# Copyright 2021 by Michiel de Hoon. All rights reserved. # This code is part of the Biopython distribution and governed by its # license. Please see the LICENSE file that should have been included # as part of this package. """Tests for Align.maf module.""" import unittest from io import StringIO from Bio import Align try: import numpy as np except ImportError: from Bio import MissingPythonDependencyError raise MissingPythonDependencyError( "Install numpy if you want to use Bio.Align.maf." ) from None class TestAlign_reading(unittest.TestCase): def test_reading_bundle_without_target(self): """Test parsing bundle_without_target.maf.""" path = "MAF/bundle_without_target.maf" alignments = Align.parse(path, "maf") self.assertEqual(alignments.metadata["MAF Version"], "1") self.assertEqual(alignments.metadata["Scoring"], "autoMZ.v1") 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.assertEqual(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.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[3009319, 3009392, 3009392, 3009481], [ 11087, 11160, 11162, 11251], ]) # fmt: on ) ) 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.assertEqual( format(alignment, "maf"), """\ a score=6441.000000 s mm8.chr10 3009319 162 + 129993255 TCATAGGTATTTATTTTTAAATATGGTTTGCTTTATGGCTAGAACACACCGATTACTTAAAATAGGATTAACC--CCCATACACTTTAAAAATGATTAAACAACATTTCTGCTGCTCGCTCACATTCTTCATAGAAGATGACATAATGTATTTTCCTTTTGGTT s oryCun1.scaffold_133159 11087 164 + 13221 TCACAGATATTTACTATTAAATATGGTTTGTTATATGGTTACGGTTCATAGGTTACTTGGAATTGGATTAACCTTCTTATTCATTGCAGAATTGGTTACACTGTGTTCTTGACCTTTGCTTGTTTTCTCCATGGAAACTGATGTCAAATACTTTCCCTTTGGTT q oryCun1.scaffold_133159 99569899999998999999999999999999999999999999999999999999999999999999999757878999975999999999999999979999999999997899999999999997997999999869999996999988997997999999 i oryCun1.scaffold_133159 N 0 N 0 """, ) def check_reading_ucsc_mm9_chr10(self, alignments): self.assertEqual(alignments.metadata["MAF Version"], "1") self.assertEqual(alignments.metadata["Scoring"], "autoMZ.v1") alignment = next(alignments) self.assertEqual(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.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[3009319, 3009392, 3009392, 3009481], [ 11087, 11160, 11162, 11251], ]) # fmt: on ) ) 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.assertEqual( format(alignment, "maf"), """\ a score=6441.000000 s mm9.chr10 3009319 162 + 129993255 TCATAGGTATTTATTTTTAAATATGGTTTGCTTTATGGCTAGAACACACCGATTACTTAAAATAGGATTAACC--CCCATACACTTTAAAAATGATTAAACAACATTTCTGCTGCTCGCTCACATTCTTCATAGAAGATGACATAATGTATTTTCCTTTTGGTT s oryCun1.scaffold_133159 11087 164 + 13221 TCACAGATATTTACTATTAAATATGGTTTGTTATATGGTTACGGTTCATAGGTTACTTGGAATTGGATTAACCTTCTTATTCATTGCAGAATTGGTTACACTGTGTTCTTGACCTTTGCTTGTTTTCTCCATGGAAACTGATGTCAAATACTTTCCCTTTGGTT q oryCun1.scaffold_133159 99569899999998999999999999999999999999999999999999999999999999999999999757878999975999999999999999979999999999997899999999999997997999999869999996999988997997999999 i oryCun1.scaffold_133159 N 0 N 0 """, ) 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.assertEqual(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.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 ), ) ) 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.assertEqual( format(alignment, "maf"), """\ a score=103072.000000 s mm9.chr10 3012076 365 + 129993255 AGTCTTTCCAATGGGACCTGTGAGTCCTAACTATGCCAGC-----ACTCCCAACAGCAAGACACTAAGTT---------CACTCATCCTTGGTGGATGGGATTTTGCTCCTGGAGTGTCAC-----CAAATTAAATAACCAGTGAGCAGAGTTG--TGACGAGCATCAGGCTCTGGATTTAGGTGAGAGACCTTAGTGTATGTCTCCTGTAGGTCGCAGCTCCCTATGGAT--------------------------GAGTCAAGTGAAGGTCCTGAGACAA-------------------CAAGTCCTC----GGCTATGTGGGGGTGAGGG-------------ATGC----AG--------CTGGAACCTCAGGGA-TCTCTGT-AAGCAGTGGCATAAATGCTTGGCGG--GAGAGAGCATGTTAGAGCTCACACGACATAGGAAGCCACTGA--GACACTG s ponAbe2.chr6 16160203 443 - 174210431 AGTCTTCATAAGTGGAAATATAAGTTTTAATTATTCCAGCCAAATCATCACAGTAAAAAGATGTTAATATTTATCTCCATACTCATCCTTACCAGATAGCCTTGTGCTCTTGGAATGTCGTACTTATGAAGTGAGCAAGCAGTATTTAGAATAGCATGAGATAGACCAGTCACCAA----AGGTTGTTGATTTCTAGGAATGTCTCATGCTGGTTGCATCTGTGTGTGAACTGGGAAGTTGAGATCGCTTTCCACAGAAATTAAGCAAAATCCTGGAGGTAAGTTGTGGA-----------TAGGGCTGCTGTAGACTCCCTGACAGCGTAGGAACT--------AGAACTCTGAAGCAAGCCACTGGTGCCTAACAAATTCTTTCTAAAGTTGTAGAGTGGATCTGTGGGGGCTGACGTGGCCTCCAACGCCTAACGTGGTTGAAAAGGCCATGGACTTGTGTTC i ponAbe2.chr6 N 0 C 0 s panTro2.chr6 16379004 443 - 173908612 AGTCTTCATAAGTGGAAATATAAGTTTTAATTATTCCAGCTAAATCATCACAGTAAAAAGATGTTAATATTTATCTCCATACTCATCCTTACCAGATAGCCTTGTGCTCTTGGAATGTCGTATTTGTGAAGTGAGCAAGCAGTATGTAGAATAGCATGAGATAGACCAGTCACCAA----AGGTTGTTGATTTCTAGGAATGTCTCATGCTGGTTGCATCTGTGTGTGAACTGGGAAGTTGAGATCGCTTTCCACAGAAATTAAGCAAAATCCTGGAGGTAAGTTGTGGA-----------TAGGGATGCTGTAGACTCCCTGACAGCATAGGAACTAGAACTCTGAAGC----AAGCCA----CTGGTGCCTAACAAATTCTTTATAAAGTTGTAGAGTGGATCTGTGGGGGCTGACGTGGCCTCCAACGCCTAACATGGTTGAAAAGGCCATGGACTTGTGTTC q panTro2.chr6 99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999----99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-----------9999999999999999999999999999999999999999999999999----999999----999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999 i panTro2.chr6 N 0 C 0 s hg18.chr6 15860456 443 - 170899992 AGTCTTCATAAGTGGAAATATAAGTTTTAATTATTCCAGCTAAATCATCACAGTAAAAAGATGTTAATATTTATCTCCATACTCATCCTTACCAGATAGCCTTGTGCTCTTGGAATGTCGTATTTGTGAAGTGAGCAAGCAGTATGTAGAATAGCATGAGATAGACCAGTCACCAA----AGGTTGTTGATTTCTAGGAATGTCTCATGCTGGTTGCATCTGTGTGTGAACTGGGAAGTTGAGATCGCTTTCCACAGAAATTAAGCAAAATCCTGGAGGTAAGTTGTGGATAGGGATGCTGTAGACTCCCT---GACAGCATAGGAAC-TAGAACTCTGAAGC---AAGC----CA--------CTGGTGCCTAACAAATTCTTTATAAAGTTGTAGAGTGGATCCATGGGGGCTGACGTGGCCTCCAACGCCTAACATGGTTGAAAAGGCCATGGACTTGTGTTC i hg18.chr6 N 0 C 0 """, ) alignment = next(alignments) self.assertEqual(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.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.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.assertEqual( format(alignment, "maf"), """\ a score=49128.000000 s mm9.chr10 3012441 125 + 129993255 TGGGTCCCCTTGGCACATCCAGATCTCCCCAGTTAACCTGTCCTGCTTAGACCACTTACCTGAATTG--AATTGGGAGGAGAGAAAGAAGCCAGTTTCCCAGAGAGGGAAAAGGAAAAGCTCGACAC s hg18.chr6 15860899 114 - 170899992 TGGGTTCCTCTAGAATAACCAAG--TCCTCACGTAACCTGGTGTGTATTGACCACCTCTCTTGACCGCTGATCTTGGGGAG----------CACCTTGCT-GAGGGCCAATGGAAAATGCTGGAAGC i hg18.chr6 C 0 C 0 s panTro2.chr6 16379447 114 - 173908612 TGGGTTCCTCTAGAATAACCAAG--TCCTCACGTAACCTGGTGTGTATTGACCACCTCTCTTGACCGCTGATCTTGGGGAG----------CACCTTGCT-GAGGGCCAATGGAAAATGCTGGAAGC q panTro2.chr6 99999999999999999999999--99999999999999999999999999999999999999999999999999999999----------999999999-99999999999999999999999999 i panTro2.chr6 C 0 C 0 s ponAbe2.chr6 16160646 114 - 174210431 TGGGTTCCTCTAGAATAACCAAG--TCCTCACGTAACCTGGTCTATATTGACCACCTGTCTTGACTGTTGATCTTGGGGAG----------CACCTTGCT-GAGGGCCAATGGAAAATGCTGGAAGC i ponAbe2.chr6 C 0 C 0 s otoGar1.scaffold_334.1-359464 180525 101 - 359464 TGGGCCCCCCTGACCTGGCCAAG--TCCTCACTCACCCGGGTTTACACTGACCACC-------------AAACTTGGGGAG----------CCCTTTGCT-GAGGGGCAACAGCAAACACGGGAAGC q otoGar1.scaffold_334.1-359464 99999999999999999999999--9999999999999999999999999999999-------------999999999999----------999999999-99999979999999999999999999 i otoGar1.scaffold_334.1-359464 N 0 C 0 """, ) 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.assertEqual(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.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 ), ) ) 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.assertEqual( format(alignment, "maf"), """\ a score=117109.000000 s mm9.chr10 3012566 262 + 129993255 --TGTGGGCTCCTCACTTTCCTG-TCTCAGGTGTGTCTGTGAGTTTCGGTGAGTGTCGTACAGGAAAGAGGGTGAAAACTCAGTCTGAGCTGTCATTCTTGCCAGCTATGTTGCTTTCCTGTCCTCTTTAGC-------TTATCTCAGGCAACCTATCTTATTTTGTT-TGCTTTC--AGAAGGCAAG---CGAtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtatgtgtgtgtgcgtgCGCGCGCGCGAGCACATGTGCATGCATGCGCACTCGTG s hg18.chr6 15861013 199 - 170899992 CATGAGCCCTCCTTGTATCCCTGATCTTAGATGGGTCTATGGTTTTTGGTGGAAGCCATCCAG-AAACAGCCTCAAAATCCAGTCTGAGTTTTCATTCCTGTCAATCAATCCTCTTATTTTTTTCCTTCACTACC----TTATTTCTAGCAACACATCTTAC-TTATTCTGTTTTCCCAGAAGA-------TGAGTTGTGTATGAGTTTTGG------------------------------------------------------------------ i hg18.chr6 C 0 C 0 s panTro2.chr6 16379561 199 - 173908612 CATGAGCCCTCCTTGTATCCCTGATCTTAGATGGGTCTATGGTTTTTGGTGGAAGCCATCCAG-AAACAGCCTCAAAATCCAGTCTGAGTTTTCATTCCTGTCAATCAATCCTCTTATTTTTTTCCTTCACTACC----TTATTTCTAGCAACACATCTTAC-TTATTTTGTTTTCCCAGAAGA-------TGAGTTGTGTATGAGTTTTGG------------------------------------------------------------------ q panTro2.chr6 999999999999999999999999999999999999999999999999999999999999999-99999999999999999999999999999999999999999999999999999999999999999999999----99999999999999999999999-999999999999999999999-------999999999999999999999------------------------------------------------------------------ i panTro2.chr6 C 0 C 0 s ponAbe2.chr6 16160760 199 - 174210431 CATGAGCCCTCCTTGTATCCCTGATCTTAGATGGGTCTATGGTTTTTGGTGGAAGCCATCCAG-AAACAGCCTCAAAATCCAGTCTGAGTTGTCATTCCTGTCAATCAATCCTCTTGTTTTTTTCCTTCATTACC----TTATTTCTAGCAACATATCTTAC-TTATTTTGTTTTCCCAGAAGA-------TGAGTTGTGTATGAGTTTTGG------------------------------------------------------------------ i ponAbe2.chr6 C 0 C 0 s otoGar1.scaffold_334.1-359464 180626 204 - 359464 CACATGCACTCATCGTGTCTCTG-TCTTAGGCGTAGCCCTGGTTTCTGGGGAAAGCTGTCCAGAAAACCACCTGAAAACCCAGTCTCTGTGGTCATTGCTGGCAATCAGTCC-CTTATTTTTAGGTTGCCTTG------TTATTTCAGGTGACATAGCTTACTTTGTTTTGTTTTCCCAGAAGACAAGTGGTGACTTGTGTATGAGTTTTGA------------------------------------------------------------------ q otoGar1.scaffold_334.1-359464 99999999999999999999999-9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-99999999999999999999------9999999999999999999999999999999999999999999999999999999999999999999999999------------------------------------------------------------------ i otoGar1.scaffold_334.1-359464 C 0 C 0 s cavPor2.scaffold_290371 310 205 - 39932 --TGCGTATCCCTTGCGATCCTGATCCGAGGTGTGGCTGTGGTTTTTGGTGAAAGCCATCCAGAAAAGAACTTCAAAACCTAGTCTAAATTGTTATTCCCTCCTGCCAATCCTCTTGTTTTTACCCCATAGTGACCTCGTTATTGCAA--AACATatcttattttgttctgttttcctggaagataaa---tgaattttgtgtgaGTTTGAG------------------------------------------------------------------ q cavPor2.scaffold_290371 --99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999997999999999999999999999999999999999999999--99999999999999999999999999999999999999---999999999999999999999------------------------------------------------------------------ i cavPor2.scaffold_290371 N 0 C 0 """, ) alignment = next(alignments) self.assertEqual(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.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 ), ) ) 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.assertEqual( format(alignment, "maf"), """\ a score=128047.000000 s mm9.chr10 3012828 168 + 129993255 TTTGCATAGACTCTCTTGGCAACAAAATAACGTTATATTTAAACATCCATTAAAATAATGCACTTAGCACAGCCTGCCCTGAGGGAT----GAACACT--ATTGTTAA-AGAACTATTCCGCTAAGGCAGCAACCTCTGGATCTTCAGCATTCTGGCGCCATCTGCTGGTCATAT s cavPor2.scaffold_290371 515 166 - 39932 -----GTGGGATGTCTTGACAGCTAAATAGTcttatatttaagcatttatGAAAATAATGAGGTTATCATGGTTCGCTCTAGTAGCTCTGAGACCTTT--ATTGTCAGCAAAGCTGTTTAGC--AGGAGGCAACTTCAGGTTCCGTGGGATTCTAGTGCCATCTGCTGGTCATAT q cavPor2.scaffold_290371 -----999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999--9999999999999999999999--999999999999999999999999999999999999999999999999999 i cavPor2.scaffold_290371 C 0 C 0 s otoGar1.scaffold_334.1-359464 180830 161 - 359464 -----GTGGACATTCGTGACAGGCAAATAGTGTTCTATTTAAACATTTGTTGAAATGATAAACTTAGCTCAGCC--CCTT---AGAAGTG-AGAGGCT--ACTGTCAGGGAAGCGGTTTTGCG-GAGCAGCAGCCTCAGGATCTGTGGGATTTTAGCGCCATCTGCTGGTCACAG q otoGar1.scaffold_334.1-359464 -----999999999999999999999999999999999999999999999999999999999999999999999--9999---9999999-9999999--99999999999999999999989-996999999999999999999999999999999999999999999999999 i otoGar1.scaffold_334.1-359464 C 0 C 0 s ponAbe2.chr6 16160959 161 - 174210431 -----GTGGACTATCCTGACAACCAAATAGCGTTATATTTAAACATTTATGAAAATAATAAGCTTAGCATAACCTGCCTTGACAGATGTG-GTATGC-------CTAGTGAAGTTGTTTAGCT-AAGGCTCAATCTCAGGATCTGTGGGACTCTAATGCCATCTGCTGGTCACAT i ponAbe2.chr6 C 0 C 0 s panTro2.chr6 16379760 161 - 173908612 -----GCGGACTATCTTGACAACCAAATAGCGTTATATTTAAACGTTTATGAAAATAATAAGCTTAGCATAACCTGCCTTGACAGATGTG-GTATGC-------CTAGTGAAGTTGCTTAGCT-ATGGCTCAATCTCAGGATCTGTGGGACTCTAATGCCATCTGCTGGTCACAC q panTro2.chr6 -----9999999999999999999999999999999999999999999999999999999999999999999999999999999999999-999999-------9999999999999999999-999999999999999999999999999999999999999999999999999 i panTro2.chr6 C 0 C 0 s hg18.chr6 15861212 161 - 170899992 -----GTGGACTATCTTGACAACCAAATAGCGTTATATTTAAACGTTTGTGAAAATAATAAGCTTAGCATAACCTGCCTTGACAGATGTG-GTATGC-------CTAGTGAAGTTGCTTAGCT-ATGGCTCAATCTCAGGATCTGTGGGACTCTAATGCCATCTGCTGGTCACAC i hg18.chr6 C 0 C 0 s echTel1.scaffold_288249 87492 169 + 100002 TTGGGGTGGATGCTCTTGGCAGTCACACAGTGCTCTATTTTAGGATTTACTAGAACAATGAGTTTGTCATAACT-GCCTCCTCCCAAGTG-GGAAGCTGAAGCACCAA-GTACTGACTCAGC--AGTCCCTGACCTCA-CATCCATGGAAATCTAGTGACATCTGCTGGACACAT q echTel1.scaffold_288249 99989999998979665899999999999676899897997899979878899999999999999999999999-999999999999999-99999999999999999-9999999999999--99999999999999-999999999999999999999999999999999999 i echTel1.scaffold_288249 N 0 I 7564 """, ) alignment = next(alignments) self.assertEqual(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.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 ), ) ) 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.assertEqual( format(alignment, "maf"), """\ a score=98097.000000 s mm9.chr10 3012996 222 + 129993255 AGATGTCTGCTGTGGAGA-------CCTGGCCAACTTTG----CTT--TCTTC-----AAAAAGGCAACAGAAGGTAATCAGTTGAATGCCCACCA-----TTAGGAAGGCGACCTCTAGTGCACAAACCTTGAC-ATTTTCCCTTTTAATGGAA-TTTAACAGAAGTTCAGGATGTTCTTTGGGTAATTTACAATT---A----GGGGGCAAAAATCAAAAGTATTTCGAGCATATCAAAACTGTTAGCTATG s cavPor2.scaffold_290371 681 177 - 39932 TGACGTCTGCAGCCACGG-------GCTGGCTAACTCCA--GTCTT--CCGCG-----CTAAAGCCGAC--------------------CACACCACATAGTGGGGAGAGTGACCTCTAGCGGAAAagctttgca-atttttttcttc----gAC-TCTGTCAG--GTTCAGAATTCCATTTAAACAATTTacagct---a----gaaaaggaaaagcagaggCATTT-------------------------- q cavPor2.scaffold_290371 999999999999999999-------99999999999999--99999--99999-----99999999999--------------------9999999999999999999999999999999999999999999999-999999999999----999-99999999--9999999999999999997999999999995---6----99999999999336991774687-------------------------- i cavPor2.scaffold_290371 C 0 N 0 s hg18.chr6 15861373 184 - 170899992 TGATGGCTGCTGCCATCA---CTTTCTTGGCCTACTCTGCTGTCTT--ACTCT-----ATAAGACTAAC--------------------AGGACCCCATAGTTAGGAGAGCGACCTCTAGCGAGCAGGCCTTGGC-ATTTTTCTTTTTAATTGAA-TTCATAAA-GGCTTAGAATGCCATTTAGACAATTTGTAATG---GTGGGGGGAGGTAAGAGTAT---------------------------------- i hg18.chr6 C 0 I 14 s panTro2.chr6 16379921 184 - 173908612 TGATGGCTGCTGCCATCA---CTTTCTTGGCCTACTCTGCTGTCTT--ATTCT-----ATAAGACTAAC--------------------AGGACCCCATGGTTAGGAGAGCGACCTCTAGCGAGCAGGCCTTGGA-ATTTTTCTTTTTAATTAAA-TTCATAAA-GGCTTAGAATGCCATTTAGACAATTTGTAATG---GTGGGGGGAGGTAAGAGTAT---------------------------------- q panTro2.chr6 999999999999999999---9999999999999999999999999--99999-----99999999999--------------------9999999999999999999999999999999999999999999999-9999999999999999999-99999999-99999999999999999999999999999999---99999999999999999999---------------------------------- i panTro2.chr6 C 0 I 14 s ponAbe2.chr6 16161120 217 - 174210431 TGATGGCTGCTGCCATCA---CTTTCTTGGCCTACTAGGCCGTCTT--ACTCT-----ATAAGACTAAC--------------------AGGACCCCATAGTTAGGAGAGCGACCTCTAGCGAGCAGGCCTTGGA-ATTTTTCTTTTTAATTGAA-TTCATAAA-GGCTTAGAATGCCATTTAGACAATTTGTAATG---GTGGGGGGAGGTAAGAGTATAAATATTGAATGTAT-TCAAACCTGTCAATGATG i ponAbe2.chr6 C 0 I 2 s otoGar1.scaffold_334.1-359464 180991 226 - 359464 GGACGGCCGCCGCCACCACCGCTTTCCCTGCCAACTCCACCGTCTTAAATTCTGCAACAAAAGAAAAAT--------------------CGGACCCTGCAGTTACTAGAGCGACCTCTGGTGAACAAGCCTTGGATTTTTTTCTTTTTAATTGAATTTTACAAC-GGCTCAAAATGCAAGTTAGACAATTCATAGTGTATGTGTGGGGACCTGAGAGTGCAAATATTGCTGGCAT-TCAGCCTTGTTA------ q otoGar1.scaffold_334.1-359464 999998999999999999999999999999999999999999999999999999999999999999999--------------------999999999999999999999999999999999999999999999999999999999999999999999999999-9999999999999999999999999999999999999999999699999999999999999999999999-999999999999------ i otoGar1.scaffold_334.1-359464 C 0 I 2931 s tupBel1.scaffold_114895.1-498454 167217 159 - 498454 TGATGGCTACAGCTGTCA---CTTTCTTGGACCACTCAGCTCTCTC--AAC-------GAAAGACAAAC--------------------TGGATCCTCCGG---GAGAGGAGACCTCTAGTGAGCAAACCTTGGA-ATTTTTCTTTAAAACAGAA-TTTATAAA-GGTTCA-AATGCCATTTAGACAACTTATAATT---A----------------------------------------------------- q tupBel1.scaffold_114895.1-498454 234233433332122232---1582112220212134443324332--133-------23732111754--------------------365002326236---2411112335242535353245936522224-1376645373578253554-58324573-545454-8444565585455465799967999---9----------------------------------------------------- i tupBel1.scaffold_114895.1-498454 N 0 I 4145 e echTel1.scaffold_288249 87661 7564 + 100002 I """, ) alignment = next(alignments) self.assertEqual(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.assertTrue( np.array_equal(alignment.coordinates, np.array([[3013218, 3013437]])) ) self.assertEqual( str(alignment), """\ mm9.chr10 3013218 agccaggcgtggtggcacacacctttactcccagcatttggggggcagaggcaggtggat mm9.chr10 3013278 ctgtgagtttgaggccagcctggtctacagagggagtctcaggacagccagagctacaca mm9.chr10 3013338 gaaataacctgcctagaaaaacaaaacaaaacaaaacatcaaaactcaaaacaaaTAAAA mm9.chr10 3013398 AAAATAAAAAACCCAACCTAAACCAAATAACAAAACACT 3013437 """, ) self.assertEqual( format(alignment, "maf"), """\ a score=0.000000 s mm9.chr10 3013218 219 + 129993255 agccaggcgtggtggcacacacctttactcccagcatttggggggcagaggcaggtggatctgtgagtttgaggccagcctggtctacagagggagtctcaggacagccagagctacacagaaataacctgcctagaaaaacaaaacaaaacaaaacatcaaaactcaaaacaaaTAAAAAAAATAAAAAACCCAACCTAAACCAAATAACAAAACACT e tupBel1.scaffold_114895.1-498454 167376 4145 - 498454 I e echTel1.scaffold_288249 87661 7564 + 100002 I e otoGar1.scaffold_334.1-359464 181217 2931 - 359464 I e hg18.chr6 15861557 14 - 170899992 I e panTro2.chr6 16380105 14 - 173908612 I e ponAbe2.chr6 16161337 2 - 174210431 I """, ) 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.assertEqual(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.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.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.assertEqual( format(alignment, "maf"), """\ a score=40604.000000 s mm9.chr10 3013437 166 + 129993255 TCCAAAATGGTTAGCTATGCCCAACTCCTTTCACTCCAAGAAAATATCCTAACCATGTAAGAGAGCTAGCCTGTTGGTGGCAGCCAAGCCTGATGGTGGCAGACTAGATTGATGGTGCCAGACTACTTTATGGCTGTATCATTTTCCATTCATGTGTTGTGTTATA s panTro2.chr6 16380119 130 - 173908612 TTCAAACCTGTCAATGATGTTCAACTCTTTTCACTGTGGATAAAGATCTTCTAGATGCAATAGAATTAGATT------------------------------------TTGGCGATTACATCCTATTTTATGGGTGTATCGTTTTGCATTCATGGGCTGTTTGATA q panTro2.chr6 999999999999999999999999999999999999999999999999999999999999999999999999------------------------------------9999999999999999999999999999999999999099999999999999999999 i panTro2.chr6 I 14 I 9106 s hg18.chr6 15861571 130 - 170899992 TTCAAACCTGTCAATGATGTTCAACTCTTTTCACTGTGGATAAAGATCTTCTAGATGCAATAGAATTAGATT------------------------------------TTGGCGATTACATCCTATTTTATGGGTGTATCGTTTTGCATTCATGGGCTGTTTGATA i hg18.chr6 I 14 I 9085 s ponAbe2.chr6 16161339 109 - 174210431 ---------------------CAACTCTTTTCACTGTGGATAAAGATCTTCTAGATGCAATAGAATTAGATT------------------------------------TTGGCGATTACATCCTATTTTATGGGTGTATCGTTTTGCATTCATGGGCTGTTTGATA i ponAbe2.chr6 I 2 I 8044 e tupBel1.scaffold_114895.1-498454 167376 4145 - 498454 I e echTel1.scaffold_288249 87661 7564 + 100002 I e otoGar1.scaffold_334.1-359464 181217 2931 - 359464 I """, ) 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.assertEqual(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.assertTrue( np.array_equal(alignment.coordinates, np.array([[3013603, 3014644]])) ) 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.assertEqual( format(alignment, "maf"), """\ a score=0.000000 s mm9.chr10 3013603 1041 + 129993255 CCTTCTTAAGAACACTAGACTCAggactggggagatggctcagcagttaagaatcggtgctgttaagagtgggagacaagtttggttcccagctcccacattggtcagctcacagccacccgtaactctaagatggtacacacctttaatcccaggagacagaggcaatcagatctgagttcaagattcagcctgagacagagcatgttccaaattcaggcatggtgggtcatacctttaatatgggacataccttctgctggaggcctacctaaggacaacggagaaaggaagtattcgttcttctcctgcttgcacttacttgccagcgcatctactggaacccacttcttcaggattccagcttatacaggagaccagctgaaatatccagcctctcgggactgaacaagtactagagtctcagacttcccattcacagctgcccattgttggttggttgtactacagactgtaagtcattgtaataatttcccttaatatatagagacattatataagttctgtgactctagagaaccctgactagtacaCGTGGCTAACTAGAAAGctctggtatgtgcttacttaatgctgaggttttaggcatggccacggtgctctgcttcttatgtgggtgctgggaatgcagactcaggtcctcatgtgtatgcagcaaacacttcatacactcagctgcttccctaacccTATGCTTGTGTCTTATTACTAACTTGTGAAAAGCTTTGAGTTTATTTTCTATGTTTTCAACCACTTTCTTGAGTATGCTCAGCTCGTGGCTTTAAACTGGATTTCCCCCTAATATGTAATGACTATAAGTATTCCTTAAATAGGACACACTTTTGTTATACTTTTTGTTATCatataaaatatttcaaaaaaatttttttGCTATTTTTATCTTTGAGCCATTGGTCATTTTGACGTGTATCTCTTGATTTTTATAGATGGTAATATTTTATGTATTGCTAGCCAATCTCGTTTTCTTGTTTGCTTGCTTGTTTGTTTTGGTCAATGCAG e tupBel1.scaffold_114895.1-498454 167376 4145 - 498454 I e echTel1.scaffold_288249 87661 7564 + 100002 I e otoGar1.scaffold_334.1-359464 181217 2931 - 359464 I e hg18.chr6 15861701 9085 - 170899992 I e panTro2.chr6 16380249 9106 - 173908612 I e ponAbe2.chr6 16161448 8044 - 174210431 I """, ) alignment = next(alignments) self.assertEqual(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.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.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.assertEqual( format(alignment, "maf"), """\ a score=19159.000000 s mm9.chr10 3014644 45 + 129993255 CCTGTACC---CTTTGGTGAGAATTTTTGTTTCAGTGTTAAAAGTTTG s hg18.chr6 15870786 46 - 170899992 CCTATACCTTTCTTTTATGAGAA-TTTTGTTTTAATCCTAAAC-TTTT i hg18.chr6 I 9085 C 0 s panTro2.chr6 16389355 46 - 173908612 CCTATACCTTTCTTTTATGAGAA-TTTTGTTTTAATCCTAAAC-TTTT q panTro2.chr6 99999999999999999999999-9999999999999999999-9999 i panTro2.chr6 I 9106 C 0 s calJac1.Contig6394 6182 46 + 133105 CCTATACCTTTCTTTCATGAGAA-TTTTGTTTGAATCCTAAAC-TTTT i calJac1.Contig6394 N 0 C 0 s loxAfr1.scaffold_75566 1167 34 - 10574 ------------TTTGGTTAGAA-TTATGCTTTAATTCAAAAC-TTCC q loxAfr1.scaffold_75566 ------------99999699899-9999999999999869998-9997 i loxAfr1.scaffold_75566 N 0 C 0 e tupBel1.scaffold_114895.1-498454 167376 4145 - 498454 I e echTel1.scaffold_288249 87661 7564 + 100002 I e otoGar1.scaffold_334.1-359464 181217 2931 - 359464 I e ponAbe2.chr6 16161448 8044 - 174210431 I """, ) 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.assertEqual(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.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.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.assertEqual( format(alignment, "maf"), """\ a score=40840.000000 s mm9.chr10 3014689 53 + 129993255 GGGAGCATAAAACTCTAAATCTGCTAAATGTCTTGTCCCT-TTGGAAAGAGTTG s hg18.chr6 15870832 53 - 170899992 GGGATCATAAACCATTTAATCTGTGAAATATCTAATCTTT-TGGGAAATAGTGG i hg18.chr6 C 0 I 401 s panTro2.chr6 16389401 53 - 173908612 GGGATCATAAACCATTTAATCTGTGAAATATCTAATCTTT-TGGGAAATAGTGG q panTro2.chr6 9999999999999999999999999999999999999999-9999999999999 i panTro2.chr6 C 0 I 400 s calJac1.Contig6394 6228 53 + 133105 GGGATCATAAGCCATTTAATCTGTGAAATGTGAAATCTTT-TGGGAAACAGTGG i calJac1.Contig6394 C 0 I 2 s otoGar1.scaffold_334.1-359464 184148 52 - 359464 GGAAGCATAAACT-TTTAATCTATGAAATATCAAATCACT-TGGGCAATAGCTG q otoGar1.scaffold_334.1-359464 7455455669566-99665699769895555689997599-9984787795599 i otoGar1.scaffold_334.1-359464 I 2931 I 2 s loxAfr1.scaffold_75566 1201 54 - 10574 GGGAGTATAAACCATTTAGTCTGCGAAATGCCAAATCTTCAGGGGAAAAAGCTG q loxAfr1.scaffold_75566 899989799999979999999999999999797999999999999999999999 i loxAfr1.scaffold_75566 C 0 I 2 e tupBel1.scaffold_114895.1-498454 167376 4145 - 498454 I e echTel1.scaffold_288249 87661 7564 + 100002 I e ponAbe2.chr6 16161448 8044 - 174210431 I """, ) 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.assertEqual(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.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.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.assertEqual( format(alignment, "maf"), """\ a score=411.000000 s mm9.chr10 3014742 36 + 129993255 AAGTTCCCTCCATAATTCCTTCCTCCCACCCCCACA s calJac1.Contig6394 6283 28 + 133105 AAATGTA-----TGATCTCCCCATCCTGCCCTG--- i calJac1.Contig6394 I 2 I 54 s otoGar1.scaffold_334.1-359464 184202 31 - 359464 AGATTTC-----TGATGCCCTCACCCCCTCCGTGCA q otoGar1.scaffold_334.1-359464 9996999-----965974999999999999999999 i otoGar1.scaffold_334.1-359464 I 2 I 24 s loxAfr1.scaffold_75566 1257 27 - 10574 AGGCTTA-----TG----CCACCCCCCACCCCCACA q loxAfr1.scaffold_75566 9999999-----99----997999999999999999 i loxAfr1.scaffold_75566 I 2 I 25 e tupBel1.scaffold_114895.1-498454 167376 4145 - 498454 I e echTel1.scaffold_288249 87661 7564 + 100002 I e hg18.chr6 15870885 401 - 170899992 I e panTro2.chr6 16389454 400 - 173908612 I e ponAbe2.chr6 16161448 8044 - 174210431 I """, ) 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.assertEqual(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.assertTrue( np.array_equal(alignment.coordinates, np.array([[3014778, 3014795]])) ) self.assertEqual( str(alignment), """\ mm9.chr10 3014778 TCCCATGTCCACCCTGA 3014795 """, ) self.assertEqual( format(alignment, "maf"), """\ a score=0.000000 s mm9.chr10 3014778 17 + 129993255 TCCCATGTCCACCCTGA e loxAfr1.scaffold_75566 1284 25 - 10574 I e calJac1.Contig6394 6311 54 + 133105 I e tupBel1.scaffold_114895.1-498454 167376 4145 - 498454 I e echTel1.scaffold_288249 87661 7564 + 100002 I e otoGar1.scaffold_334.1-359464 184233 24 - 359464 I e hg18.chr6 15870885 401 - 170899992 I e panTro2.chr6 16389454 400 - 173908612 I e ponAbe2.chr6 16161448 8044 - 174210431 I """, ) 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.assertEqual(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.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.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.assertEqual( format(alignment, "maf"), """\ a score=-12243.000000 s mm9.chr10 3014795 47 + 129993255 GTTTCAGGGGCAGCTCGCTG----------------TTAGCAG-CTAAGGCATGGTGTCTCTCA s otoGar1.scaffold_334.1-359464 184257 60 - 359464 ---TCGGGAACAAGTTGCAGTCATGGATAT-TTGGTTTAGATGGTTTAGGTGGGGTGTATTTCT q otoGar1.scaffold_334.1-359464 ---899999999999999999999999999-999999999999999999999999999999999 i otoGar1.scaffold_334.1-359464 I 24 C 0 s calJac1.Contig6394 6365 39 + 133105 -------------------GCCATGAATAT-----TTTAGAC-ATGCAGGTGTGGCGTGTTTCT i calJac1.Contig6394 I 54 C 0 s hg18.chr6 15871286 20 - 170899992 --------------------------------------------aGCAGGTGTGGCATGTTTCT i hg18.chr6 I 401 C 0 s panTro2.chr6 16389854 20 - 173908612 --------------------------------------------aGCAGGTGTGGCATGTTTCT q panTro2.chr6 --------------------------------------------99999999999999999999 i panTro2.chr6 I 400 C 0 s ponAbe2.chr6 16169492 20 - 174210431 --------------------------------------------aGCAGGTGTGGCATGTTTCT i ponAbe2.chr6 I 8044 C 0 s tupBel1.scaffold_114895.1-498454 171521 27 - 498454 ------------------------------------TTAGAAA-TGTGGGTGTGGCGCATCGCT q tupBel1.scaffold_114895.1-498454 ------------------------------------9999999-99999989998899999699 i tupBel1.scaffold_114895.1-498454 I 4145 C 0 s cavPor2.scaffold_216473 7816 26 - 10026 ------------------------------------TTAGAAA-TTTAGGTGTGGCATGGTTC- q cavPor2.scaffold_216473 ------------------------------------4255831-1324566557465575854- i cavPor2.scaffold_216473 N 0 C 0 s loxAfr1.scaffold_75566 1309 62 - 10574 GTT-TGAGAGCAAGTTTAGGACATCAATACGTTGTTTCAGAAA-TTGAGGTTTGCTGTATCTCt q loxAfr1.scaffold_75566 999-999999999999999999999999999999999999999-99999999999999999999 i loxAfr1.scaffold_75566 I 25 C 0 e echTel1.scaffold_288249 87661 7564 + 100002 I """, ) 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.assertEqual(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.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 ), ) ) 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.assertEqual( format(alignment, "maf"), """\ a score=320596.000000 s mm9.chr10 3014842 186 + 129993255 C--TTGGGA---------TGCTTTATAGTGGAAATGGAAAGCA----A-TTTATTTAGATCTTAAATCATTTT-GAAGGTTAATAAAATGACCATATTAATATTCCCATGAACAAAGCCTTCATTT----TTAAAATATTGCATCCTATAATACACATAA-ATCTTGT-----TCTCGtttttatttttt----tatt-tat-----------------------ttattttttttt------------cttt s loxAfr1.scaffold_75566 1371 245 - 10574 tatttttgatttttttttttttttaaaGCTGAAGTGAAAGTCACACTG-TTTCTTTTGGCCATAAATCCCTTT-GAAGTATAATGAAATTTTCACTTTAATATTCCTGTGAACAATACCCTCATTT-AAAAAAAAAAATTGGGTTTTATACCACACACAGCATCTTTTCAAAATCTCATTCCC-TTTTTAAGCAGGTG-TCT---TAGCAAGTTCACTCTCTCTCTCTTTTTTCATTGACTTTGGCCAAATCT q loxAfr1.scaffold_75566 999999999999999999999999999999999999999999999999-999999999999999999999999-9999999999999999999999999999999999999999999999999999-99999999999999999999999999999999999999999999999999999999-99999999999999-999---999999999999999999999999999999999999999999999999 i loxAfr1.scaffold_75566 C 0 C 0 s cavPor2.scaffold_216473 7842 198 - 10026 ---TTTGGA---------TA-TTCACAGTTGGAATGAAAGGCACCCTG-TTTCTTTAGGACTTAAATCCTTTT-GAAGTATAATAAAATGATCACATTAATATTCCTACTAACAATGCCCTCATTT----AAAAAAGTTTGGATTTTGTACCACATACAGCATATTTCCAACATCTCATTTCCTTCTTCTGGCAGGTT-TAt-----------------------tagtctctcttt------------ctct q cavPor2.scaffold_216473 ---610137---------77-200195531236266876425368858-778987956887868956898956-8988778987788768588885664786777656586678636299978766----89979789936989956687867689995888978886997659897789899998996778899997-989-----------------------998799999777------------9899 i cavPor2.scaffold_216473 C 0 C 0 s tupBel1.scaffold_114895.1-498454 171548 215 - 498454 CCTTTTGGA---------TTTTTTACAGCTGAAATAAAAAGCACACTG-TGTCTGTAGGTCTTAAATCCTTTT-GAAGTATAATAAAATGATCACTTTACTATTCCTGTGAACAATGCCCTCATTT---TACAAAATCTGGGATTTTATACCACGTACAGCATATTTCCAAAATCTCATTTCC-TTTTTTGGCAGGTT-TAT---TAGCAAGTTCCCT-------TTTTGTCTATTG------------ACTT q tupBel1.scaffold_114895.1-498454 989999999---------899999998999999999999999999999-999999999999999999999999-9999998999999999999999999999999999899999999999999999---998899999999973999999998999999999999999979999999999999-99999997699849-999---9999999999999-------999999999999------------9999 i tupBel1.scaffold_114895.1-498454 C 0 C 0 s ponAbe2.chr6 16169512 219 - 174210431 CCTTTTGGA---------CTTTTTATAGCTGAAATGGAAGGCACACTG-TTTCTTTAGGTCTTAAATACTTTT-GAAGTATAATAAAACGATCACTTTAATACTCCTGTGAGCAATGTCCTCTTTT---AAAAAAATCCTGGATTTTATACCACATGCAGCATATTTCTGAAATCTCATTTCC-TTTCTTGGCAGGTT-TATTTATAGCAAGTTATCTC------TCTCTCTTATTT------------ACTT i ponAbe2.chr6 C 0 C 0 s panTro2.chr6 16389874 168 - 173908612 CCTTTTGGA---------CTTTTTATAGCTGAAATGGAAGGCACAATA-TTTCTTTAGGTCTTAAATACTTTT-GAAGTATAAAAAAATGATCACTTTAATACTCCTGTGAACAATGCCCTCTTTTT--AAAAAAATCCTGGATTTTATACCACATGCAGCATATTTCTGAAATCCCATTT------------------------------------------------------------------------ q panTro2.chr6 999999999---------999999999999999999999999999999-999999999999999999999999-99999999999999999999999999999999999999999999999999999--9999999999999999999999999999999999999999999999999999------------------------------------------------------------------------ i panTro2.chr6 C 0 C 0 s hg18.chr6 15871306 169 - 170899992 CCTTTTGGA---------CTTTTTATAGCTGAAATGGAAGGCACAATA-TTTCTTTAGGTCTTAAATACTTTT-GAAGTATAAAAAAATGATCACTTTAATACTCCTGTGAACAATGCCCTCTTTTT-AAAAAAAATCCTGGATTTTATACCACATGCAGCATATTTCTGAAATCTCATTT------------------------------------------------------------------------ i hg18.chr6 C 0 C 0 s calJac1.Contig6394 6404 223 + 133105 TCTTTTGTA--------TTTTTTTATAGCTGAAAAGGAAGGCACACTG-TCTCTTTAGGTCTTAAATACGTTT-GAAGCATAATAAAATGATCACTTTCATACTCCTGTGAATAATGCCCTCCTTTTAAAAAGAAATCTTGGATTTTATATCACACGCAGCATATTTCTGAAATCTCATTTCC-TTTCCTGGCAGGTT-TATTAATAGCAAGTTCTCTC------TCTTATTTATTT------------ATTT i calJac1.Contig6394 C 0 C 0 s otoGar1.scaffold_334.1-359464 184317 222 - 359464 TATTTTGGG--------CTTTTTTATGGGTGAAATGAAAGGCACACTG-TTTTTTTAGGACTTAAATCCTTTT-GAAGTATAATAAAACGATTACTTTACTGTTCCTGTGAACAATGCCCTCATTT---AAAAAAATCTTGGATTTTATACCAGATCCAGCATATTTCCAAAATCTCATTT-C-CTTTTTGGCGGGTT-TGT---TAGCAAGTTCTCTCCGGCTTTCTTCTTCTTTT------------TCTC q otoGar1.scaffold_334.1-359464 999999999--------9999999999999999999999997999999-999999999999999999999999-9999999999999999999999999999999999999999999999999999---9999999999999999999999999999999999999999999999999999-9-99999999999999-999---99999999999999999999999999999999------------9999 i otoGar1.scaffold_334.1-359464 C 0 C 0 s ornAna1.chr2 14750994 201 - 54797317 --CCTTGGA---------AATGTTACTGCAAAAGTGAAAGGCTCATTGTTTTCTTTCTATCTTAAGCCTTTTTAAAAGTGTATTGTAATTATGATCTTCATTTCCCCGCTAACAAAGCCCTCATTA----AAATATCTTTGTATTTTA-ACGACATACAGCCCATTTCCAAAATCTTAGTTCC-TTTTTGGGTGCATTGTAT---TAAC----------------CGTTCTCTCTTT---------------- i ornAna1.chr2 N 0 I 5690 e echTel1.scaffold_288249 87661 7564 + 100002 I """, ) alignment = next(alignments) self.assertEqual(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.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.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.assertEqual( format(alignment, "maf"), """\ a score=-36127.000000 s mm9.chr10 3015028 58 + 129993255 ccatttt----------ttattaggtatttagctcatttacatttccaatgctatac----caaaagtcccc s loxAfr1.scaffold_75566 1616 33 - 10574 TCACTTCTA---------------------------------------CCTCCATTCCTTACAAAAGTTCTC q loxAfr1.scaffold_75566 999999999---------------------------------------999999999999999999999999 i loxAfr1.scaffold_75566 C 0 N 0 s cavPor2.scaffold_216473 8040 8 - 10026 ctgtgtc----------t------------------------------------------------------ q cavPor2.scaffold_216473 6788989----------9------------------------------------------------------ i cavPor2.scaffold_216473 C 0 I 1372 s tupBel1.scaffold_114895.1-498454 171763 1 - 498454 T----------------------------------------------------------------------- q tupBel1.scaffold_114895.1-498454 9----------------------------------------------------------------------- i tupBel1.scaffold_114895.1-498454 C 0 I 2374 s ponAbe2.chr6 16169731 12 - 174210431 TTTTGCCTTTTC------------------------------------------------------------ i ponAbe2.chr6 C 0 I 75 s calJac1.Contig6394 6627 22 + 133105 TGCTTTTTCTCAAATCTCCACT-------------------------------------------------- i calJac1.Contig6394 C 0 I 3479 s otoGar1.scaffold_334.1-359464 184539 36 - 359464 TTTTTTCTATT------------GACTTTTGCCAAATATTCACTTCCA------------------------ q otoGar1.scaffold_334.1-359464 99999999999------------9999999999999999999999999------------------------ i otoGar1.scaffold_334.1-359464 C 0 I 137 e ornAna1.chr2 14751195 5690 - 54797317 I e echTel1.scaffold_288249 87661 7564 + 100002 I e hg18.chr6 155028517 0 + 170899992 C e panTro2.chr6 157518570 0 + 173908612 C """, ) 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.assertEqual(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.assertTrue( np.array_equal(alignment.coordinates, np.array([[3015086, 3017658]])) ) 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.assertEqual( format(alignment, "maf"), """\ a score=0.000000 s mm9.chr10 3015086 2572 + 129993255 catacccacccacccccactcccctacccgcccactccccctttttggccctggcgttcccctgttctggggcatataaagtttgtgtgtccaatgggcctctctttccagtgatggccgactaggccatcttttgatacatatgcagctagagtcaagagctccggggtactggttagttcataatgttgatccacctatagggttgcagatccctttagctccttgggtactttctctagctcccccattgggagccctgtgatccatccattagctgactgtgggcatccacttctgtgtttgctaggccccggcatagtctcacaagagacagctacatctgggtcctttcgataagatcttgctagtgtatgcaatggtgtcagcgtttggatgctgattatggggtagatccctggataaggcagtctctacatggtccatcctttcatctcagctccaaactttgtctctgtaactccttccaagggtgttttgttcccacttctaaggaggggcatagtgtccacacttcagtcttcatttttcttgagtttcatgtgtttaggaaattgtatcttatatcttgggtatcctaggttttgggctaatatccacttatcagtgagtacatattgtgtgagttcctttgtgaatgtgttacctcactcaggatgatgccctccaggtccatccatttggctaggaatttcataaattaattctttttaatagctgagtagtactccattgtgtagatgtaccacattttctgtatccattcctctgttgaggggcatctgggttctttccagcttctggctattataaataaggctgctatgaacatagtggagcatgtgtccttcttaccagttggggcatcttttggatatatgcccaggagaggtattgctggatcctccggtagtactatgtccaattttctgaggaaccgccagacggatttccagagtggttgtacaagcctgcaatcccaccaacaatggaggagtgttcctctttctccacatcctcgccagcatctgctgtcacctgaatttttgatcttagccattctgactggtgtgaggtggaatctcagggttgttttgatttgcatttctctgatgattaaggatgttgaacatgttttcaggtgcttctctgccattcggtattcctcaggtgagaattctttgttcagttctgagccccattttttaatggggttatttgattttctgaagtccaccttcttgagttctttatatatgttggatattagtcccctatctgatttaggataggtaaagatcctttcccaatctgttggtggtctctttgtgttattgacggtgtcttttgccttgcagaaactttggagtttcattaggtcccatttgtcaattctcgatcttacagcacaagccattgctgttctgttcaggaatttttcccctgtgcccatatcttcaaggcttttccccactttctcctctataagtttcagtgtctctggttttatgtggagttctttgatccatttagatttgaccttagtacaaggagataagtatggatcgattcgcattcttctacatgataacaaccagttgtgccagcaccaattgttgaaaatgctgtctttcttccactggatggttttagctcccttgtcgaagatcaagtgaccataggtgtgtgggttcatttctgggtcttcaattctattccattggtctacttgtctgtctctataccagtaccatgcagtttttaccacaattgctctgtagtaaagctttaggtcaggcatggtgattccaccagaggttcttttatccttgagaagagtttttgctatcctaggttttttgttattccagatgaatttgcaaattgctccttctaattcgttgaagaattgagttggaattgtgatggggattgcattgaatctgtagattgcttttggcaagatagccatttttacaatgttgatcctgccaatccatgagcatgggagagctttccatcttctgagatcttctttaatttctttcttcagagacttgaagtttttatcatacagatctttcacttccttagttagagtcacgccgagatattttatattatttgtgactattgagaagggtgttgtttccctaatttctttctcagcctgtttattctttgtgtagagaaaggccattgacttgtttgagttaattttatatccagctacttcaccgaagctgtttatcaggtttaggagttctctggtggaatttttagggtcacttatatatactatcatatcatctgcaaaaagtgatattttgacttcctcctttccaatttgtatccccttgatctccttttgttgtcgaattgctctggctaatacttcaagtactatgttgaaaaggtagggagaaagtgggcagccttgtctagtccctgattttagtgagattgcttccagcttctctccatttactttgatgttggctactggtttgctgtagattgcttttatcatgtttaggtatgggTGTTCTCG e ornAna1.chr2 14751195 5690 - 54797317 I e calJac1.Contig6394 6649 3479 + 133105 I e tupBel1.scaffold_114895.1-498454 171764 2374 - 498454 I e echTel1.scaffold_288249 87661 7564 + 100002 I e cavPor2.scaffold_216473 8048 1372 - 10026 I e otoGar1.scaffold_334.1-359464 184575 137 - 359464 I e hg18.chr6 155028517 0 + 170899992 C e panTro2.chr6 157518570 0 + 173908612 C e ponAbe2.chr6 16169743 75 - 174210431 I """, ) alignment = next(alignments) self.assertEqual(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.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.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.assertEqual( format(alignment, "maf"), """\ a score=12170.000000 s mm9.chr10 3017658 85 + 129993255 TTTTTATTTGCAGGTTTCTTTAC----AGTTCTCTTTCATTCTTCTCCTCTTTTCTTCTGTTGACCTTTATCAGATTTCTGCTTTAACC s hg18.chr6 15871475 83 - 170899992 CCTTTCTTGGCAGGGTTATTTATAGCAAGTTATCTCTCTCTCTTA------TTTATTTTTTTGCCTTTTCCCAAATCTCCACTTCCACC i hg18.chr6 C 0 I 53 s panTro2.chr6 16390042 83 - 173908612 CCTTTCTTGGCAGGGTTATTTATAGCAAGTTATCTCTCTCTCTTA------TTTATTTTTTTGCCTTTTCCCAAATCTCCACTTCCACC q panTro2.chr6 999999999999999999999999999999999999999999999------99999999999999999999999999999999999999 i panTro2.chr6 C 0 I 53 e ornAna1.chr2 14751195 5690 - 54797317 I e calJac1.Contig6394 6649 3479 + 133105 I e tupBel1.scaffold_114895.1-498454 171764 2374 - 498454 I e echTel1.scaffold_288249 87661 7564 + 100002 I e cavPor2.scaffold_216473 8048 1372 - 10026 I e otoGar1.scaffold_334.1-359464 184575 137 - 359464 I e ponAbe2.chr6 16169743 75 - 174210431 I """, ) 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.assertEqual(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.assertTrue( np.array_equal(alignment.coordinates, np.array([[3017743, 3018161]])) ) 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.assertEqual( format(alignment, "maf"), """\ a score=0.000000 s mm9.chr10 3017743 418 + 129993255 ACCACAGACCTTCTGTTTAGTCCAAAGGACGCAAATTATGTATCCACTTtagtaggaggctgacccgcagcctacatgaaccaggtatttctggaaggcaggctggggttgaaagagaaattagatggtgagaaaagaataatgaggccaagacaaatttttctcttatcaaggcccaagagagtttactaagagactatgcttaaaagggggaaggcccatcccccccccccctcgcgccagtctatccttggtgctttgtcaccatgccatcagcacttggtcggcaggtagcagaatctcagggcagttgacacttcaaaagaaaccagccaagtcagaaagctgcactgcaggagacctgcactcagtggtgacaaggtctgtaccagcctgcttcaggctgggggaggctaca e ornAna1.chr2 14751195 5690 - 54797317 I e calJac1.Contig6394 6649 3479 + 133105 I e tupBel1.scaffold_114895.1-498454 171764 2374 - 498454 I e echTel1.scaffold_288249 87661 7564 + 100002 I e cavPor2.scaffold_216473 8048 1372 - 10026 I e otoGar1.scaffold_334.1-359464 184575 137 - 359464 I e hg18.chr6 15871558 53 - 170899992 I e panTro2.chr6 16390125 53 - 173908612 I e ponAbe2.chr6 16169743 75 - 174210431 I """, ) 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.assertEqual(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.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.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.assertEqual( format(alignment, "maf"), """\ a score=22499.000000 s mm9.chr10 3018161 69 + 129993255 ATCCACAAAAGAGAC-----AAAGAAGAAAACCAAAAGAAAAGATTGTAGCTTAAAACAATTCCATTTTATTGA s panTro2.chr6 16390178 65 - 173908612 ACCTACAAAGG---------AAAACAATTAACCATAAGAAAAGTTTGTACCATAAAACAATTTTATTTTATTGA q panTro2.chr6 99999999999---------999999999999999999999999999999999999999999999999999999 i panTro2.chr6 I 53 C 0 s hg18.chr6 15871611 65 - 170899992 ACCTACAAAGG---------AAAACAATTAACCACAAGAAAAGTTTGTACCATAAAACAATTTTATTTTATTGA i hg18.chr6 I 53 C 0 s ponAbe2.chr6 16169818 61 - 174210431 -------------ACAAAGGAAAACAATTAACCATAAGAAAAGTTTGTACCATAAAACAATTTTATTTTATTGA i ponAbe2.chr6 I 75 I 97 e ornAna1.chr2 14751195 5690 - 54797317 I e calJac1.Contig6394 6649 3479 + 133105 I e tupBel1.scaffold_114895.1-498454 171764 2374 - 498454 I e echTel1.scaffold_288249 87661 7564 + 100002 I e cavPor2.scaffold_216473 8048 1372 - 10026 I e otoGar1.scaffold_334.1-359464 184575 137 - 359464 I """, ) 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.assertEqual(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.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.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.assertEqual( format(alignment, "maf"), """\ a score=4781.000000 s mm9.chr10 3018230 129 + 129993255 AGGA-CAAAATAATACAGAtttttttttttttttttttttGCAGTACTGGAAATGGAATGAATGTCCCTCACAATCACTATCAAGGTCCCTATCAAGGCAATCACTCTGTCACCGAGCTA-CAGCCCCAGC s hg18.chr6 15871676 95 - 170899992 ATAATCCAATCAATATATAT---------------------CAGAACCTGGCTCCCAATG-----TTCTGATAGTCATTATGAA----------AAAGAATTTACACATATATAGATTTATTAGGTATATG i hg18.chr6 C 0 C 0 s panTro2.chr6 16390243 95 - 173908612 ATAATCCAATCAATATATAT---------------------CAGAACCTGGCTCCCAATG-----TTCTGATAGTCATTGTGAA----------AAAGAatttacacatatatagatttattaggtatatg q panTro2.chr6 99999999999999999999---------------------9999999999999999999-----9999999999999999999----------9999999999999999999999999999999999999 i panTro2.chr6 C 0 C 0 e ornAna1.chr2 14751195 5690 - 54797317 I e calJac1.Contig6394 6649 3479 + 133105 I e tupBel1.scaffold_114895.1-498454 171764 2374 - 498454 I e echTel1.scaffold_288249 87661 7564 + 100002 I e cavPor2.scaffold_216473 8048 1372 - 10026 I e otoGar1.scaffold_334.1-359464 184575 137 - 359464 I e ponAbe2.chr6 16169879 97 - 174210431 I """, ) 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.assertEqual(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.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.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.assertEqual( format(alignment, "maf"), """\ a score=61520.000000 s mm9.chr10 3018359 123 + 129993255 TT-CAAACATGCATACATGCATTCATGTCTCATAA-TAATTATTAACA-TTGTCTTAGGCCAGAGGCTCGACTGCCCCAAAGCAATCCACT-------TAAACTGTCCCTGAGAA-AGTCAttcctctccctaa s panTro2.chr6 16390338 131 - 173908612 -tataaatgtacaaatatatgtgtatgtCTCATAAATAATTATTAACAGTCATCTTAGGTCAGTGGCCTGAGTGATACAAACTAAGCCATCCATATTTTATATTCTCTCCGGGAAGGGTCATCCTTTTCTTT-- q panTro2.chr6 -99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999-- i panTro2.chr6 C 0 I 2400 s hg18.chr6 15871771 131 - 170899992 -TATAAACGTACAAATATATGTGTATGTCTCATAAATAATTATTAACAGTCATCTTAGGTCAGTGGCCTGAATGATACAAACTAAGCCATCCATATTTTATATTCTCTCCGGGAAGGGTCATCCTTTTCTTT-- i hg18.chr6 C 0 I 2402 s otoGar1.scaffold_334.1-359464 184712 127 - 359464 TT-TATACATGTATGTGTAAATGTAGGTCCTGTAAGTAATTATTAACATTTGTCTTAGGTTAGAGGCCCGAGTGACACAAGCTAACCCATCC------TATCCTCCCTGTGTGAAGGGTCATCCTTTCTTCTGA q otoGar1.scaffold_334.1-359464 99-99999999999999999999999999999999999999999999999999667736999999999999999999999999999995666------677755798899998999967967999999999589 i otoGar1.scaffold_334.1-359464 I 137 I 2731 s ponAbe2.chr6 16169976 129 - 174210431 ---taaatgtacaaatatatgtgtatgtgtcataaataATTATTAACAGTCATCTTAGGTCAGTGGCCTGAGTGATAGAAACTAAGCCATCCATATTTTATATTCTCTCTGGGAAGGGTCATCCTTTTCTTT-- i ponAbe2.chr6 I 97 I 2523 e ornAna1.chr2 14751195 5690 - 54797317 I e calJac1.Contig6394 6649 3479 + 133105 I e tupBel1.scaffold_114895.1-498454 171764 2374 - 498454 I e echTel1.scaffold_288249 87661 7564 + 100002 I e cavPor2.scaffold_216473 8048 1372 - 10026 I """, ) 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.assertEqual(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.assertTrue( np.array_equal(alignment.coordinates, np.array([[3018482, 3018644]])) ) self.assertEqual( str(alignment), """\ mm9.chr10 3018482 tcttcatctcctcttttcctccttttttttttctcatttctctttctctttcttttgtcc mm9.chr10 3018542 ttttccttTATAGCAAGCAAGGCAAGTAGTCTCTATTTAGAAGGCATggagagaatgggg mm9.chr10 3018602 agaggaggaaaggaggagaggggaggagaggaggggagGTAT 3018644 """, ) self.assertEqual( format(alignment, "maf"), """\ a score=0.000000 s mm9.chr10 3018482 162 + 129993255 tcttcatctcctcttttcctccttttttttttctcatttctctttctctttcttttgtccttttccttTATAGCAAGCAAGGCAAGTAGTCTCTATTTAGAAGGCATggagagaatggggagaggaggaaaggaggagaggggaggagaggaggggagGTAT e ornAna1.chr2 14751195 5690 - 54797317 I e calJac1.Contig6394 6649 3479 + 133105 I e tupBel1.scaffold_114895.1-498454 171764 2374 - 498454 I e echTel1.scaffold_288249 87661 7564 + 100002 I e cavPor2.scaffold_216473 8048 1372 - 10026 I e otoGar1.scaffold_334.1-359464 184839 2731 - 359464 I e hg18.chr6 15871902 2402 - 170899992 I e panTro2.chr6 16390469 2400 - 173908612 I e ponAbe2.chr6 16170105 2523 - 174210431 I """, ) 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.assertEqual(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.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.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.assertEqual( format(alignment, "maf"), """\ a score=1520.000000 s mm9.chr10 3018644 178 + 129993255 AGGGTAGGCCAAGTGCCTTGGGAAGTAGTTGTTGGTAGACTGAAAGTGTGTTC---TGAGTGTCAGTGATGTTCA-TGAGATTATCACCAGCAAGGATG--GCTGACGGGAACTG---CAAGAGGCATAGCCCTGAGTTCTAAAGGAGAGGGAAACGTCACAGAAAGGATG--------------------------CACTGTTTCAGCATCT s canFam2.chr1 78070420 204 - 125616256 AGAAAAGGCAAATGCCCCTGGGAGGGA-----TAGCACATTGA--GTTTATTCACATGCGTGTAAGTGATGGATACTGAGATCCTCTCC--TAAGGATGCGGTTGATGGAATCAGAAGCAAATACCACCAGCCAGAACTCTAAAATGAGAGGAAAGATCATGGATAGAATAGAATTGTAATATGAAATATAAAATTTCCCTATTGAAGAATTT q canFam2.chr1 999999999999999999999999999-----99999999999--99999999999999999999999999999999999999999999--99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999 i canFam2.chr1 N 0 I 160 e ornAna1.chr2 14751195 5690 - 54797317 I e calJac1.Contig6394 6649 3479 + 133105 I e tupBel1.scaffold_114895.1-498454 171764 2374 - 498454 I e echTel1.scaffold_288249 87661 7564 + 100002 I e cavPor2.scaffold_216473 8048 1372 - 10026 I e otoGar1.scaffold_334.1-359464 184839 2731 - 359464 I e hg18.chr6 15871902 2402 - 170899992 I e panTro2.chr6 16390469 2400 - 173908612 I e ponAbe2.chr6 16170105 2523 - 174210431 I """, ) 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.assertEqual(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.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.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.assertEqual( format(alignment, "maf"), """\ a score=1986.000000 s mm9.chr10 3018822 110 + 129993255 CTGCCTTCCATTACGATTTACTGATCACTTACAACCCTCCCACA----GAAGAGAACCTAACTTG-CTTAGGAGCATATGTACAGTTAATCAAGAC-----AAAAATAAGAATGGAGACt s canFam2.chr1 78070784 119 - 125616256 CTTTTTTTCCCTGCCCATTATTACTCACTTAAAATTCTCC-ACATTGTAAAGGGAATTCAAATCGACTTCTAGAGATGCACACAATTTAGCAAGATCAACTAAAAATAAGTATGGAAAAT q canFam2.chr1 9999999999999999999999999999999999999999-9999999999999999999999999999999999999999999999999999999999999999999999999999999 i canFam2.chr1 I 160 C 0 e ornAna1.chr2 14751195 5690 - 54797317 I e calJac1.Contig6394 6649 3479 + 133105 I e tupBel1.scaffold_114895.1-498454 171764 2374 - 498454 I e echTel1.scaffold_288249 87661 7564 + 100002 I e cavPor2.scaffold_216473 8048 1372 - 10026 I e otoGar1.scaffold_334.1-359464 184839 2731 - 359464 I e hg18.chr6 15871902 2402 - 170899992 I e panTro2.chr6 16390469 2400 - 173908612 I e ponAbe2.chr6 16170105 2523 - 174210431 I """, ) 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.assertEqual(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.assertTrue( np.array_equal(alignment.coordinates, np.array([[3018932, 3019271]])) ) 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.assertEqual( format(alignment, "maf"), """\ a score=0.000000 s mm9.chr10 3018932 339 + 129993255 gtctgagttagggttttactgctgtgaacagacaccatgaccaaggcatgtcttataaaaaaaatttaattagggctggcttacagattcagaggttcagtgggagcatcaaggtgggggcatggcagcatccaggcaggcatggtgcaggcagagctgagagttctacatcttcatccaaaggcttctagtggaagactgacttccaggcacctagggtgagggtcttaagcccacacccacagtgacacacctattccaaccaggtcacacctattccaacaaggccatacctccaaatggcaccactcctggtccaagaatatacaaaccatgaca e canFam2.chr1 47545353 0 + 125616256 C e ornAna1.chr2 14751195 5690 - 54797317 I e calJac1.Contig6394 6649 3479 + 133105 I e tupBel1.scaffold_114895.1-498454 171764 2374 - 498454 I e echTel1.scaffold_288249 87661 7564 + 100002 I e cavPor2.scaffold_216473 8048 1372 - 10026 I e otoGar1.scaffold_334.1-359464 184839 2731 - 359464 I e hg18.chr6 15871902 2402 - 170899992 I e panTro2.chr6 16390469 2400 - 173908612 I e ponAbe2.chr6 16170105 2523 - 174210431 I """, ) 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.assertEqual(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.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.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.assertEqual( format(alignment, "maf"), """\ a score=228.000000 s mm9.chr10 3019271 106 + 129993255 GAGACCAAATG------------TGGCGCTCACG-TGAGGCCAGGAGTAAATCGCACACACAGCCCATGCTTTCACCATCTGCTAGGGTGCTCTGGAGCAGGGCAGGCTTCTAACCTGG s canFam2.chr1 78070903 106 - 125616256 GAGGC-AAATGGAAAATGCCCCACGATGTCCAGGCTGTGTCCATGTGTGA--CGCACATGCTGTCC----------CACCTGCTTCTATTCACTTGACACACATAGGTCCCAAACCTGG q canFam2.chr1 99999-99999999999999999999999999999999999999999999--99999999999999----------9999999999999999999999999999999999999999999 i canFam2.chr1 C 0 C 0 e ornAna1.chr2 14751195 5690 - 54797317 I e calJac1.Contig6394 6649 3479 + 133105 I e tupBel1.scaffold_114895.1-498454 171764 2374 - 498454 I e echTel1.scaffold_288249 87661 7564 + 100002 I e cavPor2.scaffold_216473 8048 1372 - 10026 I e otoGar1.scaffold_334.1-359464 184839 2731 - 359464 I e hg18.chr6 15871902 2402 - 170899992 I e panTro2.chr6 16390469 2400 - 173908612 I e ponAbe2.chr6 16170105 2523 - 174210431 I """, ) 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.assertEqual(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.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.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.assertEqual( format(alignment, "maf"), """\ a score=10938.000000 s mm9.chr10 3019377 88 + 129993255 CCCCAGCATTCTGGCAGACACAGTG-AAAAGAGACAGATGGTCACTAATAAAATCTGT-ATAAATTAG-ATCTCAGAGGATGGATGGACCA s felCat3.scaffold_205680 72509 88 - 119354 CCCAAGTGTTCTGATAGCTAATGTGAAAAAGAAGCATGTGCCCACCAGTAAGCTTTGTGGTGAACTAGAATCTCAGAGGATG---GGACTC q felCat3.scaffold_205680 9999999999999999999999999999999999999999999999999999999999999999999999999999999999---999999 i felCat3.scaffold_205680 N 0 C 0 s canFam2.chr1 78071009 88 - 125616256 CCCAAGTGTTCTGATTGCCTCTGTGAAAAAGAAACATGGGCCCGCTAATAagatttgcaatgacctagaatctcagaggatg---ggactc q canFam2.chr1 9999999999999999999999999999999999999999999999999999999999999999999999999999999999---999999 i canFam2.chr1 C 0 C 0 e ornAna1.chr2 14751195 5690 - 54797317 I e calJac1.Contig6394 6649 3479 + 133105 I e tupBel1.scaffold_114895.1-498454 171764 2374 - 498454 I e echTel1.scaffold_288249 87661 7564 + 100002 I e cavPor2.scaffold_216473 8048 1372 - 10026 I e otoGar1.scaffold_334.1-359464 184839 2731 - 359464 I e hg18.chr6 15871902 2402 - 170899992 I e panTro2.chr6 16390469 2400 - 173908612 I e ponAbe2.chr6 16170105 2523 - 174210431 I """, ) 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.assertEqual(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.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.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.assertEqual( format(alignment, "maf"), """\ a score=36924.000000 s mm9.chr10 3019465 47 + 129993255 AAGATAGATATTTAGAAGTAGCTTTTTATGTTTTTCTGATGTGTGTT s calJac1.Contig6394 10128 47 + 133105 aacaTCTATATTTTGAAATGGCTTTTCATGTTACTCTGATGTGTGTC i calJac1.Contig6394 I 3479 C 0 s panTro2.chr6 16392869 40 - 173908612 -------atattttgaaatggcttttcatgttattctgatgTGTTTT q panTro2.chr6 -------9999999999999999999999999999999999999999 i panTro2.chr6 I 2400 C 0 s hg18.chr6 15874304 40 - 170899992 -------atattttgaaatggcttttcatgttattctgatgTGTTTT i hg18.chr6 I 2402 C 0 s canFam2.chr1 78071097 44 - 125616256 ---aggtatatttaaaaatagctcttcatgttgttctaatgtgtgtt q canFam2.chr1 ---99999999999999999999999999999999999999999999 i canFam2.chr1 C 0 C 0 s felCat3.scaffold_205680 72597 43 - 119354 ---ACGTGTTTTTAAAAATAG-TTTTCATGTTGTTCTGATGTGTGTT q felCat3.scaffold_205680 ---999999999999999999-9999999999999999999999999 i felCat3.scaffold_205680 C 0 I 193 e ornAna1.chr2 14751195 5690 - 54797317 I e tupBel1.scaffold_114895.1-498454 171764 2374 - 498454 I e echTel1.scaffold_288249 87661 7564 + 100002 I e cavPor2.scaffold_216473 8048 1372 - 10026 I e otoGar1.scaffold_334.1-359464 184839 2731 - 359464 I e ponAbe2.chr6 16170105 2523 - 174210431 I """, ) 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.assertEqual(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.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.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.assertEqual( format(alignment, "maf"), """\ a score=20303.000000 s mm9.chr10 3019512 92 + 129993255 TGCATCATTAAGACTAGAGTTCCT---------------TTCTGTCTT---TGCTTTCTTG--------ACAGGGCCATGCTCGGCAGTCATTCTTAGACTGCTTTTTGTTTgtttgg s calJac1.Contig6394 10175 86 + 133105 --CCTCATGAAGGCCCAAGTTCCTAAA-----ACATTAATTCTCTTCC---TATTTCCTAGCTGTCTCGCCTAGGCCTTGCCCGCCAGCAATTCCC---------------------- i calJac1.Contig6394 C 0 C 0 s panTro2.chr6 16392909 93 - 173908612 --CTTCATTAAGGCCCAAGTTCCTAAA-----ACATTCATTCTCTTCC---TCTTTTCTAG------AAAAGAGGTCTTGCCCGCCAGCAATTCCCACATGGGTATTGG--------- q panTro2.chr6 --9999999999999999999999999-----9999999999999999---9999999999------999999999999999999999999999999999999999999--------- i panTro2.chr6 C 0 C 0 s hg18.chr6 15874344 93 - 170899992 --CTTCATTAAGGCCCAAGTTCCTAAA-----ACATTCATTCTCTTCC---TCTTTTCTAG------AAAAGAGGTCTTGCCCGCCAGCAATTCCCACATGGGTATTGG--------- i hg18.chr6 C 0 C 0 s canFam2.chr1 78071141 97 - 125616256 --CCTCATCTAAACCCAGGTTCTTACAGGCTTATATTTTTTCTTTCTTCAACCCTTCCTCA--------TCAGTGTCTTGCCTGCCAGTCATTCCTAC-----------TTTGTTCGG q canFam2.chr1 --99999999999999999999999999999999999999999999999999999999999--------99999999999999999999999999999-----------999999999 i canFam2.chr1 C 0 C 0 e felCat3.scaffold_205680 72640 193 - 119354 I e ornAna1.chr2 14751195 5690 - 54797317 I e tupBel1.scaffold_114895.1-498454 171764 2374 - 498454 I e echTel1.scaffold_288249 87661 7564 + 100002 I e cavPor2.scaffold_216473 8048 1372 - 10026 I e otoGar1.scaffold_334.1-359464 184839 2731 - 359464 I e ponAbe2.chr6 16170105 2523 - 174210431 I """, ) 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.assertEqual(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.assertTrue( np.array_equal(alignment.coordinates, np.array([[3019604, 3019702]])) ) self.assertEqual( str(alignment), """\ mm9.chr10 3019604 tttggtttggtttggttttttcaagacagggtttctttgtatagtcctagctgtcctgga mm9.chr10 3019664 actcactttgtagaccagactggccttgaactcagaaa 3019702 """, ) self.assertEqual( format(alignment, "maf"), """\ a score=0.000000 s mm9.chr10 3019604 98 + 129993255 tttggtttggtttggttttttcaagacagggtttctttgtatagtcctagctgtcctggaactcactttgtagaccagactggccttgaactcagaaa e felCat3.scaffold_205680 72640 193 - 119354 I e canFam2.chr1 47545018 0 + 125616256 C e ornAna1.chr2 14751195 5690 - 54797317 I e calJac1.Contig6394 10261 0 + 133105 C e tupBel1.scaffold_114895.1-498454 171764 2374 - 498454 I e echTel1.scaffold_288249 87661 7564 + 100002 I e cavPor2.scaffold_216473 8048 1372 - 10026 I e otoGar1.scaffold_334.1-359464 184839 2731 - 359464 I e hg18.chr6 155025555 0 + 170899992 C e panTro2.chr6 157515610 0 + 173908612 C e ponAbe2.chr6 16170105 2523 - 174210431 I """, ) 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.assertEqual(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.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[3019702, 3019725, 3019725, 3019744], [ 46521, 46498, 46466, 46447], ]) # fmt: on ) ) 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.assertEqual( format(alignment, "maf"), """\ a score=45.000000 s mm9.chr10 3019702 42 + 129993255 tctgcctgcctctgcctcccaag--------------------------------tcctgggattaaaggcgtg s felCat3.scaffold_205680 72833 74 - 119354 tctgtctctctctctctctcaaaaataaacattaaaaaaaaCCAAACAAACAAACTCAAGTTCTTAAAGGTTTA q felCat3.scaffold_205680 99999999999999999999999999999999999999999999999999999999999999999999999999 i felCat3.scaffold_205680 I 193 C 0 e canFam2.chr1 47545018 0 + 125616256 C e ornAna1.chr2 14751195 5690 - 54797317 I e calJac1.Contig6394 10261 0 + 133105 C e tupBel1.scaffold_114895.1-498454 171764 2374 - 498454 I e echTel1.scaffold_288249 87661 7564 + 100002 I e cavPor2.scaffold_216473 8048 1372 - 10026 I e otoGar1.scaffold_334.1-359464 184839 2731 - 359464 I e hg18.chr6 155025555 0 + 170899992 C e panTro2.chr6 157515610 0 + 173908612 C e ponAbe2.chr6 16170105 2523 - 174210431 I """, ) 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.assertEqual(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.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.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.assertEqual( format(alignment, "maf"), """\ a score=-16865.000000 s mm9.chr10 3019744 33 + 129993255 -----------------cgccaccactgccctgcCT------------TAAACTGCTCTTAA s ponAbe2.chr6 16172628 27 - 174210431 -----------------CGCCAGCAATTCC------------------CACATGGGTATTGG i ponAbe2.chr6 I 2523 C 0 s tupBel1.scaffold_114895.1-498454 174138 4 - 498454 ----------------------------------------------------------TTGA q tupBel1.scaffold_114895.1-498454 ----------------------------------------------------------9999 i tupBel1.scaffold_114895.1-498454 I 2374 C 0 s calJac1.Contig6394 10261 13 + 133105 -------------------------------------------------ACATGGCTACTGG i calJac1.Contig6394 C 0 C 0 s otoGar1.scaffold_334.1-359464 187570 11 - 359464 ---------------------------------------------------ATTGGTGTTGA q otoGar1.scaffold_334.1-359464 ---------------------------------------------------87784564678 i otoGar1.scaffold_334.1-359464 I 2731 C 0 s oryCun1.scaffold_156751 192 41 - 4726 --------------------CACCATTGTCTTGCCTGTC-TCAGGTCCCATAGGGGTGTTGA q oryCun1.scaffold_156751 --------------------9999999999999999999-9999999999999999999999 i oryCun1.scaffold_156751 N 0 C 0 s felCat3.scaffold_205680 72907 62 - 119354 TGATTTCTCTTTCTCTTACTCATCAGTGTCTTGTCTTTCAGTCATTCCCACATTGGTGTAGA q felCat3.scaffold_205680 99999999999999999999999999999999999999999999999999999999999999 i felCat3.scaffold_205680 C 0 C 0 e canFam2.chr1 47545018 0 + 125616256 C e ornAna1.chr2 14751195 5690 - 54797317 I e echTel1.scaffold_288249 87661 7564 + 100002 I e cavPor2.scaffold_216473 8048 1372 - 10026 I e hg18.chr6 155025555 0 + 170899992 C e panTro2.chr6 157515610 0 + 173908612 C """, ) 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.assertEqual(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.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 ), ) ) 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.assertEqual( format(alignment, "maf"), """\ a score=367532.000000 s mm9.chr10 3019777 183 + 129993255 GGCAATGTCA-GGCTATGCGT------TCTAGACAGGGCACAAGAAAAGCTTTTAGCAGCAGAATAAACTTTT-AAAGTAAATTACTTTCCTTGATAGCAACTAGACGACCCAATTGA-TACAGT------GGAAAG-----A----------GGCCTTTGAGAAT---GCATGAGAGAATAT---TTCCTGTA------AGAGTTGAACAATTTAGAATTTACc s oryCun1.scaffold_156751 233 193 - 4726 GGCAACATCATGACCTTATGT------TCTAA----GGGACAGGAAAAGCTTTTTCCAGTAGAATAAGCCTTT-AGAGGAAACTGCTTCCCTTGCTAGTAATCAAGTGTTCAAAGTGA-TACAACAAAGAAAAAAAA-----A----------GCCTTTTGGGAAT-CAGGATGGAATAATATTACTTCCCCTATTTCTCAGAGCTAAATAGTTTAGGATT---- q oryCun1.scaffold_156751 999999999999999999999------99999----9999999999989999999998999999999999999-99999999999999999999999999999999999998989999-999899799999999999-----9----------9997999999998-978998999999999999999978999999979689999999999999999979---- i oryCun1.scaffold_156751 C 0 I 37 s hg18.chr6 15874437 190 - 170899992 GGCAACACCATGA-TACATAT------TCAAGATAAAGTACAGGAAAAGCTTTTTGCAGTGGAATAAAATGTT-AAAGGGAATTGCTTTCCTTGATAGCAATCAGGTCACCAAAGTGA-GATGA-------AGAAAA-----A----------TTTTTTTGAGAATGCAGGATAGAATAATATTATTTCCCTTATTTCTAAGAGTTAAACAATTTAGGATT---- i hg18.chr6 C 0 C 0 s panTro2.chr6 16393002 191 - 173908612 GGCAACACCATGA-TACATAT------TCAAGATAAAGTACAGGAAAAGCTTTTTGCAGTGGAATAAAATGTT-AAAGGAAATTGCTTTCCTTGATAGCAATCAGGTCACCAAAGTGA-GATGA-------AGAAAA-----A---------TTTTTTTTGAGAATGCAGGATAGAATAATATTATTTCCCTTATTTCTAAGAGTTAAACAATTTAGGATT---- q panTro2.chr6 9999999999999-9999999------9999999999999999999999999999999999999999999999-99999999999999999999999999999999999999999999-99999-------999999-----9---------999999999999999999999999999999999999999999999999999999999999999999999---- i panTro2.chr6 C 0 C 0 s ponAbe2.chr6 16172655 190 - 174210431 GGCAACACCATGA-TACATAT------TCAAGATAAAGTACAGGAAAAGCTTTTTGCGGTGGAATAAAATGTT-AAAGGAAATTGCTTTCCTTGATAGCAATCAGGTCACCAAAGTGA-GATGA-------AGAAAA-----A---------TTCTTTTTGAGAATGCAGCACAGAATAATATTATTTCCCTTATTTCT-AGAGTTAAACAATTTAGGATT---- i ponAbe2.chr6 C 0 I 21 s calJac1.Contig6394 10274 187 + 133105 GGCAACACCGTGA-TACATAT------CCGAGATAAAGTACAGGAAAAGC-TTTTGCAGTGGACGAAAATGTT-GAAGGAAATTGCTTTTCTTGATAGCAATCAGGTCACCAAAGTGA-GATGA-------AGAAA-----------------GTTTTTTGAGAATGTGGGATAGAATAATATTGTTTTCGTTATTTCTAAGAGTTAAACAATTTAGGATT---- i calJac1.Contig6394 C 0 I 21 s otoGar1.scaffold_334.1-359464 187581 197 - 359464 GGCAACGCCGTGA-TCCTTGCTGTAGATAAAGACAAAGTGCAGGAAAAGCCCTTTACGGTAGAATAAAAGGTT-AAAGGAAATTGCTTTTCTTGATAGCAATCAGGTGACCAAAGTGATTATAA-------AGAAAA-----A----------ATGTTTTGAGAATGCTGGAAAGAATAATTTTATCCACCCTCCATTTCAGAGTTAAATAATTCAGGATT---- q otoGar1.scaffold_334.1-359464 5466765345564-89977768969797886996999557766667768677897764536465578775526-67697777697779896767576676677696675376877786786858-------478887-----7----------56858859779666569356677477759968759378767656876769557597655596536566---- i otoGar1.scaffold_334.1-359464 C 0 I 358 s tupBel1.scaffold_114895.1-498454 174142 196 - 498454 GGCAATGTCATGA----ATGT------TCTAGATAAAGTACAGGAAAAGCTTTTTGCAGTAGGATAAACTTTT-AAAGGAAATTGCCTTCCTTGACAGCAATCAGGTGACCAAAGTCATACTGA-------AAAAAA-----AAACAAAAACAAACTTTTGTGGATGCAGTATAGAAGCATATTATTTTCCCTATGTCT--AAGTTAAATAACTTGGGCTT---- q tupBel1.scaffold_114895.1-498454 9999999999999----9999------9999999999999999999999999999999999999999999999-99999999999999999999999999999999999999999999999999-------999999-----999999999999999999999999999999999999999999999999999999999--99999999999999999999---- i tupBel1.scaffold_114895.1-498454 C 0 I 623 s felCat3.scaffold_205680 72969 186 - 119354 GACATC---ATAA-AGTACAT------TCTAGATAAAGTGCAGGAAAAGCATTTTG-AGTAGAATAAAATGTT-GTAGGAAATTGCTTTCTTCAAGAGACATTAGGTGATTAAAGTAA-TATAA-------AGGGAA-----T----------TTTTTTTGAGAATACAGGATACAATAATATTATTTCCCCTACATCTAAGAGttaaataatttaaaatt---- q felCat3.scaffold_205680 999999---9999-9999999------99999999999999999999999999999-9999999999999999-99999999999999999999999999999999999999999999-99999-------999999-----9----------99999999999999999999999999999999999999999999999999999999999999999999---- i felCat3.scaffold_205680 C 0 I 27 s canFam2.chr1 78071238 193 - 125616256 ------ATCATGA-TGTAAAT------TCCGGGTAAAGTACAACAAAAGGATTTTG-AACAGGATAAAATGTTAATAGGAAATTACTTTCTTTGAGAGCAATCAGGTGATTGAAGGAA-TATAA-------AGGGAAAAAACA----------AAGTTCAGTGAATCCAAGTTAGAATAATATTGTTTCCCTTACTTCTAAGAGttaaataatttaaaatttaat q canFam2.chr1 ------9999999-9999999------99999999999999999999999999999-9999999999999999999999999999999999999999999999999999999999999-99999-------999999999999----------999999999999999999999999999999999999999999999999999999999999999999999999 i canFam2.chr1 C 0 C 0 e ornAna1.chr2 14751195 5690 - 54797317 I e echTel1.scaffold_288249 87661 7564 + 100002 I e cavPor2.scaffold_216473 8048 1372 - 10026 I """, ) alignment = next(alignments) self.assertEqual(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.assertTrue( np.array_equal(alignment.coordinates, np.array([[3019960, 3020717]])) ) 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.assertEqual( format(alignment, "maf"), """\ a score=0.000000 s mm9.chr10 3019960 757 + 129993255 actagggatgggagaggctcccagaacccagtaatgatgacattaagaaatacacaacagttgggaaatggaacccaaagagaacacctccagtagataagcatgacccccagttgagggatgggcccatgcacccatcttaaaattttggacccagaattattcttctcaaaaggaaatgcagggatgaaaatggagcagagactggaagaaaggccaaccagagactgccctaactcaggatccatcgcatgtgcaggcaccaaccccaacactattgctgatgccatgttgtacttgctgatggaagcctggcatggctgtcctctgagagtctcaaatgaggcacctgacagatgcagatacttacagccaaccaatggactgagccccgggacctcaataaaagaatgaggggatggcaaccccataggaagaacaacagtatcaactccctggactcctcagagctcccggggactaagccaccaactaaagagcatacataggctgctctgaggccccagatacatatgtagcagaggactgcctcagtgggaggggatgtgcttggtcttgtgaaggcttgatgctccagagaaggaggatgctagaggggtgaggtgggagtggatgggtgggtgggcaggggagcaccctcttagaggacaagggctctggggtgggggagctcatggagggggaactgggaaggagggagaacatttgaaatgtaaataaataaaataataaaaaa e felCat3.scaffold_205680 73155 27 - 119354 I e canFam2.chr1 47544825 0 + 125616256 C e ornAna1.chr2 14751195 5690 - 54797317 I e calJac1.Contig6394 10461 21 + 133105 I e tupBel1.scaffold_114895.1-498454 174338 623 - 498454 I e echTel1.scaffold_288249 87661 7564 + 100002 I e cavPor2.scaffold_216473 8048 1372 - 10026 I e otoGar1.scaffold_334.1-359464 187778 358 - 359464 I e hg18.chr6 155025365 0 + 170899992 C e panTro2.chr6 157515419 0 + 173908612 C e ponAbe2.chr6 16172845 21 - 174210431 I e oryCun1.scaffold_156751 426 37 - 4726 I """, ) 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.assertEqual(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.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.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.assertEqual( format(alignment, "maf"), """\ a score=8951.000000 s mm9.chr10 3020717 44 + 129993255 TGTCAAACATGCATAAAGATATACT-GAGGAGCCCATGAATTTTA s canFam2.chr1 78071431 33 - 125616256 tGTT------------TAACATAATAGAGGGGCCCATGAATTTTA q canFam2.chr1 9999------------99999999999999999999999999999 i canFam2.chr1 C 0 I 9 s panTro2.chr6 16393193 38 - 173908612 ----AAAAAT---TTTAAATATACTAGAGGGGTCCATGAATTTTA q panTro2.chr6 ----999999---99999999999999999999999999999999 i panTro2.chr6 C 0 I 11 s hg18.chr6 15874627 38 - 170899992 ----AAAAAT---TTTAAATATACTAGAGGGGTCCATGAATTTTA i hg18.chr6 C 0 I 11 e felCat3.scaffold_205680 73155 27 - 119354 I e ornAna1.chr2 14751195 5690 - 54797317 I e calJac1.Contig6394 10461 21 + 133105 I e tupBel1.scaffold_114895.1-498454 174338 623 - 498454 I e echTel1.scaffold_288249 87661 7564 + 100002 I e cavPor2.scaffold_216473 8048 1372 - 10026 I e otoGar1.scaffold_334.1-359464 187778 358 - 359464 I e ponAbe2.chr6 16172845 21 - 174210431 I e oryCun1.scaffold_156751 426 37 - 4726 I """, ) 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.assertEqual(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.assertTrue( np.array_equal(alignment.coordinates, np.array([[3020761, 3020918]])) ) self.assertEqual( str(alignment), """\ mm9.chr10 3020761 TATATATGCTATCCGTGTGCTGTGATTTTTGTTTTAAATGTTATTTTATGTATATGcaag mm9.chr10 3020821 attttgcattgtagcagaaggtggcttcaaactcacgatcctcctgcctcagccttccaa mm9.chr10 3020881 gtgctgagatcatacctctgcaccatcctgcccACCT 3020918 """, ) self.assertEqual( format(alignment, "maf"), """\ a score=0.000000 s mm9.chr10 3020761 157 + 129993255 TATATATGCTATCCGTGTGCTGTGATTTTTGTTTTAAATGTTATTTTATGTATATGcaagattttgcattgtagcagaaggtggcttcaaactcacgatcctcctgcctcagccttccaagtgctgagatcatacctctgcaccatcctgcccACCT e felCat3.scaffold_205680 73155 27 - 119354 I e canFam2.chr1 78071464 9 - 125616256 I e ornAna1.chr2 14751195 5690 - 54797317 I e calJac1.Contig6394 10461 21 + 133105 I e tupBel1.scaffold_114895.1-498454 174338 623 - 498454 I e echTel1.scaffold_288249 87661 7564 + 100002 I e cavPor2.scaffold_216473 8048 1372 - 10026 I e otoGar1.scaffold_334.1-359464 187778 358 - 359464 I e hg18.chr6 15874665 11 - 170899992 I e panTro2.chr6 16393231 11 - 173908612 I e ponAbe2.chr6 16172845 21 - 174210431 I e oryCun1.scaffold_156751 426 37 - 4726 I """, ) 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.assertEqual(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.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.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.assertEqual( format(alignment, "maf"), """\ a score=85471.000000 s mm9.chr10 3020918 96 + 129993255 GAGGTTTGTGACTTTTAATA----------CTGATTGTTATCTAACATCACAGAATTCTCAGTTCTTAAGGAAACAATTGTTCTGTGTGTTATTTGTCTAGGAGGA s hg18.chr6 15874676 73 - 170899992 ---------------------------------ATGGTTATTTAATACTGCACAATCCTCAGCTTTTAAGGAAAAACATGTTTGACTTATTAATTATTTAGGACAA i hg18.chr6 I 11 C 0 s panTro2.chr6 16393242 73 - 173908612 ---------------------------------ATGGTTATTTAATACTGCACAATCCTCAGCTTTTAAGGAAAAACATGTTTGACTTATTAATTATTTAGGACAA q panTro2.chr6 ---------------------------------9999999999999999999999999999999999999999999999999999999999999999999999999 i panTro2.chr6 I 11 C 0 s canFam2.chr1 78071473 75 - 125616256 --------------------------TAATAAAATAATTCTGTACCATTATGAAGTTCTCAGCTCTTAAGGAAAAA-----GTGATTTGTTAATTACTTAGGACAA q canFam2.chr1 --------------------------99999999999999999999999999999999999999999999999999-----9999999999999999999999999 i canFam2.chr1 I 9 C 0 s felCat3.scaffold_205680 73182 76 - 119354 ---GTCCATGAATTTTAATGGTGAAGTAATGAAATAATTCTTTAATATCAC----------------------AAA-----GTAATTTATTAATTATTTAGGACAA q felCat3.scaffold_205680 ---999989999999999999999999999999999999999999999999----------------------999-----9999999999999999999999769 i felCat3.scaffold_205680 I 27 C 0 s cavPor2.scaffold_216473 9420 82 - 10026 GAGTTCTGCAAATtttaata----------ggaaaagaagatTAATATTACAAAGTTTTCAGTTCTGATGGAAaaa----------gtgtgatttttttaaa---- q cavPor2.scaffold_216473 99679966799668566465----------8567828838346568788268865663676558367765776667----------6965686997776684---- i cavPor2.scaffold_216473 I 1372 I 28 s oryCun1.scaffold_156751 463 102 - 4726 -AGATCCATGAATTTTAATA---AAGCAATGAGATAATTATTTAATGTTGGAAAATCCTCAAGTCTTAAGGAAAAAAGTGTTTGACTTGTTAATGACTTGGGATGA q oryCun1.scaffold_156751 -9999997999999999999---99999999999999999999999999999999998677999969999999999999999999999999999999999999999 i oryCun1.scaffold_156751 I 37 C 0 s calJac1.Contig6394 10482 100 + 133105 GGGGTCCATGAATTTTAATA-----GTAACAAAATGGTTATTCAATATTGCAAAATCCTCAGC-TTTAAGGAAAAACATATTTGATTTGTTAATTATTTAGGACAA i calJac1.Contig6394 I 21 C 0 s ponAbe2.chr6 16172866 101 - 174210431 GGGGTCCATGAATTTTAATA-----GTAATAAAATGGTTATTTAATATTGCAAAATCCTCAGCTTTTAAGGAAAAACGTGTTTGACTTATTAATTATTTAGGACAA i ponAbe2.chr6 I 21 C 0 e ornAna1.chr2 14751195 5690 - 54797317 I e tupBel1.scaffold_114895.1-498454 174338 623 - 498454 I e echTel1.scaffold_288249 87661 7564 + 100002 I e otoGar1.scaffold_334.1-359464 187778 358 - 359464 I """, ) 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.assertEqual(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.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.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.assertEqual( format(alignment, "maf"), """\ a score=105724.000000 s mm9.chr10 3021014 40 + 129993255 ACCTTGGTGACGCCACTGGATTTTGTATGACTGAATACTG s oryCun1.scaffold_156751 565 40 - 4726 ATCTTGATGAAGTCATTCCAACTTGGATGATTTAGGAATT q oryCun1.scaffold_156751 9999999999999969999699999999999999999999 i oryCun1.scaffold_156751 C 0 C 0 s otoGar1.scaffold_334.1-359464 188136 40 - 359464 ATCTTGGTGAAGTTATTCCAATTTATGTGATTTAGGAATG q otoGar1.scaffold_334.1-359464 9999999999999999999999999999999999999999 i otoGar1.scaffold_334.1-359464 I 358 C 0 s calJac1.Contig6394 10582 40 + 133105 ATTTTGGTGAAGTTATTCCAACTTGTGTGGCTTAGGAATG i calJac1.Contig6394 C 0 C 0 s hg18.chr6 15874749 40 - 170899992 ATTTTGGTGAAGTTATTCCAACTTGCATGGCTTAGGAATG i hg18.chr6 C 0 C 0 s panTro2.chr6 16393315 40 - 173908612 ATTTTGGTGAAGTTATTCCAACTTGCATGGCTTAGGAATG q panTro2.chr6 9999999999999999999999999999999999999999 i panTro2.chr6 C 0 C 0 s ponAbe2.chr6 16172967 40 - 174210431 ATTTTGGTGAAGTTATTCCAACTTGCATGGCTTAGGAATG i ponAbe2.chr6 C 0 C 0 s canFam2.chr1 78071548 40 - 125616256 ATCTCAGTGAAGTCATTCTGACTCGCATGATTTAGGAATG q canFam2.chr1 9999999999999999999999999999999999999999 i canFam2.chr1 C 0 C 0 s felCat3.scaffold_205680 73258 40 - 119354 ATCTCAGTGAAGTTATTCTGACTTGCATGATTTAGGTATG q felCat3.scaffold_205680 9999989999989988999997999979997996167779 i felCat3.scaffold_205680 C 0 C 0 s dasNov1.scaffold_56749 3116 40 - 10470 ACATCAGTGAAATCATTCCGACTCGTATGACTGAGCGATG q dasNov1.scaffold_56749 9759855999977756667495765475885678385647 i dasNov1.scaffold_56749 N 0 C 0 e ornAna1.chr2 14751195 5690 - 54797317 I e tupBel1.scaffold_114895.1-498454 174338 623 - 498454 I e echTel1.scaffold_288249 87661 7564 + 100002 I e cavPor2.scaffold_216473 9502 28 - 10026 I """, ) 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.assertEqual(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.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.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.assertEqual( format(alignment, "maf"), """\ a score=115790.000000 s mm9.chr10 3021054 50 + 129993255 CTCATTTGGGAACTTACAGGTCAGCAAAGGCTTCCAG--------------------GACTTACATGCAG s cavPor2.scaffold_216473 9530 38 - 10026 CTCATTTGGGAGTTCAGAGTT--------GCTATAAA--------------------TACTTGTGA---- q cavPor2.scaffold_216473 788777667898846665666--------98766677--------------------876665669---- i cavPor2.scaffold_216473 I 28 C 0 s oryCun1.scaffold_156751 605 69 - 4726 CTAATTTGGGCTCTTACATTTTATAACTGCCTAATGGAGTCTTCTTTTTTCCT-CCTTAATTACACGTAT q oryCun1.scaffold_156751 99999999999997999799999999999999999999999799799999997-9979999999495999 i oryCun1.scaffold_156751 C 0 C 0 s otoGar1.scaffold_334.1-359464 188176 69 - 359464 CTAACTTGGGGACACAGG-TTCATAAAGGCTTAATGGAGCCCACTGGTCCCTTCCCCAGACTCTATGTAC q otoGar1.scaffold_334.1-359464 999999999999999999-999999999999999999998999999689999999999999999999999 i otoGar1.scaffold_334.1-359464 C 0 C 0 s calJac1.Contig6394 10622 70 + 133105 CCAGTTTGGGGACTTAGATTTTCTAACTGCCTAATGAAGTCTGCTCTTTCCTTCCCTAGCCTATATGTAT i calJac1.Contig6394 C 0 C 0 s hg18.chr6 15874789 70 - 170899992 ACAATTTGGGGATTTACATTTCCTAACTGCCTAATGAAGTCTGCTCCTTCCTTCCCTAGACTATATGTAT i hg18.chr6 C 0 C 0 s panTro2.chr6 16393355 70 - 173908612 CCAATTTGGGGATTTACATTTCCTAACTGCCTAATGAAGTCTGCTCTTTCCTTCCCTAGACTATATGTAT q panTro2.chr6 9999999999999999999999999999999999999999999999999999999999999999999999 i panTro2.chr6 C 0 C 0 s ponAbe2.chr6 16173007 70 - 174210431 CCAATTTGGGGATTTACATTTCCTAACTGCCTAATGAAGTCTGCTCTTTCCTTCCCTAGACTATATGTAT i ponAbe2.chr6 C 0 C 0 s canFam2.chr1 78071588 70 - 125616256 CTAATTTGGTGACTCAAATTTCATAATTGCTTAATGAAAGCTGATGTTTTCTTCCCTACACCATATGTAT q canFam2.chr1 9999999999999999999999999999999999999999999999999999999999999999999999 i canFam2.chr1 C 0 C 0 s felCat3.scaffold_205680 73298 70 - 119354 CTAATTTGGTGACTTGAATTTCATAATTGCTTAAGGAAGCCTGCTGTTTCCTTCCCAAGACTATATGCAT q felCat3.scaffold_205680 9769999999975699868977669777966666596959759669595666758736585676666655 i felCat3.scaffold_205680 C 0 C 0 s dasNov1.scaffold_56749 3156 70 - 10470 CTAATTGGGGGACTCACATTTTAAAATTGCTAACCGAAGCCTGCTGTTTTCTTCTCTAGACTATAAGTAT q dasNov1.scaffold_56749 5556576999664654656985688667655565647767537567688856666555556565555656 i dasNov1.scaffold_56749 C 0 C 0 e ornAna1.chr2 14751195 5690 - 54797317 I e tupBel1.scaffold_114895.1-498454 174338 623 - 498454 I e echTel1.scaffold_288249 87661 7564 + 100002 I """, ) 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.assertEqual(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.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.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.assertEqual( format(alignment, "maf"), """\ a score=44222.000000 s mm9.chr10 3021104 32 + 129993255 CTGTTAGTGCTGTTTT---AATGTACCTCGCAGTA s cavPor2.scaffold_216473 9568 27 - 10026 -----ATTACTTTCTT---AATGTAAATTTTTATA q cavPor2.scaffold_216473 -----55455868746---7957999989884575 i cavPor2.scaffold_216473 C 0 C 0 s oryCun1.scaffold_156751 674 30 - 4726 TTGCTAGTA--TTCTC---AATGTAATATTTTATA q oryCun1.scaffold_156751 999979999--96665---6999999999999999 i oryCun1.scaffold_156751 C 0 C 0 s otoGar1.scaffold_334.1-359464 188245 32 - 359464 TTGCTGGTGTTCCCTT---AATATAATGTTTTATA q otoGar1.scaffold_334.1-359464 9999999999999999---9999999999999999 i otoGar1.scaffold_334.1-359464 C 0 C 0 s calJac1.Contig6394 10692 30 + 133105 TTACTCGTG--CCCTT---AATATAGCATTTTATA i calJac1.Contig6394 C 0 C 0 s hg18.chr6 15874859 30 - 170899992 TTGCTGGTA--CTCTT---AATATCACATTTTATA i hg18.chr6 C 0 C 0 s panTro2.chr6 16393425 30 - 173908612 TTGCTGGTA--CTCTT---AATATCACATTTTATA q panTro2.chr6 999999999--99999---9999999999999999 i panTro2.chr6 C 0 C 0 s ponAbe2.chr6 16173077 30 - 174210431 TTGCTGGTG--CTCTT---AATATAACATTTTATA i ponAbe2.chr6 C 0 C 0 s canFam2.chr1 78071658 25 - 125616256 TTGCTGGTGCTCTCAA---AATGTAGCA------- q canFam2.chr1 9999999999999999---999999999------- i canFam2.chr1 C 0 I 196 s felCat3.scaffold_205680 73368 25 - 119354 TTGCTGGTGCTCTCAA---AATATAACA------- q felCat3.scaffold_205680 8677668566555658---876555655------- i felCat3.scaffold_205680 C 0 I 6 s dasNov1.scaffold_56749 3226 33 - 10470 TTGCTGGTG--ATCTGATTAATGTAACATTTTATG q dasNov1.scaffold_56749 856647736--775356546747663745776545 i dasNov1.scaffold_56749 C 0 C 0 s echTel1.scaffold_288249 95225 21 + 100002 CTGTTAATG--CTCTG------------TTTTATG q echTel1.scaffold_288249 999999999--99999------------9999999 i echTel1.scaffold_288249 I 7564 C 0 e ornAna1.chr2 14751195 5690 - 54797317 I e tupBel1.scaffold_114895.1-498454 174338 623 - 498454 I """, ) 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.assertEqual(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.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.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.assertEqual( format(alignment, "maf"), """\ a score=43757.000000 s mm9.chr10 3021136 44 + 129993255 AGGCAAATGAGGTGATAAGA-------TTGTGTT-----TAC----TCCCTCTGTGC----------TTG s cavPor2.scaffold_216473 9595 43 - 10026 AG-CAGATGAGATAACAGTG-------ATATATT-----cat----tctctgtgtgt----------atg q cavPor2.scaffold_216473 49-96766988786798889-------8679566-----756----66896967579----------888 i cavPor2.scaffold_216473 C 0 C 0 s oryCun1.scaffold_156751 704 42 - 4726 AAGCAAATGAGGTGATGAGG---------GCATC-----TAT----TTCTTATTTGT----------GTG q oryCun1.scaffold_156751 99998999999999999999---------99999-----999----99999999999----------999 i oryCun1.scaffold_156751 C 0 C 0 s otoGar1.scaffold_334.1-359464 188277 45 - 359464 AAACAAATGAGATCACA-GG-------ACATATG-----TA--CTTGTCCCCCACGT----------GTG q otoGar1.scaffold_334.1-359464 99999999999999999-99-------9999999-----99--99939999999999----------999 i otoGar1.scaffold_334.1-359464 C 0 I 15 s calJac1.Contig6394 10722 45 + 133105 AAGCAAATGAGATCACA----------GCACATG-----TATATTTTTTCTCCGTGT----------GTG i calJac1.Contig6394 C 0 I 15 s hg18.chr6 15874889 47 - 170899992 AAACAAATGAGATCACAAGG-------GCATATA-----TGT-TTTTTTCTCTGTGT----------GTG i hg18.chr6 C 0 I 15 s panTro2.chr6 16393455 47 - 173908612 AAACAAATGAGATCACAAGG-------GCATATA-----TGT-TTTTTTCTCTGTGT----------GTG q panTro2.chr6 99999999999999999999-------9999999-----999-99999999999999----------999 i panTro2.chr6 C 0 I 15 s ponAbe2.chr6 16173107 47 - 174210431 AAACAAATGAGATCACAAGG-------GCATATG-----TAT-TTTTTTCTCTGTGT----------GTG i ponAbe2.chr6 C 0 I 15 s eriEur1.scaffold_266115 358 65 + 4589 taaataataagataagatgaaagCATAGCATGTA-----TTTTCTtgccctctccttctctgtctctgtc q eriEur1.scaffold_266115 9999999999999999999999999999999999-----9999999999999999999999999999999 i eriEur1.scaffold_266115 N 0 I 9 s canFam2.chr1 78071879 51 - 125616256 tAGAAAATGAGATACC-----------GTGTGTA-----TATGCTTTCTCTCTGTGT---GGGGTCTGTG q canFam2.chr1 9999999999999999-----------9999999-----999999999999999999---9999999999 i canFam2.chr1 I 196 I 9 s felCat3.scaffold_205680 73399 51 - 119354 AAGCAAATGAGATAAG-----------ACACGTG-----TATTCTTCCTCTCTGTGT---GGTGTCTGTG q felCat3.scaffold_205680 9755596656454353-----------5346324-----243451535354422233---3635339999 i felCat3.scaffold_205680 I 6 I 9 s dasNov1.scaffold_56749 3259 46 - 10470 AGGAAAGTGAGAGGACCAGG-------GCAAATA-----AATATTCTTTCTCTGTGT----------A-- q dasNov1.scaffold_56749 55569764556657658568-------6768555-----858686457859535656----------5-- i dasNov1.scaffold_56749 C 0 C 0 s echTel1.scaffold_288249 95246 51 + 100002 AAGAAGGTGAGATGACAAGG-------GTGTATAGATAGGATATTCTTGCTTTGGGT----------G-- q echTel1.scaffold_288249 99999999999999999999-------999999999999999999999999999999----------9-- i echTel1.scaffold_288249 C 0 C 0 e ornAna1.chr2 14751195 5690 - 54797317 I e tupBel1.scaffold_114895.1-498454 174338 623 - 498454 I """, ) 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.assertEqual(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.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.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.assertEqual( format(alignment, "maf"), """\ a score=32886.000000 s mm9.chr10 3021180 24 + 129993255 -------------------TCCC-------AGAGAGTCTGA-TAGGAGGAG s cavPor2.scaffold_216473 9638 32 - 10026 -------------------tgcctTTGTATAGTGGCTCTGAGTATAAAGTA q cavPor2.scaffold_216473 -------------------67576649966655666885655548785776 i cavPor2.scaffold_216473 C 0 C 0 s oryCun1.scaffold_156751 746 27 - 4726 -------------------TGCCTGTGTATAGCATTTCTGAATATA----- q oryCun1.scaffold_156751 -------------------999999999999999999999999999----- i oryCun1.scaffold_156751 C 0 C 0 s ponAbe2.chr6 16173169 25 - 174210431 -----------------------TCTG---AGTGTGTATGAATATGAAGTA i ponAbe2.chr6 I 15 C 0 s panTro2.chr6 16393517 25 - 173908612 -----------------------TCTG---AGTATGTATGAATATGAAGTA q panTro2.chr6 -----------------------9999---999999999999999999999 i panTro2.chr6 I 15 C 0 s hg18.chr6 15874951 25 - 170899992 -----------------------TCTG---AGTATGTATGAATATGAAGTA i hg18.chr6 I 15 C 0 s calJac1.Contig6394 10782 25 + 133105 -----------------------TCTG---AGTATGTCTGAATATGAAGTG i calJac1.Contig6394 I 15 C 0 s otoGar1.scaffold_334.1-359464 188337 25 - 359464 -----------------------TCTA---AGTGTGTCTGAACATGATGTG q otoGar1.scaffold_334.1-359464 -----------------------9999---999999999999999999999 i otoGar1.scaffold_334.1-359464 I 15 C 0 s tupBel1.scaffold_114895.1-498454 174961 25 - 498454 -----------------------TCTC---TGAGTGTCTGAACTTGAGGTA q tupBel1.scaffold_114895.1-498454 -----------------------9999---999999999999999999999 i tupBel1.scaffold_114895.1-498454 I 623 C 0 s eriEur1.scaffold_266115 432 19 + 4589 -----------------------TCTC---AGTGTGTCTGACCAG------ q eriEur1.scaffold_266115 -----------------------9999---999999999999999------ i eriEur1.scaffold_266115 I 9 C 0 s canFam2.chr1 78071939 25 - 125616256 -----------------------TCTG---AGTGTGTCTGAATGTGAGGTA q canFam2.chr1 -----------------------9999---999999999999999999999 i canFam2.chr1 I 9 C 0 s felCat3.scaffold_205680 73459 25 - 119354 -----------------------TCTG---AGTGTTCCTGAATGTGAGGTG q felCat3.scaffold_205680 -----------------------9999---999999999999999999999 i felCat3.scaffold_205680 I 9 C 0 s dasNov1.scaffold_56749 3305 47 - 10470 T-TGTGTGCCTTTGCGGAGCATTTCTG---AGCGTGTCTGAACTTGAGGTA q dasNov1.scaffold_56749 7-3659557766555777595699547---965955937797755656587 i dasNov1.scaffold_56749 C 0 C 0 s echTel1.scaffold_288249 95297 48 + 100002 TGCCCAGGACTGCGCATGGTATTTCTT---GGTGTGTCTGAAGGTGAGATA q echTel1.scaffold_288249 999999999999999999999999999---999999999999999999999 i echTel1.scaffold_288249 C 0 C 0 e ornAna1.chr2 14751195 5690 - 54797317 I """, ) 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.assertEqual(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.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 ), ) ) 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.assertEqual( format(alignment, "maf"), """\ a score=309116.000000 s mm9.chr10 3021204 71 + 129993255 TGCACTGGTTTTCC-TGCAGTGGTTCTCAGTAATAGGAAGACA-ACAGAATTTGAAGTATCCGGCTTTGGCCA s echTel1.scaffold_288249 95345 73 + 100002 GGCATTGGTTTTTAGAGAGAGAACCCACATAAGTAGGAAAACATTTTGAATTTATAGTAAATATTCTTGGCTA q echTel1.scaffold_288249 9999999999999999999999999999999999999999999999999999999999999999999999999 i echTel1.scaffold_288249 C 0 C 0 s dasNov1.scaffold_56749 3352 70 - 10470 TGCATTGATTTTCAGTGAGGGAAATCACAC---TAAGAGAGCATTTTGAATTTATAATAAATGCTCTTGGCTA q dasNov1.scaffold_56749 579663579997957596666783594865---8458696597898258979678997999677999997699 i dasNov1.scaffold_56749 C 0 C 0 s felCat3.scaffold_205680 73484 72 - 119354 TGCATTGATTTTCA-TGCATTGATTCACATGAATAGGAATGCATTTTGAAATTATAGCAAATGTTTTTGGCTG q felCat3.scaffold_205680 99999999999999-9999999999999999999999999999999999999999999999999999999999 i felCat3.scaffold_205680 C 0 C 0 s canFam2.chr1 78071964 71 - 125616256 TGCATTAATTTTCA-TGCGTTGATTCACATGAATAGGAATACA-TTTGAATTTATAGGAAATGCTTTTGGCTG q canFam2.chr1 99999999999999-9999999999999999999999999999-99999999999999999999999999999 i canFam2.chr1 C 0 C 0 s eriEur1.scaffold_266115 451 70 + 4589 -GCACTGATTCTCG-AGGGTTGATTCCCAGTAAGAGGAAACTG-CGTGAGTTTACAGTACATGGGCTTGGCTG q eriEur1.scaffold_266115 -9999999999999-9999999999999999999999999999-99999999999999999999999999799 i eriEur1.scaffold_266115 C 0 C 0 s sorAra1.scaffold_2476 3312 70 - 4997 TGCATTGATTTTTA-AGTATTGATTCACATGAAAAGGAAAGCA-CTTCAATTTATGATAAAT-GATTTGGCCA q sorAra1.scaffold_2476 89999999999989-9999999999999999999999999999-999999999799999999-9999999999 i sorAra1.scaffold_2476 N 0 C 0 s tupBel1.scaffold_114895.1-498454 174986 71 - 498454 TGCATTGAATTCCA-TGTGTTATGTCACATTAATAGGAAACGA-TTCTAATTGATAGGAAATGCTTCTGACCA q tupBel1.scaffold_114895.1-498454 99999899899999-9999999999999999999999999999-99999999999999999999999999997 i tupBel1.scaffold_114895.1-498454 C 0 C 0 s otoGar1.scaffold_334.1-359464 188362 67 - 359464 TG----GATTTTTA-CACATTGATTCACCTTAACGGGAAAACA-TGTGAATTTGTAGGAAAGGCATTTGGCCA q otoGar1.scaffold_334.1-359464 88----99999999-9899999899943848888999999999-66359999569699999923799351281 i otoGar1.scaffold_334.1-359464 C 0 I 6280 s calJac1.Contig6394 10807 71 + 133105 TGCATTGGTTTTTA-TGCCTTGATTCACATGAATAGGAAAACG-TTTGAATTTATAGGAAATGGTTTTGGCCA i calJac1.Contig6394 C 0 C 0 s hg18.chr6 15874976 71 - 170899992 TGCTTTGATTTTTA-TGCATTGATTTACATGAATAGGAAAATG-TTTGAATTTATAGTAAATGGTTTTGGCCA i hg18.chr6 C 0 C 0 s panTro2.chr6 16393542 71 - 173908612 TGCTTTGATTTTTA-TGCATTGATTTACATGAATAGGAAAACA-TTTGAATTTATAGTAAATGGTTTTGGCCA q panTro2.chr6 99999999999999-9999999999999999999999999999-99999999999999999999999999999 i panTro2.chr6 C 0 C 0 s ponAbe2.chr6 16173194 71 - 174210431 TGCTTTGATTTTTA-TGCATTGATTTACATGGATAGGAAAACG-TTTGAATTTATAGTAAATGGTTTTGGCCA i ponAbe2.chr6 C 0 C 0 s oryCun1.scaffold_156751 773 65 - 4726 ------TCTTTACA-TACTTTGATTTACATCGACGGGAAAACA-TTTGCATTTATAGCAATGGCTTTTGGTCA q oryCun1.scaffold_156751 ------99999994-9999999999999899999999999999-99999999999999899999999999999 i oryCun1.scaffold_156751 C 0 C 0 s cavPor2.scaffold_216473 9670 71 - 10026 GGCATTGATTTCCA-TGCATTAATTCACATTAATAGGAAAACA-GTCCAATTTATAGTAAATGGTTTTGGCCA q cavPor2.scaffold_216473 77888768786695-3886758796446556688656665478-68687676669688688666687574686 i cavPor2.scaffold_216473 C 0 C 0 e ornAna1.chr2 14751195 5690 - 54797317 I """, ) alignment = next(alignments) self.assertEqual(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.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 ), ) ) 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.assertEqual( format(alignment, "maf"), """\ a score=891219.000000 s mm9.chr10 3021275 146 + 129993255 CTTTCTCTGACATTACTGTAACTGAAGTAGCTC-AGAAGCACAAAAGGTCACATCATGCATCCATGCAGAATCCACTGAAGCTGTTTGGAAAGGC-----------------------CACGTGTCTTCCCAGAAGGCCAGTTACACCATCATTTCCTTCCATGTTTCAG s cavPor2.scaffold_216473 9741 169 - 10026 CCTTTGCTGATGTTACTGTAAGCGAACTAGCTG-AAAAGCACAAAAGGTCATGTCAGGCATTTATGCAAAATTTACTAGTTCCGTTCATAAAGGCACCTCGCATTTTATTACTTAGTTCATGTGTCTCGCAGGAAATCCAGTCACGCCATCATTTCCTTCCATATTTCAA q cavPor2.scaffold_216473 668536545547664539866666666666668-8787886799997788875886655536666688786768476688854689668876558688874778656675665668746666788474786888875667457786687996867886548798845555 i cavPor2.scaffold_216473 C 0 C 0 s oryCun1.scaffold_156751 838 158 - 4726 TCGTCTCTGATGTTACTCTAGCTGAAAGCGCTC-CAAAGCACAAAAGGCCATGGCAGGCATTTATGTCAAATGTACTAGCACTGTTTATAACAGCACCTTGTGTTGTATTACTTTGTTCA-----------GGAAATCCAGTCACGCCGCGATTTCCTTCCACATTTCAA q oryCun1.scaffold_156751 999999879999999999999999999997999-99999799999999898999999988999999988999999989996999999999988897996999999999999979999987-----------899998987999799998998999999999777999899 i oryCun1.scaffold_156751 C 0 C 0 s ponAbe2.chr6 16173265 169 - 174210431 CCTTCTCTGATGTTACTGTAACTGAAATAGCTC-AAAAGCACAAAAGGTCATGGGAGGCATTCATGTAAAACTTACTAGTGCTGTTTATAAGGGTACCTTGTGTTTTATTACTTTGTTAATGTATCTTTCAGGAAATTCAGTCACGCCATCATTTCCTTCCATATTTCAT i ponAbe2.chr6 C 0 C 0 s panTro2.chr6 16393613 169 - 173908612 CCTTCTCTGATGTTACTGTAACTGAAATAGCTC-AAAAGCACAAAAGGTCATGGGAGGCATTTATGTAAAACTTACTAGTGCTGTTTATAAGGGTACCTTGTGTTTTATTACTTTGTTAATGTACCTTTCAGGAAATCCAGTCATGCCATCATTTCCTTCCATATTTCAT q panTro2.chr6 999999999999999999999999999999999-9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999 i panTro2.chr6 C 0 C 0 s hg18.chr6 15875047 169 - 170899992 CCTTCTCTGATGTTACTGTAACTGAAATAGCTC-AAAAGCACAAAAGGTCATGGGAGGCATTTATGTAAAACTTACTAGTGCTGTTTATAAGGGTATCTTGTGTTTTATTACTTTGTTAATGTACCTTTCAGGAAATCCAGTCATGCCATCATTTCCTTCCATATTTCAT i hg18.chr6 C 0 C 0 s calJac1.Contig6394 10878 169 + 133105 CCTTCTCTGATATTACTGTAACTGAAATAGCTC-AAAAGCACAAAAGGTCATGGCAGGCATTTATGTAAAACTTACTAGTGCTGTTTATAAAGGCACCTTGTGTTTTATTACTTTGTTAATGTACCTTTCAGGAAATCCAGTCATGCCATCATTTCCTTCCATATTTCAT i calJac1.Contig6394 C 0 C 0 s tupBel1.scaffold_114895.1-498454 175057 156 - 498454 TCCTCTCAGATGTTCCTGTAACCAAAGTAGCTC-AGAAGCACAAAAGGTCATGCCAGGCATTGATGTAAA-------------GTTTCTGAAGGCATCTCGTGTTTTATTACTTTGTTCATGTGCCTTACAGGAAATCCAGTCGGGCCATCATTTCCTTCCATATCTCAG q tupBel1.scaffold_114895.1-498454 999999999999999999999999999999999-999999999999999999999999999999999999-------------999999999999999999999999999999999999999999999999999999999999999999999999999999999999999 i tupBel1.scaffold_114895.1-498454 C 0 C 0 s sorAra1.scaffold_2476 3382 170 - 4997 CCTTCTCTGATGTTACTGTAACTGAGGTAGCTCAAAAAGCACAAAAGGTCATGTCAGGCATTGATGTAAAATATACCAGTGCTGTTTATAAAGACCCCTTGCATATAATGTTGTTGATCATGAACTTTTCCGGAAATCCTGTAATCTCATCATTTCCTCCCATATTCCAG q sorAra1.scaffold_2476 99999999999999997999999999999999999999999999999999999999999999999999999999999979999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999 i sorAra1.scaffold_2476 C 0 C 0 s eriEur1.scaffold_266115 521 156 + 4589 CCTTCTCTGATCTGACTGTAACCGAAGTCTCTC-GAAAGCACAAAAGCTCACGGCAGGCCTTTCTGTAAAATACAGCGGCGCTGCTTCCAAAGGCaccttgca------gatgtctctcacgcATTTGGCAGGAGTCCCTGTCACTCGGCCAGTTCC-------TTCCTG q eriEur1.scaffold_266115 999999999999999999999999999999999-999999999999999999999999799999999999999999999998987999899999999999999------999999999999999999999999999999999999999999999998-------999989 i eriEur1.scaffold_266115 C 0 C 0 s canFam2.chr1 78072035 168 - 125616256 CTGTCTCTGATGTTACTGTAACTGAAGTAGCTC-AAAAGCACAAAAGGTCATGTCAGGC-TTTATGTAAAATTTACTAGAGCTGTTTATAAAGGCACCTCGTGTAATATTGCTTTGTTCATGTACTTTACAGGAAATCCTGTCATCCTGTTACTTCCTTCCATATTTCAA q canFam2.chr1 999999999999999999999999999999999-9999999999999999999999999-99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999 i canFam2.chr1 C 0 C 0 s felCat3.scaffold_205680 73556 169 - 119354 CTGTCTCTGATGTTACTGTAACTGAAATAGTTC-AAAAGCACAAAAGGTGATGTCAGGCATTTATGTAAAATTTACTAGTGCTGTTTATAAAGGTACCTTGTGTATTATTGCTTTGTTCATGCACTTTATAGGAAATCCTGTCATCCTGTCATTTCCTTCCATAGTTCAG q felCat3.scaffold_205680 999999999999999999999999999999999-9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999 i felCat3.scaffold_205680 C 0 I 34165 s dasNov1.scaffold_56749 3422 168 - 10470 CCTTCTCTGATGTTACTGTAACTGAAGAGGCTC-AAAAGCACAAAAGGTCATGTCGGGCATTGATGTAAAATTTACTAGTGCTG-TTTATAAAGGACCTTGTGTTCTATTACTTTTTCTATCCCCCTTACAGGAAATCCTGTCATACCATCATTTCCTTCCATAAGTCAC q dasNov1.scaffold_56749 989999999999999937699999999999999-79999999999999999999999999999999999999999999999999-9999999999999999999999999999999999999999999999999999999999999999999999999999999999999 i dasNov1.scaffold_56749 C 0 C 0 s echTel1.scaffold_288249 95418 169 + 100002 CCATCTCTGATATTACTGTAATGGAATTACTTT-GAAAGCACAAAAGGTCAGGACAAGCGTGTATGTGAAATTTCCTAGAGCTGTTTTCCTGCACACCTTGGATTTTATTGCTTAGTTCATTTGCTTTCCCAGAAATCCCGCCATGCCATCATTTCCTTCCACATCTCAG q echTel1.scaffold_288249 999999999999999999999999999999999-9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999 i echTel1.scaffold_288249 C 0 C 0 s ornAna1.chr2 14756885 169 - 54797317 CCACCTCTGATATCACTGTAACTCAGCTACCCA-GAAGATAGGAAAGGTCATATCAGCCAATCATGTGCAACTTAATAGCCCTGTTCATAAAGCTGCTTTGTGTTTTATGAGGCTATTCATTCACCTTAGGGGAAATCCTGTCAAGCCATCATTTCCTTCCATATCTTCA i ornAna1.chr2 I 5690 C 0 e otoGar1.scaffold_334.1-359464 188429 6280 - 359464 I """, ) alignment = next(alignments) self.assertEqual(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.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 ), ) ) 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.assertEqual( format(alignment, "maf"), """\ a score=30254.000000 s mm9.chr10 3021421 44 + 129993255 -ACGTTGCTCATTGT-----AATTGAAGCATTTATTACCAA--------TG--------------CCTTCCC s cavPor2.scaffold_216473 9910 47 - 10026 -CTGTTCCTTGTTACA----AATAAAAGTATGTTTTGCTGA--------CG-------G-----CCCCTCTG q cavPor2.scaffold_216473 -476754645667788----868678677444665235455--------76-------4-----36669356 i cavPor2.scaffold_216473 C 0 C 0 s oryCun1.scaffold_156751 996 37 - 4726 -TGGTTCCTCATTATG----GATTAAAGCATTCACTGCTAA--------T---------------------- q oryCun1.scaffold_156751 -999999999899999----887999999999999999999--------9---------------------- i oryCun1.scaffold_156751 C 0 I 2345 s ponAbe2.chr6 16173434 45 - 174210431 -CTGTTGCTCATTATA----AATAAAAGTGTTTATTGCTAA--------T--------------GCTTTCTC i ponAbe2.chr6 C 0 I 4 s panTro2.chr6 16393782 45 - 173908612 -CTGTTCCTCATTATA----AATAAAAGTGTTTATTGCTAA--------C--------------GCTTTCTC q panTro2.chr6 -999999999999999----999999999999999999999--------9--------------99999999 i panTro2.chr6 C 0 I 4 s hg18.chr6 15875216 45 - 170899992 -CTGTTCCTCATTATA----AATAAAAGTGTTTATTGCTAA--------C--------------GCTTTCTC i hg18.chr6 C 0 I 4 s calJac1.Contig6394 11047 43 + 133105 -CTGTTTCTCATTATA----AAT--AAGTGTTTATTGCTAA--------C--------------GCTTTCTC i calJac1.Contig6394 C 0 I 701 s tupBel1.scaffold_114895.1-498454 175213 35 - 498454 -CTGCTCCTCATGATA----AAT-ATAGCGTTTGTTGCTAA------------------------------- q tupBel1.scaffold_114895.1-498454 -999999999999999----999-99999999999999999------------------------------- i tupBel1.scaffold_114895.1-498454 C 0 I 10695 s sorAra1.scaffold_2476 3552 48 - 4997 -CTGTTCCTTCTTAGATTaaaaaaaGAGCGTTTATGACCAG--------CA-------GGTTCC-------- q sorAra1.scaffold_2476 -9999999999999999999999999999999997669755--------99-------999999-------- i sorAra1.scaffold_2476 C 0 N 0 s eriEur1.scaffold_266115 677 35 + 4589 -CTCCTTGTTCTTGAAGC----------CGTTTTTTATTGT--------CA-------GTG----------- q eriEur1.scaffold_266115 -98959997997999999----------9999999999999--------89-------999----------- i eriEur1.scaffold_266115 C 0 N 0 s canFam2.chr1 78072203 40 - 125616256 -CTGTTTCTCATTATA----AATAAAAGCATTTATTGCTAA--------TG-------T------------C q canFam2.chr1 -999999999999999----999999999999999999999--------99-------9------------9 i canFam2.chr1 C 0 C 0 s dasNov1.scaffold_56749 3590 44 - 10470 -CTGTTCCTCTTTAT-----AATAAAAGCATTTACTGCTAA--------CGGCTCCTC-------------- q dasNov1.scaffold_56749 -99999999999999-----999999999999999999999--------999999999-------------- i dasNov1.scaffold_56749 C 0 I 904 s echTel1.scaffold_288249 95587 38 + 100002 -CTGATCCTCATTATA----AATAAAAGTGTTTGTTACTAA--------TG--------------------- q echTel1.scaffold_288249 -999999999999999----999999999999999999999--------99--------------------- i echTel1.scaffold_288249 C 0 N 0 s ornAna1.chr2 14757054 45 - 54797317 ACTG-TCCTCATTGTA----CAGGGACTCTTTTATTACTAAAGATCCCCC---------------------- i ornAna1.chr2 C 0 C 0 e felCat3.scaffold_205680 73725 34165 - 119354 I e otoGar1.scaffold_334.1-359464 188429 6280 - 359464 I """, ) alignment = next(alignments) self.assertEqual(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.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.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.assertEqual( format(alignment, "maf"), """\ a score=-9167.000000 s mm9.chr10 3021465 29 + 129993255 CCCT--ACACTGTC----AAGTGGGAGGAGACAGT-------------------- s cavPor2.scaffold_216473 9957 28 - 10026 AGCC--acactgg-----gggtggggtgggatggt-------------------- q cavPor2.scaffold_216473 7667--6878566-----66544895554554677-------------------- i cavPor2.scaffold_216473 C 0 N 0 s ponAbe2.chr6 16173483 24 - 174210431 -------CCCTGTG----GGGGCGATAGGAGCAGC-------------------- i ponAbe2.chr6 I 4 I 9 s panTro2.chr6 16393831 24 - 173908612 -------CCATGTG----GGGGCGATAGGGGCAGC-------------------- q panTro2.chr6 -------9999999----99999999999999999-------------------- i panTro2.chr6 I 4 I 9 s hg18.chr6 15875265 24 - 170899992 -------CCATGTG----GGGGCGATAGGGGCAGC-------------------- i hg18.chr6 I 4 I 9 s canFam2.chr1 78072243 31 - 125616256 CCCTGAACCACATG----GGGGGTGTGTGTGTGTG-------------------- q canFam2.chr1 99999999999999----99999999999999999-------------------- i canFam2.chr1 C 0 I 13 s ornAna1.chr2 14757099 45 - 54797317 ----------TGTGTCATAGGAGTTTGGATGTAGCCCTCTTTCATCTTTGCTGGC i ornAna1.chr2 C 0 C 0 e dasNov1.scaffold_56749 3634 904 - 10470 I e felCat3.scaffold_205680 73725 34165 - 119354 I e calJac1.Contig6394 11090 701 + 133105 I e tupBel1.scaffold_114895.1-498454 175248 10695 - 498454 I e otoGar1.scaffold_334.1-359464 188429 6280 - 359464 I e oryCun1.scaffold_156751 1033 2345 - 4726 I """, ) 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.assertEqual(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.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.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.assertEqual( format(alignment, "maf"), """\ a score=15763.000000 s mm9.chr10 3021494 42 + 129993255 TGTTTAGTACC----ATGCTTAGGAATGATAAACTCACTTAGTGtt s ponAbe2.chr6 16173516 46 - 174210431 TGTTGCATGTCCTTTATTCTTTGGCGTGATAGGCTCACCCAATCTT i ponAbe2.chr6 I 9 I 943 s panTro2.chr6 16393864 46 - 173908612 TGTTGCATATCCTTTATTCTTTGGCGTGATAGGCTCACCCAATCTT q panTro2.chr6 9999999999999999999999999999999999999999999999 i panTro2.chr6 I 9 I 10 s hg18.chr6 15875298 46 - 170899992 TGTTGCATGTCGTTTATTCTTTGGCGTGATAGGCTCACCCAATCTT i hg18.chr6 I 9 I 931 s canFam2.chr1 78072287 46 - 125616256 TGTTAAGTCTCACTTGCTGTTCAAAGTGATAGCTTCACTCCATCAT q canFam2.chr1 9999999999999999999999999999999999999999999999 i canFam2.chr1 I 13 I 1 s ornAna1.chr2 14757144 36 - 54797317 TGTTTAAAATG----ATTGCTAGAACTTCTA--CTCACTGGA---- i ornAna1.chr2 C 0 C 0 e dasNov1.scaffold_56749 3634 904 - 10470 I e felCat3.scaffold_205680 73725 34165 - 119354 I e calJac1.Contig6394 11090 701 + 133105 I e tupBel1.scaffold_114895.1-498454 175248 10695 - 498454 I e otoGar1.scaffold_334.1-359464 188429 6280 - 359464 I e oryCun1.scaffold_156751 1033 2345 - 4726 I """, ) 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) def test_reading_ucsc_mm9_chr10(self): """Test parsing MAF file ucsc_mm9_chr10.maf.""" path = "MAF/ucsc_mm9_chr10.maf" alignments = Align.parse(path, "maf") self.check_reading_ucsc_mm9_chr10(alignments) self.assertRaises(StopIteration, next, alignments) alignments = iter(alignments) self.check_reading_ucsc_mm9_chr10(alignments) self.assertRaises(StopIteration, next, alignments) alignments = alignments[:] self.check_reading_ucsc_mm9_chr10(alignments) def test_reading_missing_signature(self): """Test parsing MAF file ucsc_mm9_chr10_big.maf with missing signature.""" path = "MAF/ucsc_mm9_chr10_big.maf" with self.assertRaises(ValueError) as cm: Align.parse(path, "maf") self.assertEqual(str(cm.exception), "header line does not start with ##maf") def test_reading_ucsc_mm9_chr10_bad(self): """Test parsing MAF file ucsc_mm9_chr10_bad.maf with incorrect sequence size.""" path = "MAF/ucsc_mm9_chr10_bad.maf" alignments = Align.parse(path, "maf") self.assertEqual(alignments.metadata["MAF Version"], "1") self.assertEqual(alignments.metadata["Scoring"], "autoMZ.v1") next(alignments) next(alignments) next(alignments) next(alignments) next(alignments) next(alignments) with self.assertRaises(ValueError) as cm: next(alignments) self.assertEqual( str(cm.exception), "sequence size is incorrect (found 219, expected 319)" ) def test_reading_length_coords_mismatch(self): """Test parsing inconsistent MAF file length_coords_mismatch.maf.""" path = "MAF/length_coords_mismatch.maf" alignments = Align.parse(path, "maf") self.assertEqual(alignments.metadata["MAF Version"], "1") self.assertEqual(alignments.metadata["Scoring"], "autoMZ.v1") alignment = next(alignments) self.assertEqual(alignment.score, 6441) self.assertEqual(len(alignment.sequences), 2) self.assertEqual(alignment.sequences[0].id, "mm8.chr10") self.assertEqual(len(alignment.sequences[0]), 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]), 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( 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.assertEqual( format(alignment, "maf"), """\ a score=6441.000000 s mm8.chr10 3009319 162 + 129993255 TCATAGGTATTTATTTTTAAATATGGTTTGCTTTATGGCTAGAACACACCGATTACTTAAAATAGGATTAACC--CCCATACACTTTAAAAATGATTAAACAACATTTCTGCTGCTCGCTCACATTCTTCATAGAAGATGACATAATGTATTTTCCTTTTGGTT s oryCun1.scaffold_133159 11087 164 + 13221 TCACAGATATTTACTATTAAATATGGTTTGTTATATGGTTACGGTTCATAGGTTACTTGGAATTGGATTAACCTTCTTATTCATTGCAGAATTGGTTACACTGTGTTCTTGACCTTTGCTTGTTTTCTCCATGGAAACTGATGTCAAATACTTTCCCTTTGGTT q oryCun1.scaffold_133159 99569899999998999999999999999999999999999999999999999999999999999999999757878999975999999999999999979999999999997899999999999997997999999869999996999988997997999999 i oryCun1.scaffold_133159 N 0 N 0 """, ) with self.assertRaises(ValueError) as cm: next(alignments) self.assertEqual( str(cm.exception), "sequence size is incorrect (found 219, expected 319)" ) def test_reading_bug2453(self): """Test parsing bug2453.maf.""" path = "MAF/bug2453.maf" alignments = Align.parse(path, "maf") self.assertEqual(len(alignments.metadata), 3) self.check_alignments(alignments) def test_reading_ucsc_test(self): """Test parsing ucsc_test.maf.""" path = "MAF/ucsc_test.maf" alignments = Align.parse(path, "maf") self.check_header(alignments) self.check_alignments(alignments) alignments = iter(alignments) self.check_header(alignments) self.check_alignments(alignments) with Align.parse(path, "maf") as alignments: self.check_header(alignments) self.check_alignments(alignments) with self.assertRaises(AttributeError): alignments._stream with Align.parse(path, "maf") as alignments: pass with self.assertRaises(AttributeError): alignments._stream def check_header(self, alignments): self.assertEqual(len(alignments.metadata), 9) self.assertEqual(alignments.metadata["name"], "euArc") self.assertEqual(alignments.metadata["visibility"], "pack") self.assertEqual(alignments.metadata["mafDot"], "off") self.assertEqual(alignments.metadata["frames"], "multiz28wayFrames") self.assertEqual( alignments.metadata["speciesOrder"], ["hg16", "panTro1", "baboon", "mm4", "rn3"], ) self.assertEqual(alignments.metadata["description"], "A sample alignment") def check_alignments(self, alignments): self.assertEqual(alignments.metadata["MAF Version"], "1") self.assertEqual(alignments.metadata["Scoring"], "tba.v8") self.assertEqual( alignments.metadata["Comments"], [ "tba.v8 (((human chimp) baboon) (mouse rat))", "multiz.v7", "maf_project.v5 _tba_right.maf3 mouse _tba_C", "single_cov2.v4 single_cov2 /dev/stdin", ], ) alignment = next(alignments) self.assertEqual(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.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.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.assertEqual( format(alignment, "maf"), """\ a score=23262.000000 s hg16.chr7 27578828 38 + 158545518 AAA-GGGAATGTTAACCAAATGA---ATTGTCTCTTACGGTG s panTro1.chr6 28741140 38 + 161576975 AAA-GGGAATGTTAACCAAATGA---ATTGTCTCTTACGGTG s baboon 116834 38 + 4622798 AAA-GGGAATGTTAACCAAATGA---GTTGTCTCTTATGGTG s mm4.chr6 53215344 38 + 151104725 -AATGGGAATGTTAAGCAAACGA---ATTGTCTCTCAGTGTG s rn3.chr4 81344243 40 + 187371129 -AA-GGGGATGCTAAGCCAATGAGTTGTTGTCTCTCAATGTG """, ) 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.assertEqual(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.assertTrue( np.array_equal( alignment.coordinates, np.array( [ # fmt: off [27699739, 27699745], [28862317, 28862323], [ 241163, 241169], [53303881, 53303887], [81444246, 81444252], # fmt: on ] ), ) ) 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.assertEqual( format(alignment, "maf"), """\ a score=5062.000000 s hg16.chr7 27699739 6 + 158545518 TAAAGA s panTro1.chr6 28862317 6 + 161576975 TAAAGA s baboon 241163 6 + 4622798 TAAAGA s mm4.chr6 53303881 6 + 151104725 TAAAGA s rn3.chr4 81444246 6 + 187371129 taagga """, ) 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.assertEqual(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.assertTrue( np.array_equal( alignment.coordinates, np.array( [ # fmt: off [27707221, 27707234], [28869787, 28869800], [ 249182, 249195], [53310102, 53310115], # fmt: on ] ), ) ) self.assertEqual( str(alignment), """\ hg16.chr7 27707221 gcagctgaaaaca 27707234 panTro1.c 28869787 gcagctgaaaaca 28869800 baboon 249182 gcagctgaaaaca 249195 mm4.chr6 53310102 ACAGCTGAAAATA 53310115 """, ) self.assertEqual( format(alignment, "maf"), """\ a score=6636.000000 s hg16.chr7 27707221 13 + 158545518 gcagctgaaaaca s panTro1.chr6 28869787 13 + 161576975 gcagctgaaaaca s baboon 249182 13 + 4622798 gcagctgaaaaca s mm4.chr6 53310102 13 + 151104725 ACAGCTGAAAATA """, ) 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_writing(unittest.TestCase): def test_writing_ucsc_test(self): """Test reading and writing ucsc_test.maf.""" path = "MAF/ucsc_test.maf" alignments = Align.parse(path, "maf") output = StringIO() n = Align.write(alignments, output, "maf") output.seek(0) with open(path) as stream: line1 = next(output) line2 = next(stream) self.assertEqual( line1, 'track name=euArc visibility=pack mafDot=off frames=multiz28wayFrames speciesOrder="hg16 panTro1 baboon mm4 rn3" description="A sample alignment"\n', ) self.assertEqual( line2, 'track name=euArc visibility=pack mafDot=off frames="multiz28wayFrames" speciesOrder="hg16 panTro1 baboon mm4 rn3" description="A sample alignment"\n', ) for line1, line2 in zip(output, stream): if line1.startswith("a score="): prefix1, score1 = line1.split("=") prefix2, score2 = line2.split("=") self.assertEqual(prefix1, prefix2) self.assertAlmostEqual(float(score1), float(score2)) else: self.assertEqual(line1.strip(), line2.strip()) def test_writing_bug2453(self): """Test reading and writing bug2453.maf.""" path = "MAF/bug2453.maf" alignments = Align.parse(path, "maf") output = StringIO() n = Align.write(alignments, output, "maf") self.assertEqual(n, 3) output.seek(0) with open(path) as stream: for line1, line2 in zip(output, stream): if line1.startswith("a score="): prefix1, score1 = line1.split("=") prefix2, score2 = line2.split("=") self.assertEqual(prefix1, prefix2) self.assertAlmostEqual(float(score1), float(score2)) else: self.assertEqual(line1.strip(), line2.strip()) def test_writing_bundle_without_target(self): """Test reading and writing bundle_without_target.maf.""" path = "MAF/bundle_without_target.maf" alignments = Align.parse(path, "maf") output = StringIO() n = Align.write(alignments, output, "maf") self.assertEqual(n, 1) output.seek(0) with open(path) as stream: for line1, line2 in zip(output, stream): self.assertEqual(line1, line2) def test_writing_ucsc_mm9_chr10(self): """Test reading and writing ucsc_mm9_chr10.maf.""" path = "MAF/ucsc_mm9_chr10.maf" alignments = Align.parse(path, "maf") output = StringIO() n = Align.write(alignments, output, "maf") self.assertEqual(n, 48) output.seek(0) with open(path) as stream: for line1, line2 in zip(output, stream): words1 = line1.split() words2 = line2.split() if line1.startswith("e "): ( prefix1, name1, start1, size1, strand1, length1, status1, ) = line1.split() ( prefix2, name2, start2, size2, strand2, length2, status2, ) = line2.split() size1 = int(size1) size2 = int(size2) if size1 == 0 and strand1 != strand2: start1 = int(start1) start2 = int(start2) size1 = int(size1) size2 = int(size2) length1 = int(length1) length2 = int(length2) self.assertEqual(prefix1, "e") self.assertEqual(prefix2, "e") self.assertEqual(name1, name2) self.assertEqual(status1, status2) self.assertEqual(size1, size2) self.assertEqual(length1, length2) self.assertEqual(start1, length2 - start2 - size2) self.assertEqual(start2, length1 - start1 - size1) continue self.assertEqual(words1, words2) if __name__ == "__main__": runner = unittest.TextTestRunner(verbosity=2) unittest.main(testRunner=runner)