATGGAATG hg18.chr6 155028316 ATAATCCAATCAATATATAT---------------------CAGAACCTGGCTCCCAATG panTro2.c 157518369 ATAATCCAATCAATATATAT---------------------CAGAACCTGGCTCCCAATG mm9.chr10 3018289 AATGTCCCTCACAATCACTATCAAGGTCCCTATCAAGGCAATCACTCTGTCACCGAGCTA hg18.chr6 155028277 -----TTCTGATAGTCATTATGAA----------AAAGAATTTACACATATATAGATTTA panTro2.c 157518330 -----TTCTGATAGTCATTGTGAA----------AAAGAatttacacatatatagattta mm9.chr10 3018349 -CAGCCCCAGC 3018359 hg18.chr6 155028232 TTAGGTATATG 155028221 panTro2.c 157518285 ttaggtatatg 157518274 """, ) self.assertTrue( np.array_equal( alignment.coordinates, np.array( # fmt: off [[ 3018230, 3018234, 3018234, 3018249, 3018270, 3018289, 3018294, 3018313, 3018323, 3018349, 3018349, 3018359], [155028316, 155028312, 155028311, 155028296, 155028296, 155028277, 155028277, 155028258, 155028258, 155028232, 155028231, 155028221], [157518369, 157518365, 157518364, 157518349, 157518349, 157518330, 157518330, 157518311, 157518311, 157518285, 157518284, 157518274], ] # fmt: on ), ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['A', 'G', 'G', 'A', '-', 'C', 'A', 'A', 'A', 'A', 'T', 'A', 'A', 'T', 'A', 'C', 'A', 'G', 'A', 't', 't', 't', 't', 't', 't', 't', 't', 't', 't', 't', 't', 't', 't', 't', 't', 't', 't', 't', 't', 't', 'G', 'C', 'A', 'G', 'T', 'A', 'C', 'T', 'G', 'G', 'A', 'A', 'A', 'T', 'G', 'G', 'A', 'A', 'T', 'G', 'A', 'A', 'T', 'G', 'T', 'C', 'C', 'C', 'T', 'C', 'A', 'C', 'A', 'A', 'T', 'C', 'A', 'C', 'T', 'A', 'T', 'C', 'A', 'A', 'G', 'G', 'T', 'C', 'C', 'C', 'T', 'A', 'T', 'C', 'A', 'A', 'G', 'G', 'C', 'A', 'A', 'T', 'C', 'A', 'C', 'T', 'C', 'T', 'G', 'T', 'C', 'A', 'C', 'C', 'G', 'A', 'G', 'C', 'T', 'A', '-', 'C', 'A', 'G', 'C', 'C', 'C', 'C', 'A', 'G', 'C'], ['A', 'T', 'A', 'A', 'T', 'C', 'C', 'A', 'A', 'T', 'C', 'A', 'A', 'T', 'A', 'T', 'A', 'T', 'A', 'T', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'C', 'A', 'G', 'A', 'A', 'C', 'C', 'T', 'G', 'G', 'C', 'T', 'C', 'C', 'C', 'A', 'A', 'T', 'G', '-', '-', '-', '-', '-', 'T', 'T', 'C', 'T', 'G', 'A', 'T', 'A', 'G', 'T', 'C', 'A', 'T', 'T', 'A', 'T', 'G', 'A', 'A', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'A', 'A', 'A', 'G', 'A', 'A', 'T', 'T', 'T', 'A', 'C', 'A', 'C', 'A', 'T', 'A', 'T', 'A', 'T', 'A', 'G', 'A', 'T', 'T', 'T', 'A', 'T', 'T', 'A', 'G', 'G', 'T', 'A', 'T', 'A', 'T', 'G'], ['A', 'T', 'A', 'A', 'T', 'C', 'C', 'A', 'A', 'T', 'C', 'A', 'A', 'T', 'A', 'T', 'A', 'T', 'A', 'T', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'C', 'A', 'G', 'A', 'A', 'C', 'C', 'T', 'G', 'G', 'C', 'T', 'C', 'C', 'C', 'A', 'A', 'T', 'G', '-', '-', '-', '-', '-', 'T', 'T', 'C', 'T', 'G', 'A', 'T', 'A', 'G', 'T', 'C', 'A', 'T', 'T', 'G', 'T', 'G', 'A', 'A', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'A', 'A', 'A', 'G', 'A', 'a', 't', 't', 't', 'a', 'c', 'a', 'c', 'a', 't', 'a', 't', 'a', 't', 'a', 'g', 'a', 't', 't', 't', 'a', 't', 't', 'a', 'g', 'g', 't', 'a', 't', 'a', 't', 'g']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.score, 61520) self.assertEqual(alignment.sequences[0].id, "mm9.chr10") self.assertEqual(len(alignment.sequences[0].seq), 129993255) self.assertEqual( alignment.sequences[0].seq[3018359 : 3018359 + 123], "TTCAAACATGCATACATGCATTCATGTCTCATAATAATTATTAACATTGTCTTAGGCCAGAGGCTCGACTGCCCCAAAGCAATCCACTTAAACTGTCCCTGAGAAAGTCAttcctctccctaa", ) self.assertEqual( alignment[0], "TT-CAAACATGCATACATGCATTCATGTCTCATAA-TAATTATTAACA-TTGTCTTAGGCCAGAGGCTCGACTGCCCCAAAGCAATCCACT-------TAAACTGTCCCTGAGAA-AGTCAttcctctccctaa", ) self.assertEqual(alignment.sequences[1].id, "panTro2.chr6") self.assertEqual(len(alignment.sequences[1].seq), 173908612) self.assertEqual( alignment.sequences[1].seq[157518143 : 157518143 + 131], "AAAGAAAAGGATGACCCTTCCCGGAGAGAATATAAAATATGGATGGCTTAGTTTGTATCACTCAGGCCACTGACCTAAGATGACTGTTAATAATTATTTATGAGacatacacatatatttgtacatttata", ) self.assertEqual( alignment[1], "-tataaatgtacaaatatatgtgtatgtCTCATAAATAATTATTAACAGTCATCTTAGGTCAGTGGCCTGAGTGATACAAACTAAGCCATCCATATTTTATATTCTCTCCGGGAAGGGTCATCCTTTTCTTT--", ) self.assertEqual( alignment.sequences[1].annotations["quality"], "99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999", ) self.assertEqual(alignment.sequences[1].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[1].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[1].annotations["rightStatus"], "I") self.assertEqual(alignment.sequences[1].annotations["rightCount"], 2400) self.assertEqual(alignment.sequences[2].id, "hg18.chr6") self.assertEqual(len(alignment.sequences[2].seq), 170899992) self.assertEqual( alignment.sequences[2].seq[155028090 : 155028090 + 131], "AAAGAAAAGGATGACCCTTCCCGGAGAGAATATAAAATATGGATGGCTTAGTTTGTATCATTCAGGCCACTGACCTAAGATGACTGTTAATAATTATTTATGAGACATACACATATATTTGTACGTTTATA", ) self.assertEqual( alignment[2], "-TATAAACGTACAAATATATGTGTATGTCTCATAAATAATTATTAACAGTCATCTTAGGTCAGTGGCCTGAATGATACAAACTAAGCCATCCATATTTTATATTCTCTCCGGGAAGGGTCATCCTTTTCTTT--", ) self.assertEqual(alignment.sequences[2].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[2].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[2].annotations["rightStatus"], "I") self.assertEqual(alignment.sequences[2].annotations["rightCount"], 2402) self.assertEqual(alignment.sequences[3].id, "otoGar1.scaffold_334.1-359464") self.assertEqual(len(alignment.sequences[3].seq), 359464) self.assertEqual( alignment.sequences[3].seq[174625 : 174625 + 127], "TCAGAAGAAAGGATGACCCTTCACACAGGGAGGATAGGATGGGTTAGCTTGTGTCACTCGGGCCTCTAACCTAAGACAAATGTTAATAATTACTTACAGGACCTACATTTACACATACATGTATAAA", ) self.assertEqual( alignment[3], "TT-TATACATGTATGTGTAAATGTAGGTCCTGTAAGTAATTATTAACATTTGTCTTAGGTTAGAGGCCCGAGTGACACAAGCTAACCCATCC------TATCCTCCCTGTGTGAAGGGTCATCCTTTCTTCTGA", ) self.assertEqual( alignment.sequences[3].annotations["quality"], "9999999999999999999999999999999999999999999999999999667736999999999999999999999999999995666677755798899998999967967999999999589", ) self.assertEqual(alignment.sequences[3].annotations["leftStatus"], "I") self.assertEqual(alignment.sequences[3].annotations["leftCount"], 137) self.assertEqual(alignment.sequences[3].annotations["rightStatus"], "I") self.assertEqual(alignment.sequences[3].annotations["rightCount"], 2731) self.assertEqual(alignment.sequences[4].id, "ponAbe2.chr6") self.assertEqual(len(alignment.sequences[4].seq), 174210431) self.assertEqual( alignment.sequences[4].seq[158040326 : 158040326 + 129], "AAAGAAAAGGATGACCCTTCCCAGAGAGAATATAAAATATGGATGGCTTAGTTTCTATCACTCAGGCCACTGACCTAAGATGACTGTTAATAATtatttatgacacatacacatatatttgtacattta", ) self.assertEqual( alignment[4], "---taaatgtacaaatatatgtgtatgtgtcataaataATTATTAACAGTCATCTTAGGTCAGTGGCCTGAGTGATAGAAACTAAGCCATCCATATTTTATATTCTCTCTGGGAAGGGTCATCCTTTTCTTT--", ) self.assertEqual(alignment.sequences[4].annotations["leftStatus"], "I") self.assertEqual(alignment.sequences[4].annotations["leftCount"], 97) self.assertEqual(alignment.sequences[4].annotations["rightStatus"], "I") self.assertEqual(alignment.sequences[4].annotations["rightCount"], 2523) empty = alignment.annotations["empty"][0] (record, segment, status) = empty self.assertEqual(record.id, "ornAna1.chr2") self.assertEqual(len(record.seq), 54797317) self.assertEqual(segment, (40046122, 40040432)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][1] (record, segment, status) = empty self.assertEqual(record.id, "calJac1.Contig6394") self.assertEqual(len(record.seq), 133105) self.assertEqual(segment, (6649, 10128)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][2] (record, segment, status) = empty self.assertEqual(record.id, "tupBel1.scaffold_114895.1-498454") self.assertEqual(len(record.seq), 498454) self.assertEqual(segment, (326690, 324316)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][3] (record, segment, status) = empty self.assertEqual(record.id, "echTel1.scaffold_288249") self.assertEqual(len(record.seq), 100002) self.assertEqual(segment, (87661, 95225)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][4] (record, segment, status) = empty self.assertEqual(record.id, "cavPor2.scaffold_216473") self.assertEqual(len(record.seq), 10026) self.assertEqual(segment, (1978, 606)) self.assertEqual(status, "I") self.assertEqual(len(alignment.sequences), 5) self.assertEqual(len(alignment.annotations["empty"]), 5) self.assertEqual( str(alignment), """\ mm9.chr10 3018359 TT-CAAACATGCATACATGCATTCATGTCTCATAA-TAATTATTAACA-TTGTCTTAGGC panTro2.c 157518274 -tataaatgtacaaatatatgtgtatgtCTCATAAATAATTATTAACAGTCATCTTAGGT hg18.chr6 155028221 -TATAAACGTACAAATATATGTGTATGTCTCATAAATAATTATTAACAGTCATCTTAGGT otoGar1.s 174752 TT-TATACATGTATGTGTAAATGTAGGTCCTGTAAGTAATTATTAACATTTGTCTTAGGT ponAbe2.c 158040455 ---taaatgtacaaatatatgtgtatgtgtcataaataATTATTAACAGTCATCTTAGGT mm9.chr10 3018416 CAGAGGCTCGACTGCCCCAAAGCAATCCACT-------TAAACTGTCCCTGAGAA-AGTC panTro2.c 157518215 CAGTGGCCTGAGTGATACAAACTAAGCCATCCATATTTTATATTCTCTCCGGGAAGGGTC hg18.chr6 155028162 CAGTGGCCTGAATGATACAAACTAAGCCATCCATATTTTATATTCTCTCCGGGAAGGGTC otoGar1.s 174693 TAGAGGCCCGAGTGACACAAGCTAACCCATCC------TATCCTCCCTGTGTGAAGGGTC ponAbe2.c 158040398 CAGTGGCCTGAGTGATAGAAACTAAGCCATCCATATTTTATATTCTCTCTGGGAAGGGTC mm9.chr10 3018468 Attcctctccctaa 3018482 panTro2.c 157518155 ATCCTTTTCTTT-- 157518143 hg18.chr6 155028102 ATCCTTTTCTTT-- 155028090 otoGar1.s 174639 ATCCTTTCTTCTGA 174625 ponAbe2.c 158040338 ATCCTTTTCTTT-- 158040326 """, ) self.assertTrue( np.array_equal( alignment.coordinates, np.array( # fmt: off [[ 3018359, 3018360, 3018361, 3018361, 3018393, 3018393, 3018405, 3018405, 3018447, 3018447, 3018447, 3018464, 3018464, 3018480, 3018482], [157518274, 157518274, 157518273, 157518272, 157518240, 157518239, 157518227, 157518226, 157518184, 157518183, 157518177, 157518160, 157518159, 157518143, 157518143], [155028221, 155028221, 155028220, 155028219, 155028187, 155028186, 155028174, 155028173, 155028131, 155028130, 155028124, 155028107, 155028106, 155028090, 155028090], [ 174752, 174751, 174750, 174750, 174718, 174717, 174705, 174704, 174662, 174661, 174661, 174644, 174643, 174627, 174625], [158040455, 158040455, 158040455, 158040455, 158040423, 158040422, 158040410, 158040409, 158040367, 158040366, 158040360, 158040343, 158040342, 158040326, 158040326], ] # fmt: on ), ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['T', 'T', '-', 'C', 'A', 'A', 'A', 'C', 'A', 'T', 'G', 'C', 'A', 'T', 'A', 'C', 'A', 'T', 'G', 'C', 'A', 'T', 'T', 'C', 'A', 'T', 'G', 'T', 'C', 'T', 'C', 'A', 'T', 'A', 'A', '-', 'T', 'A', 'A', 'T', 'T', 'A', 'T', 'T', 'A', 'A', 'C', 'A', '-', 'T', 'T', 'G', 'T', 'C', 'T', 'T', 'A', 'G', 'G', 'C', 'C', 'A', 'G', 'A', 'G', 'G', 'C', 'T', 'C', 'G', 'A', 'C', 'T', 'G', 'C', 'C', 'C', 'C', 'A', 'A', 'A', 'G', 'C', 'A', 'A', 'T', 'C', 'C', 'A', 'C', 'T', '-', '-', '-', '-', '-', '-', '-', 'T', 'A', 'A', 'A', 'C', 'T', 'G', 'T', 'C', 'C', 'C', 'T', 'G', 'A', 'G', 'A', 'A', '-', 'A', 'G', 'T', 'C', 'A', 't', 't', 'c', 'c', 't', 'c', 't', 'c', 'c', 'c', 't', 'a', 'a'], ['-', 't', 'a', 't', 'a', 'a', 'a', 't', 'g', 't', 'a', 'c', 'a', 'a', 'a', 't', 'a', 't', 'a', 't', 'g', 't', 'g', 't', 'a', 't', 'g', 't', 'C', 'T', 'C', 'A', 'T', 'A', 'A', 'A', 'T', 'A', 'A', 'T', 'T', 'A', 'T', 'T', 'A', 'A', 'C', 'A', 'G', 'T', 'C', 'A', 'T', 'C', 'T', 'T', 'A', 'G', 'G', 'T', 'C', 'A', 'G', 'T', 'G', 'G', 'C', 'C', 'T', 'G', 'A', 'G', 'T', 'G', 'A', 'T', 'A', 'C', 'A', 'A', 'A', 'C', 'T', 'A', 'A', 'G', 'C', 'C', 'A', 'T', 'C', 'C', 'A', 'T', 'A', 'T', 'T', 'T', 'T', 'A', 'T', 'A', 'T', 'T', 'C', 'T', 'C', 'T', 'C', 'C', 'G', 'G', 'G', 'A', 'A', 'G', 'G', 'G', 'T', 'C', 'A', 'T', 'C', 'C', 'T', 'T', 'T', 'T', 'C', 'T', 'T', 'T', '-', '-'], ['-', 'T', 'A', 'T', 'A', 'A', 'A', 'C', 'G', 'T', 'A', 'C', 'A', 'A', 'A', 'T', 'A', 'T', 'A', 'T', 'G', 'T', 'G', 'T', 'A', 'T', 'G', 'T', 'C', 'T', 'C', 'A', 'T', 'A', 'A', 'A', 'T', 'A', 'A', 'T', 'T', 'A', 'T', 'T', 'A', 'A', 'C', 'A', 'G', 'T', 'C', 'A', 'T', 'C', 'T', 'T', 'A', 'G', 'G', 'T', 'C', 'A', 'G', 'T', 'G', 'G', 'C', 'C', 'T', 'G', 'A', 'A', 'T', 'G', 'A', 'T', 'A', 'C', 'A', 'A', 'A', 'C', 'T', 'A', 'A', 'G', 'C', 'C', 'A', 'T', 'C', 'C', 'A', 'T', 'A', 'T', 'T', 'T', 'T', 'A', 'T', 'A', 'T', 'T', 'C', 'T', 'C', 'T', 'C', 'C', 'G', 'G', 'G', 'A', 'A', 'G', 'G', 'G', 'T', 'C', 'A', 'T', 'C', 'C', 'T', 'T', 'T', 'T', 'C', 'T', 'T', 'T', '-', '-'], ['T', 'T', '-', 'T', 'A', 'T', 'A', 'C', 'A', 'T', 'G', 'T', 'A', 'T', 'G', 'T', 'G', 'T', 'A', 'A', 'A', 'T', 'G', 'T', 'A', 'G', 'G', 'T', 'C', 'C', 'T', 'G', 'T', 'A', 'A', 'G', 'T', 'A', 'A', 'T', 'T', 'A', 'T', 'T', 'A', 'A', 'C', 'A', 'T', 'T', 'T', 'G', 'T', 'C', 'T', 'T', 'A', 'G', 'G', 'T', 'T', 'A', 'G', 'A', 'G', 'G', 'C', 'C', 'C', 'G', 'A', 'G', 'T', 'G', 'A', 'C', 'A', 'C', 'A', 'A', 'G', 'C', 'T', 'A', 'A', 'C', 'C', 'C', 'A', 'T', 'C', 'C', '-', '-', '-', '-', '-', '-', 'T', 'A', 'T', 'C', 'C', 'T', 'C', 'C', 'C', 'T', 'G', 'T', 'G', 'T', 'G', 'A', 'A', 'G', 'G', 'G', 'T', 'C', 'A', 'T', 'C', 'C', 'T', 'T', 'T', 'C', 'T', 'T', 'C', 'T', 'G', 'A'], ['-', '-', '-', 't', 'a', 'a', 'a', 't', 'g', 't', 'a', 'c', 'a', 'a', 'a', 't', 'a', 't', 'a', 't', 'g', 't', 'g', 't', 'a', 't', 'g', 't', 'g', 't', 'c', 'a', 't', 'a', 'a', 'a', 't', 'a', 'A', 'T', 'T', 'A', 'T', 'T', 'A', 'A', 'C', 'A', 'G', 'T', 'C', 'A', 'T', 'C', 'T', 'T', 'A', 'G', 'G', 'T', 'C', 'A', 'G', 'T', 'G', 'G', 'C', 'C', 'T', 'G', 'A', 'G', 'T', 'G', 'A', 'T', 'A', 'G', 'A', 'A', 'A', 'C', 'T', 'A', 'A', 'G', 'C', 'C', 'A', 'T', 'C', 'C', 'A', 'T', 'A', 'T', 'T', 'T', 'T', 'A', 'T', 'A', 'T', 'T', 'C', 'T', 'C', 'T', 'C', 'T', 'G', 'G', 'G', 'A', 'A', 'G', 'G', 'G', 'T', 'C', 'A', 'T', 'C', 'C', 'T', 'T', 'T', 'T', 'C', 'T', 'T', 'T', '-', '-']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.score, 0) self.assertEqual(alignment.sequences[0].id, "mm9.chr10") self.assertEqual(len(alignment.sequences[0].seq), 129993255) self.assertEqual( alignment.sequences[0].seq[3018482 : 3018482 + 162], "tcttcatctcctcttttcctccttttttttttctcatttctctttctctttcttttgtccttttccttTATAGCAAGCAAGGCAAGTAGTCTCTATTTAGAAGGCATggagagaatggggagaggaggaaaggaggagaggggaggagaggaggggagGTAT", ) self.assertEqual( alignment[0], "tcttcatctcctcttttcctccttttttttttctcatttctctttctctttcttttgtccttttccttTATAGCAAGCAAGGCAAGTAGTCTCTATTTAGAAGGCATggagagaatggggagaggaggaaaggaggagaggggaggagaggaggggagGTAT", ) empty = alignment.annotations["empty"][0] (record, segment, status) = empty self.assertEqual(record.id, "ornAna1.chr2") self.assertEqual(len(record.seq), 54797317) self.assertEqual(segment, (40046122, 40040432)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][1] (record, segment, status) = empty self.assertEqual(record.id, "calJac1.Contig6394") self.assertEqual(len(record.seq), 133105) self.assertEqual(segment, (6649, 10128)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][2] (record, segment, status) = empty self.assertEqual(record.id, "tupBel1.scaffold_114895.1-498454") self.assertEqual(len(record.seq), 498454) self.assertEqual(segment, (326690, 324316)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][3] (record, segment, status) = empty self.assertEqual(record.id, "echTel1.scaffold_288249") self.assertEqual(len(record.seq), 100002) self.assertEqual(segment, (87661, 95225)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][4] (record, segment, status) = empty self.assertEqual(record.id, "cavPor2.scaffold_216473") self.assertEqual(len(record.seq), 10026) self.assertEqual(segment, (1978, 606)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][5] (record, segment, status) = empty self.assertEqual(record.id, "otoGar1.scaffold_334.1-359464") self.assertEqual(len(record.seq), 359464) self.assertEqual(segment, (174625, 171894)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][6] (record, segment, status) = empty self.assertEqual(record.id, "hg18.chr6") self.assertEqual(len(record.seq), 170899992) self.assertEqual(segment, (155028090, 155025688)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][7] (record, segment, status) = empty self.assertEqual(record.id, "panTro2.chr6") self.assertEqual(len(record.seq), 173908612) self.assertEqual(segment, (157518143, 157515743)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][8] (record, segment, status) = empty self.assertEqual(record.id, "ponAbe2.chr6") self.assertEqual(len(record.seq), 174210431) self.assertEqual(segment, (158040326, 158037803)) self.assertEqual(status, "I") self.assertEqual(len(alignment.sequences), 1) self.assertEqual(len(alignment.annotations["empty"]), 9) self.assertEqual( str(alignment), """\ mm9.chr10 3018482 tcttcatctcctcttttcctccttttttttttctcatttctctttctctttcttttgtcc mm9.chr10 3018542 ttttccttTATAGCAAGCAAGGCAAGTAGTCTCTATTTAGAAGGCATggagagaatgggg mm9.chr10 3018602 agaggaggaaaggaggagaggggaggagaggaggggagGTAT 3018644 """, ) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[3018482, 3018644]])) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['t', 'c', 't', 't', 'c', 'a', 't', 'c', 't', 'c', 'c', 't', 'c', 't', 't', 't', 't', 'c', 'c', 't', 'c', 'c', 't', 't', 't', 't', 't', 't', 't', 't', 't', 't', 'c', 't', 'c', 'a', 't', 't', 't', 'c', 't', 'c', 't', 't', 't', 'c', 't', 'c', 't', 't', 't', 'c', 't', 't', 't', 't', 'g', 't', 'c', 'c', 't', 't', 't', 't', 'c', 'c', 't', 't', 'T', 'A', 'T', 'A', 'G', 'C', 'A', 'A', 'G', 'C', 'A', 'A', 'G', 'G', 'C', 'A', 'A', 'G', 'T', 'A', 'G', 'T', 'C', 'T', 'C', 'T', 'A', 'T', 'T', 'T', 'A', 'G', 'A', 'A', 'G', 'G', 'C', 'A', 'T', 'g', 'g', 'a', 'g', 'a', 'g', 'a', 'a', 't', 'g', 'g', 'g', 'g', 'a', 'g', 'a', 'g', 'g', 'a', 'g', 'g', 'a', 'a', 'a', 'g', 'g', 'a', 'g', 'g', 'a', 'g', 'a', 'g', 'g', 'g', 'g', 'a', 'g', 'g', 'a', 'g', 'a', 'g', 'g', 'a', 'g', 'g', 'g', 'g', 'a', 'g', 'G', 'T', 'A', 'T']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.score, 1520) self.assertEqual(alignment.sequences[0].id, "mm9.chr10") self.assertEqual(len(alignment.sequences[0].seq), 129993255) self.assertEqual( alignment.sequences[0].seq[3018644 : 3018644 + 178], "AGGGTAGGCCAAGTGCCTTGGGAAGTAGTTGTTGGTAGACTGAAAGTGTGTTCTGAGTGTCAGTGATGTTCATGAGATTATCACCAGCAAGGATGGCTGACGGGAACTGCAAGAGGCATAGCCCTGAGTTCTAAAGGAGAGGGAAACGTCACAGAAAGGATGCACTGTTTCAGCATCT", ) self.assertEqual( alignment[0], "AGGGTAGGCCAAGTGCCTTGGGAAGTAGTTGTTGGTAGACTGAAAGTGTGTTC---TGAGTGTCAGTGATGTTCA-TGAGATTATCACCAGCAAGGATG--GCTGACGGGAACTG---CAAGAGGCATAGCCCTGAGTTCTAAAGGAGAGGGAAACGTCACAGAAAGGATG--------------------------CACTGTTTCAGCATCT", ) self.assertEqual(alignment.sequences[1].id, "canFam2.chr1") self.assertEqual(len(alignment.sequences[1].seq), 125616256) self.assertEqual( alignment.sequences[1].seq[47545632 : 47545632 + 204], "AAATTCTTCAATAGGGAAATTTTATATTTCATATTACAATTCTATTCTATCCATGATCTTTCCTCTCATTTTAGAGTTCTGGCTGGTGGTATTTGCTTCTGATTCCATCAACCGCATCCTTAGGAGAGGATCTCAGTATCCATCACTTACACGCATGTGAATAAACTCAATGTGCTATCCCTCCCAGGGGCATTTGCCTTTTCT", ) self.assertEqual( alignment[1], "AGAAAAGGCAAATGCCCCTGGGAGGGA-----TAGCACATTGA--GTTTATTCACATGCGTGTAAGTGATGGATACTGAGATCCTCTCC--TAAGGATGCGGTTGATGGAATCAGAAGCAAATACCACCAGCCAGAACTCTAAAATGAGAGGAAAGATCATGGATAGAATAGAATTGTAATATGAAATATAAAATTTCCCTATTGAAGAATTT", ) self.assertEqual( alignment.sequences[1].annotations["quality"], "999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999", ) self.assertEqual(alignment.sequences[1].annotations["leftStatus"], "N") self.assertEqual(alignment.sequences[1].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[1].annotations["rightStatus"], "I") self.assertEqual(alignment.sequences[1].annotations["rightCount"], 160) empty = alignment.annotations["empty"][0] (record, segment, status) = empty self.assertEqual(record.id, "ornAna1.chr2") self.assertEqual(len(record.seq), 54797317) self.assertEqual(segment, (40046122, 40040432)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][1] (record, segment, status) = empty self.assertEqual(record.id, "calJac1.Contig6394") self.assertEqual(len(record.seq), 133105) self.assertEqual(segment, (6649, 10128)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][2] (record, segment, status) = empty self.assertEqual(record.id, "tupBel1.scaffold_114895.1-498454") self.assertEqual(len(record.seq), 498454) self.assertEqual(segment, (326690, 324316)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][3] (record, segment, status) = empty self.assertEqual(record.id, "echTel1.scaffold_288249") self.assertEqual(len(record.seq), 100002) self.assertEqual(segment, (87661, 95225)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][4] (record, segment, status) = empty self.assertEqual(record.id, "cavPor2.scaffold_216473") self.assertEqual(len(record.seq), 10026) self.assertEqual(segment, (1978, 606)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][5] (record, segment, status) = empty self.assertEqual(record.id, "otoGar1.scaffold_334.1-359464") self.assertEqual(len(record.seq), 359464) self.assertEqual(segment, (174625, 171894)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][6] (record, segment, status) = empty self.assertEqual(record.id, "hg18.chr6") self.assertEqual(len(record.seq), 170899992) self.assertEqual(segment, (155028090, 155025688)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][7] (record, segment, status) = empty self.assertEqual(record.id, "panTro2.chr6") self.assertEqual(len(record.seq), 173908612) self.assertEqual(segment, (157518143, 157515743)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][8] (record, segment, status) = empty self.assertEqual(record.id, "ponAbe2.chr6") self.assertEqual(len(record.seq), 174210431) self.assertEqual(segment, (158040326, 158037803)) self.assertEqual(status, "I") self.assertEqual(len(alignment.sequences), 2) self.assertEqual(len(alignment.annotations["empty"]), 9) self.assertEqual( str(alignment), """\ mm9.chr10 3018644 AGGGTAGGCCAAGTGCCTTGGGAAGTAGTTGTTGGTAGACTGAAAGTGTGTTC---TGAG 0 ||...||||.||...||.|||||.|.|-----|.|.|.|.|||--||.|.|||---||.| canFam2.c 47545836 AGAAAAGGCAAATGCCCCTGGGAGGGA-----TAGCACATTGA--GTTTATTCACATGCG mm9.chr10 3018701 TGTCAGTGATGTTCA-TGAGATTATCACCAGCAAGGATG--GCTGACGGGAACTG---CA 60 |||.|||||||...|-||||||..||.||--.|||||||--|.|||.||.|.|.|---|| canFam2.c 47545783 TGTAAGTGATGGATACTGAGATCCTCTCC--TAAGGATGCGGTTGATGGAATCAGAAGCA mm9.chr10 3018755 AGAGGCATAGCCCTGAGTTCTAAAGGAGAGGGAAACGTCACAGAAAGGATG--------- 120 |....||....||.||..||||||......|||||..|||..||.||.||.--------- canFam2.c 47545725 AATACCACCAGCCAGAACTCTAAAATGAGAGGAAAGATCATGGATAGAATAGAATTGTAA mm9.chr10 3018806 -----------------CACTGTTTCAGCATCT 3018822 180 -----------------|.||.||..||.||.| 213 canFam2.c 47545665 TATGAAATATAAAATTTCCCTATTGAAGAATTT 47545632 """, ) self.assertTrue( np.array_equal( alignment.coordinates, np.array( # fmt: off [[ 3018644, 3018671, 3018676, 3018687, 3018689, 3018697, 3018697, 3018716, 3018716, 3018729, 3018731, 3018739, 3018739, 3018753, 3018753, 3018806, 3018806, 3018822], [47545836, 47545809, 47545809, 47545798, 47545798, 47545790, 47545787, 47545768, 47545767, 47545754, 47545754, 47545746, 47545744, 47545730, 47545727, 47545674, 47545648, 47545632], ] # fmt: on ), ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['A', 'G', 'G', 'G', 'T', 'A', 'G', 'G', 'C', 'C', 'A', 'A', 'G', 'T', 'G', 'C', 'C', 'T', 'T', 'G', 'G', 'G', 'A', 'A', 'G', 'T', 'A', 'G', 'T', 'T', 'G', 'T', 'T', 'G', 'G', 'T', 'A', 'G', 'A', 'C', 'T', 'G', 'A', 'A', 'A', 'G', 'T', 'G', 'T', 'G', 'T', 'T', 'C', '-', '-', '-', 'T', 'G', 'A', 'G', 'T', 'G', 'T', 'C', 'A', 'G', 'T', 'G', 'A', 'T', 'G', 'T', 'T', 'C', 'A', '-', 'T', 'G', 'A', 'G', 'A', 'T', 'T', 'A', 'T', 'C', 'A', 'C', 'C', 'A', 'G', 'C', 'A', 'A', 'G', 'G', 'A', 'T', 'G', '-', '-', 'G', 'C', 'T', 'G', 'A', 'C', 'G', 'G', 'G', 'A', 'A', 'C', 'T', 'G', '-', '-', '-', 'C', 'A', 'A', 'G', 'A', 'G', 'G', 'C', 'A', 'T', 'A', 'G', 'C', 'C', 'C', 'T', 'G', 'A', 'G', 'T', 'T', 'C', 'T', 'A', 'A', 'A', 'G', 'G', 'A', 'G', 'A', 'G', 'G', 'G', 'A', 'A', 'A', 'C', 'G', 'T', 'C', 'A', 'C', 'A', 'G', 'A', 'A', 'A', 'G', 'G', 'A', 'T', 'G', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'C', 'A', 'C', 'T', 'G', 'T', 'T', 'T', 'C', 'A', 'G', 'C', 'A', 'T', 'C', 'T'], ['A', 'G', 'A', 'A', 'A', 'A', 'G', 'G', 'C', 'A', 'A', 'A', 'T', 'G', 'C', 'C', 'C', 'C', 'T', 'G', 'G', 'G', 'A', 'G', 'G', 'G', 'A', '-', '-', '-', '-', '-', 'T', 'A', 'G', 'C', 'A', 'C', 'A', 'T', 'T', 'G', 'A', '-', '-', 'G', 'T', 'T', 'T', 'A', 'T', 'T', 'C', 'A', 'C', 'A', 'T', 'G', 'C', 'G', 'T', 'G', 'T', 'A', 'A', 'G', 'T', 'G', 'A', 'T', 'G', 'G', 'A', 'T', 'A', 'C', 'T', 'G', 'A', 'G', 'A', 'T', 'C', 'C', 'T', 'C', 'T', 'C', 'C', '-', '-', 'T', 'A', 'A', 'G', 'G', 'A', 'T', 'G', 'C', 'G', 'G', 'T', 'T', 'G', 'A', 'T', 'G', 'G', 'A', 'A', 'T', 'C', 'A', 'G', 'A', 'A', 'G', 'C', 'A', 'A', 'A', 'T', 'A', 'C', 'C', 'A', 'C', 'C', 'A', 'G', 'C', 'C', 'A', 'G', 'A', 'A', 'C', 'T', 'C', 'T', 'A', 'A', 'A', 'A', 'T', 'G', 'A', 'G', 'A', 'G', 'G', 'A', 'A', 'A', 'G', 'A', 'T', 'C', 'A', 'T', 'G', 'G', 'A', 'T', 'A', 'G', 'A', 'A', 'T', 'A', 'G', 'A', 'A', 'T', 'T', 'G', 'T', 'A', 'A', 'T', 'A', 'T', 'G', 'A', 'A', 'A', 'T', 'A', 'T', 'A', 'A', 'A', 'A', 'T', 'T', 'T', 'C', 'C', 'C', 'T', 'A', 'T', 'T', 'G', 'A', 'A', 'G', 'A', 'A', 'T', 'T', 'T']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.score, 1986) self.assertEqual(alignment.sequences[0].id, "mm9.chr10") self.assertEqual(len(alignment.sequences[0].seq), 129993255) self.assertEqual( alignment.sequences[0].seq[3018822 : 3018822 + 110], "CTGCCTTCCATTACGATTTACTGATCACTTACAACCCTCCCACAGAAGAGAACCTAACTTGCTTAGGAGCATATGTACAGTTAATCAAGACAAAAATAAGAATGGAGACt", ) self.assertEqual( alignment[0], "CTGCCTTCCATTACGATTTACTGATCACTTACAACCCTCCCACA----GAAGAGAACCTAACTTG-CTTAGGAGCATATGTACAGTTAATCAAGAC-----AAAAATAAGAATGGAGACt", ) self.assertEqual(alignment.sequences[1].id, "canFam2.chr1") self.assertEqual(len(alignment.sequences[1].seq), 125616256) self.assertEqual( alignment.sequences[1].seq[47545353 : 47545353 + 119], "ATTTTCCATACTTATTTTTAGTTGATCTTGCTAAATTGTGTGCATCTCTAGAAGTCGATTTGAATTCCCTTTACAATGTGGAGAATTTTAAGTGAGTAATAATGGGCAGGGAAAAAAAG", ) self.assertEqual( alignment[1], "CTTTTTTTCCCTGCCCATTATTACTCACTTAAAATTCTCC-ACATTGTAAAGGGAATTCAAATCGACTTCTAGAGATGCACACAATTTAGCAAGATCAACTAAAAATAAGTATGGAAAAT", ) self.assertEqual( alignment.sequences[1].annotations["quality"], "99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999", ) self.assertEqual(alignment.sequences[1].annotations["leftStatus"], "I") self.assertEqual(alignment.sequences[1].annotations["leftCount"], 160) self.assertEqual(alignment.sequences[1].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[1].annotations["rightCount"], 0) empty = alignment.annotations["empty"][0] (record, segment, status) = empty self.assertEqual(record.id, "ornAna1.chr2") self.assertEqual(len(record.seq), 54797317) self.assertEqual(segment, (40046122, 40040432)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][1] (record, segment, status) = empty self.assertEqual(record.id, "calJac1.Contig6394") self.assertEqual(len(record.seq), 133105) self.assertEqual(segment, (6649, 10128)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][2] (record, segment, status) = empty self.assertEqual(record.id, "tupBel1.scaffold_114895.1-498454") self.assertEqual(len(record.seq), 498454) self.assertEqual(segment, (326690, 324316)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][3] (record, segment, status) = empty self.assertEqual(record.id, "echTel1.scaffold_288249") self.assertEqual(len(record.seq), 100002) self.assertEqual(segment, (87661, 95225)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][4] (record, segment, status) = empty self.assertEqual(record.id, "cavPor2.scaffold_216473") self.assertEqual(len(record.seq), 10026) self.assertEqual(segment, (1978, 606)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][5] (record, segment, status) = empty self.assertEqual(record.id, "otoGar1.scaffold_334.1-359464") self.assertEqual(len(record.seq), 359464) self.assertEqual(segment, (174625, 171894)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][6] (record, segment, status) = empty self.assertEqual(record.id, "hg18.chr6") self.assertEqual(len(record.seq), 170899992) self.assertEqual(segment, (155028090, 155025688)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][7] (record, segment, status) = empty self.assertEqual(record.id, "panTro2.chr6") self.assertEqual(len(record.seq), 173908612) self.assertEqual(segment, (157518143, 157515743)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][8] (record, segment, status) = empty self.assertEqual(record.id, "ponAbe2.chr6") self.assertEqual(len(record.seq), 174210431) self.assertEqual(segment, (158040326, 158037803)) self.assertEqual(status, "I") self.assertEqual(len(alignment.sequences), 2) self.assertEqual(len(alignment.annotations["empty"]), 9) self.assertEqual( str(alignment), """\ mm9.chr10 3018822 CTGCCTTCCATTACGATTTACTGATCACTTACAACCCTCCCACA----GAAGAGAACCTA 0 ||...||.|..|.|...|||.|..|||||||.||..||||-|||----.|||.|||...| canFam2.c 47545472 CTTTTTTTCCCTGCCCATTATTACTCACTTAAAATTCTCC-ACATTGTAAAGGGAATTCA mm9.chr10 3018878 ACTTG-CTTAGGAGCATATGTACAGTTAATCAAGAC-----AAAAATAAGAATGGAGACt 60 |.|.|-|||......||....|||.||.|.|||||.-----|||||||||.|||||.|.. canFam2.c 47545413 AATCGACTTCTAGAGATGCACACAATTTAGCAAGATCAACTAAAAATAAGTATGGAAAAT mm9.chr10 3018932 120 canFam2.c 47545353 """, ) self.assertTrue( np.array_equal( alignment.coordinates, np.array( # fmt: off [[ 3018822, 3018862, 3018863, 3018866, 3018866, 3018883, 3018883, 3018913, 3018913, 3018932], [47545472, 47545432, 47545432, 47545429, 47545425, 47545408, 47545407, 47545377, 47545372, 47545353], ] # fmt: on ), ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['C', 'T', 'G', 'C', 'C', 'T', 'T', 'C', 'C', 'A', 'T', 'T', 'A', 'C', 'G', 'A', 'T', 'T', 'T', 'A', 'C', 'T', 'G', 'A', 'T', 'C', 'A', 'C', 'T', 'T', 'A', 'C', 'A', 'A', 'C', 'C', 'C', 'T', 'C', 'C', 'C', 'A', 'C', 'A', '-', '-', '-', '-', 'G', 'A', 'A', 'G', 'A', 'G', 'A', 'A', 'C', 'C', 'T', 'A', 'A', 'C', 'T', 'T', 'G', '-', 'C', 'T', 'T', 'A', 'G', 'G', 'A', 'G', 'C', 'A', 'T', 'A', 'T', 'G', 'T', 'A', 'C', 'A', 'G', 'T', 'T', 'A', 'A', 'T', 'C', 'A', 'A', 'G', 'A', 'C', '-', '-', '-', '-', '-', 'A', 'A', 'A', 'A', 'A', 'T', 'A', 'A', 'G', 'A', 'A', 'T', 'G', 'G', 'A', 'G', 'A', 'C', 't'], ['C', 'T', 'T', 'T', 'T', 'T', 'T', 'T', 'C', 'C', 'C', 'T', 'G', 'C', 'C', 'C', 'A', 'T', 'T', 'A', 'T', 'T', 'A', 'C', 'T', 'C', 'A', 'C', 'T', 'T', 'A', 'A', 'A', 'A', 'T', 'T', 'C', 'T', 'C', 'C', '-', 'A', 'C', 'A', 'T', 'T', 'G', 'T', 'A', 'A', 'A', 'G', 'G', 'G', 'A', 'A', 'T', 'T', 'C', 'A', 'A', 'A', 'T', 'C', 'G', 'A', 'C', 'T', 'T', 'C', 'T', 'A', 'G', 'A', 'G', 'A', 'T', 'G', 'C', 'A', 'C', 'A', 'C', 'A', 'A', 'T', 'T', 'T', 'A', 'G', 'C', 'A', 'A', 'G', 'A', 'T', 'C', 'A', 'A', 'C', 'T', 'A', 'A', 'A', 'A', 'A', 'T', 'A', 'A', 'G', 'T', 'A', 'T', 'G', 'G', 'A', 'A', 'A', 'A', 'T']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.score, 0) self.assertEqual(alignment.sequences[0].id, "mm9.chr10") self.assertEqual(len(alignment.sequences[0].seq), 129993255) self.assertEqual( alignment.sequences[0].seq[3018932 : 3018932 + 339], "gtctgagttagggttttactgctgtgaacagacaccatgaccaaggcatgtcttataaaaaaaatttaattagggctggcttacagattcagaggttcagtgggagcatcaaggtgggggcatggcagcatccaggcaggcatggtgcaggcagagctgagagttctacatcttcatccaaaggcttctagtggaagactgacttccaggcacctagggtgagggtcttaagcccacacccacagtgacacacctattccaaccaggtcacacctattccaacaaggccatacctccaaatggcaccactcctggtccaagaatatacaaaccatgaca", ) self.assertEqual( alignment[0], "gtctgagttagggttttactgctgtgaacagacaccatgaccaaggcatgtcttataaaaaaaatttaattagggctggcttacagattcagaggttcagtgggagcatcaaggtgggggcatggcagcatccaggcaggcatggtgcaggcagagctgagagttctacatcttcatccaaaggcttctagtggaagactgacttccaggcacctagggtgagggtcttaagcccacacccacagtgacacacctattccaaccaggtcacacctattccaacaaggccatacctccaaatggcaccactcctggtccaagaatatacaaaccatgaca", ) empty = alignment.annotations["empty"][0] (record, segment, status) = empty self.assertEqual(record.id, "canFam2.chr1") self.assertEqual(len(record.seq), 125616256) self.assertEqual(segment, (47545353, 47545353)) self.assertEqual(status, "C") empty = alignment.annotations["empty"][1] (record, segment, status) = empty self.assertEqual(record.id, "ornAna1.chr2") self.assertEqual(len(record.seq), 54797317) self.assertEqual(segment, (40046122, 40040432)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][2] (record, segment, status) = empty self.assertEqual(record.id, "calJac1.Contig6394") self.assertEqual(len(record.seq), 133105) self.assertEqual(segment, (6649, 10128)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][3] (record, segment, status) = empty self.assertEqual(record.id, "tupBel1.scaffold_114895.1-498454") self.assertEqual(len(record.seq), 498454) self.assertEqual(segment, (326690, 324316)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][4] (record, segment, status) = empty self.assertEqual(record.id, "echTel1.scaffold_288249") self.assertEqual(len(record.seq), 100002) self.assertEqual(segment, (87661, 95225)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][5] (record, segment, status) = empty self.assertEqual(record.id, "cavPor2.scaffold_216473") self.assertEqual(len(record.seq), 10026) self.assertEqual(segment, (1978, 606)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][6] (record, segment, status) = empty self.assertEqual(record.id, "otoGar1.scaffold_334.1-359464") self.assertEqual(len(record.seq), 359464) self.assertEqual(segment, (174625, 171894)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][7] (record, segment, status) = empty self.assertEqual(record.id, "hg18.chr6") self.assertEqual(len(record.seq), 170899992) self.assertEqual(segment, (155028090, 155025688)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][8] (record, segment, status) = empty self.assertEqual(record.id, "panTro2.chr6") self.assertEqual(len(record.seq), 173908612) self.assertEqual(segment, (157518143, 157515743)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][9] (record, segment, status) = empty self.assertEqual(record.id, "ponAbe2.chr6") self.assertEqual(len(record.seq), 174210431) self.assertEqual(segment, (158040326, 158037803)) self.assertEqual(status, "I") self.assertEqual(len(alignment.sequences), 1) self.assertEqual(len(alignment.annotations["empty"]), 10) self.assertEqual( str(alignment), """\ mm9.chr10 3018932 gtctgagttagggttttactgctgtgaacagacaccatgaccaaggcatgtcttataaaa mm9.chr10 3018992 aaaatttaattagggctggcttacagattcagaggttcagtgggagcatcaaggtggggg mm9.chr10 3019052 catggcagcatccaggcaggcatggtgcaggcagagctgagagttctacatcttcatcca mm9.chr10 3019112 aaggcttctagtggaagactgacttccaggcacctagggtgagggtcttaagcccacacc mm9.chr10 3019172 cacagtgacacacctattccaaccaggtcacacctattccaacaaggccatacctccaaa mm9.chr10 3019232 tggcaccactcctggtccaagaatatacaaaccatgaca 3019271 """, ) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[3018932, 3019271]])) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['g', 't', 'c', 't', 'g', 'a', 'g', 't', 't', 'a', 'g', 'g', 'g', 't', 't', 't', 't', 'a', 'c', 't', 'g', 'c', 't', 'g', 't', 'g', 'a', 'a', 'c', 'a', 'g', 'a', 'c', 'a', 'c', 'c', 'a', 't', 'g', 'a', 'c', 'c', 'a', 'a', 'g', 'g', 'c', 'a', 't', 'g', 't', 'c', 't', 't', 'a', 't', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 't', 't', 't', 'a', 'a', 't', 't', 'a', 'g', 'g', 'g', 'c', 't', 'g', 'g', 'c', 't', 't', 'a', 'c', 'a', 'g', 'a', 't', 't', 'c', 'a', 'g', 'a', 'g', 'g', 't', 't', 'c', 'a', 'g', 't', 'g', 'g', 'g', 'a', 'g', 'c', 'a', 't', 'c', 'a', 'a', 'g', 'g', 't', 'g', 'g', 'g', 'g', 'g', 'c', 'a', 't', 'g', 'g', 'c', 'a', 'g', 'c', 'a', 't', 'c', 'c', 'a', 'g', 'g', 'c', 'a', 'g', 'g', 'c', 'a', 't', 'g', 'g', 't', 'g', 'c', 'a', 'g', 'g', 'c', 'a', 'g', 'a', 'g', 'c', 't', 'g', 'a', 'g', 'a', 'g', 't', 't', 'c', 't', 'a', 'c', 'a', 't', 'c', 't', 't', 'c', 'a', 't', 'c', 'c', 'a', 'a', 'a', 'g', 'g', 'c', 't', 't', 'c', 't', 'a', 'g', 't', 'g', 'g', 'a', 'a', 'g', 'a', 'c', 't', 'g', 'a', 'c', 't', 't', 'c', 'c', 'a', 'g', 'g', 'c', 'a', 'c', 'c', 't', 'a', 'g', 'g', 'g', 't', 'g', 'a', 'g', 'g', 'g', 't', 'c', 't', 't', 'a', 'a', 'g', 'c', 'c', 'c', 'a', 'c', 'a', 'c', 'c', 'c', 'a', 'c', 'a', 'g', 't', 'g', 'a', 'c', 'a', 'c', 'a', 'c', 'c', 't', 'a', 't', 't', 'c', 'c', 'a', 'a', 'c', 'c', 'a', 'g', 'g', 't', 'c', 'a', 'c', 'a', 'c', 'c', 't', 'a', 't', 't', 'c', 'c', 'a', 'a', 'c', 'a', 'a', 'g', 'g', 'c', 'c', 'a', 't', 'a', 'c', 'c', 't', 'c', 'c', 'a', 'a', 'a', 't', 'g', 'g', 'c', 'a', 'c', 'c', 'a', 'c', 't', 'c', 'c', 't', 'g', 'g', 't', 'c', 'c', 'a', 'a', 'g', 'a', 'a', 't', 'a', 't', 'a', 'c', 'a', 'a', 'a', 'c', 'c', 'a', 't', 'g', 'a', 'c', 'a']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.score, 228) self.assertEqual(alignment.sequences[0].id, "mm9.chr10") self.assertEqual(len(alignment.sequences[0].seq), 129993255) self.assertEqual( alignment.sequences[0].seq[3019271 : 3019271 + 106], "GAGACCAAATGTGGCGCTCACGTGAGGCCAGGAGTAAATCGCACACACAGCCCATGCTTTCACCATCTGCTAGGGTGCTCTGGAGCAGGGCAGGCTTCTAACCTGG", ) self.assertEqual( alignment[0], "GAGACCAAATG------------TGGCGCTCACG-TGAGGCCAGGAGTAAATCGCACACACAGCCCATGCTTTCACCATCTGCTAGGGTGCTCTGGAGCAGGGCAGGCTTCTAACCTGG", ) self.assertEqual(alignment.sequences[1].id, "canFam2.chr1") self.assertEqual(len(alignment.sequences[1].seq), 125616256) self.assertEqual( alignment.sequences[1].seq[47545247 : 47545247 + 106], "CCAGGTTTGGGACCTATGTGTGTCAAGTGAATAGAAGCAGGTGGGACAGCATGTGCGTCACACATGGACACAGCCTGGACATCGTGGGGCATTTTCCATTTGCCTC", ) self.assertEqual( alignment[1], "GAGGC-AAATGGAAAATGCCCCACGATGTCCAGGCTGTGTCCATGTGTGA--CGCACATGCTGTCC----------CACCTGCTTCTATTCACTTGACACACATAGGTCCCAAACCTGG", ) self.assertEqual( alignment.sequences[1].annotations["quality"], "9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999", ) self.assertEqual(alignment.sequences[1].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[1].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[1].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[1].annotations["rightCount"], 0) empty = alignment.annotations["empty"][0] (record, segment, status) = empty self.assertEqual(record.id, "ornAna1.chr2") self.assertEqual(len(record.seq), 54797317) self.assertEqual(segment, (40046122, 40040432)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][1] (record, segment, status) = empty self.assertEqual(record.id, "calJac1.Contig6394") self.assertEqual(len(record.seq), 133105) self.assertEqual(segment, (6649, 10128)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][2] (record, segment, status) = empty self.assertEqual(record.id, "tupBel1.scaffold_114895.1-498454") self.assertEqual(len(record.seq), 498454) self.assertEqual(segment, (326690, 324316)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][3] (record, segment, status) = empty self.assertEqual(record.id, "echTel1.scaffold_288249") self.assertEqual(len(record.seq), 100002) self.assertEqual(segment, (87661, 95225)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][4] (record, segment, status) = empty self.assertEqual(record.id, "cavPor2.scaffold_216473") self.assertEqual(len(record.seq), 10026) self.assertEqual(segment, (1978, 606)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][5] (record, segment, status) = empty self.assertEqual(record.id, "otoGar1.scaffold_334.1-359464") self.assertEqual(len(record.seq), 359464) self.assertEqual(segment, (174625, 171894)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][6] (record, segment, status) = empty self.assertEqual(record.id, "hg18.chr6") self.assertEqual(len(record.seq), 170899992) self.assertEqual(segment, (155028090, 155025688)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][7] (record, segment, status) = empty self.assertEqual(record.id, "panTro2.chr6") self.assertEqual(len(record.seq), 173908612) self.assertEqual(segment, (157518143, 157515743)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][8] (record, segment, status) = empty self.assertEqual(record.id, "ponAbe2.chr6") self.assertEqual(len(record.seq), 174210431) self.assertEqual(segment, (158040326, 158037803)) self.assertEqual(status, "I") self.assertEqual(len(alignment.sequences), 2) self.assertEqual(len(alignment.annotations["empty"]), 9) self.assertEqual( str(alignment), """\ mm9.chr10 3019271 GAGACCAAATG------------TGGCGCTCACG-TGAGGCCAGGAGTAAATCGCACACA 0 |||.|-|||||------------.|..|..||.|-||.|.|||.|.||.|--||||||.. canFam2.c 47545353 GAGGC-AAATGGAAAATGCCCCACGATGTCCAGGCTGTGTCCATGTGTGA--CGCACATG mm9.chr10 3019318 CAGCCCATGCTTTCACCATCTGCTAGGGTGCTCTGGAGCAGGGCAGGCTTCTAACCTGG 60 |.|.||----------||.|||||....|.|.||.||.......|||...|.||||||| canFam2.c 47545296 CTGTCC----------CACCTGCTTCTATTCACTTGACACACATAGGTCCCAAACCTGG mm9.chr10 3019377 119 canFam2.c 47545247 """, ) self.assertTrue( np.array_equal( alignment.coordinates, np.array( # fmt: off [[ 3019271, 3019276, 3019277, 3019282, 3019282, 3019293, 3019293, 3019308, 3019310, 3019324, 3019334, 3019377], [47545353, 47545348, 47545348, 47545343, 47545331, 47545320, 47545319, 47545304, 47545304, 47545290, 47545290, 47545247], ] # fmt: on ), ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['G', 'A', 'G', 'A', 'C', 'C', 'A', 'A', 'A', 'T', 'G', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'T', 'G', 'G', 'C', 'G', 'C', 'T', 'C', 'A', 'C', 'G', '-', 'T', 'G', 'A', 'G', 'G', 'C', 'C', 'A', 'G', 'G', 'A', 'G', 'T', 'A', 'A', 'A', 'T', 'C', 'G', 'C', 'A', 'C', 'A', 'C', 'A', 'C', 'A', 'G', 'C', 'C', 'C', 'A', 'T', 'G', 'C', 'T', 'T', 'T', 'C', 'A', 'C', 'C', 'A', 'T', 'C', 'T', 'G', 'C', 'T', 'A', 'G', 'G', 'G', 'T', 'G', 'C', 'T', 'C', 'T', 'G', 'G', 'A', 'G', 'C', 'A', 'G', 'G', 'G', 'C', 'A', 'G', 'G', 'C', 'T', 'T', 'C', 'T', 'A', 'A', 'C', 'C', 'T', 'G', 'G'], ['G', 'A', 'G', 'G', 'C', '-', 'A', 'A', 'A', 'T', 'G', 'G', 'A', 'A', 'A', 'A', 'T', 'G', 'C', 'C', 'C', 'C', 'A', 'C', 'G', 'A', 'T', 'G', 'T', 'C', 'C', 'A', 'G', 'G', 'C', 'T', 'G', 'T', 'G', 'T', 'C', 'C', 'A', 'T', 'G', 'T', 'G', 'T', 'G', 'A', '-', '-', 'C', 'G', 'C', 'A', 'C', 'A', 'T', 'G', 'C', 'T', 'G', 'T', 'C', 'C', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'C', 'A', 'C', 'C', 'T', 'G', 'C', 'T', 'T', 'C', 'T', 'A', 'T', 'T', 'C', 'A', 'C', 'T', 'T', 'G', 'A', 'C', 'A', 'C', 'A', 'C', 'A', 'T', 'A', 'G', 'G', 'T', 'C', 'C', 'C', 'A', 'A', 'A', 'C', 'C', 'T', 'G', 'G']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.score, 10938) self.assertEqual(alignment.sequences[0].id, "mm9.chr10") self.assertEqual(len(alignment.sequences[0].seq), 129993255) self.assertEqual( alignment.sequences[0].seq[3019377 : 3019377 + 88], "CCCCAGCATTCTGGCAGACACAGTGAAAAGAGACAGATGGTCACTAATAAAATCTGTATAAATTAGATCTCAGAGGATGGATGGACCA", ) self.assertEqual( alignment[0], "CCCCAGCATTCTGGCAGACACAGTG-AAAAGAGACAGATGGTCACTAATAAAATCTGT-ATAAATTAG-ATCTCAGAGGATGGATGGACCA", ) self.assertEqual(alignment.sequences[1].id, "felCat3.scaffold_205680") self.assertEqual(len(alignment.sequences[1].seq), 119354) self.assertEqual( alignment.sequences[1].seq[46757 : 46757 + 88], "GAGTCCCATCCTCTGAGATTCTAGTTCACCACAAAGCTTACTGGTGGGCACATGCTTCTTTTTCACATTAGCTATCAGAACACTTGGG", ) self.assertEqual( alignment[1], "CCCAAGTGTTCTGATAGCTAATGTGAAAAAGAAGCATGTGCCCACCAGTAAGCTTTGTGGTGAACTAGAATCTCAGAGGATG---GGACTC", ) self.assertEqual( alignment.sequences[1].annotations["quality"], "9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999", ) self.assertEqual(alignment.sequences[1].annotations["leftStatus"], "N") self.assertEqual(alignment.sequences[1].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[1].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[1].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[2].id, "canFam2.chr1") self.assertEqual(len(alignment.sequences[2].seq), 125616256) self.assertEqual( alignment.sequences[2].seq[47545159 : 47545159 + 88], "gagtcccatcctctgagattctaggtcattgcaaatctTATTAGCGGGCCCATGTTTCTTTTTCACAGAGGCAATCAGAACACTTGGG", ) self.assertEqual( alignment[2], "CCCAAGTGTTCTGATTGCCTCTGTGAAAAAGAAACATGGGCCCGCTAATAagatttgcaatgacctagaatctcagaggatg---ggactc", ) self.assertEqual( alignment.sequences[2].annotations["quality"], "9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999", ) self.assertEqual(alignment.sequences[2].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[2].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[2].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[2].annotations["rightCount"], 0) empty = alignment.annotations["empty"][0] (record, segment, status) = empty self.assertEqual(record.id, "ornAna1.chr2") self.assertEqual(len(record.seq), 54797317) self.assertEqual(segment, (40046122, 40040432)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][1] (record, segment, status) = empty self.assertEqual(record.id, "calJac1.Contig6394") self.assertEqual(len(record.seq), 133105) self.assertEqual(segment, (6649, 10128)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][2] (record, segment, status) = empty self.assertEqual(record.id, "tupBel1.scaffold_114895.1-498454") self.assertEqual(len(record.seq), 498454) self.assertEqual(segment, (326690, 324316)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][3] (record, segment, status) = empty self.assertEqual(record.id, "echTel1.scaffold_288249") self.assertEqual(len(record.seq), 100002) self.assertEqual(segment, (87661, 95225)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][4] (record, segment, status) = empty self.assertEqual(record.id, "cavPor2.scaffold_216473") self.assertEqual(len(record.seq), 10026) self.assertEqual(segment, (1978, 606)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][5] (record, segment, status) = empty self.assertEqual(record.id, "otoGar1.scaffold_334.1-359464") self.assertEqual(len(record.seq), 359464) self.assertEqual(segment, (174625, 171894)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][6] (record, segment, status) = empty self.assertEqual(record.id, "hg18.chr6") self.assertEqual(len(record.seq), 170899992) self.assertEqual(segment, (155028090, 155025688)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][7] (record, segment, status) = empty self.assertEqual(record.id, "panTro2.chr6") self.assertEqual(len(record.seq), 173908612) self.assertEqual(segment, (157518143, 157515743)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][8] (record, segment, status) = empty self.assertEqual(record.id, "ponAbe2.chr6") self.assertEqual(len(record.seq), 174210431) self.assertEqual(segment, (158040326, 158037803)) self.assertEqual(status, "I") self.assertEqual(len(alignment.sequences), 3) self.assertEqual(len(alignment.annotations["empty"]), 9) self.assertEqual( str(alignment), """\ mm9.chr10 3019377 CCCCAGCATTCTGGCAGACACAGTG-AAAAGAGACAGATGGTCACTAATAAAATCTGT-A felCat3.s 46845 CCCAAGTGTTCTGATAGCTAATGTGAAAAAGAAGCATGTGCCCACCAGTAAGCTTTGTGG canFam2.c 47545247 CCCAAGTGTTCTGATTGCCTCTGTGAAAAAGAAACATGGGCCCGCTAATAagatttgcaa mm9.chr10 3019435 TAAATTAG-ATCTCAGAGGATGGATGGACCA 3019465 felCat3.s 46785 TGAACTAGAATCTCAGAGGATG---GGACTC 46757 canFam2.c 47545187 tgacctagaatctcagaggatg---ggactc 47545159 """, ) self.assertTrue( np.array_equal( alignment.coordinates, np.array( # fmt: off [[ 3019377, 3019402, 3019402, 3019434, 3019434, 3019443, 3019443, 3019456, 3019459, 3019465], [ 46845, 46820, 46819, 46787, 46786, 46777, 46776, 46763, 46763, 46757], [47545247, 47545222, 47545221, 47545189, 47545188, 47545179, 47545178, 47545165, 47545165, 47545159], ] # fmt: on ), ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['C', 'C', 'C', 'C', 'A', 'G', 'C', 'A', 'T', 'T', 'C', 'T', 'G', 'G', 'C', 'A', 'G', 'A', 'C', 'A', 'C', 'A', 'G', 'T', 'G', '-', 'A', 'A', 'A', 'A', 'G', 'A', 'G', 'A', 'C', 'A', 'G', 'A', 'T', 'G', 'G', 'T', 'C', 'A', 'C', 'T', 'A', 'A', 'T', 'A', 'A', 'A', 'A', 'T', 'C', 'T', 'G', 'T', '-', 'A', 'T', 'A', 'A', 'A', 'T', 'T', 'A', 'G', '-', 'A', 'T', 'C', 'T', 'C', 'A', 'G', 'A', 'G', 'G', 'A', 'T', 'G', 'G', 'A', 'T', 'G', 'G', 'A', 'C', 'C', 'A'], ['C', 'C', 'C', 'A', 'A', 'G', 'T', 'G', 'T', 'T', 'C', 'T', 'G', 'A', 'T', 'A', 'G', 'C', 'T', 'A', 'A', 'T', 'G', 'T', 'G', 'A', 'A', 'A', 'A', 'A', 'G', 'A', 'A', 'G', 'C', 'A', 'T', 'G', 'T', 'G', 'C', 'C', 'C', 'A', 'C', 'C', 'A', 'G', 'T', 'A', 'A', 'G', 'C', 'T', 'T', 'T', 'G', 'T', 'G', 'G', 'T', 'G', 'A', 'A', 'C', 'T', 'A', 'G', 'A', 'A', 'T', 'C', 'T', 'C', 'A', 'G', 'A', 'G', 'G', 'A', 'T', 'G', '-', '-', '-', 'G', 'G', 'A', 'C', 'T', 'C'], ['C', 'C', 'C', 'A', 'A', 'G', 'T', 'G', 'T', 'T', 'C', 'T', 'G', 'A', 'T', 'T', 'G', 'C', 'C', 'T', 'C', 'T', 'G', 'T', 'G', 'A', 'A', 'A', 'A', 'A', 'G', 'A', 'A', 'A', 'C', 'A', 'T', 'G', 'G', 'G', 'C', 'C', 'C', 'G', 'C', 'T', 'A', 'A', 'T', 'A', 'a', 'g', 'a', 't', 't', 't', 'g', 'c', 'a', 'a', 't', 'g', 'a', 'c', 'c', 't', 'a', 'g', 'a', 'a', 't', 'c', 't', 'c', 'a', 'g', 'a', 'g', 'g', 'a', 't', 'g', '-', '-', '-', 'g', 'g', 'a', 'c', 't', 'c']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.score, 36924) self.assertEqual(alignment.sequences[0].id, "mm9.chr10") self.assertEqual(len(alignment.sequences[0].seq), 129993255) self.assertEqual( alignment.sequences[0].seq[3019465 : 3019465 + 47], "AAGATAGATATTTAGAAGTAGCTTTTTATGTTTTTCTGATGTGTGTT", ) self.assertEqual( alignment[0], "AAGATAGATATTTAGAAGTAGCTTTTTATGTTTTTCTGATGTGTGTT" ) self.assertEqual(alignment.sequences[1].id, "calJac1.Contig6394") self.assertEqual(len(alignment.sequences[1].seq), 133105) self.assertEqual( alignment.sequences[1].seq[10128 : 10128 + 47], "aacaTCTATATTTTGAAATGGCTTTTCATGTTACTCTGATGTGTGTC", ) self.assertEqual( alignment[1], "aacaTCTATATTTTGAAATGGCTTTTCATGTTACTCTGATGTGTGTC" ) self.assertEqual(alignment.sequences[1].annotations["leftStatus"], "I") self.assertEqual(alignment.sequences[1].annotations["leftCount"], 3479) self.assertEqual(alignment.sequences[1].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[1].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[2].id, "panTro2.chr6") self.assertEqual(len(alignment.sequences[2].seq), 173908612) self.assertEqual( alignment.sequences[2].seq[157515703 : 157515703 + 40], "AAAACAcatcagaataacatgaaaagccatttcaaaatat", ) self.assertEqual( alignment[2], "-------atattttgaaatggcttttcatgttattctgatgTGTTTT" ) self.assertEqual( alignment.sequences[2].annotations["quality"], "9999999999999999999999999999999999999999", ) self.assertEqual(alignment.sequences[2].annotations["leftStatus"], "I") self.assertEqual(alignment.sequences[2].annotations["leftCount"], 2400) self.assertEqual(alignment.sequences[2].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[2].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[3].id, "hg18.chr6") self.assertEqual(len(alignment.sequences[3].seq), 170899992) self.assertEqual( alignment.sequences[3].seq[155025648 : 155025648 + 40], "AAAACAcatcagaataacatgaaaagccatttcaaaatat", ) self.assertEqual( alignment[3], "-------atattttgaaatggcttttcatgttattctgatgTGTTTT" ) self.assertEqual(alignment.sequences[3].annotations["leftStatus"], "I") self.assertEqual(alignment.sequences[3].annotations["leftCount"], 2402) self.assertEqual(alignment.sequences[3].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[3].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[4].id, "canFam2.chr1") self.assertEqual(len(alignment.sequences[4].seq), 125616256) self.assertEqual( alignment.sequences[4].seq[47545115 : 47545115 + 44], "aacacacattagaacaacatgaagagctatttttaaatatacct", ) self.assertEqual( alignment[4], "---aggtatatttaaaaatagctcttcatgttgttctaatgtgtgtt" ) self.assertEqual( alignment.sequences[4].annotations["quality"], "99999999999999999999999999999999999999999999", ) self.assertEqual(alignment.sequences[4].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[4].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[4].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[4].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[5].id, "felCat3.scaffold_205680") self.assertEqual(len(alignment.sequences[5].seq), 119354) self.assertEqual( alignment.sequences[5].seq[46714 : 46714 + 43], "AACACACATCAGAACAACATGAAAACTATTTTTAAAAACACGT", ) self.assertEqual( alignment[5], "---ACGTGTTTTTAAAAATAG-TTTTCATGTTGTTCTGATGTGTGTT" ) self.assertEqual( alignment.sequences[5].annotations["quality"], "9999999999999999999999999999999999999999999", ) self.assertEqual(alignment.sequences[5].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[5].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[5].annotations["rightStatus"], "I") self.assertEqual(alignment.sequences[5].annotations["rightCount"], 193) empty = alignment.annotations["empty"][0] (record, segment, status) = empty self.assertEqual(record.id, "ornAna1.chr2") self.assertEqual(len(record.seq), 54797317) self.assertEqual(segment, (40046122, 40040432)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][1] (record, segment, status) = empty self.assertEqual(record.id, "tupBel1.scaffold_114895.1-498454") self.assertEqual(len(record.seq), 498454) self.assertEqual(segment, (326690, 324316)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][2] (record, segment, status) = empty self.assertEqual(record.id, "echTel1.scaffold_288249") self.assertEqual(len(record.seq), 100002) self.assertEqual(segment, (87661, 95225)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][3] (record, segment, status) = empty self.assertEqual(record.id, "cavPor2.scaffold_216473") self.assertEqual(len(record.seq), 10026) self.assertEqual(segment, (1978, 606)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][4] (record, segment, status) = empty self.assertEqual(record.id, "otoGar1.scaffold_334.1-359464") self.assertEqual(len(record.seq), 359464) self.assertEqual(segment, (174625, 171894)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][5] (record, segment, status) = empty self.assertEqual(record.id, "ponAbe2.chr6") self.assertEqual(len(record.seq), 174210431) self.assertEqual(segment, (158040326, 158037803)) self.assertEqual(status, "I") self.assertEqual(len(alignment.sequences), 6) self.assertEqual(len(alignment.annotations["empty"]), 6) self.assertEqual( str(alignment), """\ mm9.chr10 3019465 AAGATAGATATTTAGAAGTAGCTTTTTATGTTTTTCTGATGTGTGTT 3019512 calJac1.C 10128 aacaTCTATATTTTGAAATGGCTTTTCATGTTACTCTGATGTGTGTC 10175 panTro2.c 157515743 -------atattttgaaatggcttttcatgttattctgatgTGTTTT 157515703 hg18.chr6 155025688 -------atattttgaaatggcttttcatgttattctgatgTGTTTT 155025648 canFam2.c 47545159 ---aggtatatttaaaaatagctcttcatgttgttctaatgtgtgtt 47545115 felCat3.s 46757 ---ACGTGTTTTTAAAAATAG-TTTTCATGTTGTTCTGATGTGTGTT 46714 """, ) self.assertTrue( np.array_equal( alignment.coordinates, np.array( # fmt: off [[ 3019465, 3019468, 3019472, 3019486, 3019487, 3019512], [ 10128, 10131, 10135, 10149, 10150, 10175], [157515743, 157515743, 157515743, 157515729, 157515728, 157515703], [155025688, 155025688, 155025688, 155025674, 155025673, 155025648], [ 47545159, 47545159, 47545155, 47545141, 47545140, 47545115], [ 46757, 46757, 46753, 46739, 46739, 46714], ] # fmt: on ), ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['A', 'A', 'G', 'A', 'T', 'A', 'G', 'A', 'T', 'A', 'T', 'T', 'T', 'A', 'G', 'A', 'A', 'G', 'T', 'A', 'G', 'C', 'T', 'T', 'T', 'T', 'T', 'A', 'T', 'G', 'T', 'T', 'T', 'T', 'T', 'C', 'T', 'G', 'A', 'T', 'G', 'T', 'G', 'T', 'G', 'T', 'T'], ['a', 'a', 'c', 'a', 'T', 'C', 'T', 'A', 'T', 'A', 'T', 'T', 'T', 'T', 'G', 'A', 'A', 'A', 'T', 'G', 'G', 'C', 'T', 'T', 'T', 'T', 'C', 'A', 'T', 'G', 'T', 'T', 'A', 'C', 'T', 'C', 'T', 'G', 'A', 'T', 'G', 'T', 'G', 'T', 'G', 'T', 'C'], ['-', '-', '-', '-', '-', '-', '-', 'a', 't', 'a', 't', 't', 't', 't', 'g', 'a', 'a', 'a', 't', 'g', 'g', 'c', 't', 't', 't', 't', 'c', 'a', 't', 'g', 't', 't', 'a', 't', 't', 'c', 't', 'g', 'a', 't', 'g', 'T', 'G', 'T', 'T', 'T', 'T'], ['-', '-', '-', '-', '-', '-', '-', 'a', 't', 'a', 't', 't', 't', 't', 'g', 'a', 'a', 'a', 't', 'g', 'g', 'c', 't', 't', 't', 't', 'c', 'a', 't', 'g', 't', 't', 'a', 't', 't', 'c', 't', 'g', 'a', 't', 'g', 'T', 'G', 'T', 'T', 'T', 'T'], ['-', '-', '-', 'a', 'g', 'g', 't', 'a', 't', 'a', 't', 't', 't', 'a', 'a', 'a', 'a', 'a', 't', 'a', 'g', 'c', 't', 'c', 't', 't', 'c', 'a', 't', 'g', 't', 't', 'g', 't', 't', 'c', 't', 'a', 'a', 't', 'g', 't', 'g', 't', 'g', 't', 't'], ['-', '-', '-', 'A', 'C', 'G', 'T', 'G', 'T', 'T', 'T', 'T', 'T', 'A', 'A', 'A', 'A', 'A', 'T', 'A', 'G', '-', 'T', 'T', 'T', 'T', 'C', 'A', 'T', 'G', 'T', 'T', 'G', 'T', 'T', 'C', 'T', 'G', 'A', 'T', 'G', 'T', 'G', 'T', 'G', 'T', 'T']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.score, 20303) self.assertEqual(alignment.sequences[0].id, "mm9.chr10") self.assertEqual(len(alignment.sequences[0].seq), 129993255) self.assertEqual( alignment.sequences[0].seq[3019512 : 3019512 + 92], "TGCATCATTAAGACTAGAGTTCCTTTCTGTCTTTGCTTTCTTGACAGGGCCATGCTCGGCAGTCATTCTTAGACTGCTTTTTGTTTgtttgg", ) self.assertEqual( alignment[0], "TGCATCATTAAGACTAGAGTTCCT---------------TTCTGTCTT---TGCTTTCTTG--------ACAGGGCCATGCTCGGCAGTCATTCTTAGACTGCTTTTTGTTTgtttgg", ) self.assertEqual(alignment.sequences[1].id, "calJac1.Contig6394") self.assertEqual(len(alignment.sequences[1].seq), 133105) self.assertEqual( alignment.sequences[1].seq[10175 : 10175 + 86], "CCTCATGAAGGCCCAAGTTCCTAAAACATTAATTCTCTTCCTATTTCCTAGCTGTCTCGCCTAGGCCTTGCCCGCCAGCAATTCCC", ) self.assertEqual( alignment[1], "--CCTCATGAAGGCCCAAGTTCCTAAA-----ACATTAATTCTCTTCC---TATTTCCTAGCTGTCTCGCCTAGGCCTTGCCCGCCAGCAATTCCC----------------------", ) self.assertEqual(alignment.sequences[1].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[1].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[1].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[1].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[2].id, "panTro2.chr6") self.assertEqual(len(alignment.sequences[2].seq), 173908612) self.assertEqual( alignment.sequences[2].seq[157515610 : 157515610 + 93], "CCAATACCCATGTGGGAATTGCTGGCGGGCAAGACCTCTTTTCTAGAAAAGAGGAAGAGAATGAATGTTTTAGGAACTTGGGCCTTAATGAAG", ) self.assertEqual( alignment[2], "--CTTCATTAAGGCCCAAGTTCCTAAA-----ACATTCATTCTCTTCC---TCTTTTCTAG------AAAAGAGGTCTTGCCCGCCAGCAATTCCCACATGGGTATTGG---------", ) self.assertEqual( alignment.sequences[2].annotations["quality"], "999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999", ) self.assertEqual(alignment.sequences[2].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[2].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[2].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[2].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[3].id, "hg18.chr6") self.assertEqual(len(alignment.sequences[3].seq), 170899992) self.assertEqual( alignment.sequences[3].seq[155025555 : 155025555 + 93], "CCAATACCCATGTGGGAATTGCTGGCGGGCAAGACCTCTTTTCTAGAAAAGAGGAAGAGAATGAATGTTTTAGGAACTTGGGCCTTAATGAAG", ) self.assertEqual( alignment[3], "--CTTCATTAAGGCCCAAGTTCCTAAA-----ACATTCATTCTCTTCC---TCTTTTCTAG------AAAAGAGGTCTTGCCCGCCAGCAATTCCCACATGGGTATTGG---------", ) self.assertEqual(alignment.sequences[3].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[3].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[3].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[3].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[4].id, "canFam2.chr1") self.assertEqual(len(alignment.sequences[4].seq), 125616256) self.assertEqual( alignment.sequences[4].seq[47545018 : 47545018 + 97], "CCGAACAAAGTAGGAATGACTGGCAGGCAAGACACTGATGAGGAAGGGTTGAAGAAAGAAAAAATATAAGCCTGTAAGAACCTGGGTTTAGATGAGG", ) self.assertEqual( alignment[4], "--CCTCATCTAAACCCAGGTTCTTACAGGCTTATATTTTTTCTTTCTTCAACCCTTCCTCA--------TCAGTGTCTTGCCTGCCAGTCATTCCTAC-----------TTTGTTCGG", ) self.assertEqual( alignment.sequences[4].annotations["quality"], "9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999", ) self.assertEqual(alignment.sequences[4].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[4].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[4].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[4].annotations["rightCount"], 0) empty = alignment.annotations["empty"][0] (record, segment, status) = empty self.assertEqual(record.id, "felCat3.scaffold_205680") self.assertEqual(len(record.seq), 119354) self.assertEqual(segment, (46714, 46521)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][1] (record, segment, status) = empty self.assertEqual(record.id, "ornAna1.chr2") self.assertEqual(len(record.seq), 54797317) self.assertEqual(segment, (40046122, 40040432)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][2] (record, segment, status) = empty self.assertEqual(record.id, "tupBel1.scaffold_114895.1-498454") self.assertEqual(len(record.seq), 498454) self.assertEqual(segment, (326690, 324316)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][3] (record, segment, status) = empty self.assertEqual(record.id, "echTel1.scaffold_288249") self.assertEqual(len(record.seq), 100002) self.assertEqual(segment, (87661, 95225)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][4] (record, segment, status) = empty self.assertEqual(record.id, "cavPor2.scaffold_216473") self.assertEqual(len(record.seq), 10026) self.assertEqual(segment, (1978, 606)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][5] (record, segment, status) = empty self.assertEqual(record.id, "otoGar1.scaffold_334.1-359464") self.assertEqual(len(record.seq), 359464) self.assertEqual(segment, (174625, 171894)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][6] (record, segment, status) = empty self.assertEqual(record.id, "ponAbe2.chr6") self.assertEqual(len(record.seq), 174210431) self.assertEqual(segment, (158040326, 158037803)) self.assertEqual(status, "I") self.assertEqual(len(alignment.sequences), 5) self.assertEqual(len(alignment.annotations["empty"]), 7) self.assertEqual( str(alignment), """\ mm9.chr10 3019512 TGCATCATTAAGACTAGAGTTCCT---------------TTCTGTCTT---TGCTTTCTT calJac1.C 10175 --CCTCATGAAGGCCCAAGTTCCTAAA-----ACATTAATTCTCTTCC---TATTTCCTA panTro2.c 157515703 --CTTCATTAAGGCCCAAGTTCCTAAA-----ACATTCATTCTCTTCC---TCTTTTCTA hg18.chr6 155025648 --CTTCATTAAGGCCCAAGTTCCTAAA-----ACATTCATTCTCTTCC---TCTTTTCTA canFam2.c 47545115 --CCTCATCTAAACCCAGGTTCTTACAGGCTTATATTTTTTCTTTCTTCAACCCTTCCTC mm9.chr10 3019554 G--------ACAGGGCCATGCTCGGCAGTCATTCTTAGACTGCTTTTTGTTTgtttgg calJac1.C 10225 GCTGTCTCGCCTAGGCCTTGCCCGCCAGCAATTCCC---------------------- panTro2.c 157515653 G------AAAAGAGGTCTTGCCCGCCAGCAATTCCCACATGGGTATTGG--------- hg18.chr6 155025598 G------AAAAGAGGTCTTGCCCGCCAGCAATTCCCACATGGGTATTGG--------- canFam2.c 47545057 A--------TCAGTGTCTTGCCTGCCAGTCATTCCTAC-----------TTTGTTCGG mm9.chr10 3019604 calJac1.C 10261 panTro2.c 157515610 hg18.chr6 155025555 canFam2.c 47545018 """, ) self.assertTrue( np.array_equal( alignment.coordinates, np.array( # fmt: off [[ 3019512, 3019514, 3019536, 3019536, 3019536, 3019536, 3019545, 3019545, 3019555, 3019555, 3019555, 3019582, 3019584, 3019595, 3019604], [ 10175, 10175, 10197, 10200, 10200, 10207, 10216, 10216, 10226, 10232, 10234, 10261, 10261, 10261, 10261], [157515703, 157515703, 157515681, 157515678, 157515678, 157515671, 157515662, 157515662, 157515652, 157515652, 157515650, 157515623, 157515621, 157515610, 157515610], [155025648, 155025648, 155025626, 155025623, 155025623, 155025616, 155025607, 155025607, 155025597, 155025597, 155025595, 155025568, 155025566, 155025555, 155025555], [ 47545115, 47545115, 47545093, 47545090, 47545085, 47545078, 47545069, 47545066, 47545056, 47545056, 47545056, 47545029, 47545027, 47545027, 47545018], ] # fmt: on ), ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['T', 'G', 'C', 'A', 'T', 'C', 'A', 'T', 'T', 'A', 'A', 'G', 'A', 'C', 'T', 'A', 'G', 'A', 'G', 'T', 'T', 'C', 'C', 'T', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'T', 'T', 'C', 'T', 'G', 'T', 'C', 'T', 'T', '-', '-', '-', 'T', 'G', 'C', 'T', 'T', 'T', 'C', 'T', 'T', 'G', '-', '-', '-', '-', '-', '-', '-', '-', 'A', 'C', 'A', 'G', 'G', 'G', 'C', 'C', 'A', 'T', 'G', 'C', 'T', 'C', 'G', 'G', 'C', 'A', 'G', 'T', 'C', 'A', 'T', 'T', 'C', 'T', 'T', 'A', 'G', 'A', 'C', 'T', 'G', 'C', 'T', 'T', 'T', 'T', 'T', 'G', 'T', 'T', 'T', 'g', 't', 't', 't', 'g', 'g'], ['-', '-', 'C', 'C', 'T', 'C', 'A', 'T', 'G', 'A', 'A', 'G', 'G', 'C', 'C', 'C', 'A', 'A', 'G', 'T', 'T', 'C', 'C', 'T', 'A', 'A', 'A', '-', '-', '-', '-', '-', 'A', 'C', 'A', 'T', 'T', 'A', 'A', 'T', 'T', 'C', 'T', 'C', 'T', 'T', 'C', 'C', '-', '-', '-', 'T', 'A', 'T', 'T', 'T', 'C', 'C', 'T', 'A', 'G', 'C', 'T', 'G', 'T', 'C', 'T', 'C', 'G', 'C', 'C', 'T', 'A', 'G', 'G', 'C', 'C', 'T', 'T', 'G', 'C', 'C', 'C', 'G', 'C', 'C', 'A', 'G', 'C', 'A', 'A', 'T', 'T', 'C', 'C', 'C', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-'], ['-', '-', 'C', 'T', 'T', 'C', 'A', 'T', 'T', 'A', 'A', 'G', 'G', 'C', 'C', 'C', 'A', 'A', 'G', 'T', 'T', 'C', 'C', 'T', 'A', 'A', 'A', '-', '-', '-', '-', '-', 'A', 'C', 'A', 'T', 'T', 'C', 'A', 'T', 'T', 'C', 'T', 'C', 'T', 'T', 'C', 'C', '-', '-', '-', 'T', 'C', 'T', 'T', 'T', 'T', 'C', 'T', 'A', 'G', '-', '-', '-', '-', '-', '-', 'A', 'A', 'A', 'A', 'G', 'A', 'G', 'G', 'T', 'C', 'T', 'T', 'G', 'C', 'C', 'C', 'G', 'C', 'C', 'A', 'G', 'C', 'A', 'A', 'T', 'T', 'C', 'C', 'C', 'A', 'C', 'A', 'T', 'G', 'G', 'G', 'T', 'A', 'T', 'T', 'G', 'G', '-', '-', '-', '-', '-', '-', '-', '-', '-'], ['-', '-', 'C', 'T', 'T', 'C', 'A', 'T', 'T', 'A', 'A', 'G', 'G', 'C', 'C', 'C', 'A', 'A', 'G', 'T', 'T', 'C', 'C', 'T', 'A', 'A', 'A', '-', '-', '-', '-', '-', 'A', 'C', 'A', 'T', 'T', 'C', 'A', 'T', 'T', 'C', 'T', 'C', 'T', 'T', 'C', 'C', '-', '-', '-', 'T', 'C', 'T', 'T', 'T', 'T', 'C', 'T', 'A', 'G', '-', '-', '-', '-', '-', '-', 'A', 'A', 'A', 'A', 'G', 'A', 'G', 'G', 'T', 'C', 'T', 'T', 'G', 'C', 'C', 'C', 'G', 'C', 'C', 'A', 'G', 'C', 'A', 'A', 'T', 'T', 'C', 'C', 'C', 'A', 'C', 'A', 'T', 'G', 'G', 'G', 'T', 'A', 'T', 'T', 'G', 'G', '-', '-', '-', '-', '-', '-', '-', '-', '-'], ['-', '-', 'C', 'C', 'T', 'C', 'A', 'T', 'C', 'T', 'A', 'A', 'A', 'C', 'C', 'C', 'A', 'G', 'G', 'T', 'T', 'C', 'T', 'T', 'A', 'C', 'A', 'G', 'G', 'C', 'T', 'T', 'A', 'T', 'A', 'T', 'T', 'T', 'T', 'T', 'T', 'C', 'T', 'T', 'T', 'C', 'T', 'T', 'C', 'A', 'A', 'C', 'C', 'C', 'T', 'T', 'C', 'C', 'T', 'C', 'A', '-', '-', '-', '-', '-', '-', '-', '-', 'T', 'C', 'A', 'G', 'T', 'G', 'T', 'C', 'T', 'T', 'G', 'C', 'C', 'T', 'G', 'C', 'C', 'A', 'G', 'T', 'C', 'A', 'T', 'T', 'C', 'C', 'T', 'A', 'C', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'T', 'T', 'T', 'G', 'T', 'T', 'C', 'G', 'G']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.score, 0) self.assertEqual(alignment.sequences[0].id, "mm9.chr10") self.assertEqual(len(alignment.sequences[0].seq), 129993255) self.assertEqual( alignment.sequences[0].seq[3019604 : 3019604 + 98], "tttggtttggtttggttttttcaagacagggtttctttgtatagtcctagctgtcctggaactcactttgtagaccagactggccttgaactcagaaa", ) self.assertEqual( alignment[0], "tttggtttggtttggttttttcaagacagggtttctttgtatagtcctagctgtcctggaactcactttgtagaccagactggccttgaactcagaaa", ) empty = alignment.annotations["empty"][0] (record, segment, status) = empty self.assertEqual(record.id, "felCat3.scaffold_205680") self.assertEqual(len(record.seq), 119354) self.assertEqual(segment, (46714, 46521)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][1] (record, segment, status) = empty self.assertEqual(record.id, "canFam2.chr1") self.assertEqual(len(record.seq), 125616256) self.assertEqual(segment, (47545018, 47545018)) self.assertEqual(status, "C") empty = alignment.annotations["empty"][2] (record, segment, status) = empty self.assertEqual(record.id, "ornAna1.chr2") self.assertEqual(len(record.seq), 54797317) self.assertEqual(segment, (40046122, 40040432)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][3] (record, segment, status) = empty self.assertEqual(record.id, "calJac1.Contig6394") self.assertEqual(len(record.seq), 133105) self.assertEqual(segment, (10261, 10261)) self.assertEqual(status, "C") empty = alignment.annotations["empty"][4] (record, segment, status) = empty self.assertEqual(record.id, "tupBel1.scaffold_114895.1-498454") self.assertEqual(len(record.seq), 498454) self.assertEqual(segment, (326690, 324316)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][5] (record, segment, status) = empty self.assertEqual(record.id, "echTel1.scaffold_288249") self.assertEqual(len(record.seq), 100002) self.assertEqual(segment, (87661, 95225)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][6] (record, segment, status) = empty self.assertEqual(record.id, "cavPor2.scaffold_216473") self.assertEqual(len(record.seq), 10026) self.assertEqual(segment, (1978, 606)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][7] (record, segment, status) = empty self.assertEqual(record.id, "otoGar1.scaffold_334.1-359464") self.assertEqual(len(record.seq), 359464) self.assertEqual(segment, (174625, 171894)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][8] (record, segment, status) = empty self.assertEqual(record.id, "hg18.chr6") self.assertEqual(len(record.seq), 170899992) self.assertEqual(segment, (155025555, 155025555)) self.assertEqual(status, "C") empty = alignment.annotations["empty"][9] (record, segment, status) = empty self.assertEqual(record.id, "panTro2.chr6") self.assertEqual(len(record.seq), 173908612) self.assertEqual(segment, (157515610, 157515610)) self.assertEqual(status, "C") empty = alignment.annotations["empty"][10] (record, segment, status) = empty self.assertEqual(record.id, "ponAbe2.chr6") self.assertEqual(len(record.seq), 174210431) self.assertEqual(segment, (158040326, 158037803)) self.assertEqual(status, "I") self.assertEqual(len(alignment.sequences), 1) self.assertEqual(len(alignment.annotations["empty"]), 11) self.assertEqual( str(alignment), """\ mm9.chr10 3019604 tttggtttggtttggttttttcaagacagggtttctttgtatagtcctagctgtcctgga mm9.chr10 3019664 actcactttgtagaccagactggccttgaactcagaaa 3019702 """, ) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[3019604, 3019702]])) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['t', 't', 't', 'g', 'g', 't', 't', 't', 'g', 'g', 't', 't', 't', 'g', 'g', 't', 't', 't', 't', 't', 't', 'c', 'a', 'a', 'g', 'a', 'c', 'a', 'g', 'g', 'g', 't', 't', 't', 'c', 't', 't', 't', 'g', 't', 'a', 't', 'a', 'g', 't', 'c', 'c', 't', 'a', 'g', 'c', 't', 'g', 't', 'c', 'c', 't', 'g', 'g', 'a', 'a', 'c', 't', 'c', 'a', 'c', 't', 't', 't', 'g', 't', 'a', 'g', 'a', 'c', 'c', 'a', 'g', 'a', 'c', 't', 'g', 'g', 'c', 'c', 't', 't', 'g', 'a', 'a', 'c', 't', 'c', 'a', 'g', 'a', 'a', 'a']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.score, 45) self.assertEqual(alignment.sequences[0].id, "mm9.chr10") self.assertEqual(len(alignment.sequences[0].seq), 129993255) self.assertEqual( alignment.sequences[0].seq[3019702 : 3019702 + 42], "tctgcctgcctctgcctcccaagtcctgggattaaaggcgtg", ) self.assertEqual( alignment[0], "tctgcctgcctctgcctcccaag--------------------------------tcctgggattaaaggcgtg", ) self.assertEqual(alignment.sequences[1].id, "felCat3.scaffold_205680") self.assertEqual(len(alignment.sequences[1].seq), 119354) self.assertEqual( alignment.sequences[1].seq[46447 : 46447 + 74], "TAAACCTTTAAGAACTTGAGTTTGTTTGTTTGGttttttttaatgtttatttttgagagagagagagagacaga", ) self.assertEqual( alignment[1], "tctgtctctctctctctctcaaaaataaacattaaaaaaaaCCAAACAAACAAACTCAAGTTCTTAAAGGTTTA", ) self.assertEqual( alignment.sequences[1].annotations["quality"], "99999999999999999999999999999999999999999999999999999999999999999999999999", ) self.assertEqual(alignment.sequences[1].annotations["leftStatus"], "I") self.assertEqual(alignment.sequences[1].annotations["leftCount"], 193) self.assertEqual(alignment.sequences[1].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[1].annotations["rightCount"], 0) empty = alignment.annotations["empty"][0] (record, segment, status) = empty self.assertEqual(record.id, "canFam2.chr1") self.assertEqual(len(record.seq), 125616256) self.assertEqual(segment, (47545018, 47545018)) self.assertEqual(status, "C") empty = alignment.annotations["empty"][1] (record, segment, status) = empty self.assertEqual(record.id, "ornAna1.chr2") self.assertEqual(len(record.seq), 54797317) self.assertEqual(segment, (40046122, 40040432)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][2] (record, segment, status) = empty self.assertEqual(record.id, "calJac1.Contig6394") self.assertEqual(len(record.seq), 133105) self.assertEqual(segment, (10261, 10261)) self.assertEqual(status, "C") empty = alignment.annotations["empty"][3] (record, segment, status) = empty self.assertEqual(record.id, "tupBel1.scaffold_114895.1-498454") self.assertEqual(len(record.seq), 498454) self.assertEqual(segment, (326690, 324316)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][4] (record, segment, status) = empty self.assertEqual(record.id, "echTel1.scaffold_288249") self.assertEqual(len(record.seq), 100002) self.assertEqual(segment, (87661, 95225)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][5] (record, segment, status) = empty self.assertEqual(record.id, "cavPor2.scaffold_216473") self.assertEqual(len(record.seq), 10026) self.assertEqual(segment, (1978, 606)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][6] (record, segment, status) = empty self.assertEqual(record.id, "otoGar1.scaffold_334.1-359464") self.assertEqual(len(record.seq), 359464) self.assertEqual(segment, (174625, 171894)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][7] (record, segment, status) = empty self.assertEqual(record.id, "hg18.chr6") self.assertEqual(len(record.seq), 170899992) self.assertEqual(segment, (155025555, 155025555)) self.assertEqual(status, "C") empty = alignment.annotations["empty"][8] (record, segment, status) = empty self.assertEqual(record.id, "panTro2.chr6") self.assertEqual(len(record.seq), 173908612) self.assertEqual(segment, (157515610, 157515610)) self.assertEqual(status, "C") empty = alignment.annotations["empty"][9] (record, segment, status) = empty self.assertEqual(record.id, "ponAbe2.chr6") self.assertEqual(len(record.seq), 174210431) self.assertEqual(segment, (158040326, 158037803)) self.assertEqual(status, "I") self.assertEqual(len(alignment.sequences), 2) self.assertEqual(len(alignment.annotations["empty"]), 10) self.assertEqual( str(alignment), """\ mm9.chr10 3019702 tctgcctgcctctgcctcccaag--------------------------------tcctg 0 ||||.||..||||..|||.|||.--------------------------------..... felCat3.s 46521 tctgtctctctctctctctcaaaaataaacattaaaaaaaaCCAAACAAACAAACTCAAG mm9.chr10 3019730 ggattaaaggcgtg 3019744 60 .............. 74 felCat3.s 46461 TTCTTAAAGGTTTA 46447 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[3019702, 3019725, 3019725, 3019744], [ 46521, 46498, 46466, 46447], ]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['t', 'c', 't', 'g', 'c', 'c', 't', 'g', 'c', 'c', 't', 'c', 't', 'g', 'c', 'c', 't', 'c', 'c', 'c', 'a', 'a', 'g', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 't', 'c', 'c', 't', 'g', 'g', 'g', 'a', 't', 't', 'a', 'a', 'a', 'g', 'g', 'c', 'g', 't', 'g'], ['t', 'c', 't', 'g', 't', 'c', 't', 'c', 't', 'c', 't', 'c', 't', 'c', 't', 'c', 't', 'c', 't', 'c', 'a', 'a', 'a', 'a', 'a', 't', 'a', 'a', 'a', 'c', 'a', 't', 't', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'a', 'C', 'C', 'A', 'A', 'A', 'C', 'A', 'A', 'A', 'C', 'A', 'A', 'A', 'C', 'T', 'C', 'A', 'A', 'G', 'T', 'T', 'C', 'T', 'T', 'A', 'A', 'A', 'G', 'G', 'T', 'T', 'T', 'A']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.score, -16865) self.assertEqual(alignment.sequences[0].id, "mm9.chr10") self.assertEqual(len(alignment.sequences[0].seq), 129993255) self.assertEqual( alignment.sequences[0].seq[3019744 : 3019744 + 33], "cgccaccactgccctgcCTTAAACTGCTCTTAA", ) self.assertEqual( alignment[0], "-----------------cgccaccactgccctgcCT------------TAAACTGCTCTTAA", ) self.assertEqual(alignment.sequences[1].id, "ponAbe2.chr6") self.assertEqual(len(alignment.sequences[1].seq), 174210431) self.assertEqual( alignment.sequences[1].seq[158037776 : 158037776 + 27], "CCAATACCCATGTGGGAATTGCTGGCG", ) self.assertEqual( alignment[1], "-----------------CGCCAGCAATTCC------------------CACATGGGTATTGG", ) self.assertEqual(alignment.sequences[1].annotations["leftStatus"], "I") self.assertEqual(alignment.sequences[1].annotations["leftCount"], 2523) self.assertEqual(alignment.sequences[1].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[1].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[2].id, "tupBel1.scaffold_114895.1-498454") self.assertEqual(len(alignment.sequences[2].seq), 498454) self.assertEqual(alignment.sequences[2].seq[324312 : 324312 + 4], "TCAA") self.assertEqual( alignment[2], "----------------------------------------------------------TTGA", ) self.assertEqual(alignment.sequences[2].annotations["quality"], "9999") self.assertEqual(alignment.sequences[2].annotations["leftStatus"], "I") self.assertEqual(alignment.sequences[2].annotations["leftCount"], 2374) self.assertEqual(alignment.sequences[2].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[2].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[3].id, "calJac1.Contig6394") self.assertEqual(len(alignment.sequences[3].seq), 133105) self.assertEqual( alignment.sequences[3].seq[10261 : 10261 + 13], "ACATGGCTACTGG" ) self.assertEqual( alignment[3], "-------------------------------------------------ACATGGCTACTGG", ) self.assertEqual(alignment.sequences[3].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[3].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[3].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[3].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[4].id, "otoGar1.scaffold_334.1-359464") self.assertEqual(len(alignment.sequences[4].seq), 359464) self.assertEqual( alignment.sequences[4].seq[171883 : 171883 + 11], "TCAACACCAAT" ) self.assertEqual( alignment[4], "---------------------------------------------------ATTGGTGTTGA", ) self.assertEqual(alignment.sequences[4].annotations["quality"], "87784564678") self.assertEqual(alignment.sequences[4].annotations["leftStatus"], "I") self.assertEqual(alignment.sequences[4].annotations["leftCount"], 2731) self.assertEqual(alignment.sequences[4].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[4].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[5].id, "oryCun1.scaffold_156751") self.assertEqual(len(alignment.sequences[5].seq), 4726) self.assertEqual( alignment.sequences[5].seq[4493 : 4493 + 41], "TCAACACCCCTATGGGACCTGAGACAGGCAAGACAATGGTG", ) self.assertEqual( alignment[5], "--------------------CACCATTGTCTTGCCTGTC-TCAGGTCCCATAGGGGTGTTGA", ) self.assertEqual( alignment.sequences[5].annotations["quality"], "99999999999999999999999999999999999999999", ) self.assertEqual(alignment.sequences[5].annotations["leftStatus"], "N") self.assertEqual(alignment.sequences[5].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[5].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[5].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[6].id, "felCat3.scaffold_205680") self.assertEqual(len(alignment.sequences[6].seq), 119354) self.assertEqual( alignment.sequences[6].seq[46385 : 46385 + 62], "TCTACACCAATGTGGGAATGACTGAAAGACAAGACACTGATGAGTAAGAGAAAGAGAAATCA", ) self.assertEqual( alignment[6], "TGATTTCTCTTTCTCTTACTCATCAGTGTCTTGTCTTTCAGTCATTCCCACATTGGTGTAGA", ) self.assertEqual( alignment.sequences[6].annotations["quality"], "99999999999999999999999999999999999999999999999999999999999999", ) self.assertEqual(alignment.sequences[6].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[6].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[6].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[6].annotations["rightCount"], 0) empty = alignment.annotations["empty"][0] (record, segment, status) = empty self.assertEqual(record.id, "canFam2.chr1") self.assertEqual(len(record.seq), 125616256) self.assertEqual(segment, (47545018, 47545018)) self.assertEqual(status, "C") empty = alignment.annotations["empty"][1] (record, segment, status) = empty self.assertEqual(record.id, "ornAna1.chr2") self.assertEqual(len(record.seq), 54797317) self.assertEqual(segment, (40046122, 40040432)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][2] (record, segment, status) = empty self.assertEqual(record.id, "echTel1.scaffold_288249") self.assertEqual(len(record.seq), 100002) self.assertEqual(segment, (87661, 95225)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][3] (record, segment, status) = empty self.assertEqual(record.id, "cavPor2.scaffold_216473") self.assertEqual(len(record.seq), 10026) self.assertEqual(segment, (1978, 606)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][4] (record, segment, status) = empty self.assertEqual(record.id, "hg18.chr6") self.assertEqual(len(record.seq), 170899992) self.assertEqual(segment, (155025555, 155025555)) self.assertEqual(status, "C") empty = alignment.annotations["empty"][5] (record, segment, status) = empty self.assertEqual(record.id, "panTro2.chr6") self.assertEqual(len(record.seq), 173908612) self.assertEqual(segment, (157515610, 157515610)) self.assertEqual(status, "C") self.assertEqual(len(alignment.sequences), 7) self.assertEqual(len(alignment.annotations["empty"]), 6) self.assertEqual( str(alignment), """\ mm9.chr10 3019744 -----------------cgccaccactgccctgcCT------------TAAACTGCTCTT ponAbe2.c 158037803 -----------------CGCCAGCAATTCC------------------CACATGGGTATT tupBel1.s 324316 ----------------------------------------------------------TT calJac1.C 10261 -------------------------------------------------ACATGGCTACT otoGar1.s 171894 ---------------------------------------------------ATTGGTGTT oryCun1.s 4534 --------------------CACCATTGTCTTGCCTGTC-TCAGGTCCCATAGGGGTGTT felCat3.s 46447 TGATTTCTCTTTCTCTTACTCATCAGTGTCTTGTCTTTCAGTCATTCCCACATTGGTGTA mm9.chr10 3019775 AA 3019777 ponAbe2.c 158037778 GG 158037776 tupBel1.s 324314 GA 324312 calJac1.C 10272 GG 10274 otoGar1.s 171885 GA 171883 oryCun1.s 4495 GA 4493 felCat3.s 46387 GA 46385 """, ) self.assertTrue( np.array_equal( alignment.coordinates, np.array( # fmt: off [[ 3019744, 3019744, 3019747, 3019757, 3019763, 3019763, 3019763, 3019763, 3019764, 3019766, 3019773, 3019777], [158037803, 158037803, 158037800, 158037790, 158037790, 158037790, 158037790, 158037790, 158037789, 158037787, 158037780, 158037776], [ 324316, 324316, 324316, 324316, 324316, 324316, 324316, 324316, 324316, 324316, 324316, 324312], [ 10261, 10261, 10261, 10261, 10261, 10261, 10261, 10261, 10261, 10263, 10270, 10274], [ 171894, 171894, 171894, 171894, 171894, 171894, 171894, 171894, 171894, 171894, 171887, 171883], [ 4534, 4534, 4534, 4524, 4518, 4515, 4515, 4507, 4506, 4504, 4497, 4493], [ 46447, 46430, 46427, 46417, 46411, 46408, 46407, 46399, 46398, 46396, 46389, 46385], ] # fmt: on ), ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'c', 'g', 'c', 'c', 'a', 'c', 'c', 'a', 'c', 't', 'g', 'c', 'c', 'c', 't', 'g', 'c', 'C', 'T', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'T', 'A', 'A', 'A', 'C', 'T', 'G', 'C', 'T', 'C', 'T', 'T', 'A', 'A'], ['-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'C', 'G', 'C', 'C', 'A', 'G', 'C', 'A', 'A', 'T', 'T', 'C', 'C', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'C', 'A', 'C', 'A', 'T', 'G', 'G', 'G', 'T', 'A', 'T', 'T', 'G', 'G'], ['-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'T', 'T', 'G', 'A'], ['-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'A', 'C', 'A', 'T', 'G', 'G', 'C', 'T', 'A', 'C', 'T', 'G', 'G'], ['-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'A', 'T', 'T', 'G', 'G', 'T', 'G', 'T', 'T', 'G', 'A'], ['-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'C', 'A', 'C', 'C', 'A', 'T', 'T', 'G', 'T', 'C', 'T', 'T', 'G', 'C', 'C', 'T', 'G', 'T', 'C', '-', 'T', 'C', 'A', 'G', 'G', 'T', 'C', 'C', 'C', 'A', 'T', 'A', 'G', 'G', 'G', 'G', 'T', 'G', 'T', 'T', 'G', 'A'], ['T', 'G', 'A', 'T', 'T', 'T', 'C', 'T', 'C', 'T', 'T', 'T', 'C', 'T', 'C', 'T', 'T', 'A', 'C', 'T', 'C', 'A', 'T', 'C', 'A', 'G', 'T', 'G', 'T', 'C', 'T', 'T', 'G', 'T', 'C', 'T', 'T', 'T', 'C', 'A', 'G', 'T', 'C', 'A', 'T', 'T', 'C', 'C', 'C', 'A', 'C', 'A', 'T', 'T', 'G', 'G', 'T', 'G', 'T', 'A', 'G', 'A']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.score, 367532) self.assertEqual(alignment.sequences[0].id, "mm9.chr10") self.assertEqual(len(alignment.sequences[0].seq), 129993255) self.assertEqual( alignment.sequences[0].seq[3019777 : 3019777 + 183], "GGCAATGTCAGGCTATGCGTTCTAGACAGGGCACAAGAAAAGCTTTTAGCAGCAGAATAAACTTTTAAAGTAAATTACTTTCCTTGATAGCAACTAGACGACCCAATTGATACAGTGGAAAGAGGCCTTTGAGAATGCATGAGAGAATATTTCCTGTAAGAGTTGAACAATTTAGAATTTACc", ) self.assertEqual( alignment[0], "GGCAATGTCA-GGCTATGCGT------TCTAGACAGGGCACAAGAAAAGCTTTTAGCAGCAGAATAAACTTTT-AAAGTAAATTACTTTCCTTGATAGCAACTAGACGACCCAATTGA-TACAGT------GGAAAG-----A----------GGCCTTTGAGAAT---GCATGAGAGAATAT---TTCCTGTA------AGAGTTGAACAATTTAGAATTTACc", ) self.assertEqual(alignment.sequences[1].id, "oryCun1.scaffold_156751") self.assertEqual(len(alignment.sequences[1].seq), 4726) self.assertEqual( alignment.sequences[1].seq[4300 : 4300 + 193], "AATCCTAAACTATTTAGCTCTGAGAAATAGGGGAAGTAATATTATTCCATCCTGATTCCCAAAAGGCTTTTTTTTTCTTTGTTGTATCACTTTGAACACTTGATTACTAGCAAGGGAAGCAGTTTCCTCTAAAGGCTTATTCTACTGGAAAAAGCTTTTCCTGTCCCTTAGAACATAAGGTCATGATGTTGCC", ) self.assertEqual( alignment[1], "GGCAACATCATGACCTTATGT------TCTAA----GGGACAGGAAAAGCTTTTTCCAGTAGAATAAGCCTTT-AGAGGAAACTGCTTCCCTTGCTAGTAATCAAGTGTTCAAAGTGA-TACAACAAAGAAAAAAAA-----A----------GCCTTTTGGGAAT-CAGGATGGAATAATATTACTTCCCCTATTTCTCAGAGCTAAATAGTTTAGGATT----", ) self.assertEqual( alignment.sequences[1].annotations["quality"], "9999999999999999999999999999999999999899999999989999999999999999999999999999999999999999999999999999898999999989979999999999999997999999998978998999999999999999978999999979689999999999999999979", ) self.assertEqual(alignment.sequences[1].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[1].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[1].annotations["rightStatus"], "I") self.assertEqual(alignment.sequences[1].annotations["rightCount"], 37) self.assertEqual(alignment.sequences[2].id, "hg18.chr6") self.assertEqual(len(alignment.sequences[2].seq), 170899992) self.assertEqual( alignment.sequences[2].seq[155025365 : 155025365 + 190], "AATCCTAAATTGTTTAACTCTTAGAAATAAGGGAAATAATATTATTCTATCCTGCATTCTCAAAAAAATTTTTCTTCATCTCACTTTGGTGACCTGATTGCTATCAAGGAAAGCAATTCCCTTTAACATTTTATTCCACTGCAAAAAGCTTTTCCTGTACTTTATCTTGAATATGTATCATGGTGTTGCC", ) self.assertEqual( alignment[2], "GGCAACACCATGA-TACATAT------TCAAGATAAAGTACAGGAAAAGCTTTTTGCAGTGGAATAAAATGTT-AAAGGGAATTGCTTTCCTTGATAGCAATCAGGTCACCAAAGTGA-GATGA-------AGAAAA-----A----------TTTTTTTGAGAATGCAGGATAGAATAATATTATTTCCCTTATTTCTAAGAGTTAAACAATTTAGGATT----", ) self.assertEqual(alignment.sequences[2].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[2].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[2].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[2].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[3].id, "panTro2.chr6") self.assertEqual(len(alignment.sequences[3].seq), 173908612) self.assertEqual( alignment.sequences[3].seq[157515419 : 157515419 + 191], "AATCCTAAATTGTTTAACTCTTAGAAATAAGGGAAATAATATTATTCTATCCTGCATTCTCAAAAAAAATTTTTCTTCATCTCACTTTGGTGACCTGATTGCTATCAAGGAAAGCAATTTCCTTTAACATTTTATTCCACTGCAAAAAGCTTTTCCTGTACTTTATCTTGAATATGTATCATGGTGTTGCC", ) self.assertEqual( alignment[3], "GGCAACACCATGA-TACATAT------TCAAGATAAAGTACAGGAAAAGCTTTTTGCAGTGGAATAAAATGTT-AAAGGAAATTGCTTTCCTTGATAGCAATCAGGTCACCAAAGTGA-GATGA-------AGAAAA-----A---------TTTTTTTTGAGAATGCAGGATAGAATAATATTATTTCCCTTATTTCTAAGAGTTAAACAATTTAGGATT----", ) self.assertEqual( alignment.sequences[3].annotations["quality"], "99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999", ) self.assertEqual(alignment.sequences[3].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[3].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[3].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[3].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[4].id, "ponAbe2.chr6") self.assertEqual(len(alignment.sequences[4].seq), 174210431) self.assertEqual( alignment.sequences[4].seq[158037586 : 158037586 + 190], "AATCCTAAATTGTTTAACTCTAGAAATAAGGGAAATAATATTATTCTGTGCTGCATTCTCAAAAAGAATTTTTCTTCATCTCACTTTGGTGACCTGATTGCTATCAAGGAAAGCAATTTCCTTTAACATTTTATTCCACCGCAAAAAGCTTTTCCTGTACTTTATCTTGAATATGTATCATGGTGTTGCC", ) self.assertEqual( alignment[4], "GGCAACACCATGA-TACATAT------TCAAGATAAAGTACAGGAAAAGCTTTTTGCGGTGGAATAAAATGTT-AAAGGAAATTGCTTTCCTTGATAGCAATCAGGTCACCAAAGTGA-GATGA-------AGAAAA-----A---------TTCTTTTTGAGAATGCAGCACAGAATAATATTATTTCCCTTATTTCT-AGAGTTAAACAATTTAGGATT----", ) self.assertEqual(alignment.sequences[4].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[4].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[4].annotations["rightStatus"], "I") self.assertEqual(alignment.sequences[4].annotations["rightCount"], 21) self.assertEqual(alignment.sequences[5].id, "calJac1.Contig6394") self.assertEqual(len(alignment.sequences[5].seq), 133105) self.assertEqual( alignment.sequences[5].seq[10274 : 10274 + 187], "GGCAACACCGTGATACATATCCGAGATAAAGTACAGGAAAAGCTTTTGCAGTGGACGAAAATGTTGAAGGAAATTGCTTTTCTTGATAGCAATCAGGTCACCAAAGTGAGATGAAGAAAGTTTTTTGAGAATGTGGGATAGAATAATATTGTTTTCGTTATTTCTAAGAGTTAAACAATTTAGGATT", ) self.assertEqual( alignment[5], "GGCAACACCGTGA-TACATAT------CCGAGATAAAGTACAGGAAAAGC-TTTTGCAGTGGACGAAAATGTT-GAAGGAAATTGCTTTTCTTGATAGCAATCAGGTCACCAAAGTGA-GATGA-------AGAAA-----------------GTTTTTTGAGAATGTGGGATAGAATAATATTGTTTTCGTTATTTCTAAGAGTTAAACAATTTAGGATT----", ) self.assertEqual(alignment.sequences[5].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[5].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[5].annotations["rightStatus"], "I") self.assertEqual(alignment.sequences[5].annotations["rightCount"], 21) self.assertEqual(alignment.sequences[6].id, "otoGar1.scaffold_334.1-359464") self.assertEqual(len(alignment.sequences[6].seq), 359464) self.assertEqual( alignment.sequences[6].seq[171686 : 171686 + 197], "AATCCTGAATTATTTAACTCTGAAATGGAGGGTGGATAAAATTATTCTTTCCAGCATTCTCAAAACATTTTTTCTTTATAATCACTTTGGTCACCTGATTGCTATCAAGAAAAGCAATTTCCTTTAACCTTTTATTCTACCGTAAAGGGCTTTTCCTGCACTTTGTCTTTATCTACAGCAAGGATCACGGCGTTGCC", ) self.assertEqual( alignment[6], "GGCAACGCCGTGA-TCCTTGCTGTAGATAAAGACAAAGTGCAGGAAAAGCCCTTTACGGTAGAATAAAAGGTT-AAAGGAAATTGCTTTTCTTGATAGCAATCAGGTGACCAAAGTGATTATAA-------AGAAAA-----A----------ATGTTTTGAGAATGCTGGAAAGAATAATTTTATCCACCCTCCATTTCAGAGTTAAATAATTCAGGATT----", ) self.assertEqual( alignment.sequences[6].annotations["quality"], "54667653455648997776896979788699699955776666776867789776453646557877552667697777697779896767576676677696675376877786786858478887756858859779666569356677477759968759378767656876769557597655596536566", ) self.assertEqual(alignment.sequences[6].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[6].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[6].annotations["rightStatus"], "I") self.assertEqual(alignment.sequences[6].annotations["rightCount"], 358) self.assertEqual(alignment.sequences[7].id, "tupBel1.scaffold_114895.1-498454") self.assertEqual(len(alignment.sequences[7].seq), 498454) self.assertEqual( alignment.sequences[7].seq[324116 : 324116 + 196], "AAGCCCAAGTTATTTAACTTAGACATAGGGAAAATAATATGCTTCTATACTGCATCCACAAAAGTTTGTTTTTGTTTTTTTTTTCAGTATGACTTTGGTCACCTGATTGCTGTCAAGGAAGGCAATTTCCTTTAAAAGTTTATCCTACTGCAAAAAGCTTTTCCTGTACTTTATCTAGAACATTCATGACATTGCC", ) self.assertEqual( alignment[7], "GGCAATGTCATGA----ATGT------TCTAGATAAAGTACAGGAAAAGCTTTTTGCAGTAGGATAAACTTTT-AAAGGAAATTGCCTTCCTTGACAGCAATCAGGTGACCAAAGTCATACTGA-------AAAAAA-----AAACAAAAACAAACTTTTGTGGATGCAGTATAGAAGCATATTATTTTCCCTATGTCT--AAGTTAAATAACTTGGGCTT----", ) self.assertEqual( alignment.sequences[7].annotations["quality"], "9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999", ) self.assertEqual(alignment.sequences[7].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[7].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[7].annotations["rightStatus"], "I") self.assertEqual(alignment.sequences[7].annotations["rightCount"], 623) self.assertEqual(alignment.sequences[8].id, "felCat3.scaffold_205680") self.assertEqual(len(alignment.sequences[8].seq), 119354) self.assertEqual( alignment.sequences[8].seq[46199 : 46199 + 186], "aattttaaattatttaaCTCTTAGATGTAGGGGAAATAATATTATTGTATCCTGTATTCTCAAAAAAAATTCCCTTTATATTACTTTAATCACCTAATGTCTCTTGAAGAAAGCAATTTCCTACAACATTTTATTCTACTCAAAATGCTTTTCCTGCACTTTATCTAGAATGTACTTTATGATGTC", ) self.assertEqual( alignment[8], "GACATC---ATAA-AGTACAT------TCTAGATAAAGTGCAGGAAAAGCATTTTG-AGTAGAATAAAATGTT-GTAGGAAATTGCTTTCTTCAAGAGACATTAGGTGATTAAAGTAA-TATAA-------AGGGAA-----T----------TTTTTTTGAGAATACAGGATACAATAATATTATTTCCCCTACATCTAAGAGttaaataatttaaaatt----", ) self.assertEqual( alignment.sequences[8].annotations["quality"], "999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999", ) self.assertEqual(alignment.sequences[8].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[8].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[8].annotations["rightStatus"], "I") self.assertEqual(alignment.sequences[8].annotations["rightCount"], 27) self.assertEqual(alignment.sequences[9].id, "canFam2.chr1") self.assertEqual(len(alignment.sequences[9].seq), 125616256) self.assertEqual( alignment.sequences[9].seq[47544825 : 47544825 + 193], "attaaattttaaattatttaaCTCTTAGAAGTAAGGGAAACAATATTATTCTAACTTGGATTCACTGAACTTTGTTTTTTCCCTTTATATTCCTTCAATCACCTGATTGCTCTCAAAGAAAGTAATTTCCTATTAACATTTTATCCTGTTCAAAATCCTTTTGTTGTACTTTACCCGGAATTTACATCATGAT", ) self.assertEqual( alignment[9], "------ATCATGA-TGTAAAT------TCCGGGTAAAGTACAACAAAAGGATTTTG-AACAGGATAAAATGTTAATAGGAAATTACTTTCTTTGAGAGCAATCAGGTGATTGAAGGAA-TATAA-------AGGGAAAAAACA----------AAGTTCAGTGAATCCAAGTTAGAATAATATTGTTTCCCTTACTTCTAAGAGttaaataatttaaaatttaat", ) self.assertEqual( alignment.sequences[9].annotations["quality"], "9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999", ) self.assertEqual(alignment.sequences[9].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[9].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[9].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[9].annotations["rightCount"], 0) empty = alignment.annotations["empty"][0] (record, segment, status) = empty self.assertEqual(record.id, "ornAna1.chr2") self.assertEqual(len(record.seq), 54797317) self.assertEqual(segment, (40046122, 40040432)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][1] (record, segment, status) = empty self.assertEqual(record.id, "echTel1.scaffold_288249") self.assertEqual(len(record.seq), 100002) self.assertEqual(segment, (87661, 95225)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][2] (record, segment, status) = empty self.assertEqual(record.id, "cavPor2.scaffold_216473") self.assertEqual(len(record.seq), 10026) self.assertEqual(segment, (1978, 606)) self.assertEqual(status, "I") self.assertEqual(len(alignment.sequences), 10) self.assertEqual(len(alignment.annotations["empty"]), 3) self.assertEqual( str(alignment), """\ mm9.chr10 3019777 GGCAATGTCA-GGCTATGCGT------TCTAGACAGGGCACAAGAAAAGCTTTTAGCAGC oryCun1.s 4493 GGCAACATCATGACCTTATGT------TCTAA----GGGACAGGAAAAGCTTTTTCCAGT hg18.chr6 155025555 GGCAACACCATGA-TACATAT------TCAAGATAAAGTACAGGAAAAGCTTTTTGCAGT panTro2.c 157515610 GGCAACACCATGA-TACATAT------TCAAGATAAAGTACAGGAAAAGCTTTTTGCAGT ponAbe2.c 158037776 GGCAACACCATGA-TACATAT------TCAAGATAAAGTACAGGAAAAGCTTTTTGCGGT calJac1.C 10274 GGCAACACCGTGA-TACATAT------CCGAGATAAAGTACAGGAAAAGC-TTTTGCAGT otoGar1.s 171883 GGCAACGCCGTGA-TCCTTGCTGTAGATAAAGACAAAGTGCAGGAAAAGCCCTTTACGGT tupBel1.s 324312 GGCAATGTCATGA----ATGT------TCTAGATAAAGTACAGGAAAAGCTTTTTGCAGT felCat3.s 46385 GACATC---ATAA-AGTACAT------TCTAGATAAAGTGCAGGAAAAGCATTTTG-AGT canFam2.c 47545018 ------ATCATGA-TGTAAAT------TCCGGGTAAAGTACAACAAAAGGATTTTG-AAC mm9.chr10 3019830 AGAATAAACTTTT-AAAGTAAATTACTTTCCTTGATAGCAACTAGACGACCCAATTGA-T oryCun1.s 4443 AGAATAAGCCTTT-AGAGGAAACTGCTTCCCTTGCTAGTAATCAAGTGTTCAAAGTGA-T hg18.chr6 155025502 GGAATAAAATGTT-AAAGGGAATTGCTTTCCTTGATAGCAATCAGGTCACCAAAGTGA-G panTro2.c 157515557 GGAATAAAATGTT-AAAGGAAATTGCTTTCCTTGATAGCAATCAGGTCACCAAAGTGA-G ponAbe2.c 158037723 GGAATAAAATGTT-AAAGGAAATTGCTTTCCTTGATAGCAATCAGGTCACCAAAGTGA-G calJac1.C 10326 GGACGAAAATGTT-GAAGGAAATTGCTTTTCTTGATAGCAATCAGGTCACCAAAGTGA-G otoGar1.s 171824 AGAATAAAAGGTT-AAAGGAAATTGCTTTTCTTGATAGCAATCAGGTGACCAAAGTGATT tupBel1.s 324262 AGGATAAACTTTT-AAAGGAAATTGCCTTCCTTGACAGCAATCAGGTGACCAAAGTCATA felCat3.s 46336 AGAATAAAATGTT-GTAGGAAATTGCTTTCTTCAAGAGACATTAGGTGATTAAAGTAA-T canFam2.c 47544972 AGGATAAAATGTTAATAGGAAATTACTTTCTTTGAGAGCAATCAGGTGATTGAAGGAA-T mm9.chr10 3019888 ACAGT------GGAAAG-----A----------GGCCTTTGAGAAT---GCATGAGAGAA oryCun1.s 4385 ACAACAAAGAAAAAAAA-----A----------GCCTTTTGGGAAT-CAGGATGGAATAA hg18.chr6 155025444 ATGA-------AGAAAA-----A----------TTTTTTTGAGAATGCAGGATAGAATAA panTro2.c 157515499 ATGA-------AGAAAA-----A---------TTTTTTTTGAGAATGCAGGATAGAATAA ponAbe2.c 158037665 ATGA-------AGAAAA-----A---------TTCTTTTTGAGAATGCAGCACAGAATAA calJac1.C 10384 ATGA-------AGAAA-----------------GTTTTTTGAGAATGTGGGATAGAATAA otoGar1.s 171765 ATAA-------AGAAAA-----A----------ATGTTTTGAGAATGCTGGAAAGAATAA tupBel1.s 324203 CTGA-------AAAAAA-----AAACAAAAACAAACTTTTGTGGATGCAGTATAGAAGCA felCat3.s 46278 ATAA-------AGGGAA-----T----------TTTTTTTGAGAATACAGGATACAATAA canFam2.c 47544913 ATAA-------AGGGAAAAAACA----------AAGTTCAGTGAATCCAAGTTAGAATAA mm9.chr10 3019924 TAT---TTCCTGTA------AGAGTTGAACAATTTAGAATTTACc 3019960 oryCun1.s 4341 TATTACTTCCCCTATTTCTCAGAGCTAAATAGTTTAGGATT---- 4300 hg18.chr6 155025406 TATTATTTCCCTTATTTCTAAGAGTTAAACAATTTAGGATT---- 155025365 panTro2.c 157515460 TATTATTTCCCTTATTTCTAAGAGTTAAACAATTTAGGATT---- 157515419 ponAbe2.c 158037626 TATTATTTCCCTTATTTCT-AGAGTTAAACAATTTAGGATT---- 158037586 calJac1.C 10420 TATTGTTTTCGTTATTTCTAAGAGTTAAACAATTTAGGATT---- 10461 otoGar1.s 171727 TTTTATCCACCCTCCATTTCAGAGTTAAATAATTCAGGATT---- 171686 tupBel1.s 324155 TATTATTTTCCCTATGTCT--AAGTTAAATAACTTGGGCTT---- 324116 felCat3.s 46240 TATTATTTCCCCTACATCTAAGAGttaaataatttaaaatt---- 46199 canFam2.c 47544870 TATTGTTTCCCTTACTTCTAAGAGttaaataatttaaaatttaat 47544825 """, ) self.assertTrue( np.array_equal( alignment.coordinates, np.array( # fmt: off [[ 3019777, 3019783, 3019786, 3019787, 3019787, 3019789, 3019790, 3019793, 3019797, 3019797, 3019802, 3019806, 3019820, 3019821, 3019826, 3019827, 3019843, 3019843, 3019887, 3019887, 3019892, 3019893, 3019893, 3019898, 3019899, 3019899, 3019900, 3019900, 3019900, 3019913, 3019913, 3019913, 3019927, 3019927, 3019935, 3019935, 3019935, 3019936, 3019956, 3019960], [ 4493, 4487, 4484, 4483, 4482, 4480, 4479, 4476, 4472, 4472, 4467, 4467, 4453, 4452, 4447, 4446, 4430, 4430, 4386, 4386, 4381, 4380, 4374, 4369, 4368, 4368, 4367, 4367, 4367, 4354, 4354, 4352, 4338, 4335, 4327, 4322, 4321, 4320, 4300, 4300], [155025555, 155025549, 155025546, 155025545, 155025544, 155025542, 155025542, 155025539, 155025535, 155025535, 155025530, 155025526, 155025512, 155025511, 155025506, 155025505, 155025489, 155025489, 155025445, 155025445, 155025440, 155025440, 155025440, 155025435, 155025434, 155025434, 155025433, 155025433, 155025433, 155025420, 155025419, 155025417, 155025403, 155025400, 155025392, 155025387, 155025386, 155025385, 155025365, 155025365], [157515610, 157515604, 157515601, 157515600, 157515599, 157515597, 157515597, 157515594, 157515590, 157515590, 157515585, 157515581, 157515567, 157515566, 157515561, 157515560, 157515544, 157515544, 157515500, 157515500, 157515495, 157515495, 157515495, 157515490, 157515489, 157515489, 157515488, 157515488, 157515487, 157515474, 157515473, 157515471, 157515457, 157515454, 157515446, 157515441, 157515440, 157515439, 157515419, 157515419], [158037776, 158037770, 158037767, 158037766, 158037765, 158037763, 158037763, 158037760, 158037756, 158037756, 158037751, 158037747, 158037733, 158037732, 158037727, 158037726, 158037710, 158037710, 158037666, 158037666, 158037661, 158037661, 158037661, 158037656, 158037655, 158037655, 158037654, 158037654, 158037653, 158037640, 158037639, 158037637, 158037623, 158037620, 158037612, 158037607, 158037607, 158037606, 158037586, 158037586], [ 10274, 10280, 10283, 10284, 10285, 10287, 10287, 10290, 10294, 10294, 10299, 10303, 10317, 10317, 10322, 10323, 10339, 10339, 10383, 10383, 10388, 10388, 10388, 10393, 10393, 10393, 10393, 10393, 10393, 10406, 10407, 10409, 10423, 10426, 10434, 10439, 10440, 10441, 10461, 10461], [ 171883, 171877, 171874, 171873, 171872, 171870, 171870, 171867, 171863, 171857, 171852, 171848, 171834, 171833, 171828, 171827, 171811, 171811, 171767, 171766, 171761, 171761, 171761, 171756, 171755, 171755, 171754, 171754, 171754, 171741, 171740, 171738, 171724, 171721, 171713, 171708, 171707, 171706, 171686, 171686], [ 324312, 324306, 324303, 324302, 324301, 324299, 324299, 324299, 324295, 324295, 324290, 324286, 324272, 324271, 324266, 324265, 324249, 324249, 324205, 324204, 324199, 324199, 324199, 324194, 324193, 324193, 324192, 324183, 324182, 324169, 324168, 324166, 324152, 324149, 324141, 324136, 324136, 324136, 324116, 324116], [ 46385, 46379, 46379, 46378, 46377, 46375, 46375, 46372, 46368, 46368, 46363, 46359, 46345, 46344, 46339, 46339, 46323, 46323, 46279, 46279, 46274, 46274, 46274, 46269, 46268, 46268, 46267, 46267, 46267, 46254, 46253, 46251, 46237, 46234, 46226, 46221, 46220, 46219, 46199, 46199], [ 47545018, 47545018, 47545015, 47545014, 47545013, 47545011, 47545011, 47545008, 47545004, 47545004, 47544999, 47544995, 47544981, 47544980, 47544975, 47544975, 47544959, 47544958, 47544914, 47544914, 47544909, 47544909, 47544909, 47544904, 47544903, 47544898, 47544897, 47544897, 47544897, 47544884, 47544883, 47544881, 47544867, 47544864, 47544856, 47544851, 47544850, 47544849, 47544829, 47544825], ] # fmt: on ), ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.score, 0) self.assertEqual(alignment.sequences[0].id, "mm9.chr10") self.assertEqual(len(alignment.sequences[0].seq), 129993255) self.assertEqual( alignment.sequences[0].seq[3019960 : 3019960 + 757], "actagggatgggagaggctcccagaacccagtaatgatgacattaagaaatacacaacagttgggaaatggaacccaaagagaacacctccagtagataagcatgacccccagttgagggatgggcccatgcacccatcttaaaattttggacccagaattattcttctcaaaaggaaatgcagggatgaaaatggagcagagactggaagaaaggccaaccagagactgccctaactcaggatccatcgcatgtgcaggcaccaaccccaacactattgctgatgccatgttgtacttgctgatggaagcctggcatggctgtcctctgagagtctcaaatgaggcacctgacagatgcagatacttacagccaaccaatggactgagccccgggacctcaataaaagaatgaggggatggcaaccccataggaagaacaacagtatcaactccctggactcctcagagctcccggggactaagccaccaactaaagagcatacataggctgctctgaggccccagatacatatgtagcagaggactgcctcagtgggaggggatgtgcttggtcttgtgaaggcttgatgctccagagaaggaggatgctagaggggtgaggtgggagtggatgggtgggtgggcaggggagcaccctcttagaggacaagggctctggggtgggggagctcatggagggggaactgggaaggagggagaacatttgaaatgtaaataaataaaataataaaaaa", ) self.assertEqual( alignment[0], "actagggatgggagaggctcccagaacccagtaatgatgacattaagaaatacacaacagttgggaaatggaacccaaagagaacacctccagtagataagcatgacccccagttgagggatgggcccatgcacccatcttaaaattttggacccagaattattcttctcaaaaggaaatgcagggatgaaaatggagcagagactggaagaaaggccaaccagagactgccctaactcaggatccatcgcatgtgcaggcaccaaccccaacactattgctgatgccatgttgtacttgctgatggaagcctggcatggctgtcctctgagagtctcaaatgaggcacctgacagatgcagatacttacagccaaccaatggactgagccccgggacctcaataaaagaatgaggggatggcaaccccataggaagaacaacagtatcaactccctggactcctcagagctcccggggactaagccaccaactaaagagcatacataggctgctctgaggccccagatacatatgtagcagaggactgcctcagtgggaggggatgtgcttggtcttgtgaaggcttgatgctccagagaaggaggatgctagaggggtgaggtgggagtggatgggtgggtgggcaggggagcaccctcttagaggacaagggctctggggtgggggagctcatggagggggaactgggaaggagggagaacatttgaaatgtaaataaataaaataataaaaaa", ) empty = alignment.annotations["empty"][0] (record, segment, status) = empty self.assertEqual(record.id, "felCat3.scaffold_205680") self.assertEqual(len(record.seq), 119354) self.assertEqual(segment, (46199, 46172)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][1] (record, segment, status) = empty self.assertEqual(record.id, "canFam2.chr1") self.assertEqual(len(record.seq), 125616256) self.assertEqual(segment, (47544825, 47544825)) self.assertEqual(status, "C") empty = alignment.annotations["empty"][2] (record, segment, status) = empty self.assertEqual(record.id, "ornAna1.chr2") self.assertEqual(len(record.seq), 54797317) self.assertEqual(segment, (40046122, 40040432)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][3] (record, segment, status) = empty self.assertEqual(record.id, "calJac1.Contig6394") self.assertEqual(len(record.seq), 133105) self.assertEqual(segment, (10461, 10482)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][4] (record, segment, status) = empty self.assertEqual(record.id, "tupBel1.scaffold_114895.1-498454") self.assertEqual(len(record.seq), 498454) self.assertEqual(segment, (324116, 323493)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][5] (record, segment, status) = empty self.assertEqual(record.id, "echTel1.scaffold_288249") self.assertEqual(len(record.seq), 100002) self.assertEqual(segment, (87661, 95225)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][6] (record, segment, status) = empty self.assertEqual(record.id, "cavPor2.scaffold_216473") self.assertEqual(len(record.seq), 10026) self.assertEqual(segment, (1978, 606)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][7] (record, segment, status) = empty self.assertEqual(record.id, "otoGar1.scaffold_334.1-359464") self.assertEqual(len(record.seq), 359464) self.assertEqual(segment, (171686, 171328)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][8] (record, segment, status) = empty self.assertEqual(record.id, "hg18.chr6") self.assertEqual(len(record.seq), 170899992) self.assertEqual(segment, (155025365, 155025365)) self.assertEqual(status, "C") empty = alignment.annotations["empty"][9] (record, segment, status) = empty self.assertEqual(record.id, "panTro2.chr6") self.assertEqual(len(record.seq), 173908612) self.assertEqual(segment, (157515419, 157515419)) self.assertEqual(status, "C") empty = alignment.annotations["empty"][10] (record, segment, status) = empty self.assertEqual(record.id, "ponAbe2.chr6") self.assertEqual(len(record.seq), 174210431) self.assertEqual(segment, (158037586, 158037565)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][11] (record, segment, status) = empty self.assertEqual(record.id, "oryCun1.scaffold_156751") self.assertEqual(len(record.seq), 4726) self.assertEqual(segment, (4300, 4263)) self.assertEqual(status, "I") self.assertEqual(len(alignment.sequences), 1) self.assertEqual(len(alignment.annotations["empty"]), 12) self.assertEqual( str(alignment), """\ mm9.chr10 3019960 actagggatgggagaggctcccagaacccagtaatgatgacattaagaaatacacaacag mm9.chr10 3020020 ttgggaaatggaacccaaagagaacacctccagtagataagcatgacccccagttgaggg mm9.chr10 3020080 atgggcccatgcacccatcttaaaattttggacccagaattattcttctcaaaaggaaat mm9.chr10 3020140 gcagggatgaaaatggagcagagactggaagaaaggccaaccagagactgccctaactca mm9.chr10 3020200 ggatccatcgcatgtgcaggcaccaaccccaacactattgctgatgccatgttgtacttg mm9.chr10 3020260 ctgatggaagcctggcatggctgtcctctgagagtctcaaatgaggcacctgacagatgc mm9.chr10 3020320 agatacttacagccaaccaatggactgagccccgggacctcaataaaagaatgaggggat mm9.chr10 3020380 ggcaaccccataggaagaacaacagtatcaactccctggactcctcagagctcccgggga mm9.chr10 3020440 ctaagccaccaactaaagagcatacataggctgctctgaggccccagatacatatgtagc mm9.chr10 3020500 agaggactgcctcagtgggaggggatgtgcttggtcttgtgaaggcttgatgctccagag mm9.chr10 3020560 aaggaggatgctagaggggtgaggtgggagtggatgggtgggtgggcaggggagcaccct mm9.chr10 3020620 cttagaggacaagggctctggggtgggggagctcatggagggggaactgggaaggaggga mm9.chr10 3020680 gaacatttgaaatgtaaataaataaaataataaaaaa 3020717 """, ) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[3019960, 3020717]])) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['a', 'c', 't', 'a', 'g', 'g', 'g', 'a', 't', 'g', 'g', 'g', 'a', 'g', 'a', 'g', 'g', 'c', 't', 'c', 'c', 'c', 'a', 'g', 'a', 'a', 'c', 'c', 'c', 'a', 'g', 't', 'a', 'a', 't', 'g', 'a', 't', 'g', 'a', 'c', 'a', 't', 't', 'a', 'a', 'g', 'a', 'a', 'a', 't', 'a', 'c', 'a', 'c', 'a', 'a', 'c', 'a', 'g', 't', 't', 'g', 'g', 'g', 'a', 'a', 'a', 't', 'g', 'g', 'a', 'a', 'c', 'c', 'c', 'a', 'a', 'a', 'g', 'a', 'g', 'a', 'a', 'c', 'a', 'c', 'c', 't', 'c', 'c', 'a', 'g', 't', 'a', 'g', 'a', 't', 'a', 'a', 'g', 'c', 'a', 't', 'g', 'a', 'c', 'c', 'c', 'c', 'c', 'a', 'g', 't', 't', 'g', 'a', 'g', 'g', 'g', 'a', 't', 'g', 'g', 'g', 'c', 'c', 'c', 'a', 't', 'g', 'c', 'a', 'c', 'c', 'c', 'a', 't', 'c', 't', 't', 'a', 'a', 'a', 'a', 't', 't', 't', 't', 'g', 'g', 'a', 'c', 'c', 'c', 'a', 'g', 'a', 'a', 't', 't', 'a', 't', 't', 'c', 't', 't', 'c', 't', 'c', 'a', 'a', 'a', 'a', 'g', 'g', 'a', 'a', 'a', 't', 'g', 'c', 'a', 'g', 'g', 'g', 'a', 't', 'g', 'a', 'a', 'a', 'a', 't', 'g', 'g', 'a', 'g', 'c', 'a', 'g', 'a', 'g', 'a', 'c', 't', 'g', 'g', 'a', 'a', 'g', 'a', 'a', 'a', 'g', 'g', 'c', 'c', 'a', 'a', 'c', 'c', 'a', 'g', 'a', 'g', 'a', 'c', 't', 'g', 'c', 'c', 'c', 't', 'a', 'a', 'c', 't', 'c', 'a', 'g', 'g', 'a', 't', 'c', 'c', 'a', 't', 'c', 'g', 'c', 'a', 't', 'g', 't', 'g', 'c', 'a', 'g', 'g', 'c', 'a', 'c', 'c', 'a', 'a', 'c', 'c', 'c', 'c', 'a', 'a', 'c', 'a', 'c', 't', 'a', 't', 't', 'g', 'c', 't', 'g', 'a', 't', 'g', 'c', 'c', 'a', 't', 'g', 't', 't', 'g', 't', 'a', 'c', 't', 't', 'g', 'c', 't', 'g', 'a', 't', 'g', 'g', 'a', 'a', 'g', 'c', 'c', 't', 'g', 'g', 'c', 'a', 't', 'g', 'g', 'c', 't', 'g', 't', 'c', 'c', 't', 'c', 't', 'g', 'a', 'g', 'a', 'g', 't', 'c', 't', 'c', 'a', 'a', 'a', 't', 'g', 'a', 'g', 'g', 'c', 'a', 'c', 'c', 't', 'g', 'a', 'c', 'a', 'g', 'a', 't', 'g', 'c', 'a', 'g', 'a', 't', 'a', 'c', 't', 't', 'a', 'c', 'a', 'g', 'c', 'c', 'a', 'a', 'c', 'c', 'a', 'a', 't', 'g', 'g', 'a', 'c', 't', 'g', 'a', 'g', 'c', 'c', 'c', 'c', 'g', 'g', 'g', 'a', 'c', 'c', 't', 'c', 'a', 'a', 't', 'a', 'a', 'a', 'a', 'g', 'a', 'a', 't', 'g', 'a', 'g', 'g', 'g', 'g', 'a', 't', 'g', 'g', 'c', 'a', 'a', 'c', 'c', 'c', 'c', 'a', 't', 'a', 'g', 'g', 'a', 'a', 'g', 'a', 'a', 'c', 'a', 'a', 'c', 'a', 'g', 't', 'a', 't', 'c', 'a', 'a', 'c', 't', 'c', 'c', 'c', 't', 'g', 'g', 'a', 'c', 't', 'c', 'c', 't', 'c', 'a', 'g', 'a', 'g', 'c', 't', 'c', 'c', 'c', 'g', 'g', 'g', 'g', 'a', 'c', 't', 'a', 'a', 'g', 'c', 'c', 'a', 'c', 'c', 'a', 'a', 'c', 't', 'a', 'a', 'a', 'g', 'a', 'g', 'c', 'a', 't', 'a', 'c', 'a', 't', 'a', 'g', 'g', 'c', 't', 'g', 'c', 't', 'c', 't', 'g', 'a', 'g', 'g', 'c', 'c', 'c', 'c', 'a', 'g', 'a', 't', 'a', 'c', 'a', 't', 'a', 't', 'g', 't', 'a', 'g', 'c', 'a', 'g', 'a', 'g', 'g', 'a', 'c', 't', 'g', 'c', 'c', 't', 'c', 'a', 'g', 't', 'g', 'g', 'g', 'a', 'g', 'g', 'g', 'g', 'a', 't', 'g', 't', 'g', 'c', 't', 't', 'g', 'g', 't', 'c', 't', 't', 'g', 't', 'g', 'a', 'a', 'g', 'g', 'c', 't', 't', 'g', 'a', 't', 'g', 'c', 't', 'c', 'c', 'a', 'g', 'a', 'g', 'a', 'a', 'g', 'g', 'a', 'g', 'g', 'a', 't', 'g', 'c', 't', 'a', 'g', 'a', 'g', 'g', 'g', 'g', 't', 'g', 'a', 'g', 'g', 't', 'g', 'g', 'g', 'a', 'g', 't', 'g', 'g', 'a', 't', 'g', 'g', 'g', 't', 'g', 'g', 'g', 't', 'g', 'g', 'g', 'c', 'a', 'g', 'g', 'g', 'g', 'a', 'g', 'c', 'a', 'c', 'c', 'c', 't', 'c', 't', 't', 'a', 'g', 'a', 'g', 'g', 'a', 'c', 'a', 'a', 'g', 'g', 'g', 'c', 't', 'c', 't', 'g', 'g', 'g', 'g', 't', 'g', 'g', 'g', 'g', 'g', 'a', 'g', 'c', 't', 'c', 'a', 't', 'g', 'g', 'a', 'g', 'g', 'g', 'g', 'g', 'a', 'a', 'c', 't', 'g', 'g', 'g', 'a', 'a', 'g', 'g', 'a', 'g', 'g', 'g', 'a', 'g', 'a', 'a', 'c', 'a', 't', 't', 't', 'g', 'a', 'a', 'a', 't', 'g', 't', 'a', 'a', 'a', 't', 'a', 'a', 'a', 't', 'a', 'a', 'a', 'a', 't', 'a', 'a', 't', 'a', 'a', 'a', 'a', 'a', 'a']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.score, 8951) self.assertEqual(alignment.sequences[0].id, "mm9.chr10") self.assertEqual(len(alignment.sequences[0].seq), 129993255) self.assertEqual( alignment.sequences[0].seq[3020717 : 3020717 + 44], "TGTCAAACATGCATAAAGATATACTGAGGAGCCCATGAATTTTA", ) self.assertEqual(alignment[0], "TGTCAAACATGCATAAAGATATACT-GAGGAGCCCATGAATTTTA") self.assertEqual(alignment.sequences[1].id, "canFam2.chr1") self.assertEqual(len(alignment.sequences[1].seq), 125616256) self.assertEqual( alignment.sequences[1].seq[47544792 : 47544792 + 33], "TAAAATTCATGGGCCCCTCTATTATGTTAAACa", ) self.assertEqual(alignment[1], "tGTT------------TAACATAATAGAGGGGCCCATGAATTTTA") self.assertEqual( alignment.sequences[1].annotations["quality"], "999999999999999999999999999999999", ) self.assertEqual(alignment.sequences[1].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[1].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[1].annotations["rightStatus"], "I") self.assertEqual(alignment.sequences[1].annotations["rightCount"], 9) self.assertEqual(alignment.sequences[2].id, "panTro2.chr6") self.assertEqual(len(alignment.sequences[2].seq), 173908612) self.assertEqual( alignment.sequences[2].seq[157515381 : 157515381 + 38], "TAAAATTCATGGACCCCTCTAGTATATTTAAAATTTTT", ) self.assertEqual(alignment[2], "----AAAAAT---TTTAAATATACTAGAGGGGTCCATGAATTTTA") self.assertEqual( alignment.sequences[2].annotations["quality"], "99999999999999999999999999999999999999", ) self.assertEqual(alignment.sequences[2].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[2].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[2].annotations["rightStatus"], "I") self.assertEqual(alignment.sequences[2].annotations["rightCount"], 11) self.assertEqual(alignment.sequences[3].id, "hg18.chr6") self.assertEqual(len(alignment.sequences[3].seq), 170899992) self.assertEqual( alignment.sequences[3].seq[155025327 : 155025327 + 38], "TAAAATTCATGGACCCCTCTAGTATATTTAAAATTTTT", ) self.assertEqual(alignment[3], "----AAAAAT---TTTAAATATACTAGAGGGGTCCATGAATTTTA") self.assertEqual(alignment.sequences[3].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[3].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[3].annotations["rightStatus"], "I") self.assertEqual(alignment.sequences[3].annotations["rightCount"], 11) empty = alignment.annotations["empty"][0] (record, segment, status) = empty self.assertEqual(record.id, "felCat3.scaffold_205680") self.assertEqual(len(record.seq), 119354) self.assertEqual(segment, (46199, 46172)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][1] (record, segment, status) = empty self.assertEqual(record.id, "ornAna1.chr2") self.assertEqual(len(record.seq), 54797317) self.assertEqual(segment, (40046122, 40040432)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][2] (record, segment, status) = empty self.assertEqual(record.id, "calJac1.Contig6394") self.assertEqual(len(record.seq), 133105) self.assertEqual(segment, (10461, 10482)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][3] (record, segment, status) = empty self.assertEqual(record.id, "tupBel1.scaffold_114895.1-498454") self.assertEqual(len(record.seq), 498454) self.assertEqual(segment, (324116, 323493)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][4] (record, segment, status) = empty self.assertEqual(record.id, "echTel1.scaffold_288249") self.assertEqual(len(record.seq), 100002) self.assertEqual(segment, (87661, 95225)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][5] (record, segment, status) = empty self.assertEqual(record.id, "cavPor2.scaffold_216473") self.assertEqual(len(record.seq), 10026) self.assertEqual(segment, (1978, 606)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][6] (record, segment, status) = empty self.assertEqual(record.id, "otoGar1.scaffold_334.1-359464") self.assertEqual(len(record.seq), 359464) self.assertEqual(segment, (171686, 171328)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][7] (record, segment, status) = empty self.assertEqual(record.id, "ponAbe2.chr6") self.assertEqual(len(record.seq), 174210431) self.assertEqual(segment, (158037586, 158037565)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][8] (record, segment, status) = empty self.assertEqual(record.id, "oryCun1.scaffold_156751") self.assertEqual(len(record.seq), 4726) self.assertEqual(segment, (4300, 4263)) self.assertEqual(status, "I") self.assertEqual(len(alignment.sequences), 4) self.assertEqual(len(alignment.annotations["empty"]), 9) self.assertEqual( str(alignment), """\ mm9.chr10 3020717 TGTCAAACATGCATAAAGATATACT-GAGGAGCCCATGAATTTTA 3020761 canFam2.c 47544825 tGTT------------TAACATAATAGAGGGGCCCATGAATTTTA 47544792 panTro2.c 157515419 ----AAAAAT---TTTAAATATACTAGAGGGGTCCATGAATTTTA 157515381 hg18.chr6 155025365 ----AAAAAT---TTTAAATATACTAGAGGGGTCCATGAATTTTA 155025327 """, ) self.assertTrue( np.array_equal( alignment.coordinates, np.array( # fmt: off [[ 3020717, 3020721, 3020727, 3020730, 3020733, 3020742, 3020742, 3020761], [ 47544825, 47544821, 47544821, 47544821, 47544821, 47544812, 47544811, 47544792], [157515419, 157515419, 157515413, 157515413, 157515410, 157515401, 157515400, 157515381], [155025365, 155025365, 155025359, 155025359, 155025356, 155025347, 155025346, 155025327], ] # fmt: on ), ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['T', 'G', 'T', 'C', 'A', 'A', 'A', 'C', 'A', 'T', 'G', 'C', 'A', 'T', 'A', 'A', 'A', 'G', 'A', 'T', 'A', 'T', 'A', 'C', 'T', '-', 'G', 'A', 'G', 'G', 'A', 'G', 'C', 'C', 'C', 'A', 'T', 'G', 'A', 'A', 'T', 'T', 'T', 'T', 'A'], ['t', 'G', 'T', 'T', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'T', 'A', 'A', 'C', 'A', 'T', 'A', 'A', 'T', 'A', 'G', 'A', 'G', 'G', 'G', 'G', 'C', 'C', 'C', 'A', 'T', 'G', 'A', 'A', 'T', 'T', 'T', 'T', 'A'], ['-', '-', '-', '-', 'A', 'A', 'A', 'A', 'A', 'T', '-', '-', '-', 'T', 'T', 'T', 'A', 'A', 'A', 'T', 'A', 'T', 'A', 'C', 'T', 'A', 'G', 'A', 'G', 'G', 'G', 'G', 'T', 'C', 'C', 'A', 'T', 'G', 'A', 'A', 'T', 'T', 'T', 'T', 'A'], ['-', '-', '-', '-', 'A', 'A', 'A', 'A', 'A', 'T', '-', '-', '-', 'T', 'T', 'T', 'A', 'A', 'A', 'T', 'A', 'T', 'A', 'C', 'T', 'A', 'G', 'A', 'G', 'G', 'G', 'G', 'T', 'C', 'C', 'A', 'T', 'G', 'A', 'A', 'T', 'T', 'T', 'T', 'A']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.score, 0) self.assertEqual(alignment.sequences[0].id, "mm9.chr10") self.assertEqual(len(alignment.sequences[0].seq), 129993255) self.assertEqual( alignment.sequences[0].seq[3020761 : 3020761 + 157], "TATATATGCTATCCGTGTGCTGTGATTTTTGTTTTAAATGTTATTTTATGTATATGcaagattttgcattgtagcagaaggtggcttcaaactcacgatcctcctgcctcagccttccaagtgctgagatcatacctctgcaccatcctgcccACCT", ) self.assertEqual( alignment[0], "TATATATGCTATCCGTGTGCTGTGATTTTTGTTTTAAATGTTATTTTATGTATATGcaagattttgcattgtagcagaaggtggcttcaaactcacgatcctcctgcctcagccttccaagtgctgagatcatacctctgcaccatcctgcccACCT", ) empty = alignment.annotations["empty"][0] (record, segment, status) = empty self.assertEqual(record.id, "felCat3.scaffold_205680") self.assertEqual(len(record.seq), 119354) self.assertEqual(segment, (46199, 46172)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][1] (record, segment, status) = empty self.assertEqual(record.id, "canFam2.chr1") self.assertEqual(len(record.seq), 125616256) self.assertEqual(segment, (47544792, 47544783)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][2] (record, segment, status) = empty self.assertEqual(record.id, "ornAna1.chr2") self.assertEqual(len(record.seq), 54797317) self.assertEqual(segment, (40046122, 40040432)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][3] (record, segment, status) = empty self.assertEqual(record.id, "calJac1.Contig6394") self.assertEqual(len(record.seq), 133105) self.assertEqual(segment, (10461, 10482)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][4] (record, segment, status) = empty self.assertEqual(record.id, "tupBel1.scaffold_114895.1-498454") self.assertEqual(len(record.seq), 498454) self.assertEqual(segment, (324116, 323493)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][5] (record, segment, status) = empty self.assertEqual(record.id, "echTel1.scaffold_288249") self.assertEqual(len(record.seq), 100002) self.assertEqual(segment, (87661, 95225)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][6] (record, segment, status) = empty self.assertEqual(record.id, "cavPor2.scaffold_216473") self.assertEqual(len(record.seq), 10026) self.assertEqual(segment, (1978, 606)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][7] (record, segment, status) = empty self.assertEqual(record.id, "otoGar1.scaffold_334.1-359464") self.assertEqual(len(record.seq), 359464) self.assertEqual(segment, (171686, 171328)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][8] (record, segment, status) = empty self.assertEqual(record.id, "hg18.chr6") self.assertEqual(len(record.seq), 170899992) self.assertEqual(segment, (155025327, 155025316)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][9] (record, segment, status) = empty self.assertEqual(record.id, "panTro2.chr6") self.assertEqual(len(record.seq), 173908612) self.assertEqual(segment, (157515381, 157515370)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][10] (record, segment, status) = empty self.assertEqual(record.id, "ponAbe2.chr6") self.assertEqual(len(record.seq), 174210431) self.assertEqual(segment, (158037586, 158037565)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][11] (record, segment, status) = empty self.assertEqual(record.id, "oryCun1.scaffold_156751") self.assertEqual(len(record.seq), 4726) self.assertEqual(segment, (4300, 4263)) self.assertEqual(status, "I") self.assertEqual(len(alignment.sequences), 1) self.assertEqual(len(alignment.annotations["empty"]), 12) self.assertEqual( str(alignment), """\ mm9.chr10 3020761 TATATATGCTATCCGTGTGCTGTGATTTTTGTTTTAAATGTTATTTTATGTATATGcaag mm9.chr10 3020821 attttgcattgtagcagaaggtggcttcaaactcacgatcctcctgcctcagccttccaa mm9.chr10 3020881 gtgctgagatcatacctctgcaccatcctgcccACCT 3020918 """, ) self.assertTrue( np.array_equal(alignment.coordinates, np.array([[3020761, 3020918]])) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['T', 'A', 'T', 'A', 'T', 'A', 'T', 'G', 'C', 'T', 'A', 'T', 'C', 'C', 'G', 'T', 'G', 'T', 'G', 'C', 'T', 'G', 'T', 'G', 'A', 'T', 'T', 'T', 'T', 'T', 'G', 'T', 'T', 'T', 'T', 'A', 'A', 'A', 'T', 'G', 'T', 'T', 'A', 'T', 'T', 'T', 'T', 'A', 'T', 'G', 'T', 'A', 'T', 'A', 'T', 'G', 'c', 'a', 'a', 'g', 'a', 't', 't', 't', 't', 'g', 'c', 'a', 't', 't', 'g', 't', 'a', 'g', 'c', 'a', 'g', 'a', 'a', 'g', 'g', 't', 'g', 'g', 'c', 't', 't', 'c', 'a', 'a', 'a', 'c', 't', 'c', 'a', 'c', 'g', 'a', 't', 'c', 'c', 't', 'c', 'c', 't', 'g', 'c', 'c', 't', 'c', 'a', 'g', 'c', 'c', 't', 't', 'c', 'c', 'a', 'a', 'g', 't', 'g', 'c', 't', 'g', 'a', 'g', 'a', 't', 'c', 'a', 't', 'a', 'c', 'c', 't', 'c', 't', 'g', 'c', 'a', 'c', 'c', 'a', 't', 'c', 'c', 't', 'g', 'c', 'c', 'c', 'A', 'C', 'C', 'T']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.score, 85471) self.assertEqual(alignment.sequences[0].id, "mm9.chr10") self.assertEqual(len(alignment.sequences[0].seq), 129993255) self.assertEqual( alignment.sequences[0].seq[3020918 : 3020918 + 96], "GAGGTTTGTGACTTTTAATACTGATTGTTATCTAACATCACAGAATTCTCAGTTCTTAAGGAAACAATTGTTCTGTGTGTTATTTGTCTAGGAGGA", ) self.assertEqual( alignment[0], "GAGGTTTGTGACTTTTAATA----------CTGATTGTTATCTAACATCACAGAATTCTCAGTTCTTAAGGAAACAATTGTTCTGTGTGTTATTTGTCTAGGAGGA", ) self.assertEqual(alignment.sequences[1].id, "hg18.chr6") self.assertEqual(len(alignment.sequences[1].seq), 170899992) self.assertEqual( alignment.sequences[1].seq[155025243 : 155025243 + 73], "TTGTCCTAAATAATTAATAAGTCAAACATGTTTTTCCTTAAAAGCTGAGGATTGTGCAGTATTAAATAACCAT", ) self.assertEqual( alignment[1], "---------------------------------ATGGTTATTTAATACTGCACAATCCTCAGCTTTTAAGGAAAAACATGTTTGACTTATTAATTATTTAGGACAA", ) self.assertEqual(alignment.sequences[1].annotations["leftStatus"], "I") self.assertEqual(alignment.sequences[1].annotations["leftCount"], 11) self.assertEqual(alignment.sequences[1].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[1].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[2].id, "panTro2.chr6") self.assertEqual(len(alignment.sequences[2].seq), 173908612) self.assertEqual( alignment.sequences[2].seq[157515297 : 157515297 + 73], "TTGTCCTAAATAATTAATAAGTCAAACATGTTTTTCCTTAAAAGCTGAGGATTGTGCAGTATTAAATAACCAT", ) self.assertEqual( alignment[2], "---------------------------------ATGGTTATTTAATACTGCACAATCCTCAGCTTTTAAGGAAAAACATGTTTGACTTATTAATTATTTAGGACAA", ) self.assertEqual( alignment.sequences[2].annotations["quality"], "9999999999999999999999999999999999999999999999999999999999999999999999999", ) self.assertEqual(alignment.sequences[2].annotations["leftStatus"], "I") self.assertEqual(alignment.sequences[2].annotations["leftCount"], 11) self.assertEqual(alignment.sequences[2].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[2].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[3].id, "canFam2.chr1") self.assertEqual(len(alignment.sequences[3].seq), 125616256) self.assertEqual( alignment.sequences[3].seq[47544708 : 47544708 + 75], "TTGTCCTAAGTAATTAACAAATCACTTTTTCCTTAAGAGCTGAGAACTTCATAATGGTACAGAATTATTTTATTA", ) self.assertEqual( alignment[3], "--------------------------TAATAAAATAATTCTGTACCATTATGAAGTTCTCAGCTCTTAAGGAAAAA-----GTGATTTGTTAATTACTTAGGACAA", ) self.assertEqual( alignment.sequences[3].annotations["quality"], "999999999999999999999999999999999999999999999999999999999999999999999999999", ) self.assertEqual(alignment.sequences[3].annotations["leftStatus"], "I") self.assertEqual(alignment.sequences[3].annotations["leftCount"], 9) self.assertEqual(alignment.sequences[3].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[3].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[4].id, "felCat3.scaffold_205680") self.assertEqual(len(alignment.sequences[4].seq), 119354) self.assertEqual( alignment.sequences[4].seq[46096 : 46096 + 76], "TTGTCCTAAATAATTAATAAATTACTTTGTGATATTAAAGAATTATTTCATTACTTCACCATTAAAATTCATGGAC", ) self.assertEqual( alignment[4], "---GTCCATGAATTTTAATGGTGAAGTAATGAAATAATTCTTTAATATCAC----------------------AAA-----GTAATTTATTAATTATTTAGGACAA", ) self.assertEqual( alignment.sequences[4].annotations["quality"], "9999899999999999999999999999999999999999999999999999999999999999999999999769", ) self.assertEqual(alignment.sequences[4].annotations["leftStatus"], "I") self.assertEqual(alignment.sequences[4].annotations["leftCount"], 27) self.assertEqual(alignment.sequences[4].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[4].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[5].id, "cavPor2.scaffold_216473") self.assertEqual(len(alignment.sequences[5].seq), 10026) self.assertEqual( alignment.sequences[5].seq[524 : 524 + 82], "tttaaaaaaatcacactttTTCCATCAGAACTGAAAACTTTGTAATATTAatcttcttttcctattaaaATTTGCAGAACTC", ) self.assertEqual( alignment[5], "GAGTTCTGCAAATtttaata----------ggaaaagaagatTAATATTACAAAGTTTTCAGTTCTGATGGAAaaa----------gtgtgatttttttaaa----", ) self.assertEqual( alignment.sequences[5].annotations["quality"], "9967996679966856646585678288383465687882688656636765583677657766676965686997776684", ) self.assertEqual(alignment.sequences[5].annotations["leftStatus"], "I") self.assertEqual(alignment.sequences[5].annotations["leftCount"], 1372) self.assertEqual(alignment.sequences[5].annotations["rightStatus"], "I") self.assertEqual(alignment.sequences[5].annotations["rightCount"], 28) self.assertEqual(alignment.sequences[6].id, "oryCun1.scaffold_156751") self.assertEqual(len(alignment.sequences[6].seq), 4726) self.assertEqual( alignment.sequences[6].seq[4161 : 4161 + 102], "TCATCCCAAGTCATTAACAAGTCAAACACTTTTTTCCTTAAGACTTGAGGATTTTCCAACATTAAATAATTATCTCATTGCTTTATTAAAATTCATGGATCT", ) self.assertEqual( alignment[6], "-AGATCCATGAATTTTAATA---AAGCAATGAGATAATTATTTAATGTTGGAAAATCCTCAAGTCTTAAGGAAAAAAGTGTTTGACTTGTTAATGACTTGGGATGA", ) self.assertEqual( alignment.sequences[6].annotations["quality"], "999999799999999999999999999999999999999999999999999998677999969999999999999999999999999999999999999999", ) self.assertEqual(alignment.sequences[6].annotations["leftStatus"], "I") self.assertEqual(alignment.sequences[6].annotations["leftCount"], 37) self.assertEqual(alignment.sequences[6].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[6].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[7].id, "calJac1.Contig6394") self.assertEqual(len(alignment.sequences[7].seq), 133105) self.assertEqual( alignment.sequences[7].seq[10482 : 10482 + 100], "GGGGTCCATGAATTTTAATAGTAACAAAATGGTTATTCAATATTGCAAAATCCTCAGCTTTAAGGAAAAACATATTTGATTTGTTAATTATTTAGGACAA", ) self.assertEqual( alignment[7], "GGGGTCCATGAATTTTAATA-----GTAACAAAATGGTTATTCAATATTGCAAAATCCTCAGC-TTTAAGGAAAAACATATTTGATTTGTTAATTATTTAGGACAA", ) self.assertEqual(alignment.sequences[7].annotations["leftStatus"], "I") self.assertEqual(alignment.sequences[7].annotations["leftCount"], 21) self.assertEqual(alignment.sequences[7].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[7].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[8].id, "ponAbe2.chr6") self.assertEqual(len(alignment.sequences[8].seq), 174210431) self.assertEqual( alignment.sequences[8].seq[158037464 : 158037464 + 101], "TTGTCCTAAATAATTAATAAGTCAAACACGTTTTTCCTTAAAAGCTGAGGATTTTGCAATATTAAATAACCATTTTATTACTATTAAAATTCATGGACCCC", ) self.assertEqual( alignment[8], "GGGGTCCATGAATTTTAATA-----GTAATAAAATGGTTATTTAATATTGCAAAATCCTCAGCTTTTAAGGAAAAACGTGTTTGACTTATTAATTATTTAGGACAA", ) self.assertEqual(alignment.sequences[8].annotations["leftStatus"], "I") self.assertEqual(alignment.sequences[8].annotations["leftCount"], 21) self.assertEqual(alignment.sequences[8].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[8].annotations["rightCount"], 0) empty = alignment.annotations["empty"][0] (record, segment, status) = empty self.assertEqual(record.id, "ornAna1.chr2") self.assertEqual(len(record.seq), 54797317) self.assertEqual(segment, (40046122, 40040432)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][1] (record, segment, status) = empty self.assertEqual(record.id, "tupBel1.scaffold_114895.1-498454") self.assertEqual(len(record.seq), 498454) self.assertEqual(segment, (324116, 323493)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][2] (record, segment, status) = empty self.assertEqual(record.id, "echTel1.scaffold_288249") self.assertEqual(len(record.seq), 100002) self.assertEqual(segment, (87661, 95225)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][3] (record, segment, status) = empty self.assertEqual(record.id, "otoGar1.scaffold_334.1-359464") self.assertEqual(len(record.seq), 359464) self.assertEqual(segment, (171686, 171328)) self.assertEqual(status, "I") self.assertEqual(len(alignment.sequences), 9) self.assertEqual(len(alignment.annotations["empty"]), 4) self.assertEqual( str(alignment), """\ mm9.chr10 3020918 GAGGTTTGTGACTTTTAATA----------CTGATTGTTATCTAACATCACAGAATTCTC hg18.chr6 155025316 ---------------------------------ATGGTTATTTAATACTGCACAATCCTC panTro2.c 157515370 ---------------------------------ATGGTTATTTAATACTGCACAATCCTC canFam2.c 47544783 --------------------------TAATAAAATAATTCTGTACCATTATGAAGTTCTC felCat3.s 46172 ---GTCCATGAATTTTAATGGTGAAGTAATGAAATAATTCTTTAATATCAC--------- cavPor2.s 606 GAGTTCTGCAAATtttaata----------ggaaaagaagatTAATATTACAAAGTTTTC oryCun1.s 4263 -AGATCCATGAATTTTAATA---AAGCAATGAGATAATTATTTAATGTTGGAAAATCCTC calJac1.C 10482 GGGGTCCATGAATTTTAATA-----GTAACAAAATGGTTATTCAATATTGCAAAATCCTC ponAbe2.c 158037565 GGGGTCCATGAATTTTAATA-----GTAATAAAATGGTTATTTAATATTGCAAAATCCTC mm9.chr10 3020968 AGTTCTTAAGGAAACAATTGTTCTGTGTGTTATTTGTCTAGGAGGA 3021014 hg18.chr6 155025289 AGCTTTTAAGGAAAAACATGTTTGACTTATTAATTATTTAGGACAA 155025243 panTro2.c 157515343 AGCTTTTAAGGAAAAACATGTTTGACTTATTAATTATTTAGGACAA 157515297 canFam2.c 47544749 AGCTCTTAAGGAAAAA-----GTGATTTGTTAATTACTTAGGACAA 47544708 felCat3.s 46124 -------------AAA-----GTAATTTATTAATTATTTAGGACAA 46096 cavPor2.s 556 AGTTCTGATGGAAaaa----------gtgtgatttttttaaa---- 524 oryCun1.s 4207 AAGTCTTAAGGAAAAAAGTGTTTGACTTGTTAATGACTTGGGATGA 4161 calJac1.C 10537 AGC-TTTAAGGAAAAACATATTTGATTTGTTAATTATTTAGGACAA 10582 ponAbe2.c 158037510 AGCTTTTAAGGAAAAACGTGTTTGACTTATTAATTATTTAGGACAA 158037464 """, ) self.assertTrue( np.array_equal( alignment.coordinates, np.array( # fmt: off [[ 3020918, 3020919, 3020921, 3020938, 3020938, 3020938, 3020938, 3020938, 3020941, 3020959, 3020971, 3020972, 3020981, 3020984, 3020989, 3020994, 3021010, 3021014], [155025316, 155025316, 155025316, 155025316, 155025316, 155025316, 155025316, 155025316, 155025316, 155025298, 155025286, 155025285, 155025276, 155025273, 155025268, 155025263, 155025247, 155025243], [157515370, 157515370, 157515370, 157515370, 157515370, 157515370, 157515370, 157515370, 157515370, 157515352, 157515340, 157515339, 157515330, 157515327, 157515322, 157515317, 157515301, 157515297], [ 47544783, 47544783, 47544783, 47544783, 47544783, 47544783, 47544783, 47544779, 47544776, 47544758, 47544746, 47544745, 47544736, 47544733, 47544733, 47544728, 47544712, 47544708], [ 46172, 46172, 46172, 46155, 46152, 46150, 46149, 46145, 46142, 46124, 46124, 46124, 46124, 46121, 46121, 46116, 46100, 46096], [ 606, 605, 603, 586, 586, 586, 586, 586, 583, 565, 553, 552, 543, 540, 540, 540, 524, 524], [ 4263, 4263, 4261, 4244, 4244, 4242, 4241, 4237, 4234, 4216, 4204, 4203, 4194, 4191, 4186, 4181, 4165, 4161], [ 10482, 10483, 10485, 10502, 10502, 10502, 10503, 10507, 10510, 10528, 10540, 10540, 10549, 10552, 10557, 10562, 10578, 10582], [158037565, 158037564, 158037562, 158037545, 158037545, 158037545, 158037544, 158037540, 158037537, 158037519, 158037507, 158037506, 158037497, 158037494, 158037489, 158037484, 158037468, 158037464], ] # fmt: on ), ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['G', 'A', 'G', 'G', 'T', 'T', 'T', 'G', 'T', 'G', 'A', 'C', 'T', 'T', 'T', 'T', 'A', 'A', 'T', 'A', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'C', 'T', 'G', 'A', 'T', 'T', 'G', 'T', 'T', 'A', 'T', 'C', 'T', 'A', 'A', 'C', 'A', 'T', 'C', 'A', 'C', 'A', 'G', 'A', 'A', 'T', 'T', 'C', 'T', 'C', 'A', 'G', 'T', 'T', 'C', 'T', 'T', 'A', 'A', 'G', 'G', 'A', 'A', 'A', 'C', 'A', 'A', 'T', 'T', 'G', 'T', 'T', 'C', 'T', 'G', 'T', 'G', 'T', 'G', 'T', 'T', 'A', 'T', 'T', 'T', 'G', 'T', 'C', 'T', 'A', 'G', 'G', 'A', 'G', 'G', 'A'], ['-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'A', 'T', 'G', 'G', 'T', 'T', 'A', 'T', 'T', 'T', 'A', 'A', 'T', 'A', 'C', 'T', 'G', 'C', 'A', 'C', 'A', 'A', 'T', 'C', 'C', 'T', 'C', 'A', 'G', 'C', 'T', 'T', 'T', 'T', 'A', 'A', 'G', 'G', 'A', 'A', 'A', 'A', 'A', 'C', 'A', 'T', 'G', 'T', 'T', 'T', 'G', 'A', 'C', 'T', 'T', 'A', 'T', 'T', 'A', 'A', 'T', 'T', 'A', 'T', 'T', 'T', 'A', 'G', 'G', 'A', 'C', 'A', 'A'], ['-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'A', 'T', 'G', 'G', 'T', 'T', 'A', 'T', 'T', 'T', 'A', 'A', 'T', 'A', 'C', 'T', 'G', 'C', 'A', 'C', 'A', 'A', 'T', 'C', 'C', 'T', 'C', 'A', 'G', 'C', 'T', 'T', 'T', 'T', 'A', 'A', 'G', 'G', 'A', 'A', 'A', 'A', 'A', 'C', 'A', 'T', 'G', 'T', 'T', 'T', 'G', 'A', 'C', 'T', 'T', 'A', 'T', 'T', 'A', 'A', 'T', 'T', 'A', 'T', 'T', 'T', 'A', 'G', 'G', 'A', 'C', 'A', 'A'], ['-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'T', 'A', 'A', 'T', 'A', 'A', 'A', 'A', 'T', 'A', 'A', 'T', 'T', 'C', 'T', 'G', 'T', 'A', 'C', 'C', 'A', 'T', 'T', 'A', 'T', 'G', 'A', 'A', 'G', 'T', 'T', 'C', 'T', 'C', 'A', 'G', 'C', 'T', 'C', 'T', 'T', 'A', 'A', 'G', 'G', 'A', 'A', 'A', 'A', 'A', '-', '-', '-', '-', '-', 'G', 'T', 'G', 'A', 'T', 'T', 'T', 'G', 'T', 'T', 'A', 'A', 'T', 'T', 'A', 'C', 'T', 'T', 'A', 'G', 'G', 'A', 'C', 'A', 'A'], ['-', '-', '-', 'G', 'T', 'C', 'C', 'A', 'T', 'G', 'A', 'A', 'T', 'T', 'T', 'T', 'A', 'A', 'T', 'G', 'G', 'T', 'G', 'A', 'A', 'G', 'T', 'A', 'A', 'T', 'G', 'A', 'A', 'A', 'T', 'A', 'A', 'T', 'T', 'C', 'T', 'T', 'T', 'A', 'A', 'T', 'A', 'T', 'C', 'A', 'C', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'A', 'A', 'A', '-', '-', '-', '-', '-', 'G', 'T', 'A', 'A', 'T', 'T', 'T', 'A', 'T', 'T', 'A', 'A', 'T', 'T', 'A', 'T', 'T', 'T', 'A', 'G', 'G', 'A', 'C', 'A', 'A'], ['G', 'A', 'G', 'T', 'T', 'C', 'T', 'G', 'C', 'A', 'A', 'A', 'T', 't', 't', 't', 'a', 'a', 't', 'a', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'g', 'g', 'a', 'a', 'a', 'a', 'g', 'a', 'a', 'g', 'a', 't', 'T', 'A', 'A', 'T', 'A', 'T', 'T', 'A', 'C', 'A', 'A', 'A', 'G', 'T', 'T', 'T', 'T', 'C', 'A', 'G', 'T', 'T', 'C', 'T', 'G', 'A', 'T', 'G', 'G', 'A', 'A', 'a', 'a', 'a', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'g', 't', 'g', 't', 'g', 'a', 't', 't', 't', 't', 't', 't', 't', 'a', 'a', 'a', '-', '-', '-', '-'], ['-', 'A', 'G', 'A', 'T', 'C', 'C', 'A', 'T', 'G', 'A', 'A', 'T', 'T', 'T', 'T', 'A', 'A', 'T', 'A', '-', '-', '-', 'A', 'A', 'G', 'C', 'A', 'A', 'T', 'G', 'A', 'G', 'A', 'T', 'A', 'A', 'T', 'T', 'A', 'T', 'T', 'T', 'A', 'A', 'T', 'G', 'T', 'T', 'G', 'G', 'A', 'A', 'A', 'A', 'T', 'C', 'C', 'T', 'C', 'A', 'A', 'G', 'T', 'C', 'T', 'T', 'A', 'A', 'G', 'G', 'A', 'A', 'A', 'A', 'A', 'A', 'G', 'T', 'G', 'T', 'T', 'T', 'G', 'A', 'C', 'T', 'T', 'G', 'T', 'T', 'A', 'A', 'T', 'G', 'A', 'C', 'T', 'T', 'G', 'G', 'G', 'A', 'T', 'G', 'A'], ['G', 'G', 'G', 'G', 'T', 'C', 'C', 'A', 'T', 'G', 'A', 'A', 'T', 'T', 'T', 'T', 'A', 'A', 'T', 'A', '-', '-', '-', '-', '-', 'G', 'T', 'A', 'A', 'C', 'A', 'A', 'A', 'A', 'T', 'G', 'G', 'T', 'T', 'A', 'T', 'T', 'C', 'A', 'A', 'T', 'A', 'T', 'T', 'G', 'C', 'A', 'A', 'A', 'A', 'T', 'C', 'C', 'T', 'C', 'A', 'G', 'C', '-', 'T', 'T', 'T', 'A', 'A', 'G', 'G', 'A', 'A', 'A', 'A', 'A', 'C', 'A', 'T', 'A', 'T', 'T', 'T', 'G', 'A', 'T', 'T', 'T', 'G', 'T', 'T', 'A', 'A', 'T', 'T', 'A', 'T', 'T', 'T', 'A', 'G', 'G', 'A', 'C', 'A', 'A'], ['G', 'G', 'G', 'G', 'T', 'C', 'C', 'A', 'T', 'G', 'A', 'A', 'T', 'T', 'T', 'T', 'A', 'A', 'T', 'A', '-', '-', '-', '-', '-', 'G', 'T', 'A', 'A', 'T', 'A', 'A', 'A', 'A', 'T', 'G', 'G', 'T', 'T', 'A', 'T', 'T', 'T', 'A', 'A', 'T', 'A', 'T', 'T', 'G', 'C', 'A', 'A', 'A', 'A', 'T', 'C', 'C', 'T', 'C', 'A', 'G', 'C', 'T', 'T', 'T', 'T', 'A', 'A', 'G', 'G', 'A', 'A', 'A', 'A', 'A', 'C', 'G', 'T', 'G', 'T', 'T', 'T', 'G', 'A', 'C', 'T', 'T', 'A', 'T', 'T', 'A', 'A', 'T', 'T', 'A', 'T', 'T', 'T', 'A', 'G', 'G', 'A', 'C', 'A', 'A']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.score, 105724) self.assertEqual(alignment.sequences[0].id, "mm9.chr10") self.assertEqual(len(alignment.sequences[0].seq), 129993255) self.assertEqual( alignment.sequences[0].seq[3021014 : 3021014 + 40], "ACCTTGGTGACGCCACTGGATTTTGTATGACTGAATACTG", ) self.assertEqual(alignment[0], "ACCTTGGTGACGCCACTGGATTTTGTATGACTGAATACTG") self.assertEqual(alignment.sequences[1].id, "oryCun1.scaffold_156751") self.assertEqual(len(alignment.sequences[1].seq), 4726) self.assertEqual( alignment.sequences[1].seq[4121 : 4121 + 40], "AATTCCTAAATCATCCAAGTTGGAATGACTTCATCAAGAT", ) self.assertEqual(alignment[1], "ATCTTGATGAAGTCATTCCAACTTGGATGATTTAGGAATT") self.assertEqual( alignment.sequences[1].annotations["quality"], "9999999999999969999699999999999999999999", ) self.assertEqual(alignment.sequences[1].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[1].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[1].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[1].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[2].id, "otoGar1.scaffold_334.1-359464") self.assertEqual(len(alignment.sequences[2].seq), 359464) self.assertEqual( alignment.sequences[2].seq[171288 : 171288 + 40], "CATTCCTAAATCACATAAATTGGAATAACTTCACCAAGAT", ) self.assertEqual(alignment[2], "ATCTTGGTGAAGTTATTCCAATTTATGTGATTTAGGAATG") self.assertEqual( alignment.sequences[2].annotations["quality"], "9999999999999999999999999999999999999999", ) self.assertEqual(alignment.sequences[2].annotations["leftStatus"], "I") self.assertEqual(alignment.sequences[2].annotations["leftCount"], 358) self.assertEqual(alignment.sequences[2].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[2].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[3].id, "calJac1.Contig6394") self.assertEqual(len(alignment.sequences[3].seq), 133105) self.assertEqual( alignment.sequences[3].seq[10582 : 10582 + 40], "ATTTTGGTGAAGTTATTCCAACTTGTGTGGCTTAGGAATG", ) self.assertEqual(alignment[3], "ATTTTGGTGAAGTTATTCCAACTTGTGTGGCTTAGGAATG") self.assertEqual(alignment.sequences[3].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[3].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[3].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[3].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[4].id, "hg18.chr6") self.assertEqual(len(alignment.sequences[4].seq), 170899992) self.assertEqual( alignment.sequences[4].seq[155025203 : 155025203 + 40], "CATTCCTAAGCCATGCAAGTTGGAATAACTTCACCAAAAT", ) self.assertEqual(alignment[4], "ATTTTGGTGAAGTTATTCCAACTTGCATGGCTTAGGAATG") self.assertEqual(alignment.sequences[4].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[4].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[4].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[4].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[5].id, "panTro2.chr6") self.assertEqual(len(alignment.sequences[5].seq), 173908612) self.assertEqual( alignment.sequences[5].seq[157515257 : 157515257 + 40], "CATTCCTAAGCCATGCAAGTTGGAATAACTTCACCAAAAT", ) self.assertEqual(alignment[5], "ATTTTGGTGAAGTTATTCCAACTTGCATGGCTTAGGAATG") self.assertEqual( alignment.sequences[5].annotations["quality"], "9999999999999999999999999999999999999999", ) self.assertEqual(alignment.sequences[5].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[5].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[5].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[5].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[6].id, "ponAbe2.chr6") self.assertEqual(len(alignment.sequences[6].seq), 174210431) self.assertEqual( alignment.sequences[6].seq[158037424 : 158037424 + 40], "CATTCCTAAGCCATGCAAGTTGGAATAACTTCACCAAAAT", ) self.assertEqual(alignment[6], "ATTTTGGTGAAGTTATTCCAACTTGCATGGCTTAGGAATG") self.assertEqual(alignment.sequences[6].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[6].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[6].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[6].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[7].id, "canFam2.chr1") self.assertEqual(len(alignment.sequences[7].seq), 125616256) self.assertEqual( alignment.sequences[7].seq[47544668 : 47544668 + 40], "CATTCCTAAATCATGCGAGTCAGAATGACTTCACTGAGAT", ) self.assertEqual(alignment[7], "ATCTCAGTGAAGTCATTCTGACTCGCATGATTTAGGAATG") self.assertEqual( alignment.sequences[7].annotations["quality"], "9999999999999999999999999999999999999999", ) self.assertEqual(alignment.sequences[7].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[7].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[7].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[7].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[8].id, "felCat3.scaffold_205680") self.assertEqual(len(alignment.sequences[8].seq), 119354) self.assertEqual( alignment.sequences[8].seq[46056 : 46056 + 40], "CATACCTAAATCATGCAAGTCAGAATAACTTCACTGAGAT", ) self.assertEqual(alignment[8], "ATCTCAGTGAAGTTATTCTGACTTGCATGATTTAGGTATG") self.assertEqual( alignment.sequences[8].annotations["quality"], "9999989999989988999997999979997996167779", ) self.assertEqual(alignment.sequences[8].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[8].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[8].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[8].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[9].id, "dasNov1.scaffold_56749") self.assertEqual(len(alignment.sequences[9].seq), 10470) self.assertEqual( alignment.sequences[9].seq[7314 : 7314 + 40], "CATCGCTCAGTCATACGAGTCGGAATGATTTCACTGATGT", ) self.assertEqual(alignment[9], "ACATCAGTGAAATCATTCCGACTCGTATGACTGAGCGATG") self.assertEqual( alignment.sequences[9].annotations["quality"], "9759855999977756667495765475885678385647", ) self.assertEqual(alignment.sequences[9].annotations["leftStatus"], "N") self.assertEqual(alignment.sequences[9].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[9].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[9].annotations["rightCount"], 0) empty = alignment.annotations["empty"][0] (record, segment, status) = empty self.assertEqual(record.id, "ornAna1.chr2") self.assertEqual(len(record.seq), 54797317) self.assertEqual(segment, (40046122, 40040432)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][1] (record, segment, status) = empty self.assertEqual(record.id, "tupBel1.scaffold_114895.1-498454") self.assertEqual(len(record.seq), 498454) self.assertEqual(segment, (324116, 323493)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][2] (record, segment, status) = empty self.assertEqual(record.id, "echTel1.scaffold_288249") self.assertEqual(len(record.seq), 100002) self.assertEqual(segment, (87661, 95225)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][3] (record, segment, status) = empty self.assertEqual(record.id, "cavPor2.scaffold_216473") self.assertEqual(len(record.seq), 10026) self.assertEqual(segment, (524, 496)) self.assertEqual(status, "I") self.assertEqual(len(alignment.sequences), 10) self.assertEqual(len(alignment.annotations["empty"]), 4) self.assertEqual( str(alignment), """\ mm9.chr10 3021014 ACCTTGGTGACGCCACTGGATTTTGTATGACTGAATACTG 3021054 oryCun1.s 4161 ATCTTGATGAAGTCATTCCAACTTGGATGATTTAGGAATT 4121 otoGar1.s 171328 ATCTTGGTGAAGTTATTCCAATTTATGTGATTTAGGAATG 171288 calJac1.C 10582 ATTTTGGTGAAGTTATTCCAACTTGTGTGGCTTAGGAATG 10622 hg18.chr6 155025243 ATTTTGGTGAAGTTATTCCAACTTGCATGGCTTAGGAATG 155025203 panTro2.c 157515297 ATTTTGGTGAAGTTATTCCAACTTGCATGGCTTAGGAATG 157515257 ponAbe2.c 158037464 ATTTTGGTGAAGTTATTCCAACTTGCATGGCTTAGGAATG 158037424 canFam2.c 47544708 ATCTCAGTGAAGTCATTCTGACTCGCATGATTTAGGAATG 47544668 felCat3.s 46096 ATCTCAGTGAAGTTATTCTGACTTGCATGATTTAGGTATG 46056 dasNov1.s 7354 ACATCAGTGAAATCATTCCGACTCGTATGACTGAGCGATG 7314 """, ) self.assertTrue( np.array_equal( # fmt: off alignment.coordinates, np.array([[ 3021014, 3021054], [ 4161, 4121], [ 171328, 171288], [ 10582, 10622], [155025243, 155025203], [157515297, 157515257], [158037464, 158037424], [ 47544708, 47544668], [ 46096, 46056], [ 7354, 7314], ]) # fmt: on ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['A', 'C', 'C', 'T', 'T', 'G', 'G', 'T', 'G', 'A', 'C', 'G', 'C', 'C', 'A', 'C', 'T', 'G', 'G', 'A', 'T', 'T', 'T', 'T', 'G', 'T', 'A', 'T', 'G', 'A', 'C', 'T', 'G', 'A', 'A', 'T', 'A', 'C', 'T', 'G'], ['A', 'T', 'C', 'T', 'T', 'G', 'A', 'T', 'G', 'A', 'A', 'G', 'T', 'C', 'A', 'T', 'T', 'C', 'C', 'A', 'A', 'C', 'T', 'T', 'G', 'G', 'A', 'T', 'G', 'A', 'T', 'T', 'T', 'A', 'G', 'G', 'A', 'A', 'T', 'T'], ['A', 'T', 'C', 'T', 'T', 'G', 'G', 'T', 'G', 'A', 'A', 'G', 'T', 'T', 'A', 'T', 'T', 'C', 'C', 'A', 'A', 'T', 'T', 'T', 'A', 'T', 'G', 'T', 'G', 'A', 'T', 'T', 'T', 'A', 'G', 'G', 'A', 'A', 'T', 'G'], ['A', 'T', 'T', 'T', 'T', 'G', 'G', 'T', 'G', 'A', 'A', 'G', 'T', 'T', 'A', 'T', 'T', 'C', 'C', 'A', 'A', 'C', 'T', 'T', 'G', 'T', 'G', 'T', 'G', 'G', 'C', 'T', 'T', 'A', 'G', 'G', 'A', 'A', 'T', 'G'], ['A', 'T', 'T', 'T', 'T', 'G', 'G', 'T', 'G', 'A', 'A', 'G', 'T', 'T', 'A', 'T', 'T', 'C', 'C', 'A', 'A', 'C', 'T', 'T', 'G', 'C', 'A', 'T', 'G', 'G', 'C', 'T', 'T', 'A', 'G', 'G', 'A', 'A', 'T', 'G'], ['A', 'T', 'T', 'T', 'T', 'G', 'G', 'T', 'G', 'A', 'A', 'G', 'T', 'T', 'A', 'T', 'T', 'C', 'C', 'A', 'A', 'C', 'T', 'T', 'G', 'C', 'A', 'T', 'G', 'G', 'C', 'T', 'T', 'A', 'G', 'G', 'A', 'A', 'T', 'G'], ['A', 'T', 'T', 'T', 'T', 'G', 'G', 'T', 'G', 'A', 'A', 'G', 'T', 'T', 'A', 'T', 'T', 'C', 'C', 'A', 'A', 'C', 'T', 'T', 'G', 'C', 'A', 'T', 'G', 'G', 'C', 'T', 'T', 'A', 'G', 'G', 'A', 'A', 'T', 'G'], ['A', 'T', 'C', 'T', 'C', 'A', 'G', 'T', 'G', 'A', 'A', 'G', 'T', 'C', 'A', 'T', 'T', 'C', 'T', 'G', 'A', 'C', 'T', 'C', 'G', 'C', 'A', 'T', 'G', 'A', 'T', 'T', 'T', 'A', 'G', 'G', 'A', 'A', 'T', 'G'], ['A', 'T', 'C', 'T', 'C', 'A', 'G', 'T', 'G', 'A', 'A', 'G', 'T', 'T', 'A', 'T', 'T', 'C', 'T', 'G', 'A', 'C', 'T', 'T', 'G', 'C', 'A', 'T', 'G', 'A', 'T', 'T', 'T', 'A', 'G', 'G', 'T', 'A', 'T', 'G'], ['A', 'C', 'A', 'T', 'C', 'A', 'G', 'T', 'G', 'A', 'A', 'A', 'T', 'C', 'A', 'T', 'T', 'C', 'C', 'G', 'A', 'C', 'T', 'C', 'G', 'T', 'A', 'T', 'G', 'A', 'C', 'T', 'G', 'A', 'G', 'C', 'G', 'A', 'T', 'G']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.score, 115790) self.assertEqual(alignment.sequences[0].id, "mm9.chr10") self.assertEqual(len(alignment.sequences[0].seq), 129993255) self.assertEqual( alignment.sequences[0].seq[3021054 : 3021054 + 50], "CTCATTTGGGAACTTACAGGTCAGCAAAGGCTTCCAGGACTTACATGCAG", ) self.assertEqual( alignment[0], "CTCATTTGGGAACTTACAGGTCAGCAAAGGCTTCCAG--------------------GACTTACATGCAG", ) self.assertEqual(alignment.sequences[1].id, "cavPor2.scaffold_216473") self.assertEqual(len(alignment.sequences[1].seq), 10026) self.assertEqual( alignment.sequences[1].seq[458 : 458 + 38], "TCACAAGTATTTATAGCAACTCTGAACTCCCAAATGAG", ) self.assertEqual( alignment[1], "CTCATTTGGGAGTTCAGAGTT--------GCTATAAA--------------------TACTTGTGA----", ) self.assertEqual( alignment.sequences[1].annotations["quality"], "78877766789884666566698766677876665669", ) self.assertEqual(alignment.sequences[1].annotations["leftStatus"], "I") self.assertEqual(alignment.sequences[1].annotations["leftCount"], 28) self.assertEqual(alignment.sequences[1].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[1].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[2].id, "oryCun1.scaffold_156751") self.assertEqual(len(alignment.sequences[2].seq), 4726) self.assertEqual( alignment.sequences[2].seq[4052 : 4052 + 69], "ATACGTGTAATTAAGGAGGAAAAAAGAAGACTCCATTAGGCAGTTATAAAATGTAAGAGCCCAAATTAG", ) self.assertEqual( alignment[2], "CTAATTTGGGCTCTTACATTTTATAACTGCCTAATGGAGTCTTCTTTTTTCCT-CCTTAATTACACGTAT", ) self.assertEqual( alignment.sequences[2].annotations["quality"], "999999999999979997999999999999999999999997997999999979979999999495999", ) self.assertEqual(alignment.sequences[2].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[2].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[2].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[2].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[3].id, "otoGar1.scaffold_334.1-359464") self.assertEqual(len(alignment.sequences[3].seq), 359464) self.assertEqual( alignment.sequences[3].seq[171219 : 171219 + 69], "GTACATAGAGTCTGGGGAAGGGACCAGTGGGCTCCATTAAGCCTTTATGAACCTGTGTCCCCAAGTTAG", ) self.assertEqual( alignment[3], "CTAACTTGGGGACACAGG-TTCATAAAGGCTTAATGGAGCCCACTGGTCCCTTCCCCAGACTCTATGTAC", ) self.assertEqual( alignment.sequences[3].annotations["quality"], "999999999999999999999999999999999999998999999689999999999999999999999", ) self.assertEqual(alignment.sequences[3].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[3].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[3].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[3].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[4].id, "calJac1.Contig6394") self.assertEqual(len(alignment.sequences[4].seq), 133105) self.assertEqual( alignment.sequences[4].seq[10622 : 10622 + 70], "CCAGTTTGGGGACTTAGATTTTCTAACTGCCTAATGAAGTCTGCTCTTTCCTTCCCTAGCCTATATGTAT", ) self.assertEqual( alignment[4], "CCAGTTTGGGGACTTAGATTTTCTAACTGCCTAATGAAGTCTGCTCTTTCCTTCCCTAGCCTATATGTAT", ) self.assertEqual(alignment.sequences[4].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[4].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[4].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[4].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[5].id, "hg18.chr6") self.assertEqual(len(alignment.sequences[5].seq), 170899992) self.assertEqual( alignment.sequences[5].seq[155025133 : 155025133 + 70], "ATACATATAGTCTAGGGAAGGAAGGAGCAGACTTCATTAGGCAGTTAGGAAATGTAAATCCCCAAATTGT", ) self.assertEqual( alignment[5], "ACAATTTGGGGATTTACATTTCCTAACTGCCTAATGAAGTCTGCTCCTTCCTTCCCTAGACTATATGTAT", ) self.assertEqual(alignment.sequences[5].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[5].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[5].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[5].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[6].id, "panTro2.chr6") self.assertEqual(len(alignment.sequences[6].seq), 173908612) self.assertEqual( alignment.sequences[6].seq[157515187 : 157515187 + 70], "ATACATATAGTCTAGGGAAGGAAAGAGCAGACTTCATTAGGCAGTTAGGAAATGTAAATCCCCAAATTGG", ) self.assertEqual( alignment[6], "CCAATTTGGGGATTTACATTTCCTAACTGCCTAATGAAGTCTGCTCTTTCCTTCCCTAGACTATATGTAT", ) self.assertEqual( alignment.sequences[6].annotations["quality"], "9999999999999999999999999999999999999999999999999999999999999999999999", ) self.assertEqual(alignment.sequences[6].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[6].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[6].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[6].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[7].id, "ponAbe2.chr6") self.assertEqual(len(alignment.sequences[7].seq), 174210431) self.assertEqual( alignment.sequences[7].seq[158037354 : 158037354 + 70], "ATACATATAGTCTAGGGAAGGAAAGAGCAGACTTCATTAGGCAGTTAGGAAATGTAAATCCCCAAATTGG", ) self.assertEqual( alignment[7], "CCAATTTGGGGATTTACATTTCCTAACTGCCTAATGAAGTCTGCTCTTTCCTTCCCTAGACTATATGTAT", ) self.assertEqual(alignment.sequences[7].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[7].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[7].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[7].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[8].id, "canFam2.chr1") self.assertEqual(len(alignment.sequences[8].seq), 125616256) self.assertEqual( alignment.sequences[8].seq[47544598 : 47544598 + 70], "ATACATATGGTGTAGGGAAGAAAACATCAGCTTTCATTAAGCAATTATGAAATTTGAGTCACCAAATTAG", ) self.assertEqual( alignment[8], "CTAATTTGGTGACTCAAATTTCATAATTGCTTAATGAAAGCTGATGTTTTCTTCCCTACACCATATGTAT", ) self.assertEqual( alignment.sequences[8].annotations["quality"], "9999999999999999999999999999999999999999999999999999999999999999999999", ) self.assertEqual(alignment.sequences[8].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[8].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[8].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[8].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[9].id, "felCat3.scaffold_205680") self.assertEqual(len(alignment.sequences[9].seq), 119354) self.assertEqual( alignment.sequences[9].seq[45986 : 45986 + 70], "ATGCATATAGTCTTGGGAAGGAAACAGCAGGCTTCCTTAAGCAATTATGAAATTCAAGTCACCAAATTAG", ) self.assertEqual( alignment[9], "CTAATTTGGTGACTTGAATTTCATAATTGCTTAAGGAAGCCTGCTGTTTCCTTCCCAAGACTATATGCAT", ) self.assertEqual( alignment.sequences[9].annotations["quality"], "9769999999975699868977669777966666596959759669595666758736585676666655", ) self.assertEqual(alignment.sequences[9].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[9].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[9].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[9].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[10].id, "dasNov1.scaffold_56749") self.assertEqual(len(alignment.sequences[10].seq), 10470) self.assertEqual( alignment.sequences[10].seq[7244 : 7244 + 70], "ATACTTATAGTCTAGAGAAGAAAACAGCAGGCTTCGGTTAGCAATTTTAAAATGTGAGTCCCCCAATTAG", ) self.assertEqual( alignment[10], "CTAATTGGGGGACTCACATTTTAAAATTGCTAACCGAAGCCTGCTGTTTTCTTCTCTAGACTATAAGTAT", ) self.assertEqual( alignment.sequences[10].annotations["quality"], "5556576999664654656985688667655565647767537567688856666555556565555656", ) self.assertEqual(alignment.sequences[10].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[10].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[10].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[10].annotations["rightCount"], 0) empty = alignment.annotations["empty"][0] (record, segment, status) = empty self.assertEqual(record.id, "ornAna1.chr2") self.assertEqual(len(record.seq), 54797317) self.assertEqual(segment, (40046122, 40040432)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][1] (record, segment, status) = empty self.assertEqual(record.id, "tupBel1.scaffold_114895.1-498454") self.assertEqual(len(record.seq), 498454) self.assertEqual(segment, (324116, 323493)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][2] (record, segment, status) = empty self.assertEqual(record.id, "echTel1.scaffold_288249") self.assertEqual(len(record.seq), 100002) self.assertEqual(segment, (87661, 95225)) self.assertEqual(status, "I") self.assertEqual(len(alignment.sequences), 11) self.assertEqual(len(alignment.annotations["empty"]), 3) self.assertEqual( str(alignment), """\ mm9.chr10 3021054 CTCATTTGGGAACTTACAGGTCAGCAAAGGCTTCCAG--------------------GAC cavPor2.s 496 CTCATTTGGGAGTTCAGAGTT--------GCTATAAA--------------------TAC oryCun1.s 4121 CTAATTTGGGCTCTTACATTTTATAACTGCCTAATGGAGTCTTCTTTTTTCCT-CCTTAA otoGar1.s 171288 CTAACTTGGGGACACAGG-TTCATAAAGGCTTAATGGAGCCCACTGGTCCCTTCCCCAGA calJac1.C 10622 CCAGTTTGGGGACTTAGATTTTCTAACTGCCTAATGAAGTCTGCTCTTTCCTTCCCTAGC hg18.chr6 155025203 ACAATTTGGGGATTTACATTTCCTAACTGCCTAATGAAGTCTGCTCCTTCCTTCCCTAGA panTro2.c 157515257 CCAATTTGGGGATTTACATTTCCTAACTGCCTAATGAAGTCTGCTCTTTCCTTCCCTAGA ponAbe2.c 158037424 CCAATTTGGGGATTTACATTTCCTAACTGCCTAATGAAGTCTGCTCTTTCCTTCCCTAGA canFam2.c 47544668 CTAATTTGGTGACTCAAATTTCATAATTGCTTAATGAAAGCTGATGTTTTCTTCCCTACA felCat3.s 46056 CTAATTTGGTGACTTGAATTTCATAATTGCTTAAGGAAGCCTGCTGTTTCCTTCCCAAGA dasNov1.s 7314 CTAATTGGGGGACTCACATTTTAAAATTGCTAACCGAAGCCTGCTGTTTTCTTCTCTAGA mm9.chr10 3021094 TTACATGCAG 3021104 cavPor2.s 464 TTGTGA---- 458 oryCun1.s 4062 TTACACGTAT 4052 otoGar1.s 171229 CTCTATGTAC 171219 calJac1.C 10682 CTATATGTAT 10692 hg18.chr6 155025143 CTATATGTAT 155025133 panTro2.c 157515197 CTATATGTAT 157515187 ponAbe2.c 158037364 CTATATGTAT 158037354 canFam2.c 47544608 CCATATGTAT 47544598 felCat3.s 45996 CTATATGCAT 45986 dasNov1.s 7254 CTATAAGTAT 7244 """, ) self.assertTrue( np.array_equal( alignment.coordinates, np.array( # fmt: off [[ 3021054, 3021072, 3021073, 3021075, 3021083, 3021091, 3021091, 3021091, 3021091, 3021100, 3021104], [ 496, 478, 477, 475, 475, 467, 467, 467, 467, 458, 458], [ 4121, 4103, 4102, 4100, 4092, 4084, 4068, 4068, 4065, 4056, 4052], [ 171288, 171270, 171270, 171268, 171260, 171252, 171236, 171235, 171232, 171223, 171219], [ 10622, 10640, 10641, 10643, 10651, 10659, 10675, 10676, 10679, 10688, 10692], [155025203, 155025185, 155025184, 155025182, 155025174, 155025166, 155025150, 155025149, 155025146, 155025137, 155025133], [157515257, 157515239, 157515238, 157515236, 157515228, 157515220, 157515204, 157515203, 157515200, 157515191, 157515187], [158037424, 158037406, 158037405, 158037403, 158037395, 158037387, 158037371, 158037370, 158037367, 158037358, 158037354], [ 47544668, 47544650, 47544649, 47544647, 47544639, 47544631, 47544615, 47544614, 47544611, 47544602, 47544598], [ 46056, 46038, 46037, 46035, 46027, 46019, 46003, 46002, 45999, 45990, 45986], [ 7314, 7296, 7295, 7293, 7285, 7277, 7261, 7260, 7257, 7248, 7244], ] # fmt: on ), ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['C', 'T', 'C', 'A', 'T', 'T', 'T', 'G', 'G', 'G', 'A', 'A', 'C', 'T', 'T', 'A', 'C', 'A', 'G', 'G', 'T', 'C', 'A', 'G', 'C', 'A', 'A', 'A', 'G', 'G', 'C', 'T', 'T', 'C', 'C', 'A', 'G', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'G', 'A', 'C', 'T', 'T', 'A', 'C', 'A', 'T', 'G', 'C', 'A', 'G'], ['C', 'T', 'C', 'A', 'T', 'T', 'T', 'G', 'G', 'G', 'A', 'G', 'T', 'T', 'C', 'A', 'G', 'A', 'G', 'T', 'T', '-', '-', '-', '-', '-', '-', '-', '-', 'G', 'C', 'T', 'A', 'T', 'A', 'A', 'A', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'T', 'A', 'C', 'T', 'T', 'G', 'T', 'G', 'A', '-', '-', '-', '-'], ['C', 'T', 'A', 'A', 'T', 'T', 'T', 'G', 'G', 'G', 'C', 'T', 'C', 'T', 'T', 'A', 'C', 'A', 'T', 'T', 'T', 'T', 'A', 'T', 'A', 'A', 'C', 'T', 'G', 'C', 'C', 'T', 'A', 'A', 'T', 'G', 'G', 'A', 'G', 'T', 'C', 'T', 'T', 'C', 'T', 'T', 'T', 'T', 'T', 'T', 'C', 'C', 'T', '-', 'C', 'C', 'T', 'T', 'A', 'A', 'T', 'T', 'A', 'C', 'A', 'C', 'G', 'T', 'A', 'T'], ['C', 'T', 'A', 'A', 'C', 'T', 'T', 'G', 'G', 'G', 'G', 'A', 'C', 'A', 'C', 'A', 'G', 'G', '-', 'T', 'T', 'C', 'A', 'T', 'A', 'A', 'A', 'G', 'G', 'C', 'T', 'T', 'A', 'A', 'T', 'G', 'G', 'A', 'G', 'C', 'C', 'C', 'A', 'C', 'T', 'G', 'G', 'T', 'C', 'C', 'C', 'T', 'T', 'C', 'C', 'C', 'C', 'A', 'G', 'A', 'C', 'T', 'C', 'T', 'A', 'T', 'G', 'T', 'A', 'C'], ['C', 'C', 'A', 'G', 'T', 'T', 'T', 'G', 'G', 'G', 'G', 'A', 'C', 'T', 'T', 'A', 'G', 'A', 'T', 'T', 'T', 'T', 'C', 'T', 'A', 'A', 'C', 'T', 'G', 'C', 'C', 'T', 'A', 'A', 'T', 'G', 'A', 'A', 'G', 'T', 'C', 'T', 'G', 'C', 'T', 'C', 'T', 'T', 'T', 'C', 'C', 'T', 'T', 'C', 'C', 'C', 'T', 'A', 'G', 'C', 'C', 'T', 'A', 'T', 'A', 'T', 'G', 'T', 'A', 'T'], ['A', 'C', 'A', 'A', 'T', 'T', 'T', 'G', 'G', 'G', 'G', 'A', 'T', 'T', 'T', 'A', 'C', 'A', 'T', 'T', 'T', 'C', 'C', 'T', 'A', 'A', 'C', 'T', 'G', 'C', 'C', 'T', 'A', 'A', 'T', 'G', 'A', 'A', 'G', 'T', 'C', 'T', 'G', 'C', 'T', 'C', 'C', 'T', 'T', 'C', 'C', 'T', 'T', 'C', 'C', 'C', 'T', 'A', 'G', 'A', 'C', 'T', 'A', 'T', 'A', 'T', 'G', 'T', 'A', 'T'], ['C', 'C', 'A', 'A', 'T', 'T', 'T', 'G', 'G', 'G', 'G', 'A', 'T', 'T', 'T', 'A', 'C', 'A', 'T', 'T', 'T', 'C', 'C', 'T', 'A', 'A', 'C', 'T', 'G', 'C', 'C', 'T', 'A', 'A', 'T', 'G', 'A', 'A', 'G', 'T', 'C', 'T', 'G', 'C', 'T', 'C', 'T', 'T', 'T', 'C', 'C', 'T', 'T', 'C', 'C', 'C', 'T', 'A', 'G', 'A', 'C', 'T', 'A', 'T', 'A', 'T', 'G', 'T', 'A', 'T'], ['C', 'C', 'A', 'A', 'T', 'T', 'T', 'G', 'G', 'G', 'G', 'A', 'T', 'T', 'T', 'A', 'C', 'A', 'T', 'T', 'T', 'C', 'C', 'T', 'A', 'A', 'C', 'T', 'G', 'C', 'C', 'T', 'A', 'A', 'T', 'G', 'A', 'A', 'G', 'T', 'C', 'T', 'G', 'C', 'T', 'C', 'T', 'T', 'T', 'C', 'C', 'T', 'T', 'C', 'C', 'C', 'T', 'A', 'G', 'A', 'C', 'T', 'A', 'T', 'A', 'T', 'G', 'T', 'A', 'T'], ['C', 'T', 'A', 'A', 'T', 'T', 'T', 'G', 'G', 'T', 'G', 'A', 'C', 'T', 'C', 'A', 'A', 'A', 'T', 'T', 'T', 'C', 'A', 'T', 'A', 'A', 'T', 'T', 'G', 'C', 'T', 'T', 'A', 'A', 'T', 'G', 'A', 'A', 'A', 'G', 'C', 'T', 'G', 'A', 'T', 'G', 'T', 'T', 'T', 'T', 'C', 'T', 'T', 'C', 'C', 'C', 'T', 'A', 'C', 'A', 'C', 'C', 'A', 'T', 'A', 'T', 'G', 'T', 'A', 'T'], ['C', 'T', 'A', 'A', 'T', 'T', 'T', 'G', 'G', 'T', 'G', 'A', 'C', 'T', 'T', 'G', 'A', 'A', 'T', 'T', 'T', 'C', 'A', 'T', 'A', 'A', 'T', 'T', 'G', 'C', 'T', 'T', 'A', 'A', 'G', 'G', 'A', 'A', 'G', 'C', 'C', 'T', 'G', 'C', 'T', 'G', 'T', 'T', 'T', 'C', 'C', 'T', 'T', 'C', 'C', 'C', 'A', 'A', 'G', 'A', 'C', 'T', 'A', 'T', 'A', 'T', 'G', 'C', 'A', 'T'], ['C', 'T', 'A', 'A', 'T', 'T', 'G', 'G', 'G', 'G', 'G', 'A', 'C', 'T', 'C', 'A', 'C', 'A', 'T', 'T', 'T', 'T', 'A', 'A', 'A', 'A', 'T', 'T', 'G', 'C', 'T', 'A', 'A', 'C', 'C', 'G', 'A', 'A', 'G', 'C', 'C', 'T', 'G', 'C', 'T', 'G', 'T', 'T', 'T', 'T', 'C', 'T', 'T', 'C', 'T', 'C', 'T', 'A', 'G', 'A', 'C', 'T', 'A', 'T', 'A', 'A', 'G', 'T', 'A', 'T']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.score, 44222) self.assertEqual(alignment.sequences[0].id, "mm9.chr10") self.assertEqual(len(alignment.sequences[0].seq), 129993255) self.assertEqual( alignment.sequences[0].seq[3021104 : 3021104 + 32], "CTGTTAGTGCTGTTTTAATGTACCTCGCAGTA", ) self.assertEqual(alignment[0], "CTGTTAGTGCTGTTTT---AATGTACCTCGCAGTA") self.assertEqual(alignment.sequences[1].id, "cavPor2.scaffold_216473") self.assertEqual(len(alignment.sequences[1].seq), 10026) self.assertEqual( alignment.sequences[1].seq[431 : 431 + 27], "TATAAAAATTTACATTAAGAAAGTAAT" ) self.assertEqual(alignment[1], "-----ATTACTTTCTT---AATGTAAATTTTTATA") self.assertEqual( alignment.sequences[1].annotations["quality"], "554558687467957999989884575" ) self.assertEqual(alignment.sequences[1].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[1].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[1].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[1].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[2].id, "oryCun1.scaffold_156751") self.assertEqual(len(alignment.sequences[2].seq), 4726) self.assertEqual( alignment.sequences[2].seq[4022 : 4022 + 30], "TATAAAATATTACATTGAGAATACTAGCAA", ) self.assertEqual(alignment[2], "TTGCTAGTA--TTCTC---AATGTAATATTTTATA") self.assertEqual( alignment.sequences[2].annotations["quality"], "999979999966656999999999999999", ) self.assertEqual(alignment.sequences[2].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[2].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[2].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[2].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[3].id, "otoGar1.scaffold_334.1-359464") self.assertEqual(len(alignment.sequences[3].seq), 359464) self.assertEqual( alignment.sequences[3].seq[171187 : 171187 + 32], "TATAAAACATTATATTAAGGGAACACCAGCAA", ) self.assertEqual(alignment[3], "TTGCTGGTGTTCCCTT---AATATAATGTTTTATA") self.assertEqual( alignment.sequences[3].annotations["quality"], "99999999999999999999999999999999", ) self.assertEqual(alignment.sequences[3].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[3].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[3].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[3].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[4].id, "calJac1.Contig6394") self.assertEqual(len(alignment.sequences[4].seq), 133105) self.assertEqual( alignment.sequences[4].seq[10692 : 10692 + 30], "TTACTCGTGCCCTTAATATAGCATTTTATA", ) self.assertEqual(alignment[4], "TTACTCGTG--CCCTT---AATATAGCATTTTATA") self.assertEqual(alignment.sequences[4].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[4].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[4].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[4].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[5].id, "hg18.chr6") self.assertEqual(len(alignment.sequences[5].seq), 170899992) self.assertEqual( alignment.sequences[5].seq[155025103 : 155025103 + 30], "TATAAAATGTGATATTAAGAGTACCAGCAA", ) self.assertEqual(alignment[5], "TTGCTGGTA--CTCTT---AATATCACATTTTATA") self.assertEqual(alignment.sequences[5].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[5].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[5].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[5].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[6].id, "panTro2.chr6") self.assertEqual(len(alignment.sequences[6].seq), 173908612) self.assertEqual( alignment.sequences[6].seq[157515157 : 157515157 + 30], "TATAAAATGTGATATTAAGAGTACCAGCAA", ) self.assertEqual(alignment[6], "TTGCTGGTA--CTCTT---AATATCACATTTTATA") self.assertEqual( alignment.sequences[6].annotations["quality"], "999999999999999999999999999999", ) self.assertEqual(alignment.sequences[6].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[6].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[6].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[6].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[7].id, "ponAbe2.chr6") self.assertEqual(len(alignment.sequences[7].seq), 174210431) self.assertEqual( alignment.sequences[7].seq[158037324 : 158037324 + 30], "TATAAAATGTTATATTAAGAGCACCAGCAA", ) self.assertEqual(alignment[7], "TTGCTGGTG--CTCTT---AATATAACATTTTATA") self.assertEqual(alignment.sequences[7].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[7].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[7].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[7].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[8].id, "canFam2.chr1") self.assertEqual(len(alignment.sequences[8].seq), 125616256) self.assertEqual( alignment.sequences[8].seq[47544573 : 47544573 + 25], "TGCTACATTTTGAGAGCACCAGCAA", ) self.assertEqual(alignment[8], "TTGCTGGTGCTCTCAA---AATGTAGCA-------") self.assertEqual( alignment.sequences[8].annotations["quality"], "9999999999999999999999999" ) self.assertEqual(alignment.sequences[8].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[8].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[8].annotations["rightStatus"], "I") self.assertEqual(alignment.sequences[8].annotations["rightCount"], 196) self.assertEqual(alignment.sequences[9].id, "felCat3.scaffold_205680") self.assertEqual(len(alignment.sequences[9].seq), 119354) self.assertEqual( alignment.sequences[9].seq[45961 : 45961 + 25], "TGTTATATTTTGAGAGCACCAGCAA" ) self.assertEqual(alignment[9], "TTGCTGGTGCTCTCAA---AATATAACA-------") self.assertEqual( alignment.sequences[9].annotations["quality"], "8677668566555658876555655" ) self.assertEqual(alignment.sequences[9].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[9].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[9].annotations["rightStatus"], "I") self.assertEqual(alignment.sequences[9].annotations["rightCount"], 6) self.assertEqual(alignment.sequences[10].id, "dasNov1.scaffold_56749") self.assertEqual(len(alignment.sequences[10].seq), 10470) self.assertEqual( alignment.sequences[10].seq[7211 : 7211 + 33], "CATAAAATGTTACATTAATCAGATCACCAGCAA", ) self.assertEqual(alignment[10], "TTGCTGGTG--ATCTGATTAATGTAACATTTTATG") self.assertEqual( alignment.sequences[10].annotations["quality"], "856647736775356546747663745776545", ) self.assertEqual(alignment.sequences[10].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[10].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[10].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[10].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[11].id, "echTel1.scaffold_288249") self.assertEqual(len(alignment.sequences[11].seq), 100002) self.assertEqual( alignment.sequences[11].seq[95225 : 95225 + 21], "CTGTTAATGCTCTGTTTTATG" ) self.assertEqual(alignment[11], "CTGTTAATG--CTCTG------------TTTTATG") self.assertEqual( alignment.sequences[11].annotations["quality"], "999999999999999999999" ) self.assertEqual(alignment.sequences[11].annotations["leftStatus"], "I") self.assertEqual(alignment.sequences[11].annotations["leftCount"], 7564) self.assertEqual(alignment.sequences[11].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[11].annotations["rightCount"], 0) empty = alignment.annotations["empty"][0] (record, segment, status) = empty self.assertEqual(record.id, "ornAna1.chr2") self.assertEqual(len(record.seq), 54797317) self.assertEqual(segment, (40046122, 40040432)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][1] (record, segment, status) = empty self.assertEqual(record.id, "tupBel1.scaffold_114895.1-498454") self.assertEqual(len(record.seq), 498454) self.assertEqual(segment, (324116, 323493)) self.assertEqual(status, "I") self.assertEqual(len(alignment.sequences), 12) self.assertEqual(len(alignment.annotations["empty"]), 2) self.assertEqual( str(alignment), """\ mm9.chr10 3021104 CTGTTAGTGCTGTTTT---AATGTACCTCGCAGTA 3021136 cavPor2.s 458 -----ATTACTTTCTT---AATGTAAATTTTTATA 431 oryCun1.s 4052 TTGCTAGTA--TTCTC---AATGTAATATTTTATA 4022 otoGar1.s 171219 TTGCTGGTGTTCCCTT---AATATAATGTTTTATA 171187 calJac1.C 10692 TTACTCGTG--CCCTT---AATATAGCATTTTATA 10722 hg18.chr6 155025133 TTGCTGGTA--CTCTT---AATATCACATTTTATA 155025103 panTro2.c 157515187 TTGCTGGTA--CTCTT---AATATCACATTTTATA 157515157 ponAbe2.c 158037354 TTGCTGGTG--CTCTT---AATATAACATTTTATA 158037324 canFam2.c 47544598 TTGCTGGTGCTCTCAA---AATGTAGCA------- 47544573 felCat3.s 45986 TTGCTGGTGCTCTCAA---AATATAACA------- 45961 dasNov1.s 7244 TTGCTGGTG--ATCTGATTAATGTAACATTTTATG 7211 echTel1.s 95225 CTGTTAATG--CTCTG------------TTTTATG 95246 """, ) self.assertTrue( np.array_equal( alignment.coordinates, np.array( # fmt: off [[ 3021104, 3021109, 3021113, 3021115, 3021120, 3021120, 3021129, 3021136], [ 458, 458, 454, 452, 447, 447, 438, 431], [ 4052, 4047, 4043, 4043, 4038, 4038, 4029, 4022], [ 171219, 171214, 171210, 171208, 171203, 171203, 171194, 171187], [ 10692, 10697, 10701, 10701, 10706, 10706, 10715, 10722], [155025133, 155025128, 155025124, 155025124, 155025119, 155025119, 155025110, 155025103], [157515187, 157515182, 157515178, 157515178, 157515173, 157515173, 157515164, 157515157], [158037354, 158037349, 158037345, 158037345, 158037340, 158037340, 158037331, 158037324], [ 47544598, 47544593, 47544589, 47544587, 47544582, 47544582, 47544573, 47544573], [ 45986, 45981, 45977, 45975, 45970, 45970, 45961, 45961], [ 7244, 7239, 7235, 7235, 7230, 7227, 7218, 7211], [ 95225, 95230, 95234, 95234, 95239, 95239, 95239, 95246], ] # fmt: on ), ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['C', 'T', 'G', 'T', 'T', 'A', 'G', 'T', 'G', 'C', 'T', 'G', 'T', 'T', 'T', 'T', '-', '-', '-', 'A', 'A', 'T', 'G', 'T', 'A', 'C', 'C', 'T', 'C', 'G', 'C', 'A', 'G', 'T', 'A'], ['-', '-', '-', '-', '-', 'A', 'T', 'T', 'A', 'C', 'T', 'T', 'T', 'C', 'T', 'T', '-', '-', '-', 'A', 'A', 'T', 'G', 'T', 'A', 'A', 'A', 'T', 'T', 'T', 'T', 'T', 'A', 'T', 'A'], ['T', 'T', 'G', 'C', 'T', 'A', 'G', 'T', 'A', '-', '-', 'T', 'T', 'C', 'T', 'C', '-', '-', '-', 'A', 'A', 'T', 'G', 'T', 'A', 'A', 'T', 'A', 'T', 'T', 'T', 'T', 'A', 'T', 'A'], ['T', 'T', 'G', 'C', 'T', 'G', 'G', 'T', 'G', 'T', 'T', 'C', 'C', 'C', 'T', 'T', '-', '-', '-', 'A', 'A', 'T', 'A', 'T', 'A', 'A', 'T', 'G', 'T', 'T', 'T', 'T', 'A', 'T', 'A'], ['T', 'T', 'A', 'C', 'T', 'C', 'G', 'T', 'G', '-', '-', 'C', 'C', 'C', 'T', 'T', '-', '-', '-', 'A', 'A', 'T', 'A', 'T', 'A', 'G', 'C', 'A', 'T', 'T', 'T', 'T', 'A', 'T', 'A'], ['T', 'T', 'G', 'C', 'T', 'G', 'G', 'T', 'A', '-', '-', 'C', 'T', 'C', 'T', 'T', '-', '-', '-', 'A', 'A', 'T', 'A', 'T', 'C', 'A', 'C', 'A', 'T', 'T', 'T', 'T', 'A', 'T', 'A'], ['T', 'T', 'G', 'C', 'T', 'G', 'G', 'T', 'A', '-', '-', 'C', 'T', 'C', 'T', 'T', '-', '-', '-', 'A', 'A', 'T', 'A', 'T', 'C', 'A', 'C', 'A', 'T', 'T', 'T', 'T', 'A', 'T', 'A'], ['T', 'T', 'G', 'C', 'T', 'G', 'G', 'T', 'G', '-', '-', 'C', 'T', 'C', 'T', 'T', '-', '-', '-', 'A', 'A', 'T', 'A', 'T', 'A', 'A', 'C', 'A', 'T', 'T', 'T', 'T', 'A', 'T', 'A'], ['T', 'T', 'G', 'C', 'T', 'G', 'G', 'T', 'G', 'C', 'T', 'C', 'T', 'C', 'A', 'A', '-', '-', '-', 'A', 'A', 'T', 'G', 'T', 'A', 'G', 'C', 'A', '-', '-', '-', '-', '-', '-', '-'], ['T', 'T', 'G', 'C', 'T', 'G', 'G', 'T', 'G', 'C', 'T', 'C', 'T', 'C', 'A', 'A', '-', '-', '-', 'A', 'A', 'T', 'A', 'T', 'A', 'A', 'C', 'A', '-', '-', '-', '-', '-', '-', '-'], ['T', 'T', 'G', 'C', 'T', 'G', 'G', 'T', 'G', '-', '-', 'A', 'T', 'C', 'T', 'G', 'A', 'T', 'T', 'A', 'A', 'T', 'G', 'T', 'A', 'A', 'C', 'A', 'T', 'T', 'T', 'T', 'A', 'T', 'G'], ['C', 'T', 'G', 'T', 'T', 'A', 'A', 'T', 'G', '-', '-', 'C', 'T', 'C', 'T', 'G', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'T', 'T', 'T', 'T', 'A', 'T', 'G']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.score, 43757) self.assertEqual(alignment.sequences[0].id, "mm9.chr10") self.assertEqual(len(alignment.sequences[0].seq), 129993255) self.assertEqual( alignment.sequences[0].seq[3021136 : 3021136 + 44], "AGGCAAATGAGGTGATAAGATTGTGTTTACTCCCTCTGTGCTTG", ) self.assertEqual( alignment[0], "AGGCAAATGAGGTGATAAGA-------TTGTGTT-----TAC----TCCCTCTGTGC----------TTG", ) self.assertEqual(alignment.sequences[1].id, "cavPor2.scaffold_216473") self.assertEqual(len(alignment.sequences[1].seq), 10026) self.assertEqual( alignment.sequences[1].seq[388 : 388 + 43], "catacacacagagaatgAATATATCACTGTTATCTCATCTGCT", ) self.assertEqual( alignment[1], "AG-CAGATGAGATAACAGTG-------ATATATT-----cat----tctctgtgtgt----------atg", ) self.assertEqual( alignment.sequences[1].annotations["quality"], "4996766988786798889867956675666896967579888", ) self.assertEqual(alignment.sequences[1].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[1].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[1].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[1].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[2].id, "oryCun1.scaffold_156751") self.assertEqual(len(alignment.sequences[2].seq), 4726) self.assertEqual( alignment.sequences[2].seq[3980 : 3980 + 42], "CACACAAATAAGAAATAGATGCCCTCATCACCTCATTTGCTT", ) self.assertEqual( alignment[2], "AAGCAAATGAGGTGATGAGG---------GCATC-----TAT----TTCTTATTTGT----------GTG", ) self.assertEqual( alignment.sequences[2].annotations["quality"], "999989999999999999999999999999999999999999", ) self.assertEqual(alignment.sequences[2].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[2].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[2].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[2].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[3].id, "otoGar1.scaffold_334.1-359464") self.assertEqual(len(alignment.sequences[3].seq), 359464) self.assertEqual( alignment.sequences[3].seq[171142 : 171142 + 45], "CACACGTGGGGGACAAGTACATATGTCCTGTGATCTCATTTGTTT", ) self.assertEqual( alignment[3], "AAACAAATGAGATCACA-GG-------ACATATG-----TA--CTTGTCCCCCACGT----------GTG", ) self.assertEqual( alignment.sequences[3].annotations["quality"], "999999999999999999999999999999939999999999999", ) self.assertEqual(alignment.sequences[3].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[3].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[3].annotations["rightStatus"], "I") self.assertEqual(alignment.sequences[3].annotations["rightCount"], 15) self.assertEqual(alignment.sequences[4].id, "calJac1.Contig6394") self.assertEqual(len(alignment.sequences[4].seq), 133105) self.assertEqual( alignment.sequences[4].seq[10722 : 10722 + 45], "AAGCAAATGAGATCACAGCACATGTATATTTTTTCTCCGTGTGTG", ) self.assertEqual( alignment[4], "AAGCAAATGAGATCACA----------GCACATG-----TATATTTTTTCTCCGTGT----------GTG", ) self.assertEqual(alignment.sequences[4].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[4].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[4].annotations["rightStatus"], "I") self.assertEqual(alignment.sequences[4].annotations["rightCount"], 15) self.assertEqual(alignment.sequences[5].id, "hg18.chr6") self.assertEqual(len(alignment.sequences[5].seq), 170899992) self.assertEqual( alignment.sequences[5].seq[155025056 : 155025056 + 47], "CACACACAGAGAAAAAAACATATATGCCCTTGTGATCTCATTTGTTT", ) self.assertEqual( alignment[5], "AAACAAATGAGATCACAAGG-------GCATATA-----TGT-TTTTTTCTCTGTGT----------GTG", ) self.assertEqual(alignment.sequences[5].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[5].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[5].annotations["rightStatus"], "I") self.assertEqual(alignment.sequences[5].annotations["rightCount"], 15) self.assertEqual(alignment.sequences[6].id, "panTro2.chr6") self.assertEqual(len(alignment.sequences[6].seq), 173908612) self.assertEqual( alignment.sequences[6].seq[157515110 : 157515110 + 47], "CACACACAGAGAAAAAAACATATATGCCCTTGTGATCTCATTTGTTT", ) self.assertEqual( alignment[6], "AAACAAATGAGATCACAAGG-------GCATATA-----TGT-TTTTTTCTCTGTGT----------GTG", ) self.assertEqual( alignment.sequences[6].annotations["quality"], "99999999999999999999999999999999999999999999999", ) self.assertEqual(alignment.sequences[6].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[6].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[6].annotations["rightStatus"], "I") self.assertEqual(alignment.sequences[6].annotations["rightCount"], 15) self.assertEqual(alignment.sequences[7].id, "ponAbe2.chr6") self.assertEqual(len(alignment.sequences[7].seq), 174210431) self.assertEqual( alignment.sequences[7].seq[158037277 : 158037277 + 47], "CACACACAGAGAAAAAAATACATATGCCCTTGTGATCTCATTTGTTT", ) self.assertEqual( alignment[7], "AAACAAATGAGATCACAAGG-------GCATATG-----TAT-TTTTTTCTCTGTGT----------GTG", ) self.assertEqual(alignment.sequences[7].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[7].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[7].annotations["rightStatus"], "I") self.assertEqual(alignment.sequences[7].annotations["rightCount"], 15) self.assertEqual(alignment.sequences[8].id, "eriEur1.scaffold_266115") self.assertEqual(len(alignment.sequences[8].seq), 4589) self.assertEqual( alignment.sequences[8].seq[358 : 358 + 65], "taaataataagataagatgaaagCATAGCATGTATTTTCTtgccctctccttctctgtctctgtc", ) self.assertEqual( alignment[8], "taaataataagataagatgaaagCATAGCATGTA-----TTTTCTtgccctctccttctctgtctctgtc", ) self.assertEqual( alignment.sequences[8].annotations["quality"], "99999999999999999999999999999999999999999999999999999999999999999", ) self.assertEqual(alignment.sequences[8].annotations["leftStatus"], "N") self.assertEqual(alignment.sequences[8].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[8].annotations["rightStatus"], "I") self.assertEqual(alignment.sequences[8].annotations["rightCount"], 9) self.assertEqual(alignment.sequences[9].id, "canFam2.chr1") self.assertEqual(len(alignment.sequences[9].seq), 125616256) self.assertEqual( alignment.sequences[9].seq[47544326 : 47544326 + 51], "CACAGACCCCACACAGAGAGAAAGCATATACACACGGTATCTCATTTTCTa", ) self.assertEqual( alignment[9], "tAGAAAATGAGATACC-----------GTGTGTA-----TATGCTTTCTCTCTGTGT---GGGGTCTGTG", ) self.assertEqual( alignment.sequences[9].annotations["quality"], "999999999999999999999999999999999999999999999999999", ) self.assertEqual(alignment.sequences[9].annotations["leftStatus"], "I") self.assertEqual(alignment.sequences[9].annotations["leftCount"], 196) self.assertEqual(alignment.sequences[9].annotations["rightStatus"], "I") self.assertEqual(alignment.sequences[9].annotations["rightCount"], 9) self.assertEqual(alignment.sequences[10].id, "felCat3.scaffold_205680") self.assertEqual(len(alignment.sequences[10].seq), 119354) self.assertEqual( alignment.sequences[10].seq[45904 : 45904 + 51], "CACAGACACCACACAGAGAGGAAGAATACACGTGTCTTATCTCATTTGCTT", ) self.assertEqual( alignment[10], "AAGCAAATGAGATAAG-----------ACACGTG-----TATTCTTCCTCTCTGTGT---GGTGTCTGTG", ) self.assertEqual( alignment.sequences[10].annotations["quality"], "975559665645435353463242434515353544222333635339999", ) self.assertEqual(alignment.sequences[10].annotations["leftStatus"], "I") self.assertEqual(alignment.sequences[10].annotations["leftCount"], 6) self.assertEqual(alignment.sequences[10].annotations["rightStatus"], "I") self.assertEqual(alignment.sequences[10].annotations["rightCount"], 9) self.assertEqual(alignment.sequences[11].id, "dasNov1.scaffold_56749") self.assertEqual(len(alignment.sequences[11].seq), 10470) self.assertEqual( alignment.sequences[11].seq[7165 : 7165 + 46], "TACACAGAGAAAGAATATTTATTTGCCCTGGTCCTCTCACTTTCCT", ) self.assertEqual( alignment[11], "AGGAAAGTGAGAGGACCAGG-------GCAAATA-----AATATTCTTTCTCTGTGT----------A--", ) self.assertEqual( alignment.sequences[11].annotations["quality"], "5556976455665765856867685558586864578595356565", ) self.assertEqual(alignment.sequences[11].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[11].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[11].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[11].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[12].id, "echTel1.scaffold_288249") self.assertEqual(len(alignment.sequences[12].seq), 100002) self.assertEqual( alignment.sequences[12].seq[95246 : 95246 + 51], "AAGAAGGTGAGATGACAAGGGTGTATAGATAGGATATTCTTGCTTTGGGTG", ) self.assertEqual( alignment[12], "AAGAAGGTGAGATGACAAGG-------GTGTATAGATAGGATATTCTTGCTTTGGGT----------G--", ) self.assertEqual( alignment.sequences[12].annotations["quality"], "999999999999999999999999999999999999999999999999999", ) self.assertEqual(alignment.sequences[12].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[12].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[12].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[12].annotations["rightCount"], 0) empty = alignment.annotations["empty"][0] (record, segment, status) = empty self.assertEqual(record.id, "ornAna1.chr2") self.assertEqual(len(record.seq), 54797317) self.assertEqual(segment, (40046122, 40040432)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][1] (record, segment, status) = empty self.assertEqual(record.id, "tupBel1.scaffold_114895.1-498454") self.assertEqual(len(record.seq), 498454) self.assertEqual(segment, (324116, 323493)) self.assertEqual(status, "I") self.assertEqual(len(alignment.sequences), 13) self.assertEqual(len(alignment.annotations["empty"]), 2) self.assertEqual( str(alignment), """\ mm9.chr10 3021136 AGGCAAATGAGGTGATAAGA-------TTGTGTT-----TAC----TCCCTCTGTGC--- cavPor2.s 431 AG-CAGATGAGATAACAGTG-------ATATATT-----cat----tctctgtgtgt--- oryCun1.s 4022 AAGCAAATGAGGTGATGAGG---------GCATC-----TAT----TTCTTATTTGT--- otoGar1.s 171187 AAACAAATGAGATCACA-GG-------ACATATG-----TA--CTTGTCCCCCACGT--- calJac1.C 10722 AAGCAAATGAGATCACA----------GCACATG-----TATATTTTTTCTCCGTGT--- hg18.chr6 155025103 AAACAAATGAGATCACAAGG-------GCATATA-----TGT-TTTTTTCTCTGTGT--- panTro2.c 157515157 AAACAAATGAGATCACAAGG-------GCATATA-----TGT-TTTTTTCTCTGTGT--- ponAbe2.c 158037324 AAACAAATGAGATCACAAGG-------GCATATG-----TAT-TTTTTTCTCTGTGT--- eriEur1.s 358 taaataataagataagatgaaagCATAGCATGTA-----TTTTCTtgccctctccttctc canFam2.c 47544377 tAGAAAATGAGATACC-----------GTGTGTA-----TATGCTTTCTCTCTGTGT--- felCat3.s 45955 AAGCAAATGAGATAAG-----------ACACGTG-----TATTCTTCCTCTCTGTGT--- dasNov1.s 7211 AGGAAAGTGAGAGGACCAGG-------GCAAATA-----AATATTCTTTCTCTGTGT--- echTel1.s 95246 AAGAAGGTGAGATGACAAGG-------GTGTATAGATAGGATATTCTTGCTTTGGGT--- mm9.chr10 3021177 -------TTG 3021180 cavPor2.s 391 -------atg 388 oryCun1.s 3983 -------GTG 3980 otoGar1.s 171145 -------GTG 171142 calJac1.C 10764 -------GTG 10767 hg18.chr6 155025059 -------GTG 155025056 panTro2.c 157515113 -------GTG 157515110 ponAbe2.c 158037280 -------GTG 158037277 eriEur1.s 413 tgtctctgtc 423 canFam2.c 47544336 GGGGTCTGTG 47544326 felCat3.s 45914 GGTGTCTGTG 45904 dasNov1.s 7166 -------A-- 7165 echTel1.s 95296 -------G-- 95297 """, ) self.assertTrue( np.array_equal( alignment.coordinates, np.array( # fmt: off [[ 3021136, 3021138, 3021139, 3021152, 3021153, 3021154, 3021156, 3021156, 3021158, 3021163, 3021163, 3021165, 3021166, 3021166, 3021166, 3021177, 3021177, 3021177, 3021178, 3021180], [ 431, 429, 429, 416, 415, 414, 412, 412, 410, 405, 405, 403, 402, 402, 402, 391, 391, 391, 390, 388], [ 4022, 4020, 4019, 4006, 4005, 4004, 4002, 4002, 4002, 3997, 3997, 3995, 3994, 3994, 3994, 3983, 3983, 3983, 3982, 3980], [ 171187, 171185, 171184, 171171, 171170, 171170, 171168, 171168, 171166, 171161, 171161, 171159, 171159, 171159, 171156, 171145, 171145, 171145, 171144, 171142], [ 10722, 10724, 10725, 10738, 10739, 10739, 10739, 10739, 10741, 10746, 10746, 10748, 10749, 10750, 10753, 10764, 10764, 10764, 10765, 10767], [155025103, 155025101, 155025100, 155025087, 155025086, 155025085, 155025083, 155025083, 155025081, 155025076, 155025076, 155025074, 155025073, 155025073, 155025070, 155025059, 155025059, 155025059, 155025058, 155025056], [157515157, 157515155, 157515154, 157515141, 157515140, 157515139, 157515137, 157515137, 157515135, 157515130, 157515130, 157515128, 157515127, 157515127, 157515124, 157515113, 157515113, 157515113, 157515112, 157515110], [158037324, 158037322, 158037321, 158037308, 158037307, 158037306, 158037304, 158037304, 158037302, 158037297, 158037297, 158037295, 158037294, 158037294, 158037291, 158037280, 158037280, 158037280, 158037279, 158037277], [ 358, 360, 361, 374, 375, 376, 378, 385, 387, 392, 392, 394, 395, 396, 399, 410, 413, 420, 421, 423], [ 47544377, 47544375, 47544374, 47544361, 47544361, 47544361, 47544361, 47544361, 47544359, 47544354, 47544354, 47544352, 47544351, 47544350, 47544347, 47544336, 47544336, 47544329, 47544328, 47544326], [ 45955, 45953, 45952, 45939, 45939, 45939, 45939, 45939, 45937, 45932, 45932, 45930, 45929, 45928, 45925, 45914, 45914, 45907, 45906, 45904], [ 7211, 7209, 7208, 7195, 7194, 7193, 7191, 7191, 7189, 7184, 7184, 7182, 7181, 7180, 7177, 7166, 7166, 7166, 7165, 7165], [ 95246, 95248, 95249, 95262, 95263, 95264, 95266, 95266, 95268, 95273, 95278, 95280, 95281, 95282, 95285, 95296, 95296, 95296, 95297, 95297], ] # fmt: on ), ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['A', 'G', 'G', 'C', 'A', 'A', 'A', 'T', 'G', 'A', 'G', 'G', 'T', 'G', 'A', 'T', 'A', 'A', 'G', 'A', '-', '-', '-', '-', '-', '-', '-', 'T', 'T', 'G', 'T', 'G', 'T', 'T', '-', '-', '-', '-', '-', 'T', 'A', 'C', '-', '-', '-', '-', 'T', 'C', 'C', 'C', 'T', 'C', 'T', 'G', 'T', 'G', 'C', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'T', 'T', 'G'], ['A', 'G', '-', 'C', 'A', 'G', 'A', 'T', 'G', 'A', 'G', 'A', 'T', 'A', 'A', 'C', 'A', 'G', 'T', 'G', '-', '-', '-', '-', '-', '-', '-', 'A', 'T', 'A', 'T', 'A', 'T', 'T', '-', '-', '-', '-', '-', 'c', 'a', 't', '-', '-', '-', '-', 't', 'c', 't', 'c', 't', 'g', 't', 'g', 't', 'g', 't', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'a', 't', 'g'], ['A', 'A', 'G', 'C', 'A', 'A', 'A', 'T', 'G', 'A', 'G', 'G', 'T', 'G', 'A', 'T', 'G', 'A', 'G', 'G', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'G', 'C', 'A', 'T', 'C', '-', '-', '-', '-', '-', 'T', 'A', 'T', '-', '-', '-', '-', 'T', 'T', 'C', 'T', 'T', 'A', 'T', 'T', 'T', 'G', 'T', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'G', 'T', 'G'], ['A', 'A', 'A', 'C', 'A', 'A', 'A', 'T', 'G', 'A', 'G', 'A', 'T', 'C', 'A', 'C', 'A', '-', 'G', 'G', '-', '-', '-', '-', '-', '-', '-', 'A', 'C', 'A', 'T', 'A', 'T', 'G', '-', '-', '-', '-', '-', 'T', 'A', '-', '-', 'C', 'T', 'T', 'G', 'T', 'C', 'C', 'C', 'C', 'C', 'A', 'C', 'G', 'T', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'G', 'T', 'G'], ['A', 'A', 'G', 'C', 'A', 'A', 'A', 'T', 'G', 'A', 'G', 'A', 'T', 'C', 'A', 'C', 'A', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'G', 'C', 'A', 'C', 'A', 'T', 'G', '-', '-', '-', '-', '-', 'T', 'A', 'T', 'A', 'T', 'T', 'T', 'T', 'T', 'T', 'C', 'T', 'C', 'C', 'G', 'T', 'G', 'T', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'G', 'T', 'G'], ['A', 'A', 'A', 'C', 'A', 'A', 'A', 'T', 'G', 'A', 'G', 'A', 'T', 'C', 'A', 'C', 'A', 'A', 'G', 'G', '-', '-', '-', '-', '-', '-', '-', 'G', 'C', 'A', 'T', 'A', 'T', 'A', '-', '-', '-', '-', '-', 'T', 'G', 'T', '-', 'T', 'T', 'T', 'T', 'T', 'T', 'C', 'T', 'C', 'T', 'G', 'T', 'G', 'T', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'G', 'T', 'G'], ['A', 'A', 'A', 'C', 'A', 'A', 'A', 'T', 'G', 'A', 'G', 'A', 'T', 'C', 'A', 'C', 'A', 'A', 'G', 'G', '-', '-', '-', '-', '-', '-', '-', 'G', 'C', 'A', 'T', 'A', 'T', 'A', '-', '-', '-', '-', '-', 'T', 'G', 'T', '-', 'T', 'T', 'T', 'T', 'T', 'T', 'C', 'T', 'C', 'T', 'G', 'T', 'G', 'T', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'G', 'T', 'G'], ['A', 'A', 'A', 'C', 'A', 'A', 'A', 'T', 'G', 'A', 'G', 'A', 'T', 'C', 'A', 'C', 'A', 'A', 'G', 'G', '-', '-', '-', '-', '-', '-', '-', 'G', 'C', 'A', 'T', 'A', 'T', 'G', '-', '-', '-', '-', '-', 'T', 'A', 'T', '-', 'T', 'T', 'T', 'T', 'T', 'T', 'C', 'T', 'C', 'T', 'G', 'T', 'G', 'T', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'G', 'T', 'G'], ['t', 'a', 'a', 'a', 't', 'a', 'a', 't', 'a', 'a', 'g', 'a', 't', 'a', 'a', 'g', 'a', 't', 'g', 'a', 'a', 'a', 'g', 'C', 'A', 'T', 'A', 'G', 'C', 'A', 'T', 'G', 'T', 'A', '-', '-', '-', '-', '-', 'T', 'T', 'T', 'T', 'C', 'T', 't', 'g', 'c', 'c', 'c', 't', 'c', 't', 'c', 'c', 't', 't', 'c', 't', 'c', 't', 'g', 't', 'c', 't', 'c', 't', 'g', 't', 'c'], ['t', 'A', 'G', 'A', 'A', 'A', 'A', 'T', 'G', 'A', 'G', 'A', 'T', 'A', 'C', 'C', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'G', 'T', 'G', 'T', 'G', 'T', 'A', '-', '-', '-', '-', '-', 'T', 'A', 'T', 'G', 'C', 'T', 'T', 'T', 'C', 'T', 'C', 'T', 'C', 'T', 'G', 'T', 'G', 'T', '-', '-', '-', 'G', 'G', 'G', 'G', 'T', 'C', 'T', 'G', 'T', 'G'], ['A', 'A', 'G', 'C', 'A', 'A', 'A', 'T', 'G', 'A', 'G', 'A', 'T', 'A', 'A', 'G', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'A', 'C', 'A', 'C', 'G', 'T', 'G', '-', '-', '-', '-', '-', 'T', 'A', 'T', 'T', 'C', 'T', 'T', 'C', 'C', 'T', 'C', 'T', 'C', 'T', 'G', 'T', 'G', 'T', '-', '-', '-', 'G', 'G', 'T', 'G', 'T', 'C', 'T', 'G', 'T', 'G'], ['A', 'G', 'G', 'A', 'A', 'A', 'G', 'T', 'G', 'A', 'G', 'A', 'G', 'G', 'A', 'C', 'C', 'A', 'G', 'G', '-', '-', '-', '-', '-', '-', '-', 'G', 'C', 'A', 'A', 'A', 'T', 'A', '-', '-', '-', '-', '-', 'A', 'A', 'T', 'A', 'T', 'T', 'C', 'T', 'T', 'T', 'C', 'T', 'C', 'T', 'G', 'T', 'G', 'T', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'A', '-', '-'], ['A', 'A', 'G', 'A', 'A', 'G', 'G', 'T', 'G', 'A', 'G', 'A', 'T', 'G', 'A', 'C', 'A', 'A', 'G', 'G', '-', '-', '-', '-', '-', '-', '-', 'G', 'T', 'G', 'T', 'A', 'T', 'A', 'G', 'A', 'T', 'A', 'G', 'G', 'A', 'T', 'A', 'T', 'T', 'C', 'T', 'T', 'G', 'C', 'T', 'T', 'T', 'G', 'G', 'G', 'T', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'G', '-', '-']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.score, 32886) self.assertEqual(alignment.sequences[0].id, "mm9.chr10") self.assertEqual(len(alignment.sequences[0].seq), 129993255) self.assertEqual( alignment.sequences[0].seq[3021180 : 3021180 + 24], "TCCCAGAGAGTCTGATAGGAGGAG", ) self.assertEqual( alignment[0], "-------------------TCCC-------AGAGAGTCTGA-TAGGAGGAG" ) self.assertEqual(alignment.sequences[1].id, "cavPor2.scaffold_216473") self.assertEqual(len(alignment.sequences[1].seq), 10026) self.assertEqual( alignment.sequences[1].seq[356 : 356 + 32], "TACTTTATACTCAGAGCCACTATACAAaggca", ) self.assertEqual( alignment[1], "-------------------tgcctTTGTATAGTGGCTCTGAGTATAAAGTA" ) self.assertEqual( alignment.sequences[1].annotations["quality"], "67576649966655666885655548785776", ) self.assertEqual(alignment.sequences[1].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[1].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[1].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[1].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[2].id, "oryCun1.scaffold_156751") self.assertEqual(len(alignment.sequences[2].seq), 4726) self.assertEqual( alignment.sequences[2].seq[3953 : 3953 + 27], "TATATTCAGAAATGCTATACACAGGCA" ) self.assertEqual( alignment[2], "-------------------TGCCTGTGTATAGCATTTCTGAATATA-----" ) self.assertEqual( alignment.sequences[2].annotations["quality"], "999999999999999999999999999" ) self.assertEqual(alignment.sequences[2].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[2].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[2].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[2].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[3].id, "ponAbe2.chr6") self.assertEqual(len(alignment.sequences[3].seq), 174210431) self.assertEqual( alignment.sequences[3].seq[158037237 : 158037237 + 25], "TACTTCATATTCATACACACTCAGA", ) self.assertEqual( alignment[3], "-----------------------TCTG---AGTGTGTATGAATATGAAGTA" ) self.assertEqual(alignment.sequences[3].annotations["leftStatus"], "I") self.assertEqual(alignment.sequences[3].annotations["leftCount"], 15) self.assertEqual(alignment.sequences[3].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[3].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[4].id, "panTro2.chr6") self.assertEqual(len(alignment.sequences[4].seq), 173908612) self.assertEqual( alignment.sequences[4].seq[157515070 : 157515070 + 25], "TACTTCATATTCATACATACTCAGA", ) self.assertEqual( alignment[4], "-----------------------TCTG---AGTATGTATGAATATGAAGTA" ) self.assertEqual( alignment.sequences[4].annotations["quality"], "9999999999999999999999999" ) self.assertEqual(alignment.sequences[4].annotations["leftStatus"], "I") self.assertEqual(alignment.sequences[4].annotations["leftCount"], 15) self.assertEqual(alignment.sequences[4].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[4].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[5].id, "hg18.chr6") self.assertEqual(len(alignment.sequences[5].seq), 170899992) self.assertEqual( alignment.sequences[5].seq[155025016 : 155025016 + 25], "TACTTCATATTCATACATACTCAGA", ) self.assertEqual( alignment[5], "-----------------------TCTG---AGTATGTATGAATATGAAGTA" ) self.assertEqual(alignment.sequences[5].annotations["leftStatus"], "I") self.assertEqual(alignment.sequences[5].annotations["leftCount"], 15) self.assertEqual(alignment.sequences[5].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[5].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[6].id, "calJac1.Contig6394") self.assertEqual(len(alignment.sequences[6].seq), 133105) self.assertEqual( alignment.sequences[6].seq[10782 : 10782 + 25], "TCTGAGTATGTCTGAATATGAAGTG" ) self.assertEqual( alignment[6], "-----------------------TCTG---AGTATGTCTGAATATGAAGTG" ) self.assertEqual(alignment.sequences[6].annotations["leftStatus"], "I") self.assertEqual(alignment.sequences[6].annotations["leftCount"], 15) self.assertEqual(alignment.sequences[6].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[6].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[7].id, "otoGar1.scaffold_334.1-359464") self.assertEqual(len(alignment.sequences[7].seq), 359464) self.assertEqual( alignment.sequences[7].seq[171102 : 171102 + 25], "CACATCATGTTCAGACACACTTAGA", ) self.assertEqual( alignment[7], "-----------------------TCTA---AGTGTGTCTGAACATGATGTG" ) self.assertEqual( alignment.sequences[7].annotations["quality"], "9999999999999999999999999" ) self.assertEqual(alignment.sequences[7].annotations["leftStatus"], "I") self.assertEqual(alignment.sequences[7].annotations["leftCount"], 15) self.assertEqual(alignment.sequences[7].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[7].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[8].id, "tupBel1.scaffold_114895.1-498454") self.assertEqual(len(alignment.sequences[8].seq), 498454) self.assertEqual( alignment.sequences[8].seq[323468 : 323468 + 25], "TACCTCAAGTTCAGACACTCAGAGA", ) self.assertEqual( alignment[8], "-----------------------TCTC---TGAGTGTCTGAACTTGAGGTA" ) self.assertEqual( alignment.sequences[8].annotations["quality"], "9999999999999999999999999" ) self.assertEqual(alignment.sequences[8].annotations["leftStatus"], "I") self.assertEqual(alignment.sequences[8].annotations["leftCount"], 623) self.assertEqual(alignment.sequences[8].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[8].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[9].id, "eriEur1.scaffold_266115") self.assertEqual(len(alignment.sequences[9].seq), 4589) self.assertEqual( alignment.sequences[9].seq[432 : 432 + 19], "TCTCAGTGTGTCTGACCAG" ) self.assertEqual( alignment[9], "-----------------------TCTC---AGTGTGTCTGACCAG------" ) self.assertEqual( alignment.sequences[9].annotations["quality"], "9999999999999999999" ) self.assertEqual(alignment.sequences[9].annotations["leftStatus"], "I") self.assertEqual(alignment.sequences[9].annotations["leftCount"], 9) self.assertEqual(alignment.sequences[9].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[9].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[10].id, "canFam2.chr1") self.assertEqual(len(alignment.sequences[10].seq), 125616256) self.assertEqual( alignment.sequences[10].seq[47544292 : 47544292 + 25], "TACCTCACATTCAGACACACTCAGA", ) self.assertEqual( alignment[10], "-----------------------TCTG---AGTGTGTCTGAATGTGAGGTA" ) self.assertEqual( alignment.sequences[10].annotations["quality"], "9999999999999999999999999" ) self.assertEqual(alignment.sequences[10].annotations["leftStatus"], "I") self.assertEqual(alignment.sequences[10].annotations["leftCount"], 9) self.assertEqual(alignment.sequences[10].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[10].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[11].id, "felCat3.scaffold_205680") self.assertEqual(len(alignment.sequences[11].seq), 119354) self.assertEqual( alignment.sequences[11].seq[45870 : 45870 + 25], "CACCTCACATTCAGGAACACTCAGA" ) self.assertEqual( alignment[11], "-----------------------TCTG---AGTGTTCCTGAATGTGAGGTG" ) self.assertEqual( alignment.sequences[11].annotations["quality"], "9999999999999999999999999" ) self.assertEqual(alignment.sequences[11].annotations["leftStatus"], "I") self.assertEqual(alignment.sequences[11].annotations["leftCount"], 9) self.assertEqual(alignment.sequences[11].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[11].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[12].id, "dasNov1.scaffold_56749") self.assertEqual(len(alignment.sequences[12].seq), 10470) self.assertEqual( alignment.sequences[12].seq[7118 : 7118 + 47], "TACCTCAAGTTCAGACACGCTCAGAAATGCTCCGCAAAGGCACACAA", ) self.assertEqual( alignment[12], "T-TGTGTGCCTTTGCGGAGCATTTCTG---AGCGTGTCTGAACTTGAGGTA" ) self.assertEqual( alignment.sequences[12].annotations["quality"], "73659557766555777595699547965955937797755656587", ) self.assertEqual(alignment.sequences[12].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[12].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[12].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[12].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[13].id, "echTel1.scaffold_288249") self.assertEqual(len(alignment.sequences[13].seq), 100002) self.assertEqual( alignment.sequences[13].seq[95297 : 95297 + 48], "TGCCCAGGACTGCGCATGGTATTTCTTGGTGTGTCTGAAGGTGAGATA", ) self.assertEqual( alignment[13], "TGCCCAGGACTGCGCATGGTATTTCTT---GGTGTGTCTGAAGGTGAGATA" ) self.assertEqual( alignment.sequences[13].annotations["quality"], "999999999999999999999999999999999999999999999999", ) self.assertEqual(alignment.sequences[13].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[13].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[13].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[13].annotations["rightCount"], 0) empty = alignment.annotations["empty"][0] (record, segment, status) = empty self.assertEqual(record.id, "ornAna1.chr2") self.assertEqual(len(record.seq), 54797317) self.assertEqual(segment, (40046122, 40040432)) self.assertEqual(status, "I") self.assertEqual(len(alignment.sequences), 14) self.assertEqual(len(alignment.annotations["empty"]), 1) self.assertEqual( str(alignment), """\ mm9.chr10 3021180 -------------------TCCC-------AGAGAGTCTGA-TAGGAGGAG cavPor2.s 388 -------------------tgcctTTGTATAGTGGCTCTGAGTATAAAGTA oryCun1.s 3980 -------------------TGCCTGTGTATAGCATTTCTGAATATA----- ponAbe2.c 158037262 -----------------------TCTG---AGTGTGTATGAATATGAAGTA panTro2.c 157515095 -----------------------TCTG---AGTATGTATGAATATGAAGTA hg18.chr6 155025041 -----------------------TCTG---AGTATGTATGAATATGAAGTA calJac1.C 10782 -----------------------TCTG---AGTATGTCTGAATATGAAGTG otoGar1.s 171127 -----------------------TCTA---AGTGTGTCTGAACATGATGTG tupBel1.s 323493 -----------------------TCTC---TGAGTGTCTGAACTTGAGGTA eriEur1.s 432 -----------------------TCTC---AGTGTGTCTGACCAG------ canFam2.c 47544317 -----------------------TCTG---AGTGTGTCTGAATGTGAGGTA felCat3.s 45895 -----------------------TCTG---AGTGTTCCTGAATGTGAGGTG dasNov1.s 7165 T-TGTGTGCCTTTGCGGAGCATTTCTG---AGCGTGTCTGAACTTGAGGTA echTel1.s 95297 TGCCCAGGACTGCGCATGGTATTTCTT---GGTGTGTCTGAAGGTGAGATA mm9.chr10 3021204 cavPor2.s 356 oryCun1.s 3953 ponAbe2.c 158037237 panTro2.c 157515070 hg18.chr6 155025016 calJac1.C 10807 otoGar1.s 171102 tupBel1.s 323468 eriEur1.s 451 canFam2.c 47544292 felCat3.s 45870 dasNov1.s 7118 echTel1.s 95345 """, ) self.assertTrue( np.array_equal( alignment.coordinates, np.array( # fmt: off [[ 3021180, 3021180, 3021180, 3021180, 3021184, 3021184, 3021184, 3021195, 3021195, 3021198, 3021199, 3021204], [ 388, 388, 388, 388, 384, 380, 377, 366, 365, 362, 361, 356], [ 3980, 3980, 3980, 3980, 3976, 3972, 3969, 3958, 3957, 3954, 3953, 3953], [158037262, 158037262, 158037262, 158037262, 158037262, 158037258, 158037258, 158037247, 158037246, 158037243, 158037242, 158037237], [157515095, 157515095, 157515095, 157515095, 157515095, 157515091, 157515091, 157515080, 157515079, 157515076, 157515075, 157515070], [155025041, 155025041, 155025041, 155025041, 155025041, 155025037, 155025037, 155025026, 155025025, 155025022, 155025021, 155025016], [ 10782, 10782, 10782, 10782, 10782, 10786, 10786, 10797, 10798, 10801, 10802, 10807], [ 171127, 171127, 171127, 171127, 171127, 171123, 171123, 171112, 171111, 171108, 171107, 171102], [ 323493, 323493, 323493, 323493, 323493, 323489, 323489, 323478, 323477, 323474, 323473, 323468], [ 432, 432, 432, 432, 432, 436, 436, 447, 448, 451, 451, 451], [ 47544317, 47544317, 47544317, 47544317, 47544317, 47544313, 47544313, 47544302, 47544301, 47544298, 47544297, 47544292], [ 45895, 45895, 45895, 45895, 45895, 45891, 45891, 45880, 45879, 45876, 45875, 45870], [ 7165, 7164, 7164, 7147, 7143, 7139, 7139, 7128, 7127, 7124, 7123, 7118], [ 95297, 95298, 95299, 95316, 95320, 95324, 95324, 95335, 95336, 95339, 95340, 95345], ] # fmt: on ), ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'T', 'C', 'C', 'C', '-', '-', '-', '-', '-', '-', '-', 'A', 'G', 'A', 'G', 'A', 'G', 'T', 'C', 'T', 'G', 'A', '-', 'T', 'A', 'G', 'G', 'A', 'G', 'G', 'A', 'G'], ['-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 't', 'g', 'c', 'c', 't', 'T', 'T', 'G', 'T', 'A', 'T', 'A', 'G', 'T', 'G', 'G', 'C', 'T', 'C', 'T', 'G', 'A', 'G', 'T', 'A', 'T', 'A', 'A', 'A', 'G', 'T', 'A'], ['-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'T', 'G', 'C', 'C', 'T', 'G', 'T', 'G', 'T', 'A', 'T', 'A', 'G', 'C', 'A', 'T', 'T', 'T', 'C', 'T', 'G', 'A', 'A', 'T', 'A', 'T', 'A', '-', '-', '-', '-', '-'], ['-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'T', 'C', 'T', 'G', '-', '-', '-', 'A', 'G', 'T', 'G', 'T', 'G', 'T', 'A', 'T', 'G', 'A', 'A', 'T', 'A', 'T', 'G', 'A', 'A', 'G', 'T', 'A'], ['-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'T', 'C', 'T', 'G', '-', '-', '-', 'A', 'G', 'T', 'A', 'T', 'G', 'T', 'A', 'T', 'G', 'A', 'A', 'T', 'A', 'T', 'G', 'A', 'A', 'G', 'T', 'A'], ['-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'T', 'C', 'T', 'G', '-', '-', '-', 'A', 'G', 'T', 'A', 'T', 'G', 'T', 'A', 'T', 'G', 'A', 'A', 'T', 'A', 'T', 'G', 'A', 'A', 'G', 'T', 'A'], ['-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'T', 'C', 'T', 'G', '-', '-', '-', 'A', 'G', 'T', 'A', 'T', 'G', 'T', 'C', 'T', 'G', 'A', 'A', 'T', 'A', 'T', 'G', 'A', 'A', 'G', 'T', 'G'], ['-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'T', 'C', 'T', 'A', '-', '-', '-', 'A', 'G', 'T', 'G', 'T', 'G', 'T', 'C', 'T', 'G', 'A', 'A', 'C', 'A', 'T', 'G', 'A', 'T', 'G', 'T', 'G'], ['-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'T', 'C', 'T', 'C', '-', '-', '-', 'T', 'G', 'A', 'G', 'T', 'G', 'T', 'C', 'T', 'G', 'A', 'A', 'C', 'T', 'T', 'G', 'A', 'G', 'G', 'T', 'A'], ['-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'T', 'C', 'T', 'C', '-', '-', '-', 'A', 'G', 'T', 'G', 'T', 'G', 'T', 'C', 'T', 'G', 'A', 'C', 'C', 'A', 'G', '-', '-', '-', '-', '-', '-'], ['-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'T', 'C', 'T', 'G', '-', '-', '-', 'A', 'G', 'T', 'G', 'T', 'G', 'T', 'C', 'T', 'G', 'A', 'A', 'T', 'G', 'T', 'G', 'A', 'G', 'G', 'T', 'A'], ['-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'T', 'C', 'T', 'G', '-', '-', '-', 'A', 'G', 'T', 'G', 'T', 'T', 'C', 'C', 'T', 'G', 'A', 'A', 'T', 'G', 'T', 'G', 'A', 'G', 'G', 'T', 'G'], ['T', '-', 'T', 'G', 'T', 'G', 'T', 'G', 'C', 'C', 'T', 'T', 'T', 'G', 'C', 'G', 'G', 'A', 'G', 'C', 'A', 'T', 'T', 'T', 'C', 'T', 'G', '-', '-', '-', 'A', 'G', 'C', 'G', 'T', 'G', 'T', 'C', 'T', 'G', 'A', 'A', 'C', 'T', 'T', 'G', 'A', 'G', 'G', 'T', 'A'], ['T', 'G', 'C', 'C', 'C', 'A', 'G', 'G', 'A', 'C', 'T', 'G', 'C', 'G', 'C', 'A', 'T', 'G', 'G', 'T', 'A', 'T', 'T', 'T', 'C', 'T', 'T', '-', '-', '-', 'G', 'G', 'T', 'G', 'T', 'G', 'T', 'C', 'T', 'G', 'A', 'A', 'G', 'G', 'T', 'G', 'A', 'G', 'A', 'T', 'A']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.score, 309116) self.assertEqual(alignment.sequences[0].id, "mm9.chr10") self.assertEqual(len(alignment.sequences[0].seq), 129993255) self.assertEqual( alignment.sequences[0].seq[3021204 : 3021204 + 71], "TGCACTGGTTTTCCTGCAGTGGTTCTCAGTAATAGGAAGACAACAGAATTTGAAGTATCCGGCTTTGGCCA", ) self.assertEqual( alignment[0], "TGCACTGGTTTTCC-TGCAGTGGTTCTCAGTAATAGGAAGACA-ACAGAATTTGAAGTATCCGGCTTTGGCCA", ) self.assertEqual(alignment.sequences[1].id, "echTel1.scaffold_288249") self.assertEqual(len(alignment.sequences[1].seq), 100002) self.assertEqual( alignment.sequences[1].seq[95345 : 95345 + 73], "GGCATTGGTTTTTAGAGAGAGAACCCACATAAGTAGGAAAACATTTTGAATTTATAGTAAATATTCTTGGCTA", ) self.assertEqual( alignment[1], "GGCATTGGTTTTTAGAGAGAGAACCCACATAAGTAGGAAAACATTTTGAATTTATAGTAAATATTCTTGGCTA", ) self.assertEqual( alignment.sequences[1].annotations["quality"], "9999999999999999999999999999999999999999999999999999999999999999999999999", ) self.assertEqual(alignment.sequences[1].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[1].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[1].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[1].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[2].id, "dasNov1.scaffold_56749") self.assertEqual(len(alignment.sequences[2].seq), 10470) self.assertEqual( alignment.sequences[2].seq[7048 : 7048 + 70], "TAGCCAAGAGCATTTATTATAAATTCAAAATGCTCTCTTAGTGTGATTTCCCTCACTGAAAATCAATGCA", ) self.assertEqual( alignment[2], "TGCATTGATTTTCAGTGAGGGAAATCACAC---TAAGAGAGCATTTTGAATTTATAATAAATGCTCTTGGCTA", ) self.assertEqual( alignment.sequences[2].annotations["quality"], "5796635799979575966667835948658458696597898258979678997999677999997699", ) self.assertEqual(alignment.sequences[2].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[2].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[2].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[2].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[3].id, "felCat3.scaffold_205680") self.assertEqual(len(alignment.sequences[3].seq), 119354) self.assertEqual( alignment.sequences[3].seq[45798 : 45798 + 72], "CAGCCAAAAACATTTGCTATAATTTCAAAATGCATTCCTATTCATGTGAATCAATGCATGAAAATCAATGCA", ) self.assertEqual( alignment[3], "TGCATTGATTTTCA-TGCATTGATTCACATGAATAGGAATGCATTTTGAAATTATAGCAAATGTTTTTGGCTG", ) self.assertEqual( alignment.sequences[3].annotations["quality"], "999999999999999999999999999999999999999999999999999999999999999999999999", ) self.assertEqual(alignment.sequences[3].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[3].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[3].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[3].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[4].id, "canFam2.chr1") self.assertEqual(len(alignment.sequences[4].seq), 125616256) self.assertEqual( alignment.sequences[4].seq[47544221 : 47544221 + 71], "CAGCCAAAAGCATTTCCTATAAATTCAAATGTATTCCTATTCATGTGAATCAACGCATGAAAATTAATGCA", ) self.assertEqual( alignment[4], "TGCATTAATTTTCA-TGCGTTGATTCACATGAATAGGAATACA-TTTGAATTTATAGGAAATGCTTTTGGCTG", ) self.assertEqual( alignment.sequences[4].annotations["quality"], "99999999999999999999999999999999999999999999999999999999999999999999999", ) self.assertEqual(alignment.sequences[4].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[4].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[4].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[4].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[5].id, "eriEur1.scaffold_266115") self.assertEqual(len(alignment.sequences[5].seq), 4589) self.assertEqual( alignment.sequences[5].seq[451 : 451 + 70], "GCACTGATTCTCGAGGGTTGATTCCCAGTAAGAGGAAACTGCGTGAGTTTACAGTACATGGGCTTGGCTG", ) self.assertEqual( alignment[5], "-GCACTGATTCTCG-AGGGTTGATTCCCAGTAAGAGGAAACTG-CGTGAGTTTACAGTACATGGGCTTGGCTG", ) self.assertEqual( alignment.sequences[5].annotations["quality"], "9999999999999999999999999999999999999999999999999999999999999999999799", ) self.assertEqual(alignment.sequences[5].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[5].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[5].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[5].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[6].id, "sorAra1.scaffold_2476") self.assertEqual(len(alignment.sequences[6].seq), 4997) self.assertEqual( alignment.sequences[6].seq[1615 : 1615 + 70], "TGGCCAAATCATTTATCATAAATTGAAGTGCTTTCCTTTTCATGTGAATCAATACTTAAAAATCAATGCA", ) self.assertEqual( alignment[6], "TGCATTGATTTTTA-AGTATTGATTCACATGAAAAGGAAAGCA-CTTCAATTTATGATAAAT-GATTTGGCCA", ) self.assertEqual( alignment.sequences[6].annotations["quality"], "8999999999998999999999999999999999999999999999999997999999999999999999", ) self.assertEqual(alignment.sequences[6].annotations["leftStatus"], "N") self.assertEqual(alignment.sequences[6].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[6].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[6].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[7].id, "tupBel1.scaffold_114895.1-498454") self.assertEqual(len(alignment.sequences[7].seq), 498454) self.assertEqual( alignment.sequences[7].seq[323397 : 323397 + 71], "TGGTCAGAAGCATTTCCTATCAATTAGAATCGTTTCCTATTAATGTGACATAACACATGGAATTCAATGCA", ) self.assertEqual( alignment[7], "TGCATTGAATTCCA-TGTGTTATGTCACATTAATAGGAAACGA-TTCTAATTGATAGGAAATGCTTCTGACCA", ) self.assertEqual( alignment.sequences[7].annotations["quality"], "99999899899999999999999999999999999999999999999999999999999999999999997", ) self.assertEqual(alignment.sequences[7].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[7].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[7].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[7].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[8].id, "otoGar1.scaffold_334.1-359464") self.assertEqual(len(alignment.sequences[8].seq), 359464) self.assertEqual( alignment.sequences[8].seq[171035 : 171035 + 67], "TGGCCAAATGCCTTTCCTACAAATTCACATGTTTTCCCGTTAAGGTGAATCAATGTGTAAAAATCCA", ) self.assertEqual( alignment[8], "TG----GATTTTTA-CACATTGATTCACCTTAACGGGAAAACA-TGTGAATTTGTAGGAAAGGCATTTGGCCA", ) self.assertEqual( alignment.sequences[8].annotations["quality"], "8899999999989999989994384888899999999966359999569699999923799351281", ) self.assertEqual(alignment.sequences[8].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[8].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[8].annotations["rightStatus"], "I") self.assertEqual(alignment.sequences[8].annotations["rightCount"], 6280) self.assertEqual(alignment.sequences[9].id, "calJac1.Contig6394") self.assertEqual(len(alignment.sequences[9].seq), 133105) self.assertEqual( alignment.sequences[9].seq[10807 : 10807 + 71], "TGCATTGGTTTTTATGCCTTGATTCACATGAATAGGAAAACGTTTGAATTTATAGGAAATGGTTTTGGCCA", ) self.assertEqual( alignment[9], "TGCATTGGTTTTTA-TGCCTTGATTCACATGAATAGGAAAACG-TTTGAATTTATAGGAAATGGTTTTGGCCA", ) self.assertEqual(alignment.sequences[9].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[9].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[9].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[9].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[10].id, "hg18.chr6") self.assertEqual(len(alignment.sequences[10].seq), 170899992) self.assertEqual( alignment.sequences[10].seq[155024945 : 155024945 + 71], "TGGCCAAAACCATTTACTATAAATTCAAACATTTTCCTATTCATGTAAATCAATGCATAAAAATCAAAGCA", ) self.assertEqual( alignment[10], "TGCTTTGATTTTTA-TGCATTGATTTACATGAATAGGAAAATG-TTTGAATTTATAGTAAATGGTTTTGGCCA", ) self.assertEqual(alignment.sequences[10].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[10].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[10].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[10].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[11].id, "panTro2.chr6") self.assertEqual(len(alignment.sequences[11].seq), 173908612) self.assertEqual( alignment.sequences[11].seq[157514999 : 157514999 + 71], "TGGCCAAAACCATTTACTATAAATTCAAATGTTTTCCTATTCATGTAAATCAATGCATAAAAATCAAAGCA", ) self.assertEqual( alignment[11], "TGCTTTGATTTTTA-TGCATTGATTTACATGAATAGGAAAACA-TTTGAATTTATAGTAAATGGTTTTGGCCA", ) self.assertEqual( alignment.sequences[11].annotations["quality"], "99999999999999999999999999999999999999999999999999999999999999999999999", ) self.assertEqual(alignment.sequences[11].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[11].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[11].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[11].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[12].id, "ponAbe2.chr6") self.assertEqual(len(alignment.sequences[12].seq), 174210431) self.assertEqual( alignment.sequences[12].seq[158037166 : 158037166 + 71], "TGGCCAAAACCATTTACTATAAATTCAAACGTTTTCCTATCCATGTAAATCAATGCATAAAAATCAAAGCA", ) self.assertEqual( alignment[12], "TGCTTTGATTTTTA-TGCATTGATTTACATGGATAGGAAAACG-TTTGAATTTATAGTAAATGGTTTTGGCCA", ) self.assertEqual(alignment.sequences[12].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[12].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[12].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[12].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[13].id, "oryCun1.scaffold_156751") self.assertEqual(len(alignment.sequences[13].seq), 4726) self.assertEqual( alignment.sequences[13].seq[3888 : 3888 + 65], "TGACCAAAAGCCATTGCTATAAATGCAAATGTTTTCCCGTCGATGTAAATCAAAGTATGTAAAGA", ) self.assertEqual( alignment[13], "------TCTTTACA-TACTTTGATTTACATCGACGGGAAAACA-TTTGCATTTATAGCAATGGCTTTTGGTCA", ) self.assertEqual( alignment.sequences[13].annotations["quality"], "99999994999999999999989999999999999999999999999999899999999999999", ) self.assertEqual(alignment.sequences[13].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[13].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[13].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[13].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[14].id, "cavPor2.scaffold_216473") self.assertEqual(len(alignment.sequences[14].seq), 10026) self.assertEqual( alignment.sequences[14].seq[285 : 285 + 71], "TGGCCAAAACCATTTACTATAAATTGGACTGTTTTCCTATTAATGTGAATTAATGCATGGAAATCAATGCC", ) self.assertEqual( alignment[14], "GGCATTGATTTCCA-TGCATTAATTCACATTAATAGGAAAACA-GTCCAATTTATAGTAAATGGTTTTGGCCA", ) self.assertEqual( alignment.sequences[14].annotations["quality"], "77888768786695388675879644655668865666547868687676669688688666687574686", ) self.assertEqual(alignment.sequences[14].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[14].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[14].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[14].annotations["rightCount"], 0) empty = alignment.annotations["empty"][0] (record, segment, status) = empty self.assertEqual(record.id, "ornAna1.chr2") self.assertEqual(len(record.seq), 54797317) self.assertEqual(segment, (40046122, 40040432)) self.assertEqual(status, "I") self.assertEqual(len(alignment.sequences), 15) self.assertEqual(len(alignment.annotations["empty"]), 1) self.assertEqual( str(alignment), """\ mm9.chr10 3021204 TGCACTGGTTTTCC-TGCAGTGGTTCTCAGTAATAGGAAGACA-ACAGAATTTGAAGTAT echTel1.s 95345 GGCATTGGTTTTTAGAGAGAGAACCCACATAAGTAGGAAAACATTTTGAATTTATAGTAA dasNov1.s 7118 TGCATTGATTTTCAGTGAGGGAAATCACAC---TAAGAGAGCATTTTGAATTTATAATAA felCat3.s 45870 TGCATTGATTTTCA-TGCATTGATTCACATGAATAGGAATGCATTTTGAAATTATAGCAA canFam2.c 47544292 TGCATTAATTTTCA-TGCGTTGATTCACATGAATAGGAATACA-TTTGAATTTATAGGAA eriEur1.s 451 -GCACTGATTCTCG-AGGGTTGATTCCCAGTAAGAGGAAACTG-CGTGAGTTTACAGTAC sorAra1.s 1685 TGCATTGATTTTTA-AGTATTGATTCACATGAAAAGGAAAGCA-CTTCAATTTATGATAA tupBel1.s 323468 TGCATTGAATTCCA-TGTGTTATGTCACATTAATAGGAAACGA-TTCTAATTGATAGGAA otoGar1.s 171102 TG----GATTTTTA-CACATTGATTCACCTTAACGGGAAAACA-TGTGAATTTGTAGGAA calJac1.C 10807 TGCATTGGTTTTTA-TGCCTTGATTCACATGAATAGGAAAACG-TTTGAATTTATAGGAA hg18.chr6 155025016 TGCTTTGATTTTTA-TGCATTGATTTACATGAATAGGAAAATG-TTTGAATTTATAGTAA panTro2.c 157515070 TGCTTTGATTTTTA-TGCATTGATTTACATGAATAGGAAAACA-TTTGAATTTATAGTAA ponAbe2.c 158037237 TGCTTTGATTTTTA-TGCATTGATTTACATGGATAGGAAAACG-TTTGAATTTATAGTAA oryCun1.s 3953 ------TCTTTACA-TACTTTGATTTACATCGACGGGAAAACA-TTTGCATTTATAGCAA cavPor2.s 356 GGCATTGATTTCCA-TGCATTAATTCACATTAATAGGAAAACA-GTCCAATTTATAGTAA mm9.chr10 3021262 CCGGCTTTGGCCA 3021275 echTel1.s 95405 ATATTCTTGGCTA 95418 dasNov1.s 7061 ATGCTCTTGGCTA 7048 felCat3.s 45811 ATGTTTTTGGCTG 45798 canFam2.c 47544234 ATGCTTTTGGCTG 47544221 eriEur1.s 508 ATGGGCTTGGCTG 521 sorAra1.s 1627 AT-GATTTGGCCA 1615 tupBel1.s 323410 ATGCTTCTGACCA 323397 otoGar1.s 171048 AGGCATTTGGCCA 171035 calJac1.C 10865 ATGGTTTTGGCCA 10878 hg18.chr6 155024958 ATGGTTTTGGCCA 155024945 panTro2.c 157515012 ATGGTTTTGGCCA 157514999 ponAbe2.c 158037179 ATGGTTTTGGCCA 158037166 oryCun1.s 3901 TGGCTTTTGGTCA 3888 cavPor2.s 298 ATGGTTTTGGCCA 285 """, ) self.assertTrue( np.array_equal( alignment.coordinates, np.array( # fmt: off [[ 3021204, 3021205, 3021206, 3021210, 3021218, 3021218, 3021233, 3021236, 3021246, 3021246, 3021264, 3021265, 3021275], [ 95345, 95346, 95347, 95351, 95359, 95360, 95375, 95378, 95388, 95389, 95407, 95408, 95418], [ 7118, 7117, 7116, 7112, 7104, 7103, 7088, 7088, 7078, 7077, 7059, 7058, 7048], [ 45870, 45869, 45868, 45864, 45856, 45856, 45841, 45838, 45828, 45827, 45809, 45808, 45798], [ 47544292, 47544291, 47544290, 47544286, 47544278, 47544278, 47544263, 47544260, 47544250, 47544250, 47544232, 47544231, 47544221], [ 451, 451, 452, 456, 464, 464, 479, 482, 492, 492, 510, 511, 521], [ 1685, 1684, 1683, 1679, 1671, 1671, 1656, 1653, 1643, 1643, 1625, 1625, 1615], [ 323468, 323467, 323466, 323462, 323454, 323454, 323439, 323436, 323426, 323426, 323408, 323407, 323397], [ 171102, 171101, 171100, 171100, 171092, 171092, 171077, 171074, 171064, 171064, 171046, 171045, 171035], [ 10807, 10808, 10809, 10813, 10821, 10821, 10836, 10839, 10849, 10849, 10867, 10868, 10878], [155025016, 155025015, 155025014, 155025010, 155025002, 155025002, 155024987, 155024984, 155024974, 155024974, 155024956, 155024955, 155024945], [157515070, 157515069, 157515068, 157515064, 157515056, 157515056, 157515041, 157515038, 157515028, 157515028, 157515010, 157515009, 157514999], [158037237, 158037236, 158037235, 158037231, 158037223, 158037223, 158037208, 158037205, 158037195, 158037195, 158037177, 158037176, 158037166], [ 3953, 3953, 3953, 3953, 3945, 3945, 3930, 3927, 3917, 3917, 3899, 3898, 3888], [ 356, 355, 354, 350, 342, 342, 327, 324, 314, 314, 296, 295, 285], ] # fmt: on ), ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.score, 891219) self.assertEqual(alignment.sequences[0].id, "mm9.chr10") self.assertEqual(len(alignment.sequences[0].seq), 129993255) self.assertEqual( alignment.sequences[0].seq[3021275 : 3021275 + 146], "CTTTCTCTGACATTACTGTAACTGAAGTAGCTCAGAAGCACAAAAGGTCACATCATGCATCCATGCAGAATCCACTGAAGCTGTTTGGAAAGGCCACGTGTCTTCCCAGAAGGCCAGTTACACCATCATTTCCTTCCATGTTTCAG", ) self.assertEqual( alignment[0], "CTTTCTCTGACATTACTGTAACTGAAGTAGCTC-AGAAGCACAAAAGGTCACATCATGCATCCATGCAGAATCCACTGAAGCTGTTTGGAAAGGC-----------------------CACGTGTCTTCCCAGAAGGCCAGTTACACCATCATTTCCTTCCATGTTTCAG", ) self.assertEqual(alignment.sequences[1].id, "cavPor2.scaffold_216473") self.assertEqual(len(alignment.sequences[1].seq), 10026) self.assertEqual( alignment.sequences[1].seq[116 : 116 + 169], "TTGAAATATGGAAGGAAATGATGGCGTGACTGGATTTCCTGCGAGACACATGAACTAAGTAATAAAATGCGAGGTGCCTTTATGAACGGAACTAGTAAATTTTGCATAAATGCCTGACATGACCTTTTGTGCTTTTCAGCTAGTTCGCTTACAGTAACATCAGCAAAGG", ) self.assertEqual( alignment[1], "CCTTTGCTGATGTTACTGTAAGCGAACTAGCTG-AAAAGCACAAAAGGTCATGTCAGGCATTTATGCAAAATTTACTAGTTCCGTTCATAAAGGCACCTCGCATTTTATTACTTAGTTCATGTGTCTCGCAGGAAATCCAGTCACGCCATCATTTCCTTCCATATTTCAA", ) self.assertEqual( alignment.sequences[1].annotations["quality"], "6685365455476645398666666666666688787886799997788875886655536666688786768476688854689668876558688874778656675665668746666788474786888875667457786687996867886548798845555", ) self.assertEqual(alignment.sequences[1].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[1].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[1].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[1].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[2].id, "oryCun1.scaffold_156751") self.assertEqual(len(alignment.sequences[2].seq), 4726) self.assertEqual( alignment.sequences[2].seq[3730 : 3730 + 158], "TTGAAATGTGGAAGGAAATCGCGGCGTGACTGGATTTCCTGAACAAAGTAATACAACACAAGGTGCTGTTATAAACAGTGCTAGTACATTTGACATAAATGCCTGCCATGGCCTTTTGTGCTTTGGAGCGCTTTCAGCTAGAGTAACATCAGAGACGA", ) self.assertEqual( alignment[2], "TCGTCTCTGATGTTACTCTAGCTGAAAGCGCTC-CAAAGCACAAAAGGCCATGGCAGGCATTTATGTCAAATGTACTAGCACTGTTTATAACAGCACCTTGTGTTGTATTACTTTGTTCA-----------GGAAATCCAGTCACGCCGCGATTTCCTTCCACATTTCAA", ) self.assertEqual( alignment.sequences[2].annotations["quality"], "99999987999999999999999999999799999999799999999898999999988999999988999999989996999999999988897996999999999999979999987899998987999799998998999999999777999899", ) self.assertEqual(alignment.sequences[2].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[2].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[2].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[2].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[3].id, "ponAbe2.chr6") self.assertEqual(len(alignment.sequences[3].seq), 174210431) self.assertEqual( alignment.sequences[3].seq[158036997 : 158036997 + 169], "ATGAAATATGGAAGGAAATGATGGCGTGACTGAATTTCCTGAAAGATACATTAACAAAGTAATAAAACACAAGGTACCCTTATAAACAGCACTAGTAAGTTTTACATGAATGCCTCCCATGACCTTTTGTGCTTTTGAGCTATTTCAGTTACAGTAACATCAGAGAAGG", ) self.assertEqual( alignment[3], "CCTTCTCTGATGTTACTGTAACTGAAATAGCTC-AAAAGCACAAAAGGTCATGGGAGGCATTCATGTAAAACTTACTAGTGCTGTTTATAAGGGTACCTTGTGTTTTATTACTTTGTTAATGTATCTTTCAGGAAATTCAGTCACGCCATCATTTCCTTCCATATTTCAT", ) self.assertEqual(alignment.sequences[3].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[3].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[3].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[3].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[4].id, "panTro2.chr6") self.assertEqual(len(alignment.sequences[4].seq), 173908612) self.assertEqual( alignment.sequences[4].seq[157514830 : 157514830 + 169], "ATGAAATATGGAAGGAAATGATGGCATGACTGGATTTCCTGAAAGGTACATTAACAAAGTAATAAAACACAAGGTACCCTTATAAACAGCACTAGTAAGTTTTACATAAATGCCTCCCATGACCTTTTGTGCTTTTGAGCTATTTCAGTTACAGTAACATCAGAGAAGG", ) self.assertEqual( alignment[4], "CCTTCTCTGATGTTACTGTAACTGAAATAGCTC-AAAAGCACAAAAGGTCATGGGAGGCATTTATGTAAAACTTACTAGTGCTGTTTATAAGGGTACCTTGTGTTTTATTACTTTGTTAATGTACCTTTCAGGAAATCCAGTCATGCCATCATTTCCTTCCATATTTCAT", ) self.assertEqual( alignment.sequences[4].annotations["quality"], "9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999", ) self.assertEqual(alignment.sequences[4].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[4].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[4].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[4].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[5].id, "hg18.chr6") self.assertEqual(len(alignment.sequences[5].seq), 170899992) self.assertEqual( alignment.sequences[5].seq[155024776 : 155024776 + 169], "ATGAAATATGGAAGGAAATGATGGCATGACTGGATTTCCTGAAAGGTACATTAACAAAGTAATAAAACACAAGATACCCTTATAAACAGCACTAGTAAGTTTTACATAAATGCCTCCCATGACCTTTTGTGCTTTTGAGCTATTTCAGTTACAGTAACATCAGAGAAGG", ) self.assertEqual( alignment[5], "CCTTCTCTGATGTTACTGTAACTGAAATAGCTC-AAAAGCACAAAAGGTCATGGGAGGCATTTATGTAAAACTTACTAGTGCTGTTTATAAGGGTATCTTGTGTTTTATTACTTTGTTAATGTACCTTTCAGGAAATCCAGTCATGCCATCATTTCCTTCCATATTTCAT", ) self.assertEqual(alignment.sequences[5].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[5].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[5].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[5].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[6].id, "calJac1.Contig6394") self.assertEqual(len(alignment.sequences[6].seq), 133105) self.assertEqual( alignment.sequences[6].seq[10878 : 10878 + 169], "CCTTCTCTGATATTACTGTAACTGAAATAGCTCAAAAGCACAAAAGGTCATGGCAGGCATTTATGTAAAACTTACTAGTGCTGTTTATAAAGGCACCTTGTGTTTTATTACTTTGTTAATGTACCTTTCAGGAAATCCAGTCATGCCATCATTTCCTTCCATATTTCAT", ) self.assertEqual( alignment[6], "CCTTCTCTGATATTACTGTAACTGAAATAGCTC-AAAAGCACAAAAGGTCATGGCAGGCATTTATGTAAAACTTACTAGTGCTGTTTATAAAGGCACCTTGTGTTTTATTACTTTGTTAATGTACCTTTCAGGAAATCCAGTCATGCCATCATTTCCTTCCATATTTCAT", ) self.assertEqual(alignment.sequences[6].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[6].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[6].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[6].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[7].id, "tupBel1.scaffold_114895.1-498454") self.assertEqual(len(alignment.sequences[7].seq), 498454) self.assertEqual( alignment.sequences[7].seq[323241 : 323241 + 156], "CTGAGATATGGAAGGAAATGATGGCCCGACTGGATTTCCTGTAAGGCACATGAACAAAGTAATAAAACACGAGATGCCTTCAGAAACTTTACATCAATGCCTGGCATGACCTTTTGTGCTTCTGAGCTACTTTGGTTACAGGAACATCTGAGAGGA", ) self.assertEqual( alignment[7], "TCCTCTCAGATGTTCCTGTAACCAAAGTAGCTC-AGAAGCACAAAAGGTCATGCCAGGCATTGATGTAAA-------------GTTTCTGAAGGCATCTCGTGTTTTATTACTTTGTTCATGTGCCTTACAGGAAATCCAGTCGGGCCATCATTTCCTTCCATATCTCAG", ) self.assertEqual( alignment.sequences[7].annotations["quality"], "999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999", ) self.assertEqual(alignment.sequences[7].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[7].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[7].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[7].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[8].id, "sorAra1.scaffold_2476") self.assertEqual(len(alignment.sequences[8].seq), 4997) self.assertEqual( alignment.sequences[8].seq[1445 : 1445 + 170], "CTGGAATATGGGAGGAAATGATGAGATTACAGGATTTCCGGAAAAGTTCATGATCAACAACATTATATGCAAGGGGTCTTTATAAACAGCACTGGTATATTTTACATCAATGCCTGACATGACCTTTTGTGCTTTTTGAGCTACCTCAGTTACAGTAACATCAGAGAAGG", ) self.assertEqual( alignment[8], "CCTTCTCTGATGTTACTGTAACTGAGGTAGCTCAAAAAGCACAAAAGGTCATGTCAGGCATTGATGTAAAATATACCAGTGCTGTTTATAAAGACCCCTTGCATATAATGTTGTTGATCATGAACTTTTCCGGAAATCCTGTAATCTCATCATTTCCTCCCATATTCCAG", ) self.assertEqual( alignment.sequences[8].annotations["quality"], "99999999999999997999999999999999999999999999999999999999999999999999999999999979999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999", ) self.assertEqual(alignment.sequences[8].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[8].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[8].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[8].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[9].id, "eriEur1.scaffold_266115") self.assertEqual(len(alignment.sequences[9].seq), 4589) self.assertEqual( alignment.sequences[9].seq[521 : 521 + 156], "CCTTCTCTGATCTGACTGTAACCGAAGTCTCTCGAAAGCACAAAAGCTCACGGCAGGCCTTTCTGTAAAATACAGCGGCGCTGCTTCCAAAGGCaccttgcagatgtctctcacgcATTTGGCAGGAGTCCCTGTCACTCGGCCAGTTCCTTCCTG", ) self.assertEqual( alignment[9], "CCTTCTCTGATCTGACTGTAACCGAAGTCTCTC-GAAAGCACAAAAGCTCACGGCAGGCCTTTCTGTAAAATACAGCGGCGCTGCTTCCAAAGGCaccttgca------gatgtctctcacgcATTTGGCAGGAGTCCCTGTCACTCGGCCAGTTCC-------TTCCTG", ) self.assertEqual( alignment.sequences[9].annotations["quality"], "999999999999999999999999999999999999999999999999999999999799999999999999999999998987999899999999999999999999999999999999999999999999999999999999999998999989", ) self.assertEqual(alignment.sequences[9].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[9].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[9].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[9].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[10].id, "canFam2.chr1") self.assertEqual(len(alignment.sequences[10].seq), 125616256) self.assertEqual( alignment.sequences[10].seq[47544053 : 47544053 + 168], "TTGAAATATGGAAGGAAGTAACAGGATGACAGGATTTCCTGTAAAGTACATGAACAAAGCAATATTACACGAGGTGCCTTTATAAACAGCTCTAGTAAATTTTACATAAAGCCTGACATGACCTTTTGTGCTTTTGAGCTACTTCAGTTACAGTAACATCAGAGACAG", ) self.assertEqual( alignment[10], "CTGTCTCTGATGTTACTGTAACTGAAGTAGCTC-AAAAGCACAAAAGGTCATGTCAGGC-TTTATGTAAAATTTACTAGAGCTGTTTATAAAGGCACCTCGTGTAATATTGCTTTGTTCATGTACTTTACAGGAAATCCTGTCATCCTGTTACTTCCTTCCATATTTCAA", ) self.assertEqual( alignment.sequences[10].annotations["quality"], "999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999", ) self.assertEqual(alignment.sequences[10].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[10].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[10].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[10].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[11].id, "felCat3.scaffold_205680") self.assertEqual(len(alignment.sequences[11].seq), 119354) self.assertEqual( alignment.sequences[11].seq[45629 : 45629 + 169], "CTGAACTATGGAAGGAAATGACAGGATGACAGGATTTCCTATAAAGTGCATGAACAAAGCAATAATACACAAGGTACCTTTATAAACAGCACTAGTAAATTTTACATAAATGCCTGACATCACCTTTTGTGCTTTTGAACTATTTCAGTTACAGTAACATCAGAGACAG", ) self.assertEqual( alignment[11], "CTGTCTCTGATGTTACTGTAACTGAAATAGTTC-AAAAGCACAAAAGGTGATGTCAGGCATTTATGTAAAATTTACTAGTGCTGTTTATAAAGGTACCTTGTGTATTATTGCTTTGTTCATGCACTTTATAGGAAATCCTGTCATCCTGTCATTTCCTTCCATAGTTCAG", ) self.assertEqual( alignment.sequences[11].annotations["quality"], "9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999", ) self.assertEqual(alignment.sequences[11].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[11].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[11].annotations["rightStatus"], "I") self.assertEqual(alignment.sequences[11].annotations["rightCount"], 34165) self.assertEqual(alignment.sequences[12].id, "dasNov1.scaffold_56749") self.assertEqual(len(alignment.sequences[12].seq), 10470) self.assertEqual( alignment.sequences[12].seq[6880 : 6880 + 168], "GTGACTTATGGAAGGAAATGATGGTATGACAGGATTTCCTGTAAGGGGGATAGAAAAAGTAATAGAACACAAGGTCCTTTATAAACAGCACTAGTAAATTTTACATCAATGCCCGACATGACCTTTTGTGCTTTTGAGCCTCTTCAGTTACAGTAACATCAGAGAAGG", ) self.assertEqual( alignment[12], "CCTTCTCTGATGTTACTGTAACTGAAGAGGCTC-AAAAGCACAAAAGGTCATGTCGGGCATTGATGTAAAATTTACTAGTGCTG-TTTATAAAGGACCTTGTGTTCTATTACTTTTTCTATCCCCCTTACAGGAAATCCTGTCATACCATCATTTCCTTCCATAAGTCAC", ) self.assertEqual( alignment.sequences[12].annotations["quality"], "989999999999999937699999999999999799999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999", ) self.assertEqual(alignment.sequences[12].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[12].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[12].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[12].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[13].id, "echTel1.scaffold_288249") self.assertEqual(len(alignment.sequences[13].seq), 100002) self.assertEqual( alignment.sequences[13].seq[95418 : 95418 + 169], "CCATCTCTGATATTACTGTAATGGAATTACTTTGAAAGCACAAAAGGTCAGGACAAGCGTGTATGTGAAATTTCCTAGAGCTGTTTTCCTGCACACCTTGGATTTTATTGCTTAGTTCATTTGCTTTCCCAGAAATCCCGCCATGCCATCATTTCCTTCCACATCTCAG", ) self.assertEqual( alignment[13], "CCATCTCTGATATTACTGTAATGGAATTACTTT-GAAAGCACAAAAGGTCAGGACAAGCGTGTATGTGAAATTTCCTAGAGCTGTTTTCCTGCACACCTTGGATTTTATTGCTTAGTTCATTTGCTTTCCCAGAAATCCCGCCATGCCATCATTTCCTTCCACATCTCAG", ) self.assertEqual( alignment.sequences[13].annotations["quality"], "9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999", ) self.assertEqual(alignment.sequences[13].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[13].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[13].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[13].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[14].id, "ornAna1.chr2") self.assertEqual(len(alignment.sequences[14].seq), 54797317) self.assertEqual( alignment.sequences[14].seq[40040263 : 40040263 + 169], "TGAAGATATGGAAGGAAATGATGGCTTGACAGGATTTCCCCTAAGGTGAATGAATAGCCTCATAAAACACAAAGCAGCTTTATGAACAGGGCTATTAAGTTGCACATGATTGGCTGATATGACCTTTCCTATCTTCTGGGTAGCTGAGTTACAGTGATATCAGAGGTGG", ) self.assertEqual( alignment[14], "CCACCTCTGATATCACTGTAACTCAGCTACCCA-GAAGATAGGAAAGGTCATATCAGCCAATCATGTGCAACTTAATAGCCCTGTTCATAAAGCTGCTTTGTGTTTTATGAGGCTATTCATTCACCTTAGGGGAAATCCTGTCAAGCCATCATTTCCTTCCATATCTTCA", ) self.assertEqual(alignment.sequences[14].annotations["leftStatus"], "I") self.assertEqual(alignment.sequences[14].annotations["leftCount"], 5690) self.assertEqual(alignment.sequences[14].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[14].annotations["rightCount"], 0) empty = alignment.annotations["empty"][0] (record, segment, status) = empty self.assertEqual(record.id, "otoGar1.scaffold_334.1-359464") self.assertEqual(len(record.seq), 359464) self.assertEqual(segment, (171035, 164755)) self.assertEqual(status, "I") self.assertEqual(len(alignment.sequences), 15) self.assertEqual(len(alignment.annotations["empty"]), 1) self.assertEqual( str(alignment), """\ mm9.chr10 3021275 CTTTCTCTGACATTACTGTAACTGAAGTAGCTC-AGAAGCACAAAAGGTCACATCATGCA cavPor2.s 285 CCTTTGCTGATGTTACTGTAAGCGAACTAGCTG-AAAAGCACAAAAGGTCATGTCAGGCA oryCun1.s 3888 TCGTCTCTGATGTTACTCTAGCTGAAAGCGCTC-CAAAGCACAAAAGGCCATGGCAGGCA ponAbe2.c 158037166 CCTTCTCTGATGTTACTGTAACTGAAATAGCTC-AAAAGCACAAAAGGTCATGGGAGGCA panTro2.c 157514999 CCTTCTCTGATGTTACTGTAACTGAAATAGCTC-AAAAGCACAAAAGGTCATGGGAGGCA hg18.chr6 155024945 CCTTCTCTGATGTTACTGTAACTGAAATAGCTC-AAAAGCACAAAAGGTCATGGGAGGCA calJac1.C 10878 CCTTCTCTGATATTACTGTAACTGAAATAGCTC-AAAAGCACAAAAGGTCATGGCAGGCA tupBel1.s 323397 TCCTCTCAGATGTTCCTGTAACCAAAGTAGCTC-AGAAGCACAAAAGGTCATGCCAGGCA sorAra1.s 1615 CCTTCTCTGATGTTACTGTAACTGAGGTAGCTCAAAAAGCACAAAAGGTCATGTCAGGCA eriEur1.s 521 CCTTCTCTGATCTGACTGTAACCGAAGTCTCTC-GAAAGCACAAAAGCTCACGGCAGGCC canFam2.c 47544221 CTGTCTCTGATGTTACTGTAACTGAAGTAGCTC-AAAAGCACAAAAGGTCATGTCAGGC- felCat3.s 45798 CTGTCTCTGATGTTACTGTAACTGAAATAGTTC-AAAAGCACAAAAGGTGATGTCAGGCA dasNov1.s 7048 CCTTCTCTGATGTTACTGTAACTGAAGAGGCTC-AAAAGCACAAAAGGTCATGTCGGGCA echTel1.s 95418 CCATCTCTGATATTACTGTAATGGAATTACTTT-GAAAGCACAAAAGGTCAGGACAAGCG ornAna1.c 40040432 CCACCTCTGATATCACTGTAACTCAGCTACCCA-GAAGATAGGAAAGGTCATATCAGCCA mm9.chr10 3021334 TCCATGCAGAATCCACTGAAGCTGTTTGGAAAGGC-----------------------CA cavPor2.s 226 TTTATGCAAAATTTACTAGTTCCGTTCATAAAGGCACCTCGCATTTTATTACTTAGTTCA oryCun1.s 3829 TTTATGTCAAATGTACTAGCACTGTTTATAACAGCACCTTGTGTTGTATTACTTTGTTCA ponAbe2.c 158037107 TTCATGTAAAACTTACTAGTGCTGTTTATAAGGGTACCTTGTGTTTTATTACTTTGTTAA panTro2.c 157514940 TTTATGTAAAACTTACTAGTGCTGTTTATAAGGGTACCTTGTGTTTTATTACTTTGTTAA hg18.chr6 155024886 TTTATGTAAAACTTACTAGTGCTGTTTATAAGGGTATCTTGTGTTTTATTACTTTGTTAA calJac1.C 10937 TTTATGTAAAACTTACTAGTGCTGTTTATAAAGGCACCTTGTGTTTTATTACTTTGTTAA tupBel1.s 323338 TTGATGTAAA-------------GTTTCTGAAGGCATCTCGTGTTTTATTACTTTGTTCA sorAra1.s 1555 TTGATGTAAAATATACCAGTGCTGTTTATAAAGACCCCTTGCATATAATGTTGTTGATCA eriEur1.s 580 TTTCTGTAAAATACAGCGGCGCTGCTTCCAAAGGCaccttgca------gatgtctctca canFam2.c 47544163 TTTATGTAAAATTTACTAGAGCTGTTTATAAAGGCACCTCGTGTAATATTGCTTTGTTCA felCat3.s 45739 TTTATGTAAAATTTACTAGTGCTGTTTATAAAGGTACCTTGTGTATTATTGCTTTGTTCA dasNov1.s 6989 TTGATGTAAAATTTACTAGTGCTG-TTTATAAAGGACCTTGTGTTCTATTACTTTTTCTA echTel1.s 95477 TGTATGTGAAATTTCCTAGAGCTGTTTTCCTGCACACCTTGGATTTTATTGCTTAGTTCA ornAna1.c 40040373 ATCATGTGCAACTTAATAGCCCTGTTCATAAAGCTGCTTTGTGTTTTATGAGGCTATTCA mm9.chr10 3021371 CGTGTCTTCCCAGAAGGCCAGTTACACCATCATTTCCTTCCATGTTTCAG 3021421 cavPor2.s 166 TGTGTCTCGCAGGAAATCCAGTCACGCCATCATTTCCTTCCATATTTCAA 116 oryCun1.s 3769 -----------GGAAATCCAGTCACGCCGCGATTTCCTTCCACATTTCAA 3730 ponAbe2.c 158037047 TGTATCTTTCAGGAAATTCAGTCACGCCATCATTTCCTTCCATATTTCAT 158036997 panTro2.c 157514880 TGTACCTTTCAGGAAATCCAGTCATGCCATCATTTCCTTCCATATTTCAT 157514830 hg18.chr6 155024826 TGTACCTTTCAGGAAATCCAGTCATGCCATCATTTCCTTCCATATTTCAT 155024776 calJac1.C 10997 TGTACCTTTCAGGAAATCCAGTCATGCCATCATTTCCTTCCATATTTCAT 11047 tupBel1.s 323291 TGTGCCTTACAGGAAATCCAGTCGGGCCATCATTTCCTTCCATATCTCAG 323241 sorAra1.s 1495 TGAACTTTTCCGGAAATCCTGTAATCTCATCATTTCCTCCCATATTCCAG 1445 eriEur1.s 634 cgcATTTGGCAGGAGTCCCTGTCACTCGGCCAGTTCC-------TTCCTG 677 canFam2.c 47544103 TGTACTTTACAGGAAATCCTGTCATCCTGTTACTTCCTTCCATATTTCAA 47544053 felCat3.s 45679 TGCACTTTATAGGAAATCCTGTCATCCTGTCATTTCCTTCCATAGTTCAG 45629 dasNov1.s 6930 TCCCCCTTACAGGAAATCCTGTCATACCATCATTTCCTTCCATAAGTCAC 6880 echTel1.s 95537 TTTGCTTTCCCAGAAATCCCGCCATGCCATCATTTCCTTCCACATCTCAG 95587 ornAna1.c 40040313 TTCACCTTAGGGGAAATCCTGTCAAGCCATCATTTCCTTCCATATCTTCA 40040263 """, ) self.assertTrue( np.array_equal( alignment.coordinates, np.array( # fmt: off [[ 3021275, 3021308, 3021308, 3021333, 3021334, 3021344, 3021357, 3021358, 3021359, 3021369, 3021369, 3021369, 3021369, 3021371, 3021382, 3021408, 3021415, 3021421], [ 285, 252, 252, 227, 226, 216, 203, 202, 201, 191, 183, 177, 168, 166, 155, 129, 122, 116], [ 3888, 3855, 3855, 3830, 3829, 3819, 3806, 3805, 3804, 3794, 3786, 3780, 3771, 3769, 3769, 3743, 3736, 3730], [158037166, 158037133, 158037133, 158037108, 158037107, 158037097, 158037084, 158037083, 158037082, 158037072, 158037064, 158037058, 158037049, 158037047, 158037036, 158037010, 158037003, 158036997], [157514999, 157514966, 157514966, 157514941, 157514940, 157514930, 157514917, 157514916, 157514915, 157514905, 157514897, 157514891, 157514882, 157514880, 157514869, 157514843, 157514836, 157514830], [155024945, 155024912, 155024912, 155024887, 155024886, 155024876, 155024863, 155024862, 155024861, 155024851, 155024843, 155024837, 155024828, 155024826, 155024815, 155024789, 155024782, 155024776], [ 10878, 10911, 10911, 10936, 10937, 10947, 10960, 10961, 10962, 10972, 10980, 10986, 10995, 10997, 11008, 11034, 11041, 11047], [ 323397, 323364, 323364, 323339, 323338, 323328, 323328, 323327, 323326, 323316, 323308, 323302, 323293, 323291, 323280, 323254, 323247, 323241], [ 1615, 1582, 1581, 1556, 1555, 1545, 1532, 1531, 1530, 1520, 1512, 1506, 1497, 1495, 1484, 1458, 1451, 1445], [ 521, 554, 554, 579, 580, 590, 603, 604, 605, 615, 623, 623, 632, 634, 645, 671, 671, 677], [ 47544221, 47544188, 47544188, 47544163, 47544163, 47544153, 47544140, 47544139, 47544138, 47544128, 47544120, 47544114, 47544105, 47544103, 47544092, 47544066, 47544059, 47544053], [ 45798, 45765, 45765, 45740, 45739, 45729, 45716, 45715, 45714, 45704, 45696, 45690, 45681, 45679, 45668, 45642, 45635, 45629], [ 7048, 7015, 7015, 6990, 6989, 6979, 6966, 6965, 6965, 6955, 6947, 6941, 6932, 6930, 6919, 6893, 6886, 6880], [ 95418, 95451, 95451, 95476, 95477, 95487, 95500, 95501, 95502, 95512, 95520, 95526, 95535, 95537, 95548, 95574, 95581, 95587], [ 40040432, 40040399, 40040399, 40040374, 40040373, 40040363, 40040350, 40040349, 40040348, 40040338, 40040330, 40040324, 40040315, 40040313, 40040302, 40040276, 40040269, 40040263], ] # fmt: on ), ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.score, 30254) self.assertEqual(alignment.sequences[0].id, "mm9.chr10") self.assertEqual(len(alignment.sequences[0].seq), 129993255) self.assertEqual( alignment.sequences[0].seq[3021421 : 3021421 + 44], "ACGTTGCTCATTGTAATTGAAGCATTTATTACCAATGCCTTCCC", ) self.assertEqual( alignment[0], "-ACGTTGCTCATTGT-----AATTGAAGCATTTATTACCAA--------TG--------------CCTTCCC", ) self.assertEqual(alignment.sequences[1].id, "cavPor2.scaffold_216473") self.assertEqual(len(alignment.sequences[1].seq), 10026) self.assertEqual( alignment.sequences[1].seq[69 : 69 + 47], "CAGAGGGGCCGTCAGCAAAACATACTTTTATTTGTAACAAGGAACAG", ) self.assertEqual( alignment[1], "-CTGTTCCTTGTTACA----AATAAAAGTATGTTTTGCTGA--------CG-------G-----CCCCTCTG", ) self.assertEqual( alignment.sequences[1].annotations["quality"], "47675464566778886867867744466523545576436669356", ) self.assertEqual(alignment.sequences[1].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[1].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[1].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[1].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[2].id, "oryCun1.scaffold_156751") self.assertEqual(len(alignment.sequences[2].seq), 4726) self.assertEqual( alignment.sequences[2].seq[3693 : 3693 + 37], "ATTAGCAGTGAATGCTTTAATCCATAATGAGGAACCA", ) self.assertEqual( alignment[2], "-TGGTTCCTCATTATG----GATTAAAGCATTCACTGCTAA--------T----------------------", ) self.assertEqual( alignment.sequences[2].annotations["quality"], "9999999998999998879999999999999999999", ) self.assertEqual(alignment.sequences[2].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[2].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[2].annotations["rightStatus"], "I") self.assertEqual(alignment.sequences[2].annotations["rightCount"], 2345) self.assertEqual(alignment.sequences[3].id, "ponAbe2.chr6") self.assertEqual(len(alignment.sequences[3].seq), 174210431) self.assertEqual( alignment.sequences[3].seq[158036952 : 158036952 + 45], "GAGAAAGCATTAGCAATAAACACTTTTATTTATAATGAGCAACAG", ) self.assertEqual( alignment[3], "-CTGTTGCTCATTATA----AATAAAAGTGTTTATTGCTAA--------T--------------GCTTTCTC", ) self.assertEqual(alignment.sequences[3].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[3].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[3].annotations["rightStatus"], "I") self.assertEqual(alignment.sequences[3].annotations["rightCount"], 4) self.assertEqual(alignment.sequences[4].id, "panTro2.chr6") self.assertEqual(len(alignment.sequences[4].seq), 173908612) self.assertEqual( alignment.sequences[4].seq[157514785 : 157514785 + 45], "GAGAAAGCGTTAGCAATAAACACTTTTATTTATAATGAGGAACAG", ) self.assertEqual( alignment[4], "-CTGTTCCTCATTATA----AATAAAAGTGTTTATTGCTAA--------C--------------GCTTTCTC", ) self.assertEqual( alignment.sequences[4].annotations["quality"], "999999999999999999999999999999999999999999999", ) self.assertEqual(alignment.sequences[4].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[4].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[4].annotations["rightStatus"], "I") self.assertEqual(alignment.sequences[4].annotations["rightCount"], 4) self.assertEqual(alignment.sequences[5].id, "hg18.chr6") self.assertEqual(len(alignment.sequences[5].seq), 170899992) self.assertEqual( alignment.sequences[5].seq[155024731 : 155024731 + 45], "GAGAAAGCGTTAGCAATAAACACTTTTATTTATAATGAGGAACAG", ) self.assertEqual( alignment[5], "-CTGTTCCTCATTATA----AATAAAAGTGTTTATTGCTAA--------C--------------GCTTTCTC", ) self.assertEqual(alignment.sequences[5].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[5].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[5].annotations["rightStatus"], "I") self.assertEqual(alignment.sequences[5].annotations["rightCount"], 4) self.assertEqual(alignment.sequences[6].id, "calJac1.Contig6394") self.assertEqual(len(alignment.sequences[6].seq), 133105) self.assertEqual( alignment.sequences[6].seq[11047 : 11047 + 43], "CTGTTTCTCATTATAAATAAGTGTTTATTGCTAACGCTTTCTC", ) self.assertEqual( alignment[6], "-CTGTTTCTCATTATA----AAT--AAGTGTTTATTGCTAA--------C--------------GCTTTCTC", ) self.assertEqual(alignment.sequences[6].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[6].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[6].annotations["rightStatus"], "I") self.assertEqual(alignment.sequences[6].annotations["rightCount"], 701) self.assertEqual(alignment.sequences[7].id, "tupBel1.scaffold_114895.1-498454") self.assertEqual(len(alignment.sequences[7].seq), 498454) self.assertEqual( alignment.sequences[7].seq[323206 : 323206 + 35], "TTAGCAACAAACGCTATATTTATCATGAGGAGCAG", ) self.assertEqual( alignment[7], "-CTGCTCCTCATGATA----AAT-ATAGCGTTTGTTGCTAA-------------------------------", ) self.assertEqual( alignment.sequences[7].annotations["quality"], "99999999999999999999999999999999999", ) self.assertEqual(alignment.sequences[7].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[7].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[7].annotations["rightStatus"], "I") self.assertEqual(alignment.sequences[7].annotations["rightCount"], 10695) self.assertEqual(alignment.sequences[8].id, "sorAra1.scaffold_2476") self.assertEqual(len(alignment.sequences[8].seq), 4997) self.assertEqual( alignment.sequences[8].seq[1397 : 1397 + 48], "GGAACCTGCTGGTCATAAACGCTCtttttttAATCTAAGAAGGAACAG", ) self.assertEqual( alignment[8], "-CTGTTCCTTCTTAGATTaaaaaaaGAGCGTTTATGACCAG--------CA-------GGTTCC--------", ) self.assertEqual( alignment.sequences[8].annotations["quality"], "999999999999999999999999999999999766975599999999", ) self.assertEqual(alignment.sequences[8].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[8].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[8].annotations["rightStatus"], "N") self.assertEqual(alignment.sequences[8].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[9].id, "eriEur1.scaffold_266115") self.assertEqual(len(alignment.sequences[9].seq), 4589) self.assertEqual( alignment.sequences[9].seq[677 : 677 + 35], "CTCCTTGTTCTTGAAGCCGTTTTTTATTGTCAGTG", ) self.assertEqual( alignment[9], "-CTCCTTGTTCTTGAAGC----------CGTTTTTTATTGT--------CA-------GTG-----------", ) self.assertEqual( alignment.sequences[9].annotations["quality"], "98959997997999999999999999999989999", ) self.assertEqual(alignment.sequences[9].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[9].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[9].annotations["rightStatus"], "N") self.assertEqual(alignment.sequences[9].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[10].id, "canFam2.chr1") self.assertEqual(len(alignment.sequences[10].seq), 125616256) self.assertEqual( alignment.sequences[10].seq[47544013 : 47544013 + 40], "GACATTAGCAATAAATGCTTTTATTTATAATGAGAAACAG", ) self.assertEqual( alignment[10], "-CTGTTTCTCATTATA----AATAAAAGCATTTATTGCTAA--------TG-------T------------C", ) self.assertEqual( alignment.sequences[10].annotations["quality"], "9999999999999999999999999999999999999999", ) self.assertEqual(alignment.sequences[10].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[10].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[10].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[10].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[11].id, "dasNov1.scaffold_56749") self.assertEqual(len(alignment.sequences[11].seq), 10470) self.assertEqual( alignment.sequences[11].seq[6836 : 6836 + 44], "GAGGAGCCGTTAGCAGTAAATGCTTTTATTATAAAGAGGAACAG", ) self.assertEqual( alignment[11], "-CTGTTCCTCTTTAT-----AATAAAAGCATTTACTGCTAA--------CGGCTCCTC--------------", ) self.assertEqual( alignment.sequences[11].annotations["quality"], "99999999999999999999999999999999999999999999", ) self.assertEqual(alignment.sequences[11].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[11].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[11].annotations["rightStatus"], "I") self.assertEqual(alignment.sequences[11].annotations["rightCount"], 904) self.assertEqual(alignment.sequences[12].id, "echTel1.scaffold_288249") self.assertEqual(len(alignment.sequences[12].seq), 100002) self.assertEqual( alignment.sequences[12].seq[95587 : 95587 + 38], "CTGATCCTCATTATAAATAAAAGTGTTTGTTACTAATG", ) self.assertEqual( alignment[12], "-CTGATCCTCATTATA----AATAAAAGTGTTTGTTACTAA--------TG---------------------", ) self.assertEqual( alignment.sequences[12].annotations["quality"], "99999999999999999999999999999999999999", ) self.assertEqual(alignment.sequences[12].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[12].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[12].annotations["rightStatus"], "N") self.assertEqual(alignment.sequences[12].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[13].id, "ornAna1.chr2") self.assertEqual(len(alignment.sequences[13].seq), 54797317) self.assertEqual( alignment.sequences[13].seq[40040218 : 40040218 + 45], "GGGGGATCTTTAGTAATAAAAGAGTCCCTGTACAATGAGGACAGT", ) self.assertEqual( alignment[13], "ACTG-TCCTCATTGTA----CAGGGACTCTTTTATTACTAAAGATCCCCC----------------------", ) self.assertEqual(alignment.sequences[13].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[13].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[13].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[13].annotations["rightCount"], 0) empty = alignment.annotations["empty"][0] (record, segment, status) = empty self.assertEqual(record.id, "felCat3.scaffold_205680") self.assertEqual(len(record.seq), 119354) self.assertEqual(segment, (45629, 11464)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][1] (record, segment, status) = empty self.assertEqual(record.id, "otoGar1.scaffold_334.1-359464") self.assertEqual(len(record.seq), 359464) self.assertEqual(segment, (171035, 164755)) self.assertEqual(status, "I") self.assertEqual(len(alignment.sequences), 14) self.assertEqual(len(alignment.annotations["empty"]), 2) self.assertEqual( str(alignment), """\ mm9.chr10 3021421 -ACGTTGCTCATTGT-----AATTGAAGCATTTATTACCAA--------TG--------- cavPor2.s 116 -CTGTTCCTTGTTACA----AATAAAAGTATGTTTTGCTGA--------CG-------G- oryCun1.s 3730 -TGGTTCCTCATTATG----GATTAAAGCATTCACTGCTAA--------T---------- ponAbe2.c 158036997 -CTGTTGCTCATTATA----AATAAAAGTGTTTATTGCTAA--------T---------- panTro2.c 157514830 -CTGTTCCTCATTATA----AATAAAAGTGTTTATTGCTAA--------C---------- hg18.chr6 155024776 -CTGTTCCTCATTATA----AATAAAAGTGTTTATTGCTAA--------C---------- calJac1.C 11047 -CTGTTTCTCATTATA----AAT--AAGTGTTTATTGCTAA--------C---------- tupBel1.s 323241 -CTGCTCCTCATGATA----AAT-ATAGCGTTTGTTGCTAA------------------- sorAra1.s 1445 -CTGTTCCTTCTTAGATTaaaaaaaGAGCGTTTATGACCAG--------CA-------GG eriEur1.s 677 -CTCCTTGTTCTTGAAGC----------CGTTTTTTATTGT--------CA-------GT canFam2.c 47544053 -CTGTTTCTCATTATA----AATAAAAGCATTTATTGCTAA--------TG-------T- dasNov1.s 6880 -CTGTTCCTCTTTAT-----AATAAAAGCATTTACTGCTAA--------CGGCTCCTC-- echTel1.s 95587 -CTGATCCTCATTATA----AATAAAAGTGTTTGTTACTAA--------TG--------- ornAna1.c 40040263 ACTG-TCCTCATTGTA----CAGGGACTCTTTTATTACTAAAGATCCCCC---------- mm9.chr10 3021458 -----CCTTCCC 3021465 cavPor2.s 77 ----CCCCTCTG 69 oryCun1.s 3693 ------------ 3693 ponAbe2.c 158036960 ----GCTTTCTC 158036952 panTro2.c 157514793 ----GCTTTCTC 157514785 hg18.chr6 155024739 ----GCTTTCTC 155024731 calJac1.C 11082 ----GCTTTCTC 11090 tupBel1.s 323206 ------------ 323206 sorAra1.s 1401 TTCC-------- 1397 eriEur1.s 711 G----------- 712 canFam2.c 47544014 -----------C 47544013 dasNov1.s 6836 ------------ 6836 echTel1.s 95625 ------------ 95625 ornAna1.c 40040218 ------------ 40040218 """, ) self.assertTrue( np.array_equal( alignment.coordinates, np.array( # fmt: off [[ 3021421, 3021421, 3021424, 3021425, 3021435, 3021435, 3021435, 3021435, 3021438, 3021439, 3021440, 3021443, 3021456, 3021456, 3021457, 3021458, 3021458, 3021458, 3021458, 3021458, 3021458, 3021464, 3021465], [ 116, 116, 113, 112, 102, 101, 101, 101, 98, 97, 96, 93, 80, 80, 79, 78, 78, 77, 77, 77, 76, 70, 69], [ 3730, 3730, 3727, 3726, 3716, 3715, 3715, 3715, 3712, 3711, 3710, 3707, 3694, 3694, 3693, 3693, 3693, 3693, 3693, 3693, 3693, 3693, 3693], [158036997, 158036997, 158036994, 158036993, 158036983, 158036982, 158036982, 158036982, 158036979, 158036978, 158036977, 158036974, 158036961, 158036961, 158036960, 158036960, 158036960, 158036960, 158036960, 158036960, 158036959, 158036953, 158036952], [157514830, 157514830, 157514827, 157514826, 157514816, 157514815, 157514815, 157514815, 157514812, 157514811, 157514810, 157514807, 157514794, 157514794, 157514793, 157514793, 157514793, 157514793, 157514793, 157514793, 157514792, 157514786, 157514785], [155024776, 155024776, 155024773, 155024772, 155024762, 155024761, 155024761, 155024761, 155024758, 155024757, 155024756, 155024753, 155024740, 155024740, 155024739, 155024739, 155024739, 155024739, 155024739, 155024739, 155024738, 155024732, 155024731], [ 11047, 11047, 11050, 11051, 11061, 11062, 11062, 11062, 11065, 11065, 11065, 11068, 11081, 11081, 11082, 11082, 11082, 11082, 11082, 11082, 11083, 11089, 11090], [ 323241, 323241, 323238, 323237, 323227, 323226, 323226, 323226, 323223, 323223, 323222, 323219, 323206, 323206, 323206, 323206, 323206, 323206, 323206, 323206, 323206, 323206, 323206], [ 1445, 1445, 1442, 1441, 1431, 1430, 1428, 1426, 1423, 1422, 1421, 1418, 1405, 1405, 1404, 1403, 1403, 1402, 1400, 1397, 1397, 1397, 1397], [ 677, 677, 680, 681, 691, 692, 694, 694, 694, 694, 694, 694, 707, 707, 708, 709, 709, 710, 712, 712, 712, 712, 712], [ 47544053, 47544053, 47544050, 47544049, 47544039, 47544038, 47544038, 47544038, 47544035, 47544034, 47544033, 47544030, 47544017, 47544017, 47544016, 47544015, 47544015, 47544014, 47544014, 47544014, 47544014, 47544014, 47544013], [ 6880, 6880, 6877, 6876, 6866, 6866, 6866, 6866, 6863, 6862, 6861, 6858, 6845, 6845, 6844, 6843, 6836, 6836, 6836, 6836, 6836, 6836, 6836], [ 95587, 95587, 95590, 95591, 95601, 95602, 95602, 95602, 95605, 95606, 95607, 95610, 95623, 95623, 95624, 95625, 95625, 95625, 95625, 95625, 95625, 95625, 95625], [ 40040263, 40040262, 40040259, 40040259, 40040249, 40040248, 40040248, 40040248, 40040245, 40040244, 40040243, 40040240, 40040227, 40040219, 40040218, 40040218, 40040218, 40040218, 40040218, 40040218, 40040218, 40040218, 40040218], ] # fmt: on ), ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.score, -9167) self.assertEqual(alignment.sequences[0].id, "mm9.chr10") self.assertEqual(len(alignment.sequences[0].seq), 129993255) self.assertEqual( alignment.sequences[0].seq[3021465 : 3021465 + 29], "CCCTACACTGTCAAGTGGGAGGAGACAGT", ) self.assertEqual( alignment[0], "CCCT--ACACTGTC----AAGTGGGAGGAGACAGT--------------------" ) self.assertEqual(alignment.sequences[1].id, "cavPor2.scaffold_216473") self.assertEqual(len(alignment.sequences[1].seq), 10026) self.assertEqual( alignment.sequences[1].seq[41 : 41 + 28], "accatcccaccccacccccagtgtGGCT" ) self.assertEqual( alignment[1], "AGCC--acactgg-----gggtggggtgggatggt--------------------" ) self.assertEqual( alignment.sequences[1].annotations["quality"], "7667687856666544895554554677", ) self.assertEqual(alignment.sequences[1].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[1].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[1].annotations["rightStatus"], "N") self.assertEqual(alignment.sequences[1].annotations["rightCount"], 0) self.assertEqual(alignment.sequences[2].id, "ponAbe2.chr6") self.assertEqual(len(alignment.sequences[2].seq), 174210431) self.assertEqual( alignment.sequences[2].seq[158036924 : 158036924 + 24], "GCTGCTCCTATCGCCCCCACAGGG", ) self.assertEqual( alignment[2], "-------CCCTGTG----GGGGCGATAGGAGCAGC--------------------" ) self.assertEqual(alignment.sequences[2].annotations["leftStatus"], "I") self.assertEqual(alignment.sequences[2].annotations["leftCount"], 4) self.assertEqual(alignment.sequences[2].annotations["rightStatus"], "I") self.assertEqual(alignment.sequences[2].annotations["rightCount"], 9) self.assertEqual(alignment.sequences[3].id, "panTro2.chr6") self.assertEqual(len(alignment.sequences[3].seq), 173908612) self.assertEqual( alignment.sequences[3].seq[157514757 : 157514757 + 24], "GCTGCCCCTATCGCCCCCACATGG", ) self.assertEqual( alignment[3], "-------CCATGTG----GGGGCGATAGGGGCAGC--------------------" ) self.assertEqual( alignment.sequences[3].annotations["quality"], "999999999999999999999999" ) self.assertEqual(alignment.sequences[3].annotations["leftStatus"], "I") self.assertEqual(alignment.sequences[3].annotations["leftCount"], 4) self.assertEqual(alignment.sequences[3].annotations["rightStatus"], "I") self.assertEqual(alignment.sequences[3].annotations["rightCount"], 9) self.assertEqual(alignment.sequences[4].id, "hg18.chr6") self.assertEqual(len(alignment.sequences[4].seq), 170899992) self.assertEqual( alignment.sequences[4].seq[155024703 : 155024703 + 24], "GCTGCCCCTATCGCCCCCACATGG", ) self.assertEqual( alignment[4], "-------CCATGTG----GGGGCGATAGGGGCAGC--------------------" ) self.assertEqual(alignment.sequences[4].annotations["leftStatus"], "I") self.assertEqual(alignment.sequences[4].annotations["leftCount"], 4) self.assertEqual(alignment.sequences[4].annotations["rightStatus"], "I") self.assertEqual(alignment.sequences[4].annotations["rightCount"], 9) self.assertEqual(alignment.sequences[5].id, "canFam2.chr1") self.assertEqual(len(alignment.sequences[5].seq), 125616256) self.assertEqual( alignment.sequences[5].seq[47543982 : 47543982 + 31], "CACACACACACACCCCCCATGTGGTTCAGGG", ) self.assertEqual( alignment[5], "CCCTGAACCACATG----GGGGGTGTGTGTGTGTG--------------------" ) self.assertEqual( alignment.sequences[5].annotations["quality"], "9999999999999999999999999999999", ) self.assertEqual(alignment.sequences[5].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[5].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[5].annotations["rightStatus"], "I") self.assertEqual(alignment.sequences[5].annotations["rightCount"], 13) self.assertEqual(alignment.sequences[6].id, "ornAna1.chr2") self.assertEqual(len(alignment.sequences[6].seq), 54797317) self.assertEqual( alignment.sequences[6].seq[40040173 : 40040173 + 45], "GCCAGCAAAGATGAAAGAGGGCTACATCCAAACTCCTATGACACA", ) self.assertEqual( alignment[6], "----------TGTGTCATAGGAGTTTGGATGTAGCCCTCTTTCATCTTTGCTGGC" ) self.assertEqual(alignment.sequences[6].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[6].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[6].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[6].annotations["rightCount"], 0) empty = alignment.annotations["empty"][0] (record, segment, status) = empty self.assertEqual(record.id, "dasNov1.scaffold_56749") self.assertEqual(len(record.seq), 10470) self.assertEqual(segment, (6836, 5932)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][1] (record, segment, status) = empty self.assertEqual(record.id, "felCat3.scaffold_205680") self.assertEqual(len(record.seq), 119354) self.assertEqual(segment, (45629, 11464)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][2] (record, segment, status) = empty self.assertEqual(record.id, "calJac1.Contig6394") self.assertEqual(len(record.seq), 133105) self.assertEqual(segment, (11090, 11791)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][3] (record, segment, status) = empty self.assertEqual(record.id, "tupBel1.scaffold_114895.1-498454") self.assertEqual(len(record.seq), 498454) self.assertEqual(segment, (323206, 312511)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][4] (record, segment, status) = empty self.assertEqual(record.id, "otoGar1.scaffold_334.1-359464") self.assertEqual(len(record.seq), 359464) self.assertEqual(segment, (171035, 164755)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][5] (record, segment, status) = empty self.assertEqual(record.id, "oryCun1.scaffold_156751") self.assertEqual(len(record.seq), 4726) self.assertEqual(segment, (3693, 1348)) self.assertEqual(status, "I") self.assertEqual(len(alignment.sequences), 7) self.assertEqual(len(alignment.annotations["empty"]), 6) self.assertEqual( str(alignment), """\ mm9.chr10 3021465 CCCT--ACACTGTC----AAGTGGGAGGAGACAGT-------------------- cavPor2.s 69 AGCC--acactgg-----gggtggggtgggatggt-------------------- ponAbe2.c 158036948 -------CCCTGTG----GGGGCGATAGGAGCAGC-------------------- panTro2.c 157514781 -------CCATGTG----GGGGCGATAGGGGCAGC-------------------- hg18.chr6 155024727 -------CCATGTG----GGGGCGATAGGGGCAGC-------------------- canFam2.c 47544013 CCCTGAACCACATG----GGGGGTGTGTGTGTGTG-------------------- ornAna1.c 40040218 ----------TGTGTCATAGGAGTTTGGATGTAGCCCTCTTTCATCTTTGCTGGC mm9.chr10 3021494 cavPor2.s 41 ponAbe2.c 158036924 panTro2.c 157514757 hg18.chr6 155024703 canFam2.c 47543982 ornAna1.c 40040173 """, ) self.assertTrue( np.array_equal( alignment.coordinates, np.array( # fmt: off [[ 3021465, 3021469, 3021469, 3021470, 3021473, 3021476, 3021477, 3021477, 3021494, 3021494], [ 69, 65, 65, 64, 61, 58, 58, 58, 41, 41], [158036948, 158036948, 158036948, 158036948, 158036945, 158036942, 158036941, 158036941, 158036924, 158036924], [157514781, 157514781, 157514781, 157514781, 157514778, 157514775, 157514774, 157514774, 157514757, 157514757], [155024727, 155024727, 155024727, 155024727, 155024724, 155024721, 155024720, 155024720, 155024703, 155024703], [ 47544013, 47544009, 47544007, 47544006, 47544003, 47544000, 47543999, 47543999, 47543982, 47543982], [ 40040218, 40040218, 40040218, 40040218, 40040218, 40040215, 40040214, 40040210, 40040193, 40040173], ] # fmt: on ), ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['C', 'C', 'C', 'T', '-', '-', 'A', 'C', 'A', 'C', 'T', 'G', 'T', 'C', '-', '-', '-', '-', 'A', 'A', 'G', 'T', 'G', 'G', 'G', 'A', 'G', 'G', 'A', 'G', 'A', 'C', 'A', 'G', 'T', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-'], ['A', 'G', 'C', 'C', '-', '-', 'a', 'c', 'a', 'c', 't', 'g', 'g', '-', '-', '-', '-', '-', 'g', 'g', 'g', 't', 'g', 'g', 'g', 'g', 't', 'g', 'g', 'g', 'a', 't', 'g', 'g', 't', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-'], ['-', '-', '-', '-', '-', '-', '-', 'C', 'C', 'C', 'T', 'G', 'T', 'G', '-', '-', '-', '-', 'G', 'G', 'G', 'G', 'C', 'G', 'A', 'T', 'A', 'G', 'G', 'A', 'G', 'C', 'A', 'G', 'C', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-'], ['-', '-', '-', '-', '-', '-', '-', 'C', 'C', 'A', 'T', 'G', 'T', 'G', '-', '-', '-', '-', 'G', 'G', 'G', 'G', 'C', 'G', 'A', 'T', 'A', 'G', 'G', 'G', 'G', 'C', 'A', 'G', 'C', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-'], ['-', '-', '-', '-', '-', '-', '-', 'C', 'C', 'A', 'T', 'G', 'T', 'G', '-', '-', '-', '-', 'G', 'G', 'G', 'G', 'C', 'G', 'A', 'T', 'A', 'G', 'G', 'G', 'G', 'C', 'A', 'G', 'C', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-'], ['C', 'C', 'C', 'T', 'G', 'A', 'A', 'C', 'C', 'A', 'C', 'A', 'T', 'G', '-', '-', '-', '-', 'G', 'G', 'G', 'G', 'G', 'T', 'G', 'T', 'G', 'T', 'G', 'T', 'G', 'T', 'G', 'T', 'G', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-', '-'], ['-', '-', '-', '-', '-', '-', '-', '-', '-', '-', 'T', 'G', 'T', 'G', 'T', 'C', 'A', 'T', 'A', 'G', 'G', 'A', 'G', 'T', 'T', 'T', 'G', 'G', 'A', 'T', 'G', 'T', 'A', 'G', 'C', 'C', 'C', 'T', 'C', 'T', 'T', 'T', 'C', 'A', 'T', 'C', 'T', 'T', 'T', 'G', 'C', 'T', 'G', 'G', 'C']], dtype='U') # fmt: on ) ) alignment = next(alignments) self.assertAlmostEqual(alignment.score, 15763) self.assertEqual(alignment.sequences[0].id, "mm9.chr10") self.assertEqual(len(alignment.sequences[0].seq), 129993255) self.assertEqual( alignment.sequences[0].seq[3021494 : 3021494 + 42], "TGTTTAGTACCATGCTTAGGAATGATAAACTCACTTAGTGtt", ) self.assertEqual(alignment[0], "TGTTTAGTACC----ATGCTTAGGAATGATAAACTCACTTAGTGtt") self.assertEqual(alignment.sequences[1].id, "ponAbe2.chr6") self.assertEqual(len(alignment.sequences[1].seq), 174210431) self.assertEqual( alignment.sequences[1].seq[158036869 : 158036869 + 46], "AAGATTGGGTGAGCCTATCACGCCAAAGAATAAAGGACATGCAACA", ) self.assertEqual(alignment[1], "TGTTGCATGTCCTTTATTCTTTGGCGTGATAGGCTCACCCAATCTT") self.assertEqual(alignment.sequences[1].annotations["leftStatus"], "I") self.assertEqual(alignment.sequences[1].annotations["leftCount"], 9) self.assertEqual(alignment.sequences[1].annotations["rightStatus"], "I") self.assertEqual(alignment.sequences[1].annotations["rightCount"], 943) self.assertEqual(alignment.sequences[2].id, "panTro2.chr6") self.assertEqual(len(alignment.sequences[2].seq), 173908612) self.assertEqual( alignment.sequences[2].seq[157514702 : 157514702 + 46], "AAGATTGGGTGAGCCTATCACGCCAAAGAATAAAGGATATGCAACA", ) self.assertEqual(alignment[2], "TGTTGCATATCCTTTATTCTTTGGCGTGATAGGCTCACCCAATCTT") self.assertEqual( alignment.sequences[2].annotations["quality"], "9999999999999999999999999999999999999999999999", ) self.assertEqual(alignment.sequences[2].annotations["leftStatus"], "I") self.assertEqual(alignment.sequences[2].annotations["leftCount"], 9) self.assertEqual(alignment.sequences[2].annotations["rightStatus"], "I") self.assertEqual(alignment.sequences[2].annotations["rightCount"], 10) self.assertEqual(alignment.sequences[3].id, "hg18.chr6") self.assertEqual(len(alignment.sequences[3].seq), 170899992) self.assertEqual( alignment.sequences[3].seq[155024648 : 155024648 + 46], "AAGATTGGGTGAGCCTATCACGCCAAAGAATAAACGACATGCAACA", ) self.assertEqual(alignment[3], "TGTTGCATGTCGTTTATTCTTTGGCGTGATAGGCTCACCCAATCTT") self.assertEqual(alignment.sequences[3].annotations["leftStatus"], "I") self.assertEqual(alignment.sequences[3].annotations["leftCount"], 9) self.assertEqual(alignment.sequences[3].annotations["rightStatus"], "I") self.assertEqual(alignment.sequences[3].annotations["rightCount"], 931) self.assertEqual(alignment.sequences[4].id, "canFam2.chr1") self.assertEqual(len(alignment.sequences[4].seq), 125616256) self.assertEqual( alignment.sequences[4].seq[47543923 : 47543923 + 46], "ATGATGGAGTGAAGCTATCACTTTGAACAGCAAGTGAGACTTAACA", ) self.assertEqual(alignment[4], "TGTTAAGTCTCACTTGCTGTTCAAAGTGATAGCTTCACTCCATCAT") self.assertEqual( alignment.sequences[4].annotations["quality"], "9999999999999999999999999999999999999999999999", ) self.assertEqual(alignment.sequences[4].annotations["leftStatus"], "I") self.assertEqual(alignment.sequences[4].annotations["leftCount"], 13) self.assertEqual(alignment.sequences[4].annotations["rightStatus"], "I") self.assertEqual(alignment.sequences[4].annotations["rightCount"], 1) self.assertEqual(alignment.sequences[5].id, "ornAna1.chr2") self.assertEqual(len(alignment.sequences[5].seq), 54797317) self.assertEqual( alignment.sequences[5].seq[40040137 : 40040137 + 36], "TCCAGTGAGTAGAAGTTCTAGCAATCATTTTAAACA", ) self.assertEqual(alignment[5], "TGTTTAAAATG----ATTGCTAGAACTTCTA--CTCACTGGA----") self.assertEqual(alignment.sequences[5].annotations["leftStatus"], "C") self.assertEqual(alignment.sequences[5].annotations["leftCount"], 0) self.assertEqual(alignment.sequences[5].annotations["rightStatus"], "C") self.assertEqual(alignment.sequences[5].annotations["rightCount"], 0) empty = alignment.annotations["empty"][0] (record, segment, status) = empty self.assertEqual(record.id, "dasNov1.scaffold_56749") self.assertEqual(len(record.seq), 10470) self.assertEqual(segment, (6836, 5932)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][1] (record, segment, status) = empty self.assertEqual(record.id, "felCat3.scaffold_205680") self.assertEqual(len(record.seq), 119354) self.assertEqual(segment, (45629, 11464)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][2] (record, segment, status) = empty self.assertEqual(record.id, "calJac1.Contig6394") self.assertEqual(len(record.seq), 133105) self.assertEqual(segment, (11090, 11791)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][3] (record, segment, status) = empty self.assertEqual(record.id, "tupBel1.scaffold_114895.1-498454") self.assertEqual(len(record.seq), 498454) self.assertEqual(segment, (323206, 312511)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][4] (record, segment, status) = empty self.assertEqual(record.id, "otoGar1.scaffold_334.1-359464") self.assertEqual(len(record.seq), 359464) self.assertEqual(segment, (171035, 164755)) self.assertEqual(status, "I") empty = alignment.annotations["empty"][5] (record, segment, status) = empty self.assertEqual(record.id, "oryCun1.scaffold_156751") self.assertEqual(len(record.seq), 4726) self.assertEqual(segment, (3693, 1348)) self.assertEqual(status, "I") self.assertEqual(len(alignment.sequences), 6) self.assertEqual(len(alignment.annotations["empty"]), 6) self.assertEqual( str(alignment), """\ mm9.chr10 3021494 TGTTTAGTACC----ATGCTTAGGAATGATAAACTCACTTAGTGtt 3021536 ponAbe2.c 158036915 TGTTGCATGTCCTTTATTCTTTGGCGTGATAGGCTCACCCAATCTT 158036869 panTro2.c 157514748 TGTTGCATATCCTTTATTCTTTGGCGTGATAGGCTCACCCAATCTT 157514702 hg18.chr6 155024694 TGTTGCATGTCGTTTATTCTTTGGCGTGATAGGCTCACCCAATCTT 155024648 canFam2.c 47543969 TGTTAAGTCTCACTTGCTGTTCAAAGTGATAGCTTCACTCCATCAT 47543923 ornAna1.c 40040173 TGTTTAAAATG----ATTGCTAGAACTTCTA--CTCACTGGA---- 40040137 """, ) self.assertTrue( np.array_equal( alignment.coordinates, np.array( # fmt: off [[ 3021494, 3021505, 3021505, 3021521, 3021523, 3021532, 3021536], [158036915, 158036904, 158036900, 158036884, 158036882, 158036873, 158036869], [157514748, 157514737, 157514733, 157514717, 157514715, 157514706, 157514702], [155024694, 155024683, 155024679, 155024663, 155024661, 155024652, 155024648], [ 47543969, 47543958, 47543954, 47543938, 47543936, 47543927, 47543923], [ 40040173, 40040162, 40040162, 40040146, 40040146, 40040137, 40040137], ] # fmt: on ), ) ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['T', 'G', 'T', 'T', 'T', 'A', 'G', 'T', 'A', 'C', 'C', '-', '-', '-', '-', 'A', 'T', 'G', 'C', 'T', 'T', 'A', 'G', 'G', 'A', 'A', 'T', 'G', 'A', 'T', 'A', 'A', 'A', 'C', 'T', 'C', 'A', 'C', 'T', 'T', 'A', 'G', 'T', 'G', 't', 't'], ['T', 'G', 'T', 'T', 'G', 'C', 'A', 'T', 'G', 'T', 'C', 'C', 'T', 'T', 'T', 'A', 'T', 'T', 'C', 'T', 'T', 'T', 'G', 'G', 'C', 'G', 'T', 'G', 'A', 'T', 'A', 'G', 'G', 'C', 'T', 'C', 'A', 'C', 'C', 'C', 'A', 'A', 'T', 'C', 'T', 'T'], ['T', 'G', 'T', 'T', 'G', 'C', 'A', 'T', 'A', 'T', 'C', 'C', 'T', 'T', 'T', 'A', 'T', 'T', 'C', 'T', 'T', 'T', 'G', 'G', 'C', 'G', 'T', 'G', 'A', 'T', 'A', 'G', 'G', 'C', 'T', 'C', 'A', 'C', 'C', 'C', 'A', 'A', 'T', 'C', 'T', 'T'], ['T', 'G', 'T', 'T', 'G', 'C', 'A', 'T', 'G', 'T', 'C', 'G', 'T', 'T', 'T', 'A', 'T', 'T', 'C', 'T', 'T', 'T', 'G', 'G', 'C', 'G', 'T', 'G', 'A', 'T', 'A', 'G', 'G', 'C', 'T', 'C', 'A', 'C', 'C', 'C', 'A', 'A', 'T', 'C', 'T', 'T'], ['T', 'G', 'T', 'T', 'A', 'A', 'G', 'T', 'C', 'T', 'C', 'A', 'C', 'T', 'T', 'G', 'C', 'T', 'G', 'T', 'T', 'C', 'A', 'A', 'A', 'G', 'T', 'G', 'A', 'T', 'A', 'G', 'C', 'T', 'T', 'C', 'A', 'C', 'T', 'C', 'C', 'A', 'T', 'C', 'A', 'T'], ['T', 'G', 'T', 'T', 'T', 'A', 'A', 'A', 'A', 'T', 'G', '-', '-', '-', '-', 'A', 'T', 'T', 'G', 'C', 'T', 'A', 'G', 'A', 'A', 'C', 'T', 'T', 'C', 'T', 'A', '-', '-', 'C', 'T', 'C', 'A', 'C', 'T', 'G', 'G', 'A', '-', '-', '-', '-']], dtype='U') # fmt: on ) ) self.assertRaises(StopIteration, next, alignments) class TestAlign_searching(unittest.TestCase): def test_search_chromosome(self): path = "MAF/ucsc_test.bb" alignments = Align.parse(path, "bigmaf") selected_alignments = alignments.search("hg16.chr7") alignment = next(selected_alignments) self.assertEqual(alignment.coordinates[0, 0], 27578828) self.assertEqual(alignment.coordinates[0, -1], 27578866) self.assertAlmostEqual(alignment.score, 23262.0) self.assertEqual( str(alignment), """\ hg16.chr7 27578828 AAA-GGGAATGTTAACCAAATGA---ATTGTCTCTTACGGTG 27578866 panTro1.c 28741140 AAA-GGGAATGTTAACCAAATGA---ATTGTCTCTTACGGTG 28741178 baboon 116834 AAA-GGGAATGTTAACCAAATGA---GTTGTCTCTTATGGTG 116872 mm4.chr6 53215344 -AATGGGAATGTTAAGCAAACGA---ATTGTCTCTCAGTGTG 53215382 rn3.chr4 81344243 -AA-GGGGATGCTAAGCCAATGAGTTGTTGTCTCTCAATGTG 81344283 """, ) alignment = next(selected_alignments) self.assertEqual(alignment.coordinates[0, 0], 27699739) self.assertEqual(alignment.coordinates[0, -1], 27699745) self.assertAlmostEqual(alignment.score, 5062.0) self.assertEqual( str(alignment), """\ hg16.chr7 27699739 TAAAGA 27699745 panTro1.c 28862317 TAAAGA 28862323 baboon 241163 TAAAGA 241169 mm4.chr6 53303881 TAAAGA 53303887 rn3.chr4 81444246 taagga 81444252 """, ) alignment = next(selected_alignments) self.assertEqual(alignment.coordinates[0, 0], 27707221) self.assertEqual(alignment.coordinates[0, -1], 27707234) self.assertAlmostEqual(alignment.score, 6636.0) self.assertEqual( str(alignment), """\ hg16.chr7 27707221 gcagctgaaaaca 27707234 panTro1.c 28869787 gcagctgaaaaca 28869800 baboon 249182 gcagctgaaaaca 249195 mm4.chr6 53310102 ACAGCTGAAAATA 53310115 """, ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['g', 'c', 'a', 'g', 'c', 't', 'g', 'a', 'a', 'a', 'a', 'c', 'a'], ['g', 'c', 'a', 'g', 'c', 't', 'g', 'a', 'a', 'a', 'a', 'c', 'a'], ['g', 'c', 'a', 'g', 'c', 't', 'g', 'a', 'a', 'a', 'a', 'c', 'a'], ['A', 'C', 'A', 'G', 'C', 'T', 'G', 'A', 'A', 'A', 'A', 'T', 'A']], dtype='U') # fmt: on ) ) self.assertRaises(StopIteration, next, selected_alignments) def test_search_region(self): path = "MAF/ucsc_mm9_chr10.bb" alignments = Align.parse(path, "bigmaf") self.assertEqual(len(alignments), 48) selected_alignments = alignments.search("mm9.chr10", 3014000, 3015000) alignment = next(selected_alignments) self.assertEqual(alignment.coordinates[0, 0], 3013603) self.assertEqual(alignment.coordinates[0, -1], 3014644) self.assertAlmostEqual(alignment.score, 0.0) self.assertEqual( str(alignment), """\ mm9.chr10 3013603 CCTTCTTAAGAACACTAGACTCAggactggggagatggctcagcagttaagaatcggtgc mm9.chr10 3013663 tgttaagagtgggagacaagtttggttcccagctcccacattggtcagctcacagccacc mm9.chr10 3013723 cgtaactctaagatggtacacacctttaatcccaggagacagaggcaatcagatctgagt mm9.chr10 3013783 tcaagattcagcctgagacagagcatgttccaaattcaggcatggtgggtcataccttta mm9.chr10 3013843 atatgggacataccttctgctggaggcctacctaaggacaacggagaaaggaagtattcg mm9.chr10 3013903 ttcttctcctgcttgcacttacttgccagcgcatctactggaacccacttcttcaggatt mm9.chr10 3013963 ccagcttatacaggagaccagctgaaatatccagcctctcgggactgaacaagtactaga mm9.chr10 3014023 gtctcagacttcccattcacagctgcccattgttggttggttgtactacagactgtaagt mm9.chr10 3014083 cattgtaataatttcccttaatatatagagacattatataagttctgtgactctagagaa mm9.chr10 3014143 ccctgactagtacaCGTGGCTAACTAGAAAGctctggtatgtgcttacttaatgctgagg mm9.chr10 3014203 ttttaggcatggccacggtgctctgcttcttatgtgggtgctgggaatgcagactcaggt mm9.chr10 3014263 cctcatgtgtatgcagcaaacacttcatacactcagctgcttccctaacccTATGCTTGT mm9.chr10 3014323 GTCTTATTACTAACTTGTGAAAAGCTTTGAGTTTATTTTCTATGTTTTCAACCACTTTCT mm9.chr10 3014383 TGAGTATGCTCAGCTCGTGGCTTTAAACTGGATTTCCCCCTAATATGTAATGACTATAAG mm9.chr10 3014443 TATTCCTTAAATAGGACACACTTTTGTTATACTTTTTGTTATCatataaaatatttcaaa mm9.chr10 3014503 aaaatttttttGCTATTTTTATCTTTGAGCCATTGGTCATTTTGACGTGTATCTCTTGAT mm9.chr10 3014563 TTTTATAGATGGTAATATTTTATGTATTGCTAGCCAATCTCGTTTTCTTGTTTGCTTGCT mm9.chr10 3014623 TGTTTGTTTTGGTCAATGCAG 3014644 """, ) alignment = next(selected_alignments) self.assertEqual(alignment.coordinates[0, 0], 3014644) self.assertEqual(alignment.coordinates[0, -1], 3014689) self.assertAlmostEqual(alignment.score, 19159.0) self.assertEqual( str(alignment), """\ mm9.chr10 3014644 CCTGTACC---CTTTGGTGAGAATTTTTGTTTCAGTGTTAAAAGTTTG 3014689 hg18.chr6 155029206 CCTATACCTTTCTTTTATGAGAA-TTTTGTTTTAATCCTAAAC-TTTT 155029160 panTro2.c 157519257 CCTATACCTTTCTTTTATGAGAA-TTTTGTTTTAATCCTAAAC-TTTT 157519211 calJac1.C 6182 CCTATACCTTTCTTTCATGAGAA-TTTTGTTTGAATCCTAAAC-TTTT 6228 loxAfr1.s 9407 ------------TTTGGTTAGAA-TTATGCTTTAATTCAAAAC-TTCC 9373 """, ) alignment = next(selected_alignments) self.assertAlmostEqual(alignment.score, 40840.0) self.assertEqual(alignment.coordinates[0, 0], 3014689) self.assertEqual(alignment.coordinates[0, -1], 3014742) self.assertEqual( str(alignment), """\ mm9.chr10 3014689 GGGAGCATAAAACTCTAAATCTGCTAAATGTCTTGTCCCT-TTGGAAAGAGTTG hg18.chr6 155029160 GGGATCATAAACCATTTAATCTGTGAAATATCTAATCTTT-TGGGAAATAGTGG panTro2.c 157519211 GGGATCATAAACCATTTAATCTGTGAAATATCTAATCTTT-TGGGAAATAGTGG calJac1.C 6228 GGGATCATAAGCCATTTAATCTGTGAAATGTGAAATCTTT-TGGGAAACAGTGG otoGar1.s 175316 GGAAGCATAAACT-TTTAATCTATGAAATATCAAATCACT-TGGGCAATAGCTG loxAfr1.s 9373 GGGAGTATAAACCATTTAGTCTGCGAAATGCCAAATCTTCAGGGGAAAAAGCTG mm9.chr10 3014742 hg18.chr6 155029107 panTro2.c 157519158 calJac1.C 6281 otoGar1.s 175264 loxAfr1.s 9319 """, ) alignment = next(selected_alignments) self.assertAlmostEqual(alignment.score, 411.0) self.assertEqual(alignment.coordinates[0, 0], 3014742) self.assertEqual(alignment.coordinates[0, -1], 3014778) self.assertEqual( str(alignment), """\ mm9.chr10 3014742 AAGTTCCCTCCATAATTCCTTCCTCCCACCCCCACA 3014778 calJac1.C 6283 AAATGTA-----TGATCTCCCCATCCTGCCCTG--- 6311 otoGar1.s 175262 AGATTTC-----TGATGCCCTCACCCCCTCCGTGCA 175231 loxAfr1.s 9317 AGGCTTA-----TG----CCACCCCCCACCCCCACA 9290 """, ) alignment = next(selected_alignments) self.assertAlmostEqual(alignment.score, 0.0) self.assertEqual(alignment.coordinates[0, 0], 3014778) self.assertEqual(alignment.coordinates[0, -1], 3014795) self.assertEqual( str(alignment), """\ mm9.chr10 3014778 TCCCATGTCCACCCTGA 3014795 """, ) alignment = next(selected_alignments) self.assertAlmostEqual(alignment.score, -12243.0) self.assertEqual(alignment.coordinates[0, 0], 3014795) self.assertEqual(alignment.coordinates[0, -1], 3014842) self.assertEqual( str(alignment), """\ mm9.chr10 3014795 GTTTCAGGGGCAGCTCGCTG----------------TTAGCAG-CTAAGGCATGGTGTCT otoGar1.s 175207 ---TCGGGAACAAGTTGCAGTCATGGATAT-TTGGTTTAGATGGTTTAGGTGGGGTGTAT calJac1.C 6365 -------------------GCCATGAATAT-----TTTAGAC-ATGCAGGTGTGGCGTGT hg18.chr6 155028706 --------------------------------------------aGCAGGTGTGGCATGT panTro2.c 157518758 --------------------------------------------aGCAGGTGTGGCATGT ponAbe2.c 158040939 --------------------------------------------aGCAGGTGTGGCATGT tupBel1.s 326933 ------------------------------------TTAGAAA-TGTGGGTGTGGCGCAT cavPor2.s 2210 ------------------------------------TTAGAAA-TTTAGGTGTGGCATGG loxAfr1.s 9265 GTT-TGAGAGCAAGTTTAGGACATCAATACGTTGTTTCAGAAA-TTGAGGTTTGCTGTAT mm9.chr10 3014838 CTCA 3014842 otoGar1.s 175151 TTCT 175147 calJac1.C 6400 TTCT 6404 hg18.chr6 155028690 TTCT 155028686 panTro2.c 157518742 TTCT 157518738 ponAbe2.c 158040923 TTCT 158040919 tupBel1.s 326910 CGCT 326906 cavPor2.s 2187 TTC- 2184 loxAfr1.s 9207 CTCt 9203 """, ) alignment = next(selected_alignments) self.assertAlmostEqual(alignment.score, 320596.0) self.assertEqual(alignment.coordinates[0, 0], 3014842) self.assertEqual(alignment.coordinates[0, -1], 3015028) self.assertEqual( str(alignment), """\ mm9.chr10 3014842 C--TTGGGA---------TGCTTTATAGTGGAAATGGAAAGCA----A-TTTATTTAGAT loxAfr1.s 9203 tatttttgatttttttttttttttaaaGCTGAAGTGAAAGTCACACTG-TTTCTTTTGGC cavPor2.s 2184 ---TTTGGA---------TA-TTCACAGTTGGAATGAAAGGCACCCTG-TTTCTTTAGGA tupBel1.s 326906 CCTTTTGGA---------TTTTTTACAGCTGAAATAAAAAGCACACTG-TGTCTGTAGGT ponAbe2.c 158040919 CCTTTTGGA---------CTTTTTATAGCTGAAATGGAAGGCACACTG-TTTCTTTAGGT panTro2.c 157518738 CCTTTTGGA---------CTTTTTATAGCTGAAATGGAAGGCACAATA-TTTCTTTAGGT hg18.chr6 155028686 CCTTTTGGA---------CTTTTTATAGCTGAAATGGAAGGCACAATA-TTTCTTTAGGT calJac1.C 6404 TCTTTTGTA--------TTTTTTTATAGCTGAAAAGGAAGGCACACTG-TCTCTTTAGGT otoGar1.s 175147 TATTTTGGG--------CTTTTTTATGGGTGAAATGAAAGGCACACTG-TTTTTTTAGGA ornAna1.c 40046323 --CCTTGGA---------AATGTTACTGCAAAAGTGAAAGGCTCATTGTTTTCTTTCTAT mm9.chr10 3014886 CTTAAATCATTTT-GAAGGTTAATAAAATGACCATATTAATATTCCCATGAACAAAGCCT loxAfr1.s 9144 CATAAATCCCTTT-GAAGTATAATGAAATTTTCACTTTAATATTCCTGTGAACAATACCC cavPor2.s 2138 CTTAAATCCTTTT-GAAGTATAATAAAATGATCACATTAATATTCCTACTAACAATGCCC tupBel1.s 326856 CTTAAATCCTTTT-GAAGTATAATAAAATGATCACTTTACTATTCCTGTGAACAATGCCC ponAbe2.c 158040869 CTTAAATACTTTT-GAAGTATAATAAAACGATCACTTTAATACTCCTGTGAGCAATGTCC panTro2.c 157518688 CTTAAATACTTTT-GAAGTATAAAAAAATGATCACTTTAATACTCCTGTGAACAATGCCC hg18.chr6 155028636 CTTAAATACTTTT-GAAGTATAAAAAAATGATCACTTTAATACTCCTGTGAACAATGCCC calJac1.C 6455 CTTAAATACGTTT-GAAGCATAATAAAATGATCACTTTCATACTCCTGTGAATAATGCCC otoGar1.s 175096 CTTAAATCCTTTT-GAAGTATAATAAAACGATTACTTTACTGTTCCTGTGAACAATGCCC ornAna1.c 40046274 CTTAAGCCTTTTTAAAAGTGTATTGTAATTATGATCTTCATTTCCCCGCTAACAAAGCCC mm9.chr10 3014945 TCATTT----TTAAAATATTGCATCCTATAATACACATAA-ATCTTGT-----TCTCGtt loxAfr1.s 9085 TCATTT-AAAAAAAAAAATTGGGTTTTATACCACACACAGCATCTTTTCAAAATCTCATT cavPor2.s 2079 TCATTT----AAAAAAGTTTGGATTTTGTACCACATACAGCATATTTCCAACATCTCATT tupBel1.s 326797 TCATTT---TACAAAATCTGGGATTTTATACCACGTACAGCATATTTCCAAAATCTCATT ponAbe2.c 158040810 TCTTTT---AAAAAAATCCTGGATTTTATACCACATGCAGCATATTTCTGAAATCTCATT panTro2.c 157518629 TCTTTTT--AAAAAAATCCTGGATTTTATACCACATGCAGCATATTTCTGAAATCCCATT hg18.chr6 155028577 TCTTTTT-AAAAAAAATCCTGGATTTTATACCACATGCAGCATATTTCTGAAATCTCATT calJac1.C 6514 TCCTTTTAAAAAGAAATCTTGGATTTTATATCACACGCAGCATATTTCTGAAATCTCATT otoGar1.s 175037 TCATTT---AAAAAAATCTTGGATTTTATACCAGATCCAGCATATTTCCAAAATCTCATT ornAna1.c 40046214 TCATTA----AAATATCTTTGTATTTTA-ACGACATACAGCCCATTTCCAAAATCTTAGT mm9.chr10 3014995 tttatttttt----tatt-tat-----------------------ttattttttttt--- loxAfr1.s 9026 CCC-TTTTTAAGCAGGTG-TCT---TAGCAAGTTCACTCTCTCTCTCTTTTTTCATTGAC cavPor2.s 2023 TCCTTCTTCTGGCAGGTT-TAt-----------------------tagtctctcttt--- tupBel1.s 326740 TCC-TTTTTTGGCAGGTT-TAT---TAGCAAGTTCCCT-------TTTTGTCTATTG--- ponAbe2.c 158040753 TCC-TTTCTTGGCAGGTT-TATTTATAGCAAGTTATCTC------TCTCTCTTATTT--- panTro2.c 157518571 T----------------------------------------------------------- hg18.chr6 155028518 T----------------------------------------------------------- calJac1.C 6574 TCC-TTTCCTGGCAGGTT-TATTAATAGCAAGTTCTCTC------TCTTATTTATTT--- otoGar1.s 174980 T-C-CTTTTTGGCGGGTT-TGT---TAGCAAGTTCTCTCCGGCTTTCTTCTTCTTTT--- ornAna1.c 40046159 TCC-TTTTTGGGTGCATTGTAT---TAAC----------------CGTTCTCTCTTT--- mm9.chr10 3015024 ---------cttt 3015028 loxAfr1.s 8971 TTTGGCCAAATCT 8958 cavPor2.s 1990 ---------ctct 1986 tupBel1.s 326695 ---------ACTT 326691 ponAbe2.c 158040704 ---------ACTT 158040700 panTro2.c 157518570 ------------- 157518570 hg18.chr6 155028517 ------------- 155028517 calJac1.C 6623 ---------ATTT 6627 otoGar1.s 174929 ---------TCTC 174925 ornAna1.c 40046122 ------------- 40046122 """, ) self.assertRaises(StopIteration, next, selected_alignments) def test_search_position(self): path = "MAF/ucsc_mm9_chr10.bb" alignments = Align.parse(path, "bigmaf") self.assertEqual(len(alignments), 48) selected_alignments = alignments.search("mm9.chr10", 3015000) alignment = next(selected_alignments) self.assertEqual(alignment.coordinates[0, 0], 3014842) self.assertEqual(alignment.coordinates[0, -1], 3015028) self.assertAlmostEqual(alignment.score, 320596.0) self.assertEqual( str(alignment), """\ mm9.chr10 3014842 C--TTGGGA---------TGCTTTATAGTGGAAATGGAAAGCA----A-TTTATTTAGAT loxAfr1.s 9203 tatttttgatttttttttttttttaaaGCTGAAGTGAAAGTCACACTG-TTTCTTTTGGC cavPor2.s 2184 ---TTTGGA---------TA-TTCACAGTTGGAATGAAAGGCACCCTG-TTTCTTTAGGA tupBel1.s 326906 CCTTTTGGA---------TTTTTTACAGCTGAAATAAAAAGCACACTG-TGTCTGTAGGT ponAbe2.c 158040919 CCTTTTGGA---------CTTTTTATAGCTGAAATGGAAGGCACACTG-TTTCTTTAGGT panTro2.c 157518738 CCTTTTGGA---------CTTTTTATAGCTGAAATGGAAGGCACAATA-TTTCTTTAGGT hg18.chr6 155028686 CCTTTTGGA---------CTTTTTATAGCTGAAATGGAAGGCACAATA-TTTCTTTAGGT calJac1.C 6404 TCTTTTGTA--------TTTTTTTATAGCTGAAAAGGAAGGCACACTG-TCTCTTTAGGT otoGar1.s 175147 TATTTTGGG--------CTTTTTTATGGGTGAAATGAAAGGCACACTG-TTTTTTTAGGA ornAna1.c 40046323 --CCTTGGA---------AATGTTACTGCAAAAGTGAAAGGCTCATTGTTTTCTTTCTAT mm9.chr10 3014886 CTTAAATCATTTT-GAAGGTTAATAAAATGACCATATTAATATTCCCATGAACAAAGCCT loxAfr1.s 9144 CATAAATCCCTTT-GAAGTATAATGAAATTTTCACTTTAATATTCCTGTGAACAATACCC cavPor2.s 2138 CTTAAATCCTTTT-GAAGTATAATAAAATGATCACATTAATATTCCTACTAACAATGCCC tupBel1.s 326856 CTTAAATCCTTTT-GAAGTATAATAAAATGATCACTTTACTATTCCTGTGAACAATGCCC ponAbe2.c 158040869 CTTAAATACTTTT-GAAGTATAATAAAACGATCACTTTAATACTCCTGTGAGCAATGTCC panTro2.c 157518688 CTTAAATACTTTT-GAAGTATAAAAAAATGATCACTTTAATACTCCTGTGAACAATGCCC hg18.chr6 155028636 CTTAAATACTTTT-GAAGTATAAAAAAATGATCACTTTAATACTCCTGTGAACAATGCCC calJac1.C 6455 CTTAAATACGTTT-GAAGCATAATAAAATGATCACTTTCATACTCCTGTGAATAATGCCC otoGar1.s 175096 CTTAAATCCTTTT-GAAGTATAATAAAACGATTACTTTACTGTTCCTGTGAACAATGCCC ornAna1.c 40046274 CTTAAGCCTTTTTAAAAGTGTATTGTAATTATGATCTTCATTTCCCCGCTAACAAAGCCC mm9.chr10 3014945 TCATTT----TTAAAATATTGCATCCTATAATACACATAA-ATCTTGT-----TCTCGtt loxAfr1.s 9085 TCATTT-AAAAAAAAAAATTGGGTTTTATACCACACACAGCATCTTTTCAAAATCTCATT cavPor2.s 2079 TCATTT----AAAAAAGTTTGGATTTTGTACCACATACAGCATATTTCCAACATCTCATT tupBel1.s 326797 TCATTT---TACAAAATCTGGGATTTTATACCACGTACAGCATATTTCCAAAATCTCATT ponAbe2.c 158040810 TCTTTT---AAAAAAATCCTGGATTTTATACCACATGCAGCATATTTCTGAAATCTCATT panTro2.c 157518629 TCTTTTT--AAAAAAATCCTGGATTTTATACCACATGCAGCATATTTCTGAAATCCCATT hg18.chr6 155028577 TCTTTTT-AAAAAAAATCCTGGATTTTATACCACATGCAGCATATTTCTGAAATCTCATT calJac1.C 6514 TCCTTTTAAAAAGAAATCTTGGATTTTATATCACACGCAGCATATTTCTGAAATCTCATT otoGar1.s 175037 TCATTT---AAAAAAATCTTGGATTTTATACCAGATCCAGCATATTTCCAAAATCTCATT ornAna1.c 40046214 TCATTA----AAATATCTTTGTATTTTA-ACGACATACAGCCCATTTCCAAAATCTTAGT mm9.chr10 3014995 tttatttttt----tatt-tat-----------------------ttattttttttt--- loxAfr1.s 9026 CCC-TTTTTAAGCAGGTG-TCT---TAGCAAGTTCACTCTCTCTCTCTTTTTTCATTGAC cavPor2.s 2023 TCCTTCTTCTGGCAGGTT-TAt-----------------------tagtctctcttt--- tupBel1.s 326740 TCC-TTTTTTGGCAGGTT-TAT---TAGCAAGTTCCCT-------TTTTGTCTATTG--- ponAbe2.c 158040753 TCC-TTTCTTGGCAGGTT-TATTTATAGCAAGTTATCTC------TCTCTCTTATTT--- panTro2.c 157518571 T----------------------------------------------------------- hg18.chr6 155028518 T----------------------------------------------------------- calJac1.C 6574 TCC-TTTCCTGGCAGGTT-TATTAATAGCAAGTTCTCTC------TCTTATTTATTT--- otoGar1.s 174980 T-C-CTTTTTGGCGGGTT-TGT---TAGCAAGTTCTCTCCGGCTTTCTTCTTCTTTT--- ornAna1.c 40046159 TCC-TTTTTGGGTGCATTGTAT---TAAC----------------CGTTCTCTCTTT--- mm9.chr10 3015024 ---------cttt 3015028 loxAfr1.s 8971 TTTGGCCAAATCT 8958 cavPor2.s 1990 ---------ctct 1986 tupBel1.s 326695 ---------ACTT 326691 ponAbe2.c 158040704 ---------ACTT 158040700 panTro2.c 157518570 ------------- 157518570 hg18.chr6 155028517 ------------- 155028517 calJac1.C 6623 ---------ATTT 6627 otoGar1.s 174929 ---------TCTC 174925 ornAna1.c 40046122 ------------- 40046122 """, ) self.assertRaises(StopIteration, next, selected_alignments) if __name__ == "__main__": runner = unittest.TextTestRunner(verbosity=2) unittest.main(testRunner=runner)