# Copyright 2022 by Michiel de Hoon. All rights reserved. # This code is part of the Biopython distribution and governed by its # license. Please see the LICENSE file that should have been included # as part of this package. """Tests for Align.psl module.""" import unittest from io import StringIO from Bio import Align from Bio import SeqIO from Bio.Align import Alignment from Bio.Seq import reverse_complement from Bio.Seq import Seq from Bio.SeqFeature import CompoundLocation from Bio.SeqFeature import ExactPosition from Bio.SeqFeature import SimpleLocation from Bio.SeqRecord import SeqRecord try: import numpy as np except ImportError: from Bio import MissingPythonDependencyError raise MissingPythonDependencyError( "Install numpy if you want to use Bio.Align.psl." ) from None class TestAlign_dna_rna(unittest.TestCase): # The PSL file dna_rna.psl was generated using this command: # blat -mask=lower hg38.2bit rna.fa dna_rna.unsorted.psl # pslSort dirs dna_rna.psl . dna_rna.unsorted.psl def setUp(self): data = {} records = SeqIO.parse("Blat/dna.fa", "fasta") for record in records: name, start_end = record.id.split(":") assert name == "chr3" start, end = start_end.split("-") start = int(start) end = int(end) sequence = str(record.seq) assert len(sequence) == end - start data[start] = sequence self.dna = data records = SeqIO.parse("Blat/rna.fa", "fasta") self.rna = {record.id: record.seq for record in records} def test_reading(self): """Test parsing dna_rna.psl.""" path = "Blat/dna_rna.psl" alignments = Align.parse(path, "psl") self.check_alignments(alignments) alignments = iter(alignments) self.check_alignments(alignments) with Align.parse(path, "psl") as alignments: self.check_alignments(alignments) with self.assertRaises(AttributeError): alignments._stream with Align.parse(path, "psl") as alignments: pass with self.assertRaises(AttributeError): alignments._stream def check_alignments(self, alignments): self.assertEqual(alignments.metadata["psLayout version"], "3") alignment = next(alignments) self.assertEqual(alignment.matches, 175) self.assertEqual(alignment.misMatches, 0) self.assertEqual(alignment.repMatches, 6) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.shape, (2, 1711)) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr3") self.assertEqual(alignment.query.id, "NR_046654.1") self.assertEqual(len(alignment.target.seq), 198295559) self.assertEqual(len(alignment.query.seq), 181) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[42530895, 42530958, 42532020, 42532095, 42532563, 42532606], [ 181, 118, 118, 43, 43, 0]]) # fmt: on ) ) dna = Seq(self.dna, length=len(alignment.target)) alignment.target.seq = dna alignment.query.seq = self.rna[alignment.query.id] self.assertTrue( np.array_equal( alignment.substitutions, # fmt: off np.array([[36., 0., 0., 0., 0., 0., 0., 0.], [ 0., 40., 0., 0., 0., 0., 0., 0.], [ 0., 0., 57., 0., 0., 0., 0., 0.], [ 0., 0., 0., 42., 0., 0., 0., 0.], [ 2., 0., 0., 0., 0., 0., 0., 0.], [ 0., 1., 0., 0., 0., 0., 0., 0.], [ 0., 0., 3., 0., 0., 0., 0., 0.], [ 0., 0., 0., 0., 0., 0., 0., 0.], ]) # fmt: on ) ) self.assertEqual(alignment.substitutions.alphabet, "ACGTacgt") matches = sum( alignment.substitutions[c, c] for c in alignment.substitutions.alphabet ) repMatches = sum( alignment.substitutions[c, c.swapcase()] for c in alignment.substitutions.alphabet ) self.assertEqual(matches, alignment.matches) self.assertEqual(repMatches, alignment.repMatches) self.assertEqual( str(alignment), """\ chr3 42530895 CGGAAGTACTTCTGGGGGTACATACTCATCGGCTGGGGTATGGTACCAGGGAGGGCTTCC 0 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| NR_046654 181 CGGAAGTACTTCTGGGGGTACATACTCATCGGCTGGGGTATGGTACCAGGGAGGGCTTCC chr3 42530955 AGGCTGGGGACAGAGGGGGCAAGGCCTGGAGAACTCCCTAGGGGGAGGGTGCCAACCCAG 60 |||--------------------------------------------------------- NR_046654 121 AGG--------------------------------------------------------- chr3 42531015 CTTGCAGTCCTACGTCTTGCTTAGCTGCAGGTCCTGCCTGCAAGGATATCAGCCAAGGGT 120 ------------------------------------------------------------ NR_046654 118 ------------------------------------------------------------ chr3 42531075 CAAGAAAGTCCTCAAAATGTCTGATCCCAGGACAAGTCCCTCAGGTTGCAGCTGCACCTA 180 ------------------------------------------------------------ NR_046654 118 ------------------------------------------------------------ chr3 42531135 GGGCTGACCTGTGGGACAGATTTTGTGAACATCTTTCCATTTCCCTTTAGTTCCCGAAAT 240 ------------------------------------------------------------ NR_046654 118 ------------------------------------------------------------ chr3 42531195 ACAcagggccactgctaatctataaagggcctctgtcacaattagaaagagaatgtccgt 300 ------------------------------------------------------------ NR_046654 118 ------------------------------------------------------------ chr3 42531255 ctaggtagacacagcccttcaggcatacagcttCACCCCCTCAGTGGAGCATCCCTCCGT 360 ------------------------------------------------------------ NR_046654 118 ------------------------------------------------------------ chr3 42531315 GGTGAACAACCTATGCAACCAAAGACAGCAGACTGACAACCCACCCTTTtctctctccct 420 ------------------------------------------------------------ NR_046654 118 ------------------------------------------------------------ chr3 42531375 ccctctccctgcttttctccaaaatctctccctcatgccctctacccctgcttcctgtgc 480 ------------------------------------------------------------ NR_046654 118 ------------------------------------------------------------ chr3 42531435 cctctctgctctttcactctccctGGGCCTGACAGGGGTACCCAGCACATTCACCATGGT 540 ------------------------------------------------------------ NR_046654 118 ------------------------------------------------------------ chr3 42531495 GTGGACCATCGCCAGGATCCATTTTGAGGATTATGGGTGAGCTGCTGCCCCACACACTCC 600 ------------------------------------------------------------ NR_046654 118 ------------------------------------------------------------ chr3 42531555 CCCGGCCGCCATCACTTGGGCAGGCCCCCTGGGTGGGATGATAATGCCATCTGGCCTTGG 660 ------------------------------------------------------------ NR_046654 118 ------------------------------------------------------------ chr3 42531615 TGAGTGGACAAAAACCACAGCTCTCGGGCCAGAGGGGAGGCTGGAGGAGGACCTGGGGAG 720 ------------------------------------------------------------ NR_046654 118 ------------------------------------------------------------ chr3 42531675 CAACAGACTCTGGGCCCGGGGTTGCTAAAGTGCTCAGGAGCAGAGCTGGGGACAACTGGG 780 ------------------------------------------------------------ NR_046654 118 ------------------------------------------------------------ chr3 42531735 GGAGGTGCTGCTGAGTCTCTCTCTGGCTGAGGACAATCCCTCTCATTCCTCCCCACGGTC 840 ------------------------------------------------------------ NR_046654 118 ------------------------------------------------------------ chr3 42531795 TGCTCAGGTGCTGGGACACCATCAACTCCTCACTGTGGTGGATCATAAAGGGCCCCATCC 900 ------------------------------------------------------------ NR_046654 118 ------------------------------------------------------------ chr3 42531855 TCACCTCCATCTTGGTAAGATaccctcccaccacctagagatggggaaacaggcccaaag 960 ------------------------------------------------------------ NR_046654 118 ------------------------------------------------------------ chr3 42531915 ggcaggcaacttagcccaaggtcacatgggaaattagtatctaggtcagaactgaaacgt 1020 ------------------------------------------------------------ NR_046654 118 ------------------------------------------------------------ chr3 42531975 agcttcctaatgcccaatgcaggatcatccccacccctgtcctaccagTTCTTCCTTGAG 1080 ---------------------------------------------...|||||||||||| NR_046654 118 ---------------------------------------------CAGTTCTTCCTTGAG chr3 42532035 CGTAAGCGGATTGGGAGCACAGTCCTTAGGGATTTGAAGGAGGTAGAGTTCCCGGATGAC 1140 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| NR_046654 103 CGTAAGCGGATTGGGAGCACAGTCCTTAGGGATTTGAAGGAGGTAGAGTTCCCGGATGAC chr3 42532095 CTGCCCAAAGGGGAAATGCCAGAGGAGAGGTAAGATAGAGAGAGGGGCAGCAGGACCCTG 1200 ------------------------------------------------------------ NR_046654 43 ------------------------------------------------------------ chr3 42532155 GGAAAGAAGACAGGCCAGCAGTCAAGGGGCCTGAACACCTCAGCCTTCCCGCTCTGACTG 1260 ------------------------------------------------------------ NR_046654 43 ------------------------------------------------------------ chr3 42532215 CCCGAACTCGGGTCCCCACCCACTAGGTAAACTTCATCCTGTTTATTTGCATCATCCGAA 1320 ------------------------------------------------------------ NR_046654 43 ------------------------------------------------------------ chr3 42532275 TCCTGCTTCAGAAACTGCGGCCCCCAGATATCAGGAAGAGTGACAGCAGTCCATACTCGT 1380 ------------------------------------------------------------ NR_046654 43 ------------------------------------------------------------ chr3 42532335 GAGTGTGGGCCTAGTGCCTCAGCCCCCAGTACCTCCATCCCCAGTCCTCAAATCATCCCA 1440 ------------------------------------------------------------ NR_046654 43 ------------------------------------------------------------ chr3 42532395 CATCTCCTTGAAGTCCTCCCACCCCAAACATCCAGAGTCACCAAAGAGCCACATTGTTCT 1500 ------------------------------------------------------------ NR_046654 43 ------------------------------------------------------------ chr3 42532455 TTCCCACCTCCACCATGGCCTGGCTcagcccaccaccatcccctgctccagccccaccct 1560 ------------------------------------------------------------ NR_046654 43 ------------------------------------------------------------ chr3 42532515 caCCAGGCTGCACTCAGAGCCCTGCATGCTTCTCCTGCCCACACTCACCTAGCATCCTTC 1620 ------------------------------------------------|||||||||||| NR_046654 43 ------------------------------------------------CTAGCATCCTTC chr3 42532575 CCAGGTATGCATCTGCTGCCAAGCCAGGgag 42532606 1680 ||||||||||||||||||||||||||||... 1711 NR_046654 31 CCAGGTATGCATCTGCTGCCAAGCCAGGGAG 0 """, ) self.assertEqual( format(alignment, "psl"), """\ 175 0 6 0 0 0 2 1530 - NR_046654.1 181 0 181 chr3 198295559 42530895 42532606 3 63,75,43, 0,63,138, 42530895,42532020,42532563, """, ) alignment = next(alignments) self.assertEqual(alignment.matches, 172) self.assertEqual(alignment.misMatches, 1) self.assertEqual(alignment.repMatches, 6) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.shape, (2, 1714)) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr3") self.assertEqual(alignment.query.id, "NR_046654.1_modified") self.assertEqual(len(alignment.target.seq), 198295559) self.assertEqual(len(alignment.query.seq), 190) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[42530895, 42530922, 42530922, 42530958, 42532020, 42532037, 42532039, 42532095, 42532563, 42532606], [ 185, 158, 155, 119, 119, 102, 102, 46, 46, 3], ]) # fmt: on ) ) dna = Seq(self.dna, length=len(alignment.target)) alignment.target.seq = dna alignment.query.seq = self.rna[alignment.query.id] self.assertTrue( np.array_equal( alignment.substitutions, # fmt: off np.array([[34., 0., 0., 1., 0., 0., 0., 0.], [ 0., 40., 0., 0., 0., 0., 0., 0.], [ 0., 0., 57., 0., 0., 0., 0., 0.], [ 0., 0., 0., 41., 0., 0., 0., 0.], [ 2., 0., 0., 0., 0., 0., 0., 0.], [ 0., 1., 0., 0., 0., 0., 0., 0.], [ 0., 0., 3., 0., 0., 0., 0., 0.], [ 0., 0., 0., 0., 0., 0., 0., 0.], ]), # fmt: on ) ) self.assertEqual(alignment.substitutions.alphabet, "ACGTacgt") matches = sum( alignment.substitutions[c, c] for c in alignment.substitutions.alphabet ) repMatches = sum( alignment.substitutions[c, c.swapcase()] for c in alignment.substitutions.alphabet if c != "X" ) self.assertEqual(matches, alignment.matches) self.assertEqual(repMatches, alignment.repMatches) self.assertEqual( str(alignment), """\ chr3 42530895 CGGAAGTACTTCTGGGGGTACATACTC---ATCGGCTGGGGTATGGTACCAGGGAGGGCT 0 |||||||||||||||||||||||||||---|||||||||||||||||||||||||||||| NR_046654 185 CGGAAGTACTTCTGGGGGTACATACTCCCCATCGGCTGGGGTATGGTACCAGGGAGGGCT chr3 42530952 TCCAGGCTGGGGACAGAGGGGGCAAGGCCTGGAGAACTCCCTAGGGGGAGGGTGCCAACC 60 ||||||------------------------------------------------------ NR_046654 125 TCCAGG------------------------------------------------------ chr3 42531012 CAGCTTGCAGTCCTACGTCTTGCTTAGCTGCAGGTCCTGCCTGCAAGGATATCAGCCAAG 120 ------------------------------------------------------------ NR_046654 119 ------------------------------------------------------------ chr3 42531072 GGTCAAGAAAGTCCTCAAAATGTCTGATCCCAGGACAAGTCCCTCAGGTTGCAGCTGCAC 180 ------------------------------------------------------------ NR_046654 119 ------------------------------------------------------------ chr3 42531132 CTAGGGCTGACCTGTGGGACAGATTTTGTGAACATCTTTCCATTTCCCTTTAGTTCCCGA 240 ------------------------------------------------------------ NR_046654 119 ------------------------------------------------------------ chr3 42531192 AATACAcagggccactgctaatctataaagggcctctgtcacaattagaaagagaatgtc 300 ------------------------------------------------------------ NR_046654 119 ------------------------------------------------------------ chr3 42531252 cgtctaggtagacacagcccttcaggcatacagcttCACCCCCTCAGTGGAGCATCCCTC 360 ------------------------------------------------------------ NR_046654 119 ------------------------------------------------------------ chr3 42531312 CGTGGTGAACAACCTATGCAACCAAAGACAGCAGACTGACAACCCACCCTTTtctctctc 420 ------------------------------------------------------------ NR_046654 119 ------------------------------------------------------------ chr3 42531372 cctccctctccctgcttttctccaaaatctctccctcatgccctctacccctgcttcctg 480 ------------------------------------------------------------ NR_046654 119 ------------------------------------------------------------ chr3 42531432 tgccctctctgctctttcactctccctGGGCCTGACAGGGGTACCCAGCACATTCACCAT 540 ------------------------------------------------------------ NR_046654 119 ------------------------------------------------------------ chr3 42531492 GGTGTGGACCATCGCCAGGATCCATTTTGAGGATTATGGGTGAGCTGCTGCCCCACACAC 600 ------------------------------------------------------------ NR_046654 119 ------------------------------------------------------------ chr3 42531552 TCCCCCGGCCGCCATCACTTGGGCAGGCCCCCTGGGTGGGATGATAATGCCATCTGGCCT 660 ------------------------------------------------------------ NR_046654 119 ------------------------------------------------------------ chr3 42531612 TGGTGAGTGGACAAAAACCACAGCTCTCGGGCCAGAGGGGAGGCTGGAGGAGGACCTGGG 720 ------------------------------------------------------------ NR_046654 119 ------------------------------------------------------------ chr3 42531672 GAGCAACAGACTCTGGGCCCGGGGTTGCTAAAGTGCTCAGGAGCAGAGCTGGGGACAACT 780 ------------------------------------------------------------ NR_046654 119 ------------------------------------------------------------ chr3 42531732 GGGGGAGGTGCTGCTGAGTCTCTCTCTGGCTGAGGACAATCCCTCTCATTCCTCCCCACG 840 ------------------------------------------------------------ NR_046654 119 ------------------------------------------------------------ chr3 42531792 GTCTGCTCAGGTGCTGGGACACCATCAACTCCTCACTGTGGTGGATCATAAAGGGCCCCA 900 ------------------------------------------------------------ NR_046654 119 ------------------------------------------------------------ chr3 42531852 TCCTCACCTCCATCTTGGTAAGATaccctcccaccacctagagatggggaaacaggccca 960 ------------------------------------------------------------ NR_046654 119 ------------------------------------------------------------ chr3 42531912 aagggcaggcaacttagcccaaggtcacatgggaaattagtatctaggtcagaactgaaa 1020 ------------------------------------------------------------ NR_046654 119 ------------------------------------------------------------ chr3 42531972 cgtagcttcctaatgcccaatgcaggatcatccccacccctgtcctaccagTTCTTCCTT 1080 ------------------------------------------------...||||||||| NR_046654 119 ------------------------------------------------CAGTTCTTCCTT chr3 42532032 GAGCGTAAGCGGATTGGGAGCACAGTCCTTAGGGATTTGAAGGAGGTAGAGTTCCCGGAT 1140 |||||--|||||||||||.||||||||||||||||||||||||||||||||||||||||| NR_046654 107 GAGCG--AGCGGATTGGGTGCACAGTCCTTAGGGATTTGAAGGAGGTAGAGTTCCCGGAT chr3 42532092 GACCTGCCCAAAGGGGAAATGCCAGAGGAGAGGTAAGATAGAGAGAGGGGCAGCAGGACC 1200 |||--------------------------------------------------------- NR_046654 49 GAC--------------------------------------------------------- chr3 42532152 CTGGGAAAGAAGACAGGCCAGCAGTCAAGGGGCCTGAACACCTCAGCCTTCCCGCTCTGA 1260 ------------------------------------------------------------ NR_046654 46 ------------------------------------------------------------ chr3 42532212 CTGCCCGAACTCGGGTCCCCACCCACTAGGTAAACTTCATCCTGTTTATTTGCATCATCC 1320 ------------------------------------------------------------ NR_046654 46 ------------------------------------------------------------ chr3 42532272 GAATCCTGCTTCAGAAACTGCGGCCCCCAGATATCAGGAAGAGTGACAGCAGTCCATACT 1380 ------------------------------------------------------------ NR_046654 46 ------------------------------------------------------------ chr3 42532332 CGTGAGTGTGGGCCTAGTGCCTCAGCCCCCAGTACCTCCATCCCCAGTCCTCAAATCATC 1440 ------------------------------------------------------------ NR_046654 46 ------------------------------------------------------------ chr3 42532392 CCACATCTCCTTGAAGTCCTCCCACCCCAAACATCCAGAGTCACCAAAGAGCCACATTGT 1500 ------------------------------------------------------------ NR_046654 46 ------------------------------------------------------------ chr3 42532452 TCTTTCCCACCTCCACCATGGCCTGGCTcagcccaccaccatcccctgctccagccccac 1560 ------------------------------------------------------------ NR_046654 46 ------------------------------------------------------------ chr3 42532512 cctcaCCAGGCTGCACTCAGAGCCCTGCATGCTTCTCCTGCCCACACTCACCTAGCATCC 1620 ---------------------------------------------------||||||||| NR_046654 46 ---------------------------------------------------CTAGCATCC chr3 42532572 TTCCCAGGTATGCATCTGCTGCCAAGCCAGGgag 42532606 1680 |||||||||||||||||||||||||||||||... 1714 NR_046654 37 TTCCCAGGTATGCATCTGCTGCCAAGCCAGGGAG 3 """, ) self.assertEqual( format(alignment, "psl"), """\ 172 1 6 0 1 3 3 1532 - NR_046654.1_modified 190 3 185 chr3 198295559 42530895 42532606 5 27,36,17,56,43, 5,35,71,88,144, 42530895,42530922,42532020,42532039,42532563, """, ) alignment = next(alignments) self.assertEqual(alignment.matches, 165) self.assertEqual(alignment.misMatches, 0) self.assertEqual(alignment.repMatches, 39) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.shape, (2, 5407)) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr3") self.assertEqual(alignment.query.id, "NR_111921.1") self.assertEqual(len(alignment.target.seq), 198295559) self.assertEqual(len(alignment.query.seq), 216) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array( [[48663767, 48663813, 48665640, 48665722, 48669098, 48669174], [ 0, 46, 46, 128, 128, 204]]), # fmt: on ) ) dna = Seq(self.dna, length=len(alignment.target.seq)) alignment.target.seq = dna alignment.query.seq = self.rna[alignment.query.id] self.assertTrue( np.array_equal( alignment.substitutions, # fmt: off np.array([[53., 0., 0., 0., 0., 0., 0., 0.], [ 0., 35., 0., 0., 0., 0., 0., 0.], [ 0., 0., 50., 0., 0., 0., 0., 0.], [ 0., 0., 0., 27., 0., 0., 0., 0.], [ 9., 0., 0., 0., 0., 0., 0., 0.], [ 0., 7., 0., 0., 0., 0., 0., 0.], [ 0., 0., 16., 0., 0., 0., 0., 0.], [ 0., 0., 0., 7., 0., 0., 0., 0.], ]) # fmt: on ) ) self.assertEqual(alignment.substitutions.alphabet, "ACGTacgt") matches = sum( alignment.substitutions[c, c] for c in alignment.substitutions.alphabet ) repMatches = sum( alignment.substitutions[c, c.swapcase()] for c in alignment.substitutions.alphabet ) self.assertEqual(matches, alignment.matches) self.assertEqual(repMatches, alignment.repMatches) self.assertEqual( str(alignment), """\ chr3 48663767 CACGAGAGGAGCGGAGGCGAGGGGTGAACGCGGAGCACTCCAATCGGTCAGTCATTGTTT 0 ||||||||||||||||||||||||||||||||||||||||||||||-------------- NR_111921 0 CACGAGAGGAGCGGAGGCGAGGGGTGAACGCGGAGCACTCCAATCG-------------- chr3 48663827 CTATTGGCACAATGGGAGGCCCCGCCCCTCACGGCGGACTCATCGCATGGGGGAGGGGGC 60 ------------------------------------------------------------ NR_111921 46 ------------------------------------------------------------ chr3 48663887 TCCGCGGGTTGCCGGCTAACCGTGAGAGAGTCCGGGAGGTACACTATACGGACCGGCCTC 120 ------------------------------------------------------------ NR_111921 46 ------------------------------------------------------------ chr3 48663947 CAAAGGCGGAATCGATAACGAGCTGCAGCGCCGGGTGCAGAGGACGCGGGCATCCCGAAG 180 ------------------------------------------------------------ NR_111921 46 ------------------------------------------------------------ chr3 48664007 CCCAGGAAGAGGTCAGGGCCGGGACCCCAGAACGCTCCACAGGGTGCGGCTCCCGCGATG 240 ------------------------------------------------------------ NR_111921 46 ------------------------------------------------------------ chr3 48664067 GGGTGGATCCTGGTTCTAACAGGCGAGGAACTCCTGGCCAAGGCCTCTGGCCCGCCCCGA 300 ------------------------------------------------------------ NR_111921 46 ------------------------------------------------------------ chr3 48664127 ACGGTCCCTATGACATCACCATCAACCAATCAGTCGGCGCATCCTTTCGCCCCTTGACTG 360 ------------------------------------------------------------ NR_111921 46 ------------------------------------------------------------ chr3 48664187 CTCCGCTTCCGGGAGGCGGGGCTTCTGCGGGTTCCACCTCCCGAGCGCCCCTTGTGGCTA 420 ------------------------------------------------------------ NR_111921 46 ------------------------------------------------------------ chr3 48664247 CCAAGGTCAGGCAACAGGTGTCCAGTTGTTCCCTCTCCTGTCTACGAATCTGAGGACCTC 480 ------------------------------------------------------------ NR_111921 46 ------------------------------------------------------------ chr3 48664307 CCCAGGATCAGAGCTCTGGGCCTGATACACGGCCGGGGTTCCTACGGGTTTGTGAGTGGG 540 ------------------------------------------------------------ NR_111921 46 ------------------------------------------------------------ chr3 48664367 GGTGGAAGATCTGCAGAGGCACTTAGGGCTGAACTCCTTTGAATGGGAGCCAATCGGTGC 600 ------------------------------------------------------------ NR_111921 46 ------------------------------------------------------------ chr3 48664427 AGGGGCTGGAGGAGCGAGTCCCCCAAAGTAGttttatttatctatttagagacaaggtct 660 ------------------------------------------------------------ NR_111921 46 ------------------------------------------------------------ chr3 48664487 cactctttcggagtgcagtggtgatcacagctcaccgtagcctcgaactccccaggcgat 720 ------------------------------------------------------------ NR_111921 46 ------------------------------------------------------------ chr3 48664547 tctctcacctcagcctcccgagtagctgggactacgggtacatgtcatcacacttggcta 780 ------------------------------------------------------------ NR_111921 46 ------------------------------------------------------------ chr3 48664607 atttttgcattttttatagagacagggtctcaccatgtaggccagattagtcttgaactc 840 ------------------------------------------------------------ NR_111921 46 ------------------------------------------------------------ chr3 48664667 ctgggctcaagcaatccgcccatcttggcctcccaaagtgctgggattataggtgtgagc 900 ------------------------------------------------------------ NR_111921 46 ------------------------------------------------------------ chr3 48664727 caccgcgcccggcAACCCAGAAGTGGTTTTGACAGCAccagcgctttctgtgtccacaat 960 ------------------------------------------------------------ NR_111921 46 ------------------------------------------------------------ chr3 48664787 ctagtgagtagagggcacaaaacctgacaccacggaggcagacaggcaggggctctgccg 1020 ------------------------------------------------------------ NR_111921 46 ------------------------------------------------------------ chr3 48664847 gggaagggtgttggagtcccaaaggaggcgtctgagtcaccttcgcaacctgggacgcct 1080 ------------------------------------------------------------ NR_111921 46 ------------------------------------------------------------ chr3 48664907 tcttgcataagatgcctgagcagtgccttgaatgaccaaggggagatccgcatctgcaaa 1140 ------------------------------------------------------------ NR_111921 46 ------------------------------------------------------------ chr3 48664967 ggaagggcagggagggatagggattgggggtgggcatcctaggtcttggagactgtgtgg 1200 ------------------------------------------------------------ NR_111921 46 ------------------------------------------------------------ chr3 48665027 gcaaatgtgcagagacataaagggactatggctgagggaaatcaagCCCTGCCCTCTCAC 1260 ------------------------------------------------------------ NR_111921 46 ------------------------------------------------------------ chr3 48665087 CAATAGGGCTGGCGCTGGTCCCAGCTAACACTCCTTTTGGAGAGCAAAGCTCCTCACTTC 1320 ------------------------------------------------------------ NR_111921 46 ------------------------------------------------------------ chr3 48665147 TGAGTAGTGAGATTGATTGCGGATCACTCTCCATGTTGCTGCCTGCTGTGTGTCATCCCA 1380 ------------------------------------------------------------ NR_111921 46 ------------------------------------------------------------ chr3 48665207 CTGTCATCCTCCCTTTGTGGCTGTTCTGTGGAGCCCCTCTCCCTCAATCTGCACTCACCT 1440 ------------------------------------------------------------ NR_111921 46 ------------------------------------------------------------ chr3 48665267 CTATGCCCCAGCCCCATTGGCAGCTCCTAATGCACTCCCGGTaaaaaaaaaaaaacaaaa 1500 ------------------------------------------------------------ NR_111921 46 ------------------------------------------------------------ chr3 48665327 aCCAGATGTTAGTGATAGTGGTGGTAGTTCTTCTCTCCACCTCCAAATCTTGCCCTTGCC 1560 ------------------------------------------------------------ NR_111921 46 ------------------------------------------------------------ chr3 48665387 TCCTAATAAGACCCCTATGTGGTTTAACCTCAttttttttttttttttttttttttgaga 1620 ------------------------------------------------------------ NR_111921 46 ------------------------------------------------------------ chr3 48665447 tggagtttcactctgtcacccaggctggagtgaagtggtgtgatGGGGCTTCACCATGTg 1680 ------------------------------------------------------------ NR_111921 46 ------------------------------------------------------------ chr3 48665507 atggggcttcaccatgttggccaggctggtatcaaactcctgacctctagtgatctgccc 1740 ------------------------------------------------------------ NR_111921 46 ------------------------------------------------------------ chr3 48665567 gcctcagcctcccaaagtgctgggattaccggcatgaggcaccgtgcccagccTATCCTC 1800 ------------------------------------------------------------ NR_111921 46 ------------------------------------------------------------ chr3 48665627 CTTCTCTTATCAGCTCCCAACTAGAGGTCCACCCAGGACCCAGAGACCTGGATTTGAGGC 1860 -------------||||||||||||||||||||||||||||||||||||||||||||||| NR_111921 46 -------------CTCCCAACTAGAGGTCCACCCAGGACCCAGAGACCTGGATTTGAGGC chr3 48665687 TGCTGGGCGGCAGATGGAGCGATCAGAAGACCAGGGTAAGGGTGTGGCAGATACTGCCAC 1920 |||||||||||||||||||||||||||||||||||------------------------- NR_111921 93 TGCTGGGCGGCAGATGGAGCGATCAGAAGACCAGG------------------------- chr3 48665747 TAACACTTCTCAGCCTTTCCTTCTCCTGCCTTTTCCACCCCACCCTGTGTTTGTCTACTC 1980 ------------------------------------------------------------ NR_111921 128 ------------------------------------------------------------ chr3 48665807 CCAGCCAGGTGTACCTTTCCAGGGGAAGACCTGGCCAACCTGTCCAGCTCAATTAtccag 2040 ------------------------------------------------------------ NR_111921 128 ------------------------------------------------------------ chr3 48665867 cagttctttgacctcactgagatctcgagtccattgttcatcacctcagctattgacctg 2100 ------------------------------------------------------------ NR_111921 128 ------------------------------------------------------------ chr3 48665927 tgtcattagccttatagagttcagtgccacggaaactccctgccctgttctttttctttt 2160 ------------------------------------------------------------ NR_111921 128 ------------------------------------------------------------ chr3 48665987 tctttttttttttttttttgagacagagccttgctctgtcgcccaggctggagtgcagtg 2220 ------------------------------------------------------------ NR_111921 128 ------------------------------------------------------------ chr3 48666047 gcgcgatctcggctcactgcaagctctgcctcccaggttcacaccattctcctgactcag 2280 ------------------------------------------------------------ NR_111921 128 ------------------------------------------------------------ chr3 48666107 cctcccgagtagctgggactacaggcgtccaccaccatgcccagctaatttttttttttg 2340 ------------------------------------------------------------ NR_111921 128 ------------------------------------------------------------ chr3 48666167 tatttttagtagagacggcgtttcaccgtgttagccaggctggtctcgatctcctgacct 2400 ------------------------------------------------------------ NR_111921 128 ------------------------------------------------------------ chr3 48666227 tgtgatgctcccgcctcggcctcccaaagtgctgggattacaggcatgagccattgtgcc 2460 ------------------------------------------------------------ NR_111921 128 ------------------------------------------------------------ chr3 48666287 cggcctgccctgttcttcttagacaaacttgctgggctaaaatctaaccccgttaaaata 2520 ------------------------------------------------------------ NR_111921 128 ------------------------------------------------------------ chr3 48666347 gactatttacgtattgtttgcctctagcgcagcagaacattgctggagaaaaacaaacaa 2580 ------------------------------------------------------------ NR_111921 128 ------------------------------------------------------------ chr3 48666407 ccgtgctaattggtctcattttatattcatgaccacaagcctcagtattatatcggaggg 2640 ------------------------------------------------------------ NR_111921 128 ------------------------------------------------------------ chr3 48666467 cctatccagtgcagtagggcaagaaaaataataagttatgaagattggaagggaaaaaaa 2700 ------------------------------------------------------------ NR_111921 128 ------------------------------------------------------------ chr3 48666527 actaattcacaagcagtaggattgtatatgtaaaaatttcaaaggaacctataggtaagt 2760 ------------------------------------------------------------ NR_111921 128 ------------------------------------------------------------ chr3 48666587 tgttagaatgagttcagcaaagttgttggacacaagatcaatatataaaaatcagttgca 2820 ------------------------------------------------------------ NR_111921 128 ------------------------------------------------------------ chr3 48666647 atttctatatgtcaccaacagttagaaaataaatttcttgcctgggcatgttggctcaag 2880 ------------------------------------------------------------ NR_111921 128 ------------------------------------------------------------ chr3 48666707 cctgtaatcccagcactttgggtggccaaggcgggcagatcacctgaggtcaggagtttg 2940 ------------------------------------------------------------ NR_111921 128 ------------------------------------------------------------ chr3 48666767 agaccagtttggccaacatggtgaaatcccgtctctactaaaaatacagaaattagccgg 3000 ------------------------------------------------------------ NR_111921 128 ------------------------------------------------------------ chr3 48666827 gcgtggtggtgggcacctgtagtcccagctactgaggaggctgaggcaggagaatcactt 3060 ------------------------------------------------------------ NR_111921 128 ------------------------------------------------------------ chr3 48666887 gaacctgggaggcagaggttgcagtgaacgagaaaaaaaaattttttttcttaaaaacaa 3120 ------------------------------------------------------------ NR_111921 128 ------------------------------------------------------------ chr3 48666947 tgatgtttacaatagcatcaagtaatatcaaatgctgaggaataaacctaatgaaagatg 3180 ------------------------------------------------------------ NR_111921 128 ------------------------------------------------------------ chr3 48667007 tgcaaagactacatacacacatacaaaaaaactataaaacattattgagggaaataaaga 3240 ------------------------------------------------------------ NR_111921 128 ------------------------------------------------------------ chr3 48667067 cataggcctggcattggtggctcatgcctgaaatctcagcactttggagggccaaggtgg 3300 ------------------------------------------------------------ NR_111921 128 ------------------------------------------------------------ chr3 48667127 gtggatcatttgaggtcaggagttagagatcagtccggccaacatggtgaaacctcatct 3360 ------------------------------------------------------------ NR_111921 128 ------------------------------------------------------------ chr3 48667187 ctactaaaaatacaaaaaaattagcttggccaggtgcagtggctcacacctgtaatccca 3420 ------------------------------------------------------------ NR_111921 128 ------------------------------------------------------------ chr3 48667247 gcactttgggaggctgaggcgggcggatcatgaggtcaggagatcgagaccatcctggct 3480 ------------------------------------------------------------ NR_111921 128 ------------------------------------------------------------ chr3 48667307 aacacggtgaaaccctgtctctactaaaaatacaaaaaaaaattagccgggcctgatggc 3540 ------------------------------------------------------------ NR_111921 128 ------------------------------------------------------------ chr3 48667367 gggcgcccgtagtcccagctactcgggaggctgaggtagcagaatggcgtgaacctggga 3600 ------------------------------------------------------------ NR_111921 128 ------------------------------------------------------------ chr3 48667427 ggtgcagcttgcagtgagcctaaattgcgccactgcactccagcctgggtaacagagcga 3660 ------------------------------------------------------------ NR_111921 128 ------------------------------------------------------------ chr3 48667487 gactccgtttcaaaaaaaaaaaaaaaaattagctgggcatgctgttgtgcacctgcaatc 3720 ------------------------------------------------------------ NR_111921 128 ------------------------------------------------------------ chr3 48667547 ccagctactctggaggatgaggcagaagtgcctgaacctgggacacagaggttgcagtga 3780 ------------------------------------------------------------ NR_111921 128 ------------------------------------------------------------ chr3 48667607 gccaagatcatgccattgcactccagcctggacaacacagccagacgctatctgaaaaaa 3840 ------------------------------------------------------------ NR_111921 128 ------------------------------------------------------------ chr3 48667667 aaaaaaaaaaaaaaagtaaaaaaaatgagaaataaagacataaataaagtgaaaaattgt 3900 ------------------------------------------------------------ NR_111921 128 ------------------------------------------------------------ chr3 48667727 tccaatattggaaaagtcaatattataaaggtgccaattttcccaaattgatatatggat 3960 ------------------------------------------------------------ NR_111921 128 ------------------------------------------------------------ chr3 48667787 tcgatgcaacttcagttaaaaatcccactaaattttggctgggtgcggtggctcacacct 4020 ------------------------------------------------------------ NR_111921 128 ------------------------------------------------------------ chr3 48667847 gtaatcccagcactttgggaggctgaggcgggcggatcacaaggtcaggagatcgagacc 4080 ------------------------------------------------------------ NR_111921 128 ------------------------------------------------------------ chr3 48667907 atcttggctaacatggtgaaaccgtctctactaaaaatacaaaagttagccgggtgtggt 4140 ------------------------------------------------------------ NR_111921 128 ------------------------------------------------------------ chr3 48667967 ggcgggcacctgtagtcccagctacttgggaggctgagacagaatggcgtgaacctgggg 4200 ------------------------------------------------------------ NR_111921 128 ------------------------------------------------------------ chr3 48668027 aggcggagcttgcagtgagccaagttgacgccactgcactccagcctgggcgacagagca 4260 ------------------------------------------------------------ NR_111921 128 ------------------------------------------------------------ chr3 48668087 agactctgtctcaaaaaaaaaaaaaaaaaaaTCCCACTAGATTTTGTGTGTGTGTAAACT 4320 ------------------------------------------------------------ NR_111921 128 ------------------------------------------------------------ chr3 48668147 GACAAACTAGATTTAGcagcctgagcaacacagcaaaaccccatctctacaaaaaataca 4380 ------------------------------------------------------------ NR_111921 128 ------------------------------------------------------------ chr3 48668207 aaaattttgcacatgcctgtatagtcccagctacttgggaggctgaagtgggaggatcat 4440 ------------------------------------------------------------ NR_111921 128 ------------------------------------------------------------ chr3 48668267 gtgagctctggggaggtcgaggctgtagtgagctatgatcacatgctgcactctagcctg 4500 ------------------------------------------------------------ NR_111921 128 ------------------------------------------------------------ chr3 48668327 ggcaacagagcaagagaccctgtatctaaaaaaagaatgaaaattaaaaaataaaaaGAa 4560 ------------------------------------------------------------ NR_111921 128 ------------------------------------------------------------ chr3 48668387 accaagattgtgtggtactggtacgaggataggaagactaaaggaacgaaatccagagac 4620 ------------------------------------------------------------ NR_111921 128 ------------------------------------------------------------ chr3 48668447 aggcctgaagatgtgtggaaacttgaattttgacaagggtgGTTCTTCAGAGCTAACATG 4680 ------------------------------------------------------------ NR_111921 128 ------------------------------------------------------------ chr3 48668507 AAGAAAGGGTTGTTTTCTTTTTTTTGTTTCCCcaggagcaactctattaactgaaagaat 4740 ------------------------------------------------------------ NR_111921 128 ------------------------------------------------------------ chr3 48668567 aggcttttcaataaatgatgctgggtcagttggatatccatatagaaaaaattaaatgag 4800 ------------------------------------------------------------ NR_111921 128 ------------------------------------------------------------ chr3 48668627 atctctatttcacactgcttgcataatcaattccatataaatttgacatctgaaaatata 4860 ------------------------------------------------------------ NR_111921 128 ------------------------------------------------------------ chr3 48668687 cagtttctagaaaacagtatTAAGACCttgttttgttttttgttgttgttgttttttgtt 4920 ------------------------------------------------------------ NR_111921 128 ------------------------------------------------------------ chr3 48668747 ttgttttttgttttttgagacagagtctcgctctgtcgccaggctggaatacagtggtgc 4980 ------------------------------------------------------------ NR_111921 128 ------------------------------------------------------------ chr3 48668807 aaccttggctcactgcaacctctgactccctagttcaagcaattctcctgcctcagcctc 5040 ------------------------------------------------------------ NR_111921 128 ------------------------------------------------------------ chr3 48668867 ccgagtagctgcgattacaggcacatgccaccacgcccagctaatttttgtatttttagt 5100 ------------------------------------------------------------ NR_111921 128 ------------------------------------------------------------ chr3 48668927 agagatgggggtttcaccatgttggccaggatggtctcgatctcctgaccctgtaatccg 5160 ------------------------------------------------------------ NR_111921 128 ------------------------------------------------------------ chr3 48668987 cccacctcggcctcccaaagtgctgggattacaggcgtgagccactgcacctggccAAGA 5220 ------------------------------------------------------------ NR_111921 128 ------------------------------------------------------------ chr3 48669047 GAAGATCTTAAAGGTGACTTTAAGCAAACttttttttttttttttttacagagacgggag 5280 ---------------------------------------------------......... NR_111921 128 ---------------------------------------------------AGACGGGAG chr3 48669107 ctggagtgcagtggctgttcacaagcgtgaAAGCAAAGATTAAAAAATTTGTTTTTATAT 5340 ..............................|||||||||||||||||||||||||||||| NR_111921 137 CTGGAGTGCAGTGGCTGTTCACAAGCGTGAAAGCAAAGATTAAAAAATTTGTTTTTATAT chr3 48669167 TAAAAAA 48669174 5400 ||||||| 5407 NR_111921 197 TAAAAAA 204 """, ) self.assertEqual( format(alignment, "psl"), """\ 165 0 39 0 0 0 2 5203 + NR_111921.1 216 0 204 chr3 198295559 48663767 48669174 3 46,82,76, 0,46,128, 48663767,48665640,48669098, """, ) alignment = next(alignments) self.assertEqual(alignment.matches, 162) self.assertEqual(alignment.misMatches, 2) self.assertEqual(alignment.repMatches, 39) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.shape, (2, 5409)) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr3") self.assertEqual(alignment.query.id, "NR_111921.1_modified") self.assertEqual(len(alignment.target.seq), 198295559) self.assertEqual(len(alignment.query.seq), 220) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[48663767, 48663795, 48663796, 48663813, 48665640, 48665716, 48665716, 48665722, 48669098, 48669174], [ 3, 31, 31, 48, 48, 124, 126, 132, 132, 208] ]) # fmt: on ) ) dna = Seq(self.dna, length=len(alignment.target)) alignment.target.seq = dna alignment.query.seq = self.rna[alignment.query.id] self.assertTrue( np.array_equal( alignment.substitutions, # fmt: off np.array([[53., 0., 0., 0., 0., 0., 0., 0.], [ 0., 34., 0., 0., 0., 0., 0., 0.], [ 0., 2., 48., 0., 0., 0., 0., 0.], [ 0., 0., 0., 27., 0., 0., 0., 0.], [ 9., 0., 0., 0., 0., 0., 0., 0.], [ 0., 7., 0., 0., 0., 0., 0., 0.], [ 0., 0., 16., 0., 0., 0., 0., 0.], [ 0., 0., 0., 7., 0., 0., 0., 0.], ]), # fmt: on ) ) self.assertEqual(alignment.substitutions.alphabet, "ACGTacgt") matches = sum( alignment.substitutions[c, c] for c in alignment.substitutions.alphabet ) repMatches = sum( alignment.substitutions[c, c.swapcase()] for c in alignment.substitutions.alphabet if c != "X" ) self.assertEqual(matches, alignment.matches) self.assertEqual(repMatches, alignment.repMatches) self.assertEqual( str(alignment), """\ chr3 48663767 CACGAGAGGAGCGGAGGCGAGGGGTGAACGCGGAGCACTCCAATCGGTCAGTCATTGTTT 0 ||||||||||||||||||||||||||||-|||||||||||||||||-------------- NR_111921 3 CACGAGAGGAGCGGAGGCGAGGGGTGAA-GCGGAGCACTCCAATCG-------------- chr3 48663827 CTATTGGCACAATGGGAGGCCCCGCCCCTCACGGCGGACTCATCGCATGGGGGAGGGGGC 60 ------------------------------------------------------------ NR_111921 48 ------------------------------------------------------------ chr3 48663887 TCCGCGGGTTGCCGGCTAACCGTGAGAGAGTCCGGGAGGTACACTATACGGACCGGCCTC 120 ------------------------------------------------------------ NR_111921 48 ------------------------------------------------------------ chr3 48663947 CAAAGGCGGAATCGATAACGAGCTGCAGCGCCGGGTGCAGAGGACGCGGGCATCCCGAAG 180 ------------------------------------------------------------ NR_111921 48 ------------------------------------------------------------ chr3 48664007 CCCAGGAAGAGGTCAGGGCCGGGACCCCAGAACGCTCCACAGGGTGCGGCTCCCGCGATG 240 ------------------------------------------------------------ NR_111921 48 ------------------------------------------------------------ chr3 48664067 GGGTGGATCCTGGTTCTAACAGGCGAGGAACTCCTGGCCAAGGCCTCTGGCCCGCCCCGA 300 ------------------------------------------------------------ NR_111921 48 ------------------------------------------------------------ chr3 48664127 ACGGTCCCTATGACATCACCATCAACCAATCAGTCGGCGCATCCTTTCGCCCCTTGACTG 360 ------------------------------------------------------------ NR_111921 48 ------------------------------------------------------------ chr3 48664187 CTCCGCTTCCGGGAGGCGGGGCTTCTGCGGGTTCCACCTCCCGAGCGCCCCTTGTGGCTA 420 ------------------------------------------------------------ NR_111921 48 ------------------------------------------------------------ chr3 48664247 CCAAGGTCAGGCAACAGGTGTCCAGTTGTTCCCTCTCCTGTCTACGAATCTGAGGACCTC 480 ------------------------------------------------------------ NR_111921 48 ------------------------------------------------------------ chr3 48664307 CCCAGGATCAGAGCTCTGGGCCTGATACACGGCCGGGGTTCCTACGGGTTTGTGAGTGGG 540 ------------------------------------------------------------ NR_111921 48 ------------------------------------------------------------ chr3 48664367 GGTGGAAGATCTGCAGAGGCACTTAGGGCTGAACTCCTTTGAATGGGAGCCAATCGGTGC 600 ------------------------------------------------------------ NR_111921 48 ------------------------------------------------------------ chr3 48664427 AGGGGCTGGAGGAGCGAGTCCCCCAAAGTAGttttatttatctatttagagacaaggtct 660 ------------------------------------------------------------ NR_111921 48 ------------------------------------------------------------ chr3 48664487 cactctttcggagtgcagtggtgatcacagctcaccgtagcctcgaactccccaggcgat 720 ------------------------------------------------------------ NR_111921 48 ------------------------------------------------------------ chr3 48664547 tctctcacctcagcctcccgagtagctgggactacgggtacatgtcatcacacttggcta 780 ------------------------------------------------------------ NR_111921 48 ------------------------------------------------------------ chr3 48664607 atttttgcattttttatagagacagggtctcaccatgtaggccagattagtcttgaactc 840 ------------------------------------------------------------ NR_111921 48 ------------------------------------------------------------ chr3 48664667 ctgggctcaagcaatccgcccatcttggcctcccaaagtgctgggattataggtgtgagc 900 ------------------------------------------------------------ NR_111921 48 ------------------------------------------------------------ chr3 48664727 caccgcgcccggcAACCCAGAAGTGGTTTTGACAGCAccagcgctttctgtgtccacaat 960 ------------------------------------------------------------ NR_111921 48 ------------------------------------------------------------ chr3 48664787 ctagtgagtagagggcacaaaacctgacaccacggaggcagacaggcaggggctctgccg 1020 ------------------------------------------------------------ NR_111921 48 ------------------------------------------------------------ chr3 48664847 gggaagggtgttggagtcccaaaggaggcgtctgagtcaccttcgcaacctgggacgcct 1080 ------------------------------------------------------------ NR_111921 48 ------------------------------------------------------------ chr3 48664907 tcttgcataagatgcctgagcagtgccttgaatgaccaaggggagatccgcatctgcaaa 1140 ------------------------------------------------------------ NR_111921 48 ------------------------------------------------------------ chr3 48664967 ggaagggcagggagggatagggattgggggtgggcatcctaggtcttggagactgtgtgg 1200 ------------------------------------------------------------ NR_111921 48 ------------------------------------------------------------ chr3 48665027 gcaaatgtgcagagacataaagggactatggctgagggaaatcaagCCCTGCCCTCTCAC 1260 ------------------------------------------------------------ NR_111921 48 ------------------------------------------------------------ chr3 48665087 CAATAGGGCTGGCGCTGGTCCCAGCTAACACTCCTTTTGGAGAGCAAAGCTCCTCACTTC 1320 ------------------------------------------------------------ NR_111921 48 ------------------------------------------------------------ chr3 48665147 TGAGTAGTGAGATTGATTGCGGATCACTCTCCATGTTGCTGCCTGCTGTGTGTCATCCCA 1380 ------------------------------------------------------------ NR_111921 48 ------------------------------------------------------------ chr3 48665207 CTGTCATCCTCCCTTTGTGGCTGTTCTGTGGAGCCCCTCTCCCTCAATCTGCACTCACCT 1440 ------------------------------------------------------------ NR_111921 48 ------------------------------------------------------------ chr3 48665267 CTATGCCCCAGCCCCATTGGCAGCTCCTAATGCACTCCCGGTaaaaaaaaaaaaacaaaa 1500 ------------------------------------------------------------ NR_111921 48 ------------------------------------------------------------ chr3 48665327 aCCAGATGTTAGTGATAGTGGTGGTAGTTCTTCTCTCCACCTCCAAATCTTGCCCTTGCC 1560 ------------------------------------------------------------ NR_111921 48 ------------------------------------------------------------ chr3 48665387 TCCTAATAAGACCCCTATGTGGTTTAACCTCAttttttttttttttttttttttttgaga 1620 ------------------------------------------------------------ NR_111921 48 ------------------------------------------------------------ chr3 48665447 tggagtttcactctgtcacccaggctggagtgaagtggtgtgatGGGGCTTCACCATGTg 1680 ------------------------------------------------------------ NR_111921 48 ------------------------------------------------------------ chr3 48665507 atggggcttcaccatgttggccaggctggtatcaaactcctgacctctagtgatctgccc 1740 ------------------------------------------------------------ NR_111921 48 ------------------------------------------------------------ chr3 48665567 gcctcagcctcccaaagtgctgggattaccggcatgaggcaccgtgcccagccTATCCTC 1800 ------------------------------------------------------------ NR_111921 48 ------------------------------------------------------------ chr3 48665627 CTTCTCTTATCAGCTCCCAACTAGAGGTCCACCCAGGACCCAGAGACCTGGATTTGAGGC 1860 -------------||||||||||||||||||||||||||||||||||||||||||||||| NR_111921 48 -------------CTCCCAACTAGAGGTCCACCCAGGACCCAGAGACCTGGATTTGAGGC chr3 48665687 TGCTGGGCGGCAGATGGAGCGATCAGAAG--ACCAGGGTAAGGGTGTGGCAGATACTGCC 1920 |||||..||||||||||||||||||||||--||||||----------------------- NR_111921 95 TGCTGCCCGGCAGATGGAGCGATCAGAAGCCACCAGG----------------------- chr3 48665745 ACTAACACTTCTCAGCCTTTCCTTCTCCTGCCTTTTCCACCCCACCCTGTGTTTGTCTAC 1980 ------------------------------------------------------------ NR_111921 132 ------------------------------------------------------------ chr3 48665805 TCCCAGCCAGGTGTACCTTTCCAGGGGAAGACCTGGCCAACCTGTCCAGCTCAATTAtcc 2040 ------------------------------------------------------------ NR_111921 132 ------------------------------------------------------------ chr3 48665865 agcagttctttgacctcactgagatctcgagtccattgttcatcacctcagctattgacc 2100 ------------------------------------------------------------ NR_111921 132 ------------------------------------------------------------ chr3 48665925 tgtgtcattagccttatagagttcagtgccacggaaactccctgccctgttctttttctt 2160 ------------------------------------------------------------ NR_111921 132 ------------------------------------------------------------ chr3 48665985 tttctttttttttttttttttgagacagagccttgctctgtcgcccaggctggagtgcag 2220 ------------------------------------------------------------ NR_111921 132 ------------------------------------------------------------ chr3 48666045 tggcgcgatctcggctcactgcaagctctgcctcccaggttcacaccattctcctgactc 2280 ------------------------------------------------------------ NR_111921 132 ------------------------------------------------------------ chr3 48666105 agcctcccgagtagctgggactacaggcgtccaccaccatgcccagctaatttttttttt 2340 ------------------------------------------------------------ NR_111921 132 ------------------------------------------------------------ chr3 48666165 tgtatttttagtagagacggcgtttcaccgtgttagccaggctggtctcgatctcctgac 2400 ------------------------------------------------------------ NR_111921 132 ------------------------------------------------------------ chr3 48666225 cttgtgatgctcccgcctcggcctcccaaagtgctgggattacaggcatgagccattgtg 2460 ------------------------------------------------------------ NR_111921 132 ------------------------------------------------------------ chr3 48666285 cccggcctgccctgttcttcttagacaaacttgctgggctaaaatctaaccccgttaaaa 2520 ------------------------------------------------------------ NR_111921 132 ------------------------------------------------------------ chr3 48666345 tagactatttacgtattgtttgcctctagcgcagcagaacattgctggagaaaaacaaac 2580 ------------------------------------------------------------ NR_111921 132 ------------------------------------------------------------ chr3 48666405 aaccgtgctaattggtctcattttatattcatgaccacaagcctcagtattatatcggag 2640 ------------------------------------------------------------ NR_111921 132 ------------------------------------------------------------ chr3 48666465 ggcctatccagtgcagtagggcaagaaaaataataagttatgaagattggaagggaaaaa 2700 ------------------------------------------------------------ NR_111921 132 ------------------------------------------------------------ chr3 48666525 aaactaattcacaagcagtaggattgtatatgtaaaaatttcaaaggaacctataggtaa 2760 ------------------------------------------------------------ NR_111921 132 ------------------------------------------------------------ chr3 48666585 gttgttagaatgagttcagcaaagttgttggacacaagatcaatatataaaaatcagttg 2820 ------------------------------------------------------------ NR_111921 132 ------------------------------------------------------------ chr3 48666645 caatttctatatgtcaccaacagttagaaaataaatttcttgcctgggcatgttggctca 2880 ------------------------------------------------------------ NR_111921 132 ------------------------------------------------------------ chr3 48666705 agcctgtaatcccagcactttgggtggccaaggcgggcagatcacctgaggtcaggagtt 2940 ------------------------------------------------------------ NR_111921 132 ------------------------------------------------------------ chr3 48666765 tgagaccagtttggccaacatggtgaaatcccgtctctactaaaaatacagaaattagcc 3000 ------------------------------------------------------------ NR_111921 132 ------------------------------------------------------------ chr3 48666825 gggcgtggtggtgggcacctgtagtcccagctactgaggaggctgaggcaggagaatcac 3060 ------------------------------------------------------------ NR_111921 132 ------------------------------------------------------------ chr3 48666885 ttgaacctgggaggcagaggttgcagtgaacgagaaaaaaaaattttttttcttaaaaac 3120 ------------------------------------------------------------ NR_111921 132 ------------------------------------------------------------ chr3 48666945 aatgatgtttacaatagcatcaagtaatatcaaatgctgaggaataaacctaatgaaaga 3180 ------------------------------------------------------------ NR_111921 132 ------------------------------------------------------------ chr3 48667005 tgtgcaaagactacatacacacatacaaaaaaactataaaacattattgagggaaataaa 3240 ------------------------------------------------------------ NR_111921 132 ------------------------------------------------------------ chr3 48667065 gacataggcctggcattggtggctcatgcctgaaatctcagcactttggagggccaaggt 3300 ------------------------------------------------------------ NR_111921 132 ------------------------------------------------------------ chr3 48667125 gggtggatcatttgaggtcaggagttagagatcagtccggccaacatggtgaaacctcat 3360 ------------------------------------------------------------ NR_111921 132 ------------------------------------------------------------ chr3 48667185 ctctactaaaaatacaaaaaaattagcttggccaggtgcagtggctcacacctgtaatcc 3420 ------------------------------------------------------------ NR_111921 132 ------------------------------------------------------------ chr3 48667245 cagcactttgggaggctgaggcgggcggatcatgaggtcaggagatcgagaccatcctgg 3480 ------------------------------------------------------------ NR_111921 132 ------------------------------------------------------------ chr3 48667305 ctaacacggtgaaaccctgtctctactaaaaatacaaaaaaaaattagccgggcctgatg 3540 ------------------------------------------------------------ NR_111921 132 ------------------------------------------------------------ chr3 48667365 gcgggcgcccgtagtcccagctactcgggaggctgaggtagcagaatggcgtgaacctgg 3600 ------------------------------------------------------------ NR_111921 132 ------------------------------------------------------------ chr3 48667425 gaggtgcagcttgcagtgagcctaaattgcgccactgcactccagcctgggtaacagagc 3660 ------------------------------------------------------------ NR_111921 132 ------------------------------------------------------------ chr3 48667485 gagactccgtttcaaaaaaaaaaaaaaaaattagctgggcatgctgttgtgcacctgcaa 3720 ------------------------------------------------------------ NR_111921 132 ------------------------------------------------------------ chr3 48667545 tcccagctactctggaggatgaggcagaagtgcctgaacctgggacacagaggttgcagt 3780 ------------------------------------------------------------ NR_111921 132 ------------------------------------------------------------ chr3 48667605 gagccaagatcatgccattgcactccagcctggacaacacagccagacgctatctgaaaa 3840 ------------------------------------------------------------ NR_111921 132 ------------------------------------------------------------ chr3 48667665 aaaaaaaaaaaaaaaaagtaaaaaaaatgagaaataaagacataaataaagtgaaaaatt 3900 ------------------------------------------------------------ NR_111921 132 ------------------------------------------------------------ chr3 48667725 gttccaatattggaaaagtcaatattataaaggtgccaattttcccaaattgatatatgg 3960 ------------------------------------------------------------ NR_111921 132 ------------------------------------------------------------ chr3 48667785 attcgatgcaacttcagttaaaaatcccactaaattttggctgggtgcggtggctcacac 4020 ------------------------------------------------------------ NR_111921 132 ------------------------------------------------------------ chr3 48667845 ctgtaatcccagcactttgggaggctgaggcgggcggatcacaaggtcaggagatcgaga 4080 ------------------------------------------------------------ NR_111921 132 ------------------------------------------------------------ chr3 48667905 ccatcttggctaacatggtgaaaccgtctctactaaaaatacaaaagttagccgggtgtg 4140 ------------------------------------------------------------ NR_111921 132 ------------------------------------------------------------ chr3 48667965 gtggcgggcacctgtagtcccagctacttgggaggctgagacagaatggcgtgaacctgg 4200 ------------------------------------------------------------ NR_111921 132 ------------------------------------------------------------ chr3 48668025 ggaggcggagcttgcagtgagccaagttgacgccactgcactccagcctgggcgacagag 4260 ------------------------------------------------------------ NR_111921 132 ------------------------------------------------------------ chr3 48668085 caagactctgtctcaaaaaaaaaaaaaaaaaaaTCCCACTAGATTTTGTGTGTGTGTAAA 4320 ------------------------------------------------------------ NR_111921 132 ------------------------------------------------------------ chr3 48668145 CTGACAAACTAGATTTAGcagcctgagcaacacagcaaaaccccatctctacaaaaaata 4380 ------------------------------------------------------------ NR_111921 132 ------------------------------------------------------------ chr3 48668205 caaaaattttgcacatgcctgtatagtcccagctacttgggaggctgaagtgggaggatc 4440 ------------------------------------------------------------ NR_111921 132 ------------------------------------------------------------ chr3 48668265 atgtgagctctggggaggtcgaggctgtagtgagctatgatcacatgctgcactctagcc 4500 ------------------------------------------------------------ NR_111921 132 ------------------------------------------------------------ chr3 48668325 tgggcaacagagcaagagaccctgtatctaaaaaaagaatgaaaattaaaaaataaaaaG 4560 ------------------------------------------------------------ NR_111921 132 ------------------------------------------------------------ chr3 48668385 Aaaccaagattgtgtggtactggtacgaggataggaagactaaaggaacgaaatccagag 4620 ------------------------------------------------------------ NR_111921 132 ------------------------------------------------------------ chr3 48668445 acaggcctgaagatgtgtggaaacttgaattttgacaagggtgGTTCTTCAGAGCTAACA 4680 ------------------------------------------------------------ NR_111921 132 ------------------------------------------------------------ chr3 48668505 TGAAGAAAGGGTTGTTTTCTTTTTTTTGTTTCCCcaggagcaactctattaactgaaaga 4740 ------------------------------------------------------------ NR_111921 132 ------------------------------------------------------------ chr3 48668565 ataggcttttcaataaatgatgctgggtcagttggatatccatatagaaaaaattaaatg 4800 ------------------------------------------------------------ NR_111921 132 ------------------------------------------------------------ chr3 48668625 agatctctatttcacactgcttgcataatcaattccatataaatttgacatctgaaaata 4860 ------------------------------------------------------------ NR_111921 132 ------------------------------------------------------------ chr3 48668685 tacagtttctagaaaacagtatTAAGACCttgttttgttttttgttgttgttgttttttg 4920 ------------------------------------------------------------ NR_111921 132 ------------------------------------------------------------ chr3 48668745 ttttgttttttgttttttgagacagagtctcgctctgtcgccaggctggaatacagtggt 4980 ------------------------------------------------------------ NR_111921 132 ------------------------------------------------------------ chr3 48668805 gcaaccttggctcactgcaacctctgactccctagttcaagcaattctcctgcctcagcc 5040 ------------------------------------------------------------ NR_111921 132 ------------------------------------------------------------ chr3 48668865 tcccgagtagctgcgattacaggcacatgccaccacgcccagctaatttttgtattttta 5100 ------------------------------------------------------------ NR_111921 132 ------------------------------------------------------------ chr3 48668925 gtagagatgggggtttcaccatgttggccaggatggtctcgatctcctgaccctgtaatc 5160 ------------------------------------------------------------ NR_111921 132 ------------------------------------------------------------ chr3 48668985 cgcccacctcggcctcccaaagtgctgggattacaggcgtgagccactgcacctggccAA 5220 ------------------------------------------------------------ NR_111921 132 ------------------------------------------------------------ chr3 48669045 GAGAAGATCTTAAAGGTGACTTTAAGCAAACttttttttttttttttttacagagacggg 5280 -----------------------------------------------------....... NR_111921 132 -----------------------------------------------------AGACGGG chr3 48669105 agctggagtgcagtggctgttcacaagcgtgaAAGCAAAGATTAAAAAATTTGTTTTTAT 5340 ................................|||||||||||||||||||||||||||| NR_111921 139 AGCTGGAGTGCAGTGGCTGTTCACAAGCGTGAAAGCAAAGATTAAAAAATTTGTTTTTAT chr3 48669165 ATTAAAAAA 48669174 5400 ||||||||| 5409 NR_111921 199 ATTAAAAAA 208 """, ) self.assertEqual( format(alignment, "psl"), """\ 162 2 39 0 1 2 3 5204 + NR_111921.1_modified 220 3 208 chr3 198295559 48663767 48669174 5 28,17,76,6,76, 3,31,48,126,132, 48663767,48663796,48665640,48665716,48669098, """, ) self.assertRaises(StopIteration, next, alignments) def test_writing(self): """Test writing the alignments in dna_rna.psl.""" path = "Blat/dna_rna.psl" with open(path) as stream: original_data = stream.read() alignments = Align.parse(path, "psl") stream = StringIO() n = Align.write(alignments, stream, "psl") self.assertEqual(n, 4) stream.seek(0) written_data = stream.read() stream.close() self.assertEqual(original_data, written_data) # Try this again. This time, we first strip the matches, misMatches, # repMatches, and nCount attributes from each alignment, and insert the # appropriate sequence data in each alignment. The writer will then # recalculate the matches, misMatches, repMatches, and nCount values # from the sequence data and the alignment, and store those values in # the PSL file. alignments = [] for alignment in Align.parse(path, "psl"): del alignment.matches del alignment.misMatches del alignment.repMatches del alignment.nCount dna = Seq(self.dna, length=len(alignment.target)) alignment.target.seq = dna alignment.query.seq = self.rna[alignment.sequences[1].id] alignments.append(alignment) stream = StringIO() n = Align.write(alignments, stream, "psl", mask="lower") self.assertEqual(n, 4) stream.seek(0) written_data = stream.read() stream.close() self.assertEqual(original_data, written_data) class TestAlign_dna(unittest.TestCase): queries = { record.id: str(record.seq) for record in SeqIO.parse("Blat/fasta_34.fa", "fasta") } def test_reading_psl_34_001(self): """Test parsing psl_34_001.psl and pslx_34_001.pslx.""" self.check_reading_psl_34_001("psl") self.check_reading_psl_34_001("pslx") def check_reading_psl_34_001(self, fmt): """Check parsing psl_34_001.psl or pslx_34_001.pslx.""" path = "Blat/%s_34_001.%s" % (fmt, fmt) alignments = Align.parse(path, "psl") self.assertEqual(alignments.metadata["psLayout version"], "3") alignment = next(alignments) self.assertEqual(alignment.matches, 16) self.assertEqual(alignment.misMatches, 0) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.shape, (2, 16)) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr4") self.assertEqual(alignment.query.id, "hg18_dna") self.assertEqual(len(alignment.target.seq), 191154276) self.assertEqual(len(alignment.query.seq), 33) if fmt == "psl": self.assertEqual( str(alignment), """\ chr4 61646095 ???????????????? 61646111 0 |||||||||||||||| 16 hg18_dna 11 ???????????????? 27 """, ) elif fmt == "pslx": self.assertEqual( alignment.target.seq[61646095:61646111], "aggtaaactgccttca" ) self.assertEqual( alignment.query.seq[11:27], self.queries[alignment.query.id][11:27] ) self.assertEqual( str(alignment), """\ chr4 61646095 aggtaaactgccttca 61646111 0 |||||||||||||||| 16 hg18_dna 11 aggtaaactgccttca 27 """, ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['a', 'g', 'g', 't', 'a', 'a', 'a', 'c', 't', 'g', 'c', 'c', 't', 't', 'c', 'a'], ['a', 'g', 'g', 't', 'a', 'a', 'a', 'c', 't', 'g', 'c', 'c', 't', 't', 'c', 'a']], dtype='U') # fmt: on ) ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[61646095, 61646111], [ 11, 27]]), # fmt: on ) ) self.assertEqual( format(alignment, "psl"), """\ 16 0 0 0 0 0 0 0 + hg18_dna 33 11 27 chr4 191154276 61646095 61646111 1 16, 11, 61646095, """, ) alignment = next(alignments) self.assertEqual(alignment.matches, 33) self.assertEqual(alignment.misMatches, 0) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.shape, (2, 33)) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr1") self.assertEqual(alignment.query.id, "hg18_dna") self.assertEqual(len(alignment.target.seq), 249250621) self.assertEqual(len(alignment.query.seq), 33) if fmt == "psl": self.assertEqual( str(alignment), """\ chr1 10271783 ????????????????????????????????? 10271816 0 ||||||||||||||||||||||||||||||||| 33 hg18_dna 0 ????????????????????????????????? 33 """, ) elif fmt == "pslx": self.assertEqual( alignment.target.seq[10271783:10271816], "atgagcttccaaggtaaactgccttcaagattc", ) self.assertEqual(alignment.query.seq, self.queries[alignment.query.id]) self.assertEqual( str(alignment), """\ chr1 10271783 atgagcttccaaggtaaactgccttcaagattc 10271816 0 ||||||||||||||||||||||||||||||||| 33 hg18_dna 0 atgagcttccaaggtaaactgccttcaagattc 33 """, ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['a', 't', 'g', 'a', 'g', 'c', 't', 't', 'c', 'c', 'a', 'a', 'g', 'g', 't', 'a', 'a', 'a', 'c', 't', 'g', 'c', 'c', 't', 't', 'c', 'a', 'a', 'g', 'a', 't', 't', 'c'], ['a', 't', 'g', 'a', 'g', 'c', 't', 't', 'c', 'c', 'a', 'a', 'g', 'g', 't', 'a', 'a', 'a', 'c', 't', 'g', 'c', 'c', 't', 't', 'c', 'a', 'a', 'g', 'a', 't', 't', 'c']], dtype='U') # fmt: on ) ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[10271783, 10271816], [ 0, 33]]), # fmt: on ) ) self.assertEqual( format(alignment, "psl"), """\ 33 0 0 0 0 0 0 0 + hg18_dna 33 0 33 chr1 249250621 10271783 10271816 1 33, 0, 10271783, """, ) alignment = next(alignments) self.assertEqual(alignment.matches, 17) self.assertEqual(alignment.misMatches, 0) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.shape, (2, 17)) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr2") self.assertEqual(alignment.query.id, "hg18_dna") self.assertEqual(len(alignment.target.seq), 243199373) self.assertEqual(len(alignment.query.seq), 33) if fmt == "psl": self.assertEqual( str(alignment), """\ chr2 53575980 ????????????????? 53575997 0 ||||||||||||||||| 17 hg18_dna 25 ????????????????? 8 """, ) elif fmt == "pslx": self.assertEqual( alignment.target.seq[53575980:53575997], "aaggcagtttaccttgg" ) self.assertEqual( alignment.query.seq[8:25], self.queries[alignment.query.id][8:25] ) self.assertEqual( str(alignment), """\ chr2 53575980 aaggcagtttaccttgg 53575997 0 ||||||||||||||||| 17 hg18_dna 25 aaggcagtttaccttgg 8 """, ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['a', 'a', 'g', 'g', 'c', 'a', 'g', 't', 't', 't', 'a', 'c', 'c', 't', 't', 'g', 'g'], ['a', 'a', 'g', 'g', 'c', 'a', 'g', 't', 't', 't', 'a', 'c', 'c', 't', 't', 'g', 'g']], dtype='U') # fmt: on ) ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[53575980, 53575997], [ 25, 8]]), # fmt: on ) ) self.assertEqual( format(alignment, "psl"), """\ 17 0 0 0 0 0 0 0 - hg18_dna 33 8 25 chr2 243199373 53575980 53575997 1 17, 8, 53575980, """, ) alignment = next(alignments) self.assertEqual(alignment.matches, 38) self.assertEqual(alignment.misMatches, 3) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.shape, (2, 41)) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr9") self.assertEqual(alignment.query.id, "hg19_dna") self.assertEqual(len(alignment.target.seq), 141213431) self.assertEqual(len(alignment.query.seq), 50) if fmt == "psl": self.assertEqual( str(alignment), """\ chr9 85737865 ????????????????????????????????????????? 85737906 0 ||||||||||||||||||||||||||||||||||||||||| 41 hg19_dna 9 ????????????????????????????????????????? 50 """, ) elif fmt == "pslx": self.assertEqual( alignment.target.seq[85737865:85737906], "acaaaggggctgggcgcagtggctcacgcctgtaatcccaa", ) self.assertEqual( alignment.query.seq[9:50], self.queries[alignment.query.id][9:50] ) self.assertEqual( str(alignment), """\ chr9 85737865 acaaaggggctgggcgcagtggctcacgcctgtaatcccaa 85737906 0 ||||||||||||||||..|||||||||.||||||||||||| 41 hg19_dna 9 acaaaggggctgggcgtggtggctcacacctgtaatcccaa 50 """, ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['a', 'c', 'a', 'a', 'a', 'g', 'g', 'g', 'g', 'c', 't', 'g', 'g', 'g', 'c', 'g', 'c', 'a', 'g', 't', 'g', 'g', 'c', 't', 'c', 'a', 'c', 'g', 'c', 'c', 't', 'g', 't', 'a', 'a', 't', 'c', 'c', 'c', 'a', 'a'], ['a', 'c', 'a', 'a', 'a', 'g', 'g', 'g', 'g', 'c', 't', 'g', 'g', 'g', 'c', 'g', 't', 'g', 'g', 't', 'g', 'g', 'c', 't', 'c', 'a', 'c', 'a', 'c', 'c', 't', 'g', 't', 'a', 'a', 't', 'c', 'c', 'c', 'a', 'a']], dtype='U') # fmt: on ) ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[85737865, 85737906], [ 9, 50]]), # fmt: on ) ) self.assertEqual( format(alignment, "psl"), """\ 38 3 0 0 0 0 0 0 + hg19_dna 50 9 50 chr9 141213431 85737865 85737906 1 41, 9, 85737865, """, ) alignment = next(alignments) self.assertEqual(alignment.matches, 41) self.assertEqual(alignment.misMatches, 0) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.shape, (2, 41)) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr8") self.assertEqual(alignment.query.id, "hg19_dna") self.assertEqual(len(alignment.target.seq), 146364022) self.assertEqual(len(alignment.query.seq), 50) if fmt == "psl": self.assertEqual( str(alignment), """\ chr8 95160479 ????????????????????????????????????????? 95160520 0 ||||||||||||||||||||||||||||||||||||||||| 41 hg19_dna 8 ????????????????????????????????????????? 49 """, ) elif fmt == "pslx": self.assertEqual( alignment.target.seq[95160479:95160520], "cacaaaggggctgggcgtggtggctcacacctgtaatccca", ) self.assertEqual( alignment.query.seq[8:49], self.queries[alignment.query.id][8:49] ) self.assertEqual( str(alignment), """\ chr8 95160479 cacaaaggggctgggcgtggtggctcacacctgtaatccca 95160520 0 ||||||||||||||||||||||||||||||||||||||||| 41 hg19_dna 8 cacaaaggggctgggcgtggtggctcacacctgtaatccca 49 """, ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['c', 'a', 'c', 'a', 'a', 'a', 'g', 'g', 'g', 'g', 'c', 't', 'g', 'g', 'g', 'c', 'g', 't', 'g', 'g', 't', 'g', 'g', 'c', 't', 'c', 'a', 'c', 'a', 'c', 'c', 't', 'g', 't', 'a', 'a', 't', 'c', 'c', 'c', 'a'], ['c', 'a', 'c', 'a', 'a', 'a', 'g', 'g', 'g', 'g', 'c', 't', 'g', 'g', 'g', 'c', 'g', 't', 'g', 'g', 't', 'g', 'g', 'c', 't', 'c', 'a', 'c', 'a', 'c', 'c', 't', 'g', 't', 'a', 'a', 't', 'c', 'c', 'c', 'a']], dtype='U') # fmt: on ) ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[95160479, 95160520], [ 8, 49]]), # fmt: on ) ) self.assertEqual( format(alignment, "psl"), """\ 41 0 0 0 0 0 0 0 + hg19_dna 50 8 49 chr8 146364022 95160479 95160520 1 41, 8, 95160479, """, ) alignment = next(alignments) self.assertEqual(alignment.matches, 33) self.assertEqual(alignment.misMatches, 3) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.shape, (2, 36)) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr22") self.assertEqual(alignment.query.id, "hg19_dna") self.assertEqual(len(alignment.target.seq), 51304566) self.assertEqual(len(alignment.query.seq), 50) if fmt == "psl": self.assertEqual( str(alignment), """\ chr22 42144400 ???????????????????????????????????? 42144436 0 |||||||||||||||||||||||||||||||||||| 36 hg19_dna 11 ???????????????????????????????????? 47 """, ) elif fmt == "pslx": self.assertEqual( alignment.target.seq[42144400:42144436], "aaaggggctgggcgtggtagctcatgcctgtaatcc", ) self.assertEqual( alignment.query.seq[11:47], self.queries[alignment.query.id][11:47] ) self.assertEqual( str(alignment), """\ chr22 42144400 aaaggggctgggcgtggtagctcatgcctgtaatcc 42144436 0 ||||||||||||||||||.|||||..|||||||||| 36 hg19_dna 11 aaaggggctgggcgtggtggctcacacctgtaatcc 47 """, ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['a', 'a', 'a', 'g', 'g', 'g', 'g', 'c', 't', 'g', 'g', 'g', 'c', 'g', 't', 'g', 'g', 't', 'a', 'g', 'c', 't', 'c', 'a', 't', 'g', 'c', 'c', 't', 'g', 't', 'a', 'a', 't', 'c', 'c'], ['a', 'a', 'a', 'g', 'g', 'g', 'g', 'c', 't', 'g', 'g', 'g', 'c', 'g', 't', 'g', 'g', 't', 'g', 'g', 'c', 't', 'c', 'a', 'c', 'a', 'c', 'c', 't', 'g', 't', 'a', 'a', 't', 'c', 'c']], dtype='U') # fmt: on ) ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[42144400, 42144436], [ 11, 47]]), # fmt: on ) ) self.assertEqual( format(alignment, "psl"), """\ 33 3 0 0 0 0 0 0 + hg19_dna 50 11 47 chr22 51304566 42144400 42144436 1 36, 11, 42144400, """, ) alignment = next(alignments) self.assertEqual(alignment.matches, 43) self.assertEqual(alignment.misMatches, 1) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.shape, (2, 48)) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr2") self.assertEqual(alignment.query.id, "hg19_dna") self.assertEqual(len(alignment.target.seq), 243199373) self.assertEqual(len(alignment.query.seq), 50) if fmt == "psl": self.assertEqual( str(alignment), """\ chr2 183925984 ??????----?????????????????????????????????????? 183926028 0 ||||||----|||||||||||||||||||||||||||||||||||||| 48 hg19_dna 1 ???????????????????????????????????????????????? 49 """, ) elif fmt == "pslx": self.assertEqual(alignment.target.seq[183925984:183925990], "aaaaat") self.assertEqual( alignment.target.seq[183925990:183926028], "aaaggggctgggcgtggtggctcacgcctgtaatccca", ) self.assertEqual( alignment.query.seq[1:7], self.queries[alignment.query.id][1:7] ) self.assertEqual( alignment.query.seq[38:49], self.queries[alignment.query.id][38:49] ) self.assertEqual( str(alignment), """\ chr2 183925984 aaaaat----aaaggggctgggcgtggtggctcacgcctgtaatccca 183926028 0 ||||||----|||||||||||||||||||||||||.|||||||||||| 48 hg19_dna 1 aaaaat????aaaggggctgggcgtggtggctcacacctgtaatccca 49 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[183925984, 183925990, 183925990, 183926028], [ 1, 7, 11, 49]]), # fmt: on ) ) self.assertEqual( format(alignment, "psl"), """\ 43 1 0 0 1 4 0 0 + hg19_dna 50 1 49 chr2 243199373 183925984 183926028 2 6,38, 1,11, 183925984,183925990, """, ) alignment = next(alignments) self.assertEqual(alignment.matches, 34) self.assertEqual(alignment.misMatches, 2) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.shape, (2, 170)) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr19") self.assertEqual(alignment.query.id, "hg19_dna") self.assertEqual(len(alignment.target.seq), 59128983) self.assertEqual(len(alignment.query.seq), 50) if fmt == "psl": self.assertEqual( str(alignment), """\ chr19 35483340 ???????????????????????????????????????????????????????????? 0 |||||||||||||||||||||||||----------------------------------- hg19_dna 10 ?????????????????????????----------------------------------- chr19 35483400 ???????????????????????????????????????????????????????????? 60 ------------------------------------------------------------ hg19_dna 35 ------------------------------------------------------------ chr19 35483460 ?????????????????????????????????????????????????? 35483510 120 ---------------------------------------||||||||||| 170 hg19_dna 35 ---------------------------------------??????????? 46 """, ) elif fmt == "pslx": self.assertEqual( alignment.target.seq[35483340:35483365], "caaaggggctgggcgtagtggctga" ) self.assertEqual(alignment.target.seq[35483499:35483510], "cacctgtaatc") self.assertEqual( alignment.query.seq[10:46], self.queries[alignment.query.id][10:46] ) self.assertEqual( str(alignment), """\ chr19 35483340 caaaggggctgggcgtagtggctga??????????????????????????????????? 0 ||||||||||||||||.||||||.|----------------------------------- hg19_dna 10 caaaggggctgggcgtggtggctca----------------------------------- chr19 35483400 ???????????????????????????????????????????????????????????? 60 ------------------------------------------------------------ hg19_dna 35 ------------------------------------------------------------ chr19 35483460 ???????????????????????????????????????cacctgtaatc 35483510 120 ---------------------------------------||||||||||| 170 hg19_dna 35 ---------------------------------------cacctgtaatc 46 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[35483340, 35483365, 35483499, 35483510], [ 10, 35, 35, 46]]), # fmt: on ) ) self.assertEqual( format(alignment, "psl"), """\ 34 2 0 0 0 0 1 134 + hg19_dna 50 10 46 chr19 59128983 35483340 35483510 2 25,11, 10,35, 35483340,35483499, """, ) alignment = next(alignments) self.assertEqual(alignment.matches, 39) self.assertEqual(alignment.misMatches, 0) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.shape, (2, 39)) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr18") self.assertEqual(alignment.query.id, "hg19_dna") self.assertEqual(len(alignment.target.seq), 78077248) self.assertEqual(len(alignment.query.seq), 50) if fmt == "psl": self.assertEqual( str(alignment), """\ chr18 23891310 ??????????????????????????????????????? 23891349 0 ||||||||||||||||||||||||||||||||||||||| 39 hg19_dna 10 ??????????????????????????????????????? 49 """, ) elif fmt == "pslx": self.assertEqual( alignment.target.seq[23891310:23891349], "caaaggggctgggcgtggtggctcacacctgtaatccca", ) self.assertEqual( alignment.query.seq[10:49], self.queries[alignment.query.id][10:49] ) self.assertEqual( str(alignment), """\ chr18 23891310 caaaggggctgggcgtggtggctcacacctgtaatccca 23891349 0 ||||||||||||||||||||||||||||||||||||||| 39 hg19_dna 10 caaaggggctgggcgtggtggctcacacctgtaatccca 49 """, ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['c', 'a', 'a', 'a', 'g', 'g', 'g', 'g', 'c', 't', 'g', 'g', 'g', 'c', 'g', 't', 'g', 'g', 't', 'g', 'g', 'c', 't', 'c', 'a', 'c', 'a', 'c', 'c', 't', 'g', 't', 'a', 'a', 't', 'c', 'c', 'c', 'a'], ['c', 'a', 'a', 'a', 'g', 'g', 'g', 'g', 'c', 't', 'g', 'g', 'g', 'c', 'g', 't', 'g', 'g', 't', 'g', 'g', 'c', 't', 'c', 'a', 'c', 'a', 'c', 'c', 't', 'g', 't', 'a', 'a', 't', 'c', 'c', 'c', 'a']], dtype='U') # fmt: on ) ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[23891310, 23891349], [ 10, 49]]), # fmt: on ) ) self.assertEqual( format(alignment, "psl"), """\ 39 0 0 0 0 0 0 0 + hg19_dna 50 10 49 chr18 78077248 23891310 23891349 1 39, 10, 23891310, """, ) alignment = next(alignments) self.assertEqual(alignment.matches, 27) self.assertEqual(alignment.misMatches, 1) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.shape, (2, 28)) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr18") self.assertEqual(alignment.query.id, "hg19_dna") self.assertEqual(len(alignment.target.seq), 78077248) self.assertEqual(len(alignment.query.seq), 50) if fmt == "psl": self.assertEqual( str(alignment), """\ chr18 43252217 ???????????????????????????? 43252245 0 |||||||||||||||||||||||||||| 28 hg19_dna 21 ???????????????????????????? 49 """, ) elif fmt == "pslx": self.assertEqual( alignment.target.seq[43252217:43252245], "ggcgtggtggctcacgcctgtaatccca" ) self.assertEqual( alignment.query.seq[21:49], self.queries[alignment.query.id][21:49] ) self.assertEqual( str(alignment), """\ chr18 43252217 ggcgtggtggctcacgcctgtaatccca 43252245 0 |||||||||||||||.|||||||||||| 28 hg19_dna 21 ggcgtggtggctcacacctgtaatccca 49 """, ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['g', 'g', 'c', 'g', 't', 'g', 'g', 't', 'g', 'g', 'c', 't', 'c', 'a', 'c', 'g', 'c', 'c', 't', 'g', 't', 'a', 'a', 't', 'c', 'c', 'c', 'a'], ['g', 'g', 'c', 'g', 't', 'g', 'g', 't', 'g', 'g', 'c', 't', 'c', 'a', 'c', 'a', 'c', 'c', 't', 'g', 't', 'a', 'a', 't', 'c', 'c', 'c', 'a']], dtype='U') # fmt: on ) ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[43252217, 43252245], [ 21, 49]]), # fmt: on ) ) self.assertEqual( format(alignment, "psl"), """\ 27 1 0 0 0 0 0 0 + hg19_dna 50 21 49 chr18 78077248 43252217 43252245 1 28, 21, 43252217, """, ) alignment = next(alignments) self.assertEqual(alignment.matches, 44) self.assertEqual(alignment.misMatches, 1) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.shape, (2, 54)) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr13") self.assertEqual(alignment.query.id, "hg19_dna") self.assertEqual(len(alignment.target.seq), 115169878) self.assertEqual(len(alignment.query.seq), 50) if fmt == "psl": self.assertEqual( str(alignment), """\ chr13 52759147 ?????????????---?????????????????????????????????????? 0 |||||||---------|||||||||||||||||||||||||||||||||||||| hg19_dna 1 ???????------????????????????????????????????????????? chr13 52759198 54 hg19_dna 49 """, ) elif fmt == "pslx": self.assertEqual(alignment.target.seq[52759147:52759154], "aaaaatt") self.assertEqual( alignment.target.seq[52759160:52759198], "aaaggggctgggcgtggtggctcacgcctgtaatccca", ) self.assertEqual( alignment.query.seq[1:8], self.queries[alignment.query.id][1:8] ) self.assertEqual( alignment.query.seq[38:49], self.queries[alignment.query.id][38:49] ) self.assertEqual( str(alignment), """\ chr13 52759147 aaaaatt??????---aaaggggctgggcgtggtggctcacgcctgtaatccca 0 |||||||---------|||||||||||||||||||||||||.|||||||||||| hg19_dna 1 aaaaatt------???aaaggggctgggcgtggtggctcacacctgtaatccca chr13 52759198 54 hg19_dna 49 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[52759147, 52759154, 52759160, 52759160, 52759198], [ 1, 8, 8, 11, 49]]), # fmt: on ) ) self.assertEqual( format(alignment, "psl"), """\ 44 1 0 0 1 3 1 6 + hg19_dna 50 1 49 chr13 115169878 52759147 52759198 2 7,38, 1,11, 52759147,52759160, """, ) alignment = next(alignments) self.assertEqual(alignment.matches, 50) self.assertEqual(alignment.misMatches, 0) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.shape, (2, 50)) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr1") self.assertEqual(alignment.query.id, "hg19_dna") self.assertEqual(len(alignment.target.seq), 249250621) self.assertEqual(len(alignment.query.seq), 50) if fmt == "psl": self.assertEqual( str(alignment), """\ chr1 1207056 ?????????????????????????????????????????????????? 1207106 0 |||||||||||||||||||||||||||||||||||||||||||||||||| 50 hg19_dna 0 ?????????????????????????????????????????????????? 50 """, ) elif fmt == "pslx": self.assertEqual( alignment.target.seq[1207056:1207106], "caaaaattcacaaaggggctgggcgtggtggctcacacctgtaatcccaa", ) self.assertEqual(alignment.query.seq, self.queries[alignment.query.id]) self.assertEqual( str(alignment), """\ chr1 1207056 caaaaattcacaaaggggctgggcgtggtggctcacacctgtaatcccaa 1207106 0 |||||||||||||||||||||||||||||||||||||||||||||||||| 50 hg19_dna 0 caaaaattcacaaaggggctgggcgtggtggctcacacctgtaatcccaa 50 """, ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['c', 'a', 'a', 'a', 'a', 'a', 't', 't', 'c', 'a', 'c', 'a', 'a', 'a', 'g', 'g', 'g', 'g', 'c', 't', 'g', 'g', 'g', 'c', 'g', 't', 'g', 'g', 't', 'g', 'g', 'c', 't', 'c', 'a', 'c', 'a', 'c', 'c', 't', 'g', 't', 'a', 'a', 't', 'c', 'c', 'c', 'a', 'a'], ['c', 'a', 'a', 'a', 'a', 'a', 't', 't', 'c', 'a', 'c', 'a', 'a', 'a', 'g', 'g', 'g', 'g', 'c', 't', 'g', 'g', 'g', 'c', 'g', 't', 'g', 'g', 't', 'g', 'g', 'c', 't', 'c', 'a', 'c', 'a', 'c', 'c', 't', 'g', 't', 'a', 'a', 't', 'c', 'c', 'c', 'a', 'a']], dtype='U') # fmt: on ) ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[1207056, 1207106], [ 0, 50]]), # fmt: on ) ) self.assertEqual( format(alignment, "psl"), """\ 50 0 0 0 0 0 0 0 + hg19_dna 50 0 50 chr1 249250621 1207056 1207106 1 50, 0, 1207056, """, ) alignment = next(alignments) self.assertEqual(alignment.matches, 31) self.assertEqual(alignment.misMatches, 3) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.shape, (2, 34)) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr1") self.assertEqual(alignment.query.id, "hg19_dna") self.assertEqual(len(alignment.target.seq), 249250621) self.assertEqual(len(alignment.query.seq), 50) if fmt == "psl": self.assertEqual( str(alignment), """\ chr1 61700837 ?????????????????????????????????? 61700871 0 |||||||||||||||||||||||||||||||||| 34 hg19_dna 1 ?????????????????????????????????? 35 """, ) elif fmt == "pslx": self.assertEqual( alignment.target.seq[61700837:61700871], "aaaaatgaacaaaggggctgggcgcggtggctca", ) self.assertEqual( alignment.query.seq[1:35], self.queries[alignment.query.id][1:35] ) self.assertEqual( str(alignment), """\ chr1 61700837 aaaaatgaacaaaggggctgggcgcggtggctca 61700871 0 ||||||..||||||||||||||||.||||||||| 34 hg19_dna 1 aaaaattcacaaaggggctgggcgtggtggctca 35 """, ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['a', 'a', 'a', 'a', 'a', 't', 'g', 'a', 'a', 'c', 'a', 'a', 'a', 'g', 'g', 'g', 'g', 'c', 't', 'g', 'g', 'g', 'c', 'g', 'c', 'g', 'g', 't', 'g', 'g', 'c', 't', 'c', 'a'], ['a', 'a', 'a', 'a', 'a', 't', 't', 'c', 'a', 'c', 'a', 'a', 'a', 'g', 'g', 'g', 'g', 'c', 't', 'g', 'g', 'g', 'c', 'g', 't', 'g', 'g', 't', 'g', 'g', 'c', 't', 'c', 'a']], dtype='U') # fmt: on ) ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[61700837, 61700871], [ 1, 35]]), # fmt: on ) ) self.assertEqual( format(alignment, "psl"), """\ 31 3 0 0 0 0 0 0 + hg19_dna 50 1 35 chr1 249250621 61700837 61700871 1 34, 1, 61700837, """, ) alignment = next(alignments) self.assertEqual(alignment.matches, 28) self.assertEqual(alignment.misMatches, 0) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.shape, (2, 44)) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr4") self.assertEqual(alignment.query.id, "hg19_dna") self.assertEqual(len(alignment.target.seq), 191154276) self.assertEqual(len(alignment.query.seq), 50) if fmt == "psl": self.assertEqual( str(alignment), """\ chr4 37558157 ????????????????----------?????????????????? 37558191 0 ||||||||||----------------|||||||||||||||||| 44 hg19_dna 49 ??????????------???????????????????????????? 11 """, ) elif fmt == "pslx": self.assertEqual(alignment.target.seq[37558157:37558167], "tgggattaca") self.assertEqual( alignment.target.seq[37558173:37558191], "accacgcccagccccttt" ) self.assertEqual( alignment.query.seq[11:29], self.queries[alignment.query.id][11:29] ) self.assertEqual( alignment.query.seq[39:49], self.queries[alignment.query.id][39:49] ) self.assertEqual( str(alignment), """\ chr4 37558157 tgggattaca??????----------accacgcccagccccttt 37558191 0 ||||||||||----------------|||||||||||||||||| 44 hg19_dna 49 tgggattaca------??????????accacgcccagccccttt 11 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[37558157, 37558167, 37558173, 37558173, 37558191], [ 49, 39, 39, 29, 11]]), # fmt: on ) ) self.assertEqual( format(alignment, "psl"), """\ 28 0 0 0 1 10 1 6 - hg19_dna 50 11 49 chr4 191154276 37558157 37558191 2 10,18, 1,21, 37558157,37558173, """, ) alignment = next(alignments) self.assertEqual(alignment.matches, 35) self.assertEqual(alignment.misMatches, 2) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.shape, (2, 37)) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr22") self.assertEqual(alignment.query.id, "hg19_dna") self.assertEqual(len(alignment.target.seq), 51304566) self.assertEqual(len(alignment.query.seq), 50) if fmt == "psl": self.assertEqual( str(alignment), """\ chr22 48997405 ????????????????????????????????????? 48997442 0 ||||||||||||||||||||||||||||||||||||| 37 hg19_dna 49 ????????????????????????????????????? 12 """, ) elif fmt == "pslx": self.assertEqual( alignment.target.seq[48997405:48997442], "tgggattacaggcgggagccaccacgcccagcccctt", ) self.assertEqual( alignment.query.seq[12:49], self.queries[alignment.query.id][12:49] ) self.assertEqual( str(alignment), """\ chr22 48997405 tgggattacaggcgggagccaccacgcccagcccctt 48997442 0 ||||||||||||.|.|||||||||||||||||||||| 37 hg19_dna 49 tgggattacaggtgtgagccaccacgcccagcccctt 12 """, ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['t', 'g', 'g', 'g', 'a', 't', 't', 'a', 'c', 'a', 'g', 'g', 'c', 'g', 'g', 'g', 'a', 'g', 'c', 'c', 'a', 'c', 'c', 'a', 'c', 'g', 'c', 'c', 'c', 'a', 'g', 'c', 'c', 'c', 'c', 't', 't'], ['t', 'g', 'g', 'g', 'a', 't', 't', 'a', 'c', 'a', 'g', 'g', 't', 'g', 't', 'g', 'a', 'g', 'c', 'c', 'a', 'c', 'c', 'a', 'c', 'g', 'c', 'c', 'c', 'a', 'g', 'c', 'c', 'c', 'c', 't', 't']], dtype='U') # fmt: on ) ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[48997405, 48997442], [ 49, 12]]), # fmt: on ) ) self.assertEqual( format(alignment, "psl"), """\ 35 2 0 0 0 0 0 0 - hg19_dna 50 12 49 chr22 51304566 48997405 48997442 1 37, 1, 48997405, """, ) alignment = next(alignments) self.assertEqual(alignment.matches, 35) self.assertEqual(alignment.misMatches, 1) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.shape, (2, 36)) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr2") self.assertEqual(alignment.query.id, "hg19_dna") self.assertEqual(len(alignment.target.seq), 243199373) self.assertEqual(len(alignment.query.seq), 50) if fmt == "psl": self.assertEqual( str(alignment), """\ chr2 120641740 ???????????????????????????????????? 120641776 0 |||||||||||||||||||||||||||||||||||| 36 hg19_dna 49 ???????????????????????????????????? 13 """, ) elif fmt == "pslx": self.assertEqual( alignment.target.seq[120641740:120641776], "tgggattacaggcgtgagccaccacgcccagcccct", ) self.assertEqual( alignment.query.seq[13:49], self.queries[alignment.query.id][13:49] ) self.assertEqual( str(alignment), """\ chr2 120641740 tgggattacaggcgtgagccaccacgcccagcccct 120641776 0 ||||||||||||.||||||||||||||||||||||| 36 hg19_dna 49 tgggattacaggtgtgagccaccacgcccagcccct 13 """, ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['t', 'g', 'g', 'g', 'a', 't', 't', 'a', 'c', 'a', 'g', 'g', 'c', 'g', 't', 'g', 'a', 'g', 'c', 'c', 'a', 'c', 'c', 'a', 'c', 'g', 'c', 'c', 'c', 'a', 'g', 'c', 'c', 'c', 'c', 't'], ['t', 'g', 'g', 'g', 'a', 't', 't', 'a', 'c', 'a', 'g', 'g', 't', 'g', 't', 'g', 'a', 'g', 'c', 'c', 'a', 'c', 'c', 'a', 'c', 'g', 'c', 'c', 'c', 'a', 'g', 'c', 'c', 'c', 'c', 't']], dtype='U') # fmt: on ) ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[120641740, 120641776], [ 49, 13]]), # fmt: on ) ) self.assertEqual( format(alignment, "psl"), """\ 35 1 0 0 0 0 0 0 - hg19_dna 50 13 49 chr2 243199373 120641740 120641776 1 36, 1, 120641740, """, ) alignment = next(alignments) self.assertEqual(alignment.matches, 39) self.assertEqual(alignment.misMatches, 0) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.shape, (2, 39)) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr19") self.assertEqual(alignment.query.id, "hg19_dna") self.assertEqual(len(alignment.target.seq), 59128983) self.assertEqual(len(alignment.query.seq), 50) if fmt == "psl": self.assertEqual( str(alignment), """\ chr19 54017130 ??????????????????????????????????????? 54017169 0 ||||||||||||||||||||||||||||||||||||||| 39 hg19_dna 49 ??????????????????????????????????????? 10 """, ) elif fmt == "pslx": self.assertEqual( alignment.target.seq[54017130:54017169], "tgggattacaggtgtgagccaccacgcccagcccctttg", ) self.assertEqual( alignment.query.seq[10:49], self.queries[alignment.query.id][10:49] ) self.assertEqual( str(alignment), """\ chr19 54017130 tgggattacaggtgtgagccaccacgcccagcccctttg 54017169 0 ||||||||||||||||||||||||||||||||||||||| 39 hg19_dna 49 tgggattacaggtgtgagccaccacgcccagcccctttg 10 """, ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['t', 'g', 'g', 'g', 'a', 't', 't', 'a', 'c', 'a', 'g', 'g', 't', 'g', 't', 'g', 'a', 'g', 'c', 'c', 'a', 'c', 'c', 'a', 'c', 'g', 'c', 'c', 'c', 'a', 'g', 'c', 'c', 'c', 'c', 't', 't', 't', 'g'], ['t', 'g', 'g', 'g', 'a', 't', 't', 'a', 'c', 'a', 'g', 'g', 't', 'g', 't', 'g', 'a', 'g', 'c', 'c', 'a', 'c', 'c', 'a', 'c', 'g', 'c', 'c', 'c', 'a', 'g', 'c', 'c', 'c', 'c', 't', 't', 't', 'g']], dtype='U') # fmt: on ) ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[54017130, 54017169], [ 49, 10]]), # fmt: on ) ) self.assertEqual( format(alignment, "psl"), """\ 39 0 0 0 0 0 0 0 - hg19_dna 50 10 49 chr19 59128983 54017130 54017169 1 39, 1, 54017130, """, ) alignment = next(alignments) self.assertEqual(alignment.matches, 36) self.assertEqual(alignment.misMatches, 3) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.shape, (2, 39)) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr19") self.assertEqual(alignment.query.id, "hg19_dna") self.assertEqual(len(alignment.target.seq), 59128983) self.assertEqual(len(alignment.query.seq), 50) if fmt == "psl": self.assertEqual( str(alignment), """\ chr19 553742 ??????????????????????????????????????? 553781 0 ||||||||||||||||||||||||||||||||||||||| 39 hg19_dna 49 ??????????????????????????????????????? 10 """, ) elif fmt == "pslx": self.assertEqual( alignment.target.seq[553742:553781], "tgggatgacaggggtgaggcaccacgcccagcccctttg", ) self.assertEqual( alignment.query.seq[10:49], self.queries[alignment.query.id][10:49] ) self.assertEqual( str(alignment), """\ chr19 553742 tgggatgacaggggtgaggcaccacgcccagcccctttg 553781 0 ||||||.|||||.|||||.|||||||||||||||||||| 39 hg19_dna 49 tgggattacaggtgtgagccaccacgcccagcccctttg 10 """, ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['t', 'g', 'g', 'g', 'a', 't', 'g', 'a', 'c', 'a', 'g', 'g', 'g', 'g', 't', 'g', 'a', 'g', 'g', 'c', 'a', 'c', 'c', 'a', 'c', 'g', 'c', 'c', 'c', 'a', 'g', 'c', 'c', 'c', 'c', 't', 't', 't', 'g'], ['t', 'g', 'g', 'g', 'a', 't', 't', 'a', 'c', 'a', 'g', 'g', 't', 'g', 't', 'g', 'a', 'g', 'c', 'c', 'a', 'c', 'c', 'a', 'c', 'g', 'c', 'c', 'c', 'a', 'g', 'c', 'c', 'c', 'c', 't', 't', 't', 'g']], dtype='U') # fmt: on ) ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[553742, 553781], [ 49, 10]]), # fmt: on ) ) self.assertEqual( format(alignment, "psl"), """\ 36 3 0 0 0 0 0 0 - hg19_dna 50 10 49 chr19 59128983 553742 553781 1 39, 1, 553742, """, ) alignment = next(alignments) self.assertEqual(alignment.matches, 33) self.assertEqual(alignment.misMatches, 3) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.shape, (2, 36)) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr10") self.assertEqual(alignment.query.id, "hg19_dna") self.assertEqual(len(alignment.target.seq), 135534747) self.assertEqual(len(alignment.query.seq), 50) if fmt == "psl": self.assertEqual( str(alignment), """\ chr10 99388555 ???????????????????????????????????? 99388591 0 |||||||||||||||||||||||||||||||||||| 36 hg19_dna 49 ???????????????????????????????????? 13 """, ) elif fmt == "pslx": self.assertEqual( alignment.target.seq[99388555:99388591], "tgggattataggcatgagccaccacgcccagcccct", ) self.assertEqual( alignment.query.seq[13:49], self.queries[alignment.query.id][13:49] ) self.assertEqual( str(alignment), """\ chr10 99388555 tgggattataggcatgagccaccacgcccagcccct 99388591 0 ||||||||.|||..|||||||||||||||||||||| 36 hg19_dna 49 tgggattacaggtgtgagccaccacgcccagcccct 13 """, ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['t', 'g', 'g', 'g', 'a', 't', 't', 'a', 't', 'a', 'g', 'g', 'c', 'a', 't', 'g', 'a', 'g', 'c', 'c', 'a', 'c', 'c', 'a', 'c', 'g', 'c', 'c', 'c', 'a', 'g', 'c', 'c', 'c', 'c', 't'], ['t', 'g', 'g', 'g', 'a', 't', 't', 'a', 'c', 'a', 'g', 'g', 't', 'g', 't', 'g', 'a', 'g', 'c', 'c', 'a', 'c', 'c', 'a', 'c', 'g', 'c', 'c', 'c', 'a', 'g', 'c', 'c', 'c', 'c', 't']], dtype='U') # fmt: on ) ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[99388555, 99388591], [ 49, 13]]), # fmt: on ) ) self.assertEqual( format(alignment, "psl"), """\ 33 3 0 0 0 0 0 0 - hg19_dna 50 13 49 chr10 135534747 99388555 99388591 1 36, 1, 99388555, """, ) alignment = next(alignments) self.assertEqual(alignment.matches, 24) self.assertEqual(alignment.misMatches, 1) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.shape, (2, 25)) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr10") self.assertEqual(alignment.query.id, "hg19_dna") self.assertEqual(len(alignment.target.seq), 135534747) self.assertEqual(len(alignment.query.seq), 50) if fmt == "psl": self.assertEqual( str(alignment), """\ chr10 112178171 ????????????????????????? 112178196 0 ||||||||||||||||||||||||| 25 hg19_dna 35 ????????????????????????? 10 """, ) elif fmt == "pslx": self.assertEqual( alignment.target.seq[112178171:112178196], "tgagtcaccacgcccagcccctttg" ) self.assertEqual( alignment.query.seq[10:35], self.queries[alignment.query.id][10:35] ) self.assertEqual( str(alignment), """\ chr10 112178171 tgagtcaccacgcccagcccctttg 112178196 0 ||||.|||||||||||||||||||| 25 hg19_dna 35 tgagccaccacgcccagcccctttg 10 """, ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['t', 'g', 'a', 'g', 't', 'c', 'a', 'c', 'c', 'a', 'c', 'g', 'c', 'c', 'c', 'a', 'g', 'c', 'c', 'c', 'c', 't', 't', 't', 'g'], ['t', 'g', 'a', 'g', 'c', 'c', 'a', 'c', 'c', 'a', 'c', 'g', 'c', 'c', 'c', 'a', 'g', 'c', 'c', 'c', 'c', 't', 't', 't', 'g']], dtype='U') # fmt: on ) ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[112178171, 112178196], [ 35, 10]]), # fmt: on ) ) self.assertEqual( format(alignment, "psl"), """\ 24 1 0 0 0 0 0 0 - hg19_dna 50 10 35 chr10 135534747 112178171 112178196 1 25, 15, 112178171, """, ) alignment = next(alignments) self.assertEqual(alignment.matches, 35) self.assertEqual(alignment.misMatches, 1) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.shape, (2, 36)) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr1") self.assertEqual(alignment.query.id, "hg19_dna") self.assertEqual(len(alignment.target.seq), 249250621) self.assertEqual(len(alignment.query.seq), 50) if fmt == "psl": self.assertEqual( str(alignment), """\ chr1 39368490 ???????????????????????????????????? 39368526 0 |||||||||||||||||||||||||||||||||||| 36 hg19_dna 49 ???????????????????????????????????? 13 """, ) elif fmt == "pslx": self.assertEqual( alignment.target.seq[39368490:39368526], "tgggattacaggcgtgagccaccacgcccagcccct", ) self.assertEqual( alignment.query.seq[13:49], self.queries[alignment.query.id][13:49] ) self.assertEqual( str(alignment), """\ chr1 39368490 tgggattacaggcgtgagccaccacgcccagcccct 39368526 0 ||||||||||||.||||||||||||||||||||||| 36 hg19_dna 49 tgggattacaggtgtgagccaccacgcccagcccct 13 """, ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['t', 'g', 'g', 'g', 'a', 't', 't', 'a', 'c', 'a', 'g', 'g', 'c', 'g', 't', 'g', 'a', 'g', 'c', 'c', 'a', 'c', 'c', 'a', 'c', 'g', 'c', 'c', 'c', 'a', 'g', 'c', 'c', 'c', 'c', 't'], ['t', 'g', 'g', 'g', 'a', 't', 't', 'a', 'c', 'a', 'g', 'g', 't', 'g', 't', 'g', 'a', 'g', 'c', 'c', 'a', 'c', 'c', 'a', 'c', 'g', 'c', 'c', 'c', 'a', 'g', 'c', 'c', 'c', 'c', 't']], dtype='U') # fmt: on ) ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[39368490, 39368526], [ 49, 13]]), # fmt: on ) ) self.assertEqual( format(alignment, "psl"), """\ 35 1 0 0 0 0 0 0 - hg19_dna 50 13 49 chr1 249250621 39368490 39368526 1 36, 1, 39368490, """, ) alignment = next(alignments) self.assertEqual(alignment.matches, 33) self.assertEqual(alignment.misMatches, 1) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.shape, (2, 34)) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr1") self.assertEqual(alignment.query.id, "hg19_dna") self.assertEqual(len(alignment.target.seq), 249250621) self.assertEqual(len(alignment.query.seq), 50) if fmt == "psl": self.assertEqual( str(alignment), """\ chr1 220325687 ?????????????????????????????????? 220325721 0 |||||||||||||||||||||||||||||||||| 34 hg19_dna 47 ?????????????????????????????????? 13 """, ) elif fmt == "pslx": self.assertEqual( alignment.target.seq[220325687:220325721], "ggattacaggcgtgagccaccacgcccagcccct", ) self.assertEqual( alignment.query.seq[13:47], self.queries[alignment.query.id][13:47] ) self.assertEqual( str(alignment), """\ chr1 220325687 ggattacaggcgtgagccaccacgcccagcccct 220325721 0 ||||||||||.||||||||||||||||||||||| 34 hg19_dna 47 ggattacaggtgtgagccaccacgcccagcccct 13 """, ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['g', 'g', 'a', 't', 't', 'a', 'c', 'a', 'g', 'g', 'c', 'g', 't', 'g', 'a', 'g', 'c', 'c', 'a', 'c', 'c', 'a', 'c', 'g', 'c', 'c', 'c', 'a', 'g', 'c', 'c', 'c', 'c', 't'], ['g', 'g', 'a', 't', 't', 'a', 'c', 'a', 'g', 'g', 't', 'g', 't', 'g', 'a', 'g', 'c', 'c', 'a', 'c', 'c', 'a', 'c', 'g', 'c', 'c', 'c', 'a', 'g', 'c', 'c', 'c', 'c', 't']], dtype='U') # fmt: on ) ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[220325687, 220325721], [ 47, 13]]), # fmt: on ) ) self.assertEqual( format(alignment, "psl"), """\ 33 1 0 0 0 0 0 0 - hg19_dna 50 13 47 chr1 249250621 220325687 220325721 1 34, 3, 220325687, """, ) self.assertRaises(StopIteration, next, alignments) def test_writing_psl_34_001(self): """Test writing the alignments in psl_34_001.psl.""" path = "Blat/psl_34_001.psl" with open(path) as stream: original_data = stream.read() alignments = Align.parse(path, "psl") stream = StringIO() n = Align.write(alignments, stream, "psl") self.assertEqual(n, 22) stream.seek(0) written_data = stream.read() stream.close() self.assertEqual(original_data, written_data) def test_reading_psl_34_002(self): """Test parsing psl_34_002.psl and pslx_34_002.pslx.""" path = "Blat/psl_34_002.psl" self.check_reading_psl_34_002(path) path = "Blat/pslx_34_002.pslx" self.check_reading_psl_34_002(path) def check_reading_psl_34_002(self, path): """Check parsing psl_34_002.psl or pslx_34_002.pslx.""" alignments = Align.parse(path, "psl") self.assertEqual(alignments.metadata["psLayout version"], "3") self.assertRaises(StopIteration, next, alignments) def test_writing_psl_34_002(self): """Test writing the alignments in psl_34_002.psl.""" path = "Blat/psl_34_002.psl" with open(path) as stream: original_data = stream.read() alignments = Align.parse(path, "psl") stream = StringIO() n = Align.write(alignments, stream, "psl") self.assertEqual(n, 0) stream.seek(0) written_data = stream.read() stream.close() self.assertEqual(original_data, written_data) def test_reading_psl_34_003(self): """Test parsing psl_34_003.psl and pslx_34_003.pslx.""" self.check_reading_psl_34_003("psl") self.check_reading_psl_34_003("pslx") def check_reading_psl_34_003(self, fmt): """Check parsing psl_34_003.psl or pslx_34_003.pslx.""" path = "Blat/%s_34_003.%s" % (fmt, fmt) alignments = Align.parse(path, "psl") self.assertEqual(alignments.metadata["psLayout version"], "3") alignment = next(alignments) self.assertEqual(alignment.matches, 16) self.assertEqual(alignment.misMatches, 0) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.shape, (2, 16)) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr4") self.assertEqual(alignment.query.id, "hg18_dna") self.assertEqual(len(alignment.target.seq), 191154276) self.assertEqual(len(alignment.query.seq), 33) if fmt == "psl": self.assertEqual( str(alignment), """\ chr4 61646095 ???????????????? 61646111 0 |||||||||||||||| 16 hg18_dna 11 ???????????????? 27 """, ) elif fmt == "pslx": self.assertEqual( alignment.target.seq[61646095:61646111], "aggtaaactgccttca" ) self.assertEqual( alignment.query.seq[11:27], self.queries[alignment.query.id][11:27] ) self.assertEqual( str(alignment), """\ chr4 61646095 aggtaaactgccttca 61646111 0 |||||||||||||||| 16 hg18_dna 11 aggtaaactgccttca 27 """, ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['a', 'g', 'g', 't', 'a', 'a', 'a', 'c', 't', 'g', 'c', 'c', 't', 't', 'c', 'a'], ['a', 'g', 'g', 't', 'a', 'a', 'a', 'c', 't', 'g', 'c', 'c', 't', 't', 'c', 'a']], dtype='U') # fmt: on ) ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[61646095, 61646111], [ 11, 27]]), # fmt: on ) ) self.assertEqual( format(alignment, "psl"), """\ 16 0 0 0 0 0 0 0 + hg18_dna 33 11 27 chr4 191154276 61646095 61646111 1 16, 11, 61646095, """, ) alignment = next(alignments) self.assertEqual(alignment.matches, 33) self.assertEqual(alignment.misMatches, 0) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.shape, (2, 33)) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr1") self.assertEqual(alignment.query.id, "hg18_dna") self.assertEqual(len(alignment.target.seq), 249250621) self.assertEqual(len(alignment.query.seq), 33) if fmt == "psl": self.assertEqual( str(alignment), """\ chr1 10271783 ????????????????????????????????? 10271816 0 ||||||||||||||||||||||||||||||||| 33 hg18_dna 0 ????????????????????????????????? 33 """, ) elif fmt == "pslx": self.assertEqual( alignment.target.seq[10271783:10271816], "atgagcttccaaggtaaactgccttcaagattc", ) self.assertEqual(alignment.query.seq, self.queries[alignment.query.id]) self.assertEqual( str(alignment), """\ chr1 10271783 atgagcttccaaggtaaactgccttcaagattc 10271816 0 ||||||||||||||||||||||||||||||||| 33 hg18_dna 0 atgagcttccaaggtaaactgccttcaagattc 33 """, ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['a', 't', 'g', 'a', 'g', 'c', 't', 't', 'c', 'c', 'a', 'a', 'g', 'g', 't', 'a', 'a', 'a', 'c', 't', 'g', 'c', 'c', 't', 't', 'c', 'a', 'a', 'g', 'a', 't', 't', 'c'], ['a', 't', 'g', 'a', 'g', 'c', 't', 't', 'c', 'c', 'a', 'a', 'g', 'g', 't', 'a', 'a', 'a', 'c', 't', 'g', 'c', 'c', 't', 't', 'c', 'a', 'a', 'g', 'a', 't', 't', 'c']], dtype='U') # fmt: on ) ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[10271783, 10271816], [ 0, 33]]), # fmt: on ) ) self.assertEqual( format(alignment, "psl"), """\ 33 0 0 0 0 0 0 0 + hg18_dna 33 0 33 chr1 249250621 10271783 10271816 1 33, 0, 10271783, """, ) alignment = next(alignments) self.assertEqual(alignment.matches, 17) self.assertEqual(alignment.misMatches, 0) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.shape, (2, 17)) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr2") self.assertEqual(alignment.query.id, "hg18_dna") self.assertEqual(len(alignment.target.seq), 243199373) self.assertEqual(len(alignment.query.seq), 33) if fmt == "psl": self.assertEqual( str(alignment), """\ chr2 53575980 ????????????????? 53575997 0 ||||||||||||||||| 17 hg18_dna 25 ????????????????? 8 """, ) elif fmt == "pslx": self.assertEqual( alignment.target.seq[53575980:53575997], "aaggcagtttaccttgg" ) self.assertEqual( alignment.query.seq[8:25], self.queries[alignment.query.id][8:25] ) self.assertEqual( str(alignment), """\ chr2 53575980 aaggcagtttaccttgg 53575997 0 ||||||||||||||||| 17 hg18_dna 25 aaggcagtttaccttgg 8 """, ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['a', 'a', 'g', 'g', 'c', 'a', 'g', 't', 't', 't', 'a', 'c', 'c', 't', 't', 'g', 'g'], ['a', 'a', 'g', 'g', 'c', 'a', 'g', 't', 't', 't', 'a', 'c', 'c', 't', 't', 'g', 'g']], dtype='U') # fmt: on ) ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[53575980, 53575997], [ 25, 8]]), # fmt: on ) ) self.assertEqual( format(alignment, "psl"), """\ 17 0 0 0 0 0 0 0 - hg18_dna 33 8 25 chr2 243199373 53575980 53575997 1 17, 8, 53575980, """, ) self.assertRaises(StopIteration, next, alignments) def test_writing_psl_34_003(self): """Test writing the alignments in psl_34_003.psl.""" path = "Blat/psl_34_003.psl" with open(path) as stream: original_data = stream.read() alignments = Align.parse(path, "psl") stream = StringIO() n = Align.write(alignments, stream, "psl") self.assertEqual(n, 3) stream.seek(0) written_data = stream.read() stream.close() self.assertEqual(original_data, written_data) def test_reading_psl_34_004(self): """Test parsing psl_34_004.psl and pslx_34_004.pslx.""" self.check_reading_psl_34_004("psl") self.check_reading_psl_34_004("pslx") def check_reading_psl_34_004(self, fmt): """Check parsing psl_34_004.psl or pslx_34_004.pslx.""" path = "Blat/%s_34_004.%s" % (fmt, fmt) alignments = Align.parse(path, "psl") self.assertEqual(alignments.metadata["psLayout version"], "3") alignment = next(alignments) self.assertEqual(alignment.matches, 38) self.assertEqual(alignment.misMatches, 3) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.shape, (2, 41)) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr9") self.assertEqual(alignment.query.id, "hg19_dna") self.assertEqual(len(alignment.target.seq), 141213431) self.assertEqual(len(alignment.query.seq), 50) if fmt == "psl": self.assertEqual( str(alignment), """\ chr9 85737865 ????????????????????????????????????????? 85737906 0 ||||||||||||||||||||||||||||||||||||||||| 41 hg19_dna 9 ????????????????????????????????????????? 50 """, ) elif fmt == "pslx": self.assertEqual( alignment.target.seq[85737865:85737906], "acaaaggggctgggcgcagtggctcacgcctgtaatcccaa", ) self.assertEqual( alignment.query.seq[9:50], self.queries[alignment.query.id][9:50] ) self.assertEqual( str(alignment), """\ chr9 85737865 acaaaggggctgggcgcagtggctcacgcctgtaatcccaa 85737906 0 ||||||||||||||||..|||||||||.||||||||||||| 41 hg19_dna 9 acaaaggggctgggcgtggtggctcacacctgtaatcccaa 50 """, ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['a', 'c', 'a', 'a', 'a', 'g', 'g', 'g', 'g', 'c', 't', 'g', 'g', 'g', 'c', 'g', 'c', 'a', 'g', 't', 'g', 'g', 'c', 't', 'c', 'a', 'c', 'g', 'c', 'c', 't', 'g', 't', 'a', 'a', 't', 'c', 'c', 'c', 'a', 'a'], ['a', 'c', 'a', 'a', 'a', 'g', 'g', 'g', 'g', 'c', 't', 'g', 'g', 'g', 'c', 'g', 't', 'g', 'g', 't', 'g', 'g', 'c', 't', 'c', 'a', 'c', 'a', 'c', 'c', 't', 'g', 't', 'a', 'a', 't', 'c', 'c', 'c', 'a', 'a']], dtype='U') # fmt: on ) ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[85737865, 85737906], [ 9, 50]]), # fmt: on ) ) self.assertEqual( format(alignment, "psl"), """\ 38 3 0 0 0 0 0 0 + hg19_dna 50 9 50 chr9 141213431 85737865 85737906 1 41, 9, 85737865, """, ) alignment = next(alignments) self.assertEqual(alignment.matches, 41) self.assertEqual(alignment.misMatches, 0) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.shape, (2, 41)) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr8") self.assertEqual(alignment.query.id, "hg19_dna") self.assertEqual(len(alignment.target.seq), 146364022) self.assertEqual(len(alignment.query.seq), 50) if fmt == "psl": self.assertEqual( str(alignment), """\ chr8 95160479 ????????????????????????????????????????? 95160520 0 ||||||||||||||||||||||||||||||||||||||||| 41 hg19_dna 8 ????????????????????????????????????????? 49 """, ) elif fmt == "pslx": self.assertEqual( alignment.target.seq[95160479:95160520], "cacaaaggggctgggcgtggtggctcacacctgtaatccca", ) self.assertEqual( alignment.query.seq[8:49], self.queries[alignment.query.id][8:49] ) self.assertEqual( str(alignment), """\ chr8 95160479 cacaaaggggctgggcgtggtggctcacacctgtaatccca 95160520 0 ||||||||||||||||||||||||||||||||||||||||| 41 hg19_dna 8 cacaaaggggctgggcgtggtggctcacacctgtaatccca 49 """, ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['c', 'a', 'c', 'a', 'a', 'a', 'g', 'g', 'g', 'g', 'c', 't', 'g', 'g', 'g', 'c', 'g', 't', 'g', 'g', 't', 'g', 'g', 'c', 't', 'c', 'a', 'c', 'a', 'c', 'c', 't', 'g', 't', 'a', 'a', 't', 'c', 'c', 'c', 'a'], ['c', 'a', 'c', 'a', 'a', 'a', 'g', 'g', 'g', 'g', 'c', 't', 'g', 'g', 'g', 'c', 'g', 't', 'g', 'g', 't', 'g', 'g', 'c', 't', 'c', 'a', 'c', 'a', 'c', 'c', 't', 'g', 't', 'a', 'a', 't', 'c', 'c', 'c', 'a']], dtype='U') # fmt: on ) ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[95160479, 95160520], [ 8, 49]]), # fmt: on ) ) self.assertEqual( format(alignment, "psl"), """\ 41 0 0 0 0 0 0 0 + hg19_dna 50 8 49 chr8 146364022 95160479 95160520 1 41, 8, 95160479, """, ) alignment = next(alignments) self.assertEqual(alignment.matches, 33) self.assertEqual(alignment.misMatches, 3) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.shape, (2, 36)) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr22") self.assertEqual(alignment.query.id, "hg19_dna") self.assertEqual(len(alignment.target.seq), 51304566) self.assertEqual(len(alignment.query.seq), 50) if fmt == "psl": self.assertEqual( str(alignment), """\ chr22 42144400 ???????????????????????????????????? 42144436 0 |||||||||||||||||||||||||||||||||||| 36 hg19_dna 11 ???????????????????????????????????? 47 """, ) elif fmt == "pslx": self.assertEqual( alignment.target.seq[42144400:42144436], "aaaggggctgggcgtggtagctcatgcctgtaatcc", ) self.assertEqual( alignment.query.seq[11:47], self.queries[alignment.query.id][11:47] ) self.assertEqual( str(alignment), """\ chr22 42144400 aaaggggctgggcgtggtagctcatgcctgtaatcc 42144436 0 ||||||||||||||||||.|||||..|||||||||| 36 hg19_dna 11 aaaggggctgggcgtggtggctcacacctgtaatcc 47 """, ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['a', 'a', 'a', 'g', 'g', 'g', 'g', 'c', 't', 'g', 'g', 'g', 'c', 'g', 't', 'g', 'g', 't', 'a', 'g', 'c', 't', 'c', 'a', 't', 'g', 'c', 'c', 't', 'g', 't', 'a', 'a', 't', 'c', 'c'], ['a', 'a', 'a', 'g', 'g', 'g', 'g', 'c', 't', 'g', 'g', 'g', 'c', 'g', 't', 'g', 'g', 't', 'g', 'g', 'c', 't', 'c', 'a', 'c', 'a', 'c', 'c', 't', 'g', 't', 'a', 'a', 't', 'c', 'c']], dtype='U') # fmt: on ) ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[42144400, 42144436], [ 11, 47]]), # fmt: on ) ) self.assertEqual( format(alignment, "psl"), """\ 33 3 0 0 0 0 0 0 + hg19_dna 50 11 47 chr22 51304566 42144400 42144436 1 36, 11, 42144400, """, ) alignment = next(alignments) self.assertEqual(alignment.matches, 43) self.assertEqual(alignment.misMatches, 1) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.shape, (2, 48)) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr2") self.assertEqual(alignment.query.id, "hg19_dna") self.assertEqual(len(alignment.target.seq), 243199373) self.assertEqual(len(alignment.query.seq), 50) if fmt == "psl": self.assertEqual( str(alignment), """\ chr2 183925984 ??????----?????????????????????????????????????? 183926028 0 ||||||----|||||||||||||||||||||||||||||||||||||| 48 hg19_dna 1 ???????????????????????????????????????????????? 49 """, ) elif fmt == "pslx": self.assertEqual(alignment.target.seq[183925984:183925990], "aaaaat") self.assertEqual( alignment.target.seq[183925990:183926028], "aaaggggctgggcgtggtggctcacgcctgtaatccca", ) self.assertEqual( str(alignment), """\ chr2 183925984 aaaaat----aaaggggctgggcgtggtggctcacgcctgtaatccca 183926028 0 ||||||----|||||||||||||||||||||||||.|||||||||||| 48 hg19_dna 1 aaaaat????aaaggggctgggcgtggtggctcacacctgtaatccca 49 """, ) self.assertEqual( alignment.query.seq[1:7], self.queries[alignment.query.id][1:7] ) self.assertEqual( alignment.query.seq[38:49], self.queries[alignment.query.id][38:49] ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[183925984, 183925990, 183925990, 183926028], [ 1, 7, 11, 49]]), # fmt: on ) ) self.assertEqual( format(alignment, "psl"), """\ 43 1 0 0 1 4 0 0 + hg19_dna 50 1 49 chr2 243199373 183925984 183926028 2 6,38, 1,11, 183925984,183925990, """, ) alignment = next(alignments) self.assertEqual(alignment.matches, 34) self.assertEqual(alignment.misMatches, 2) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.shape, (2, 170)) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr19") self.assertEqual(alignment.query.id, "hg19_dna") self.assertEqual(len(alignment.target.seq), 59128983) self.assertEqual(len(alignment.query.seq), 50) if fmt == "psl": self.assertEqual( str(alignment), """\ chr19 35483340 ???????????????????????????????????????????????????????????? 0 |||||||||||||||||||||||||----------------------------------- hg19_dna 10 ?????????????????????????----------------------------------- chr19 35483400 ???????????????????????????????????????????????????????????? 60 ------------------------------------------------------------ hg19_dna 35 ------------------------------------------------------------ chr19 35483460 ?????????????????????????????????????????????????? 35483510 120 ---------------------------------------||||||||||| 170 hg19_dna 35 ---------------------------------------??????????? 46 """, ) elif fmt == "pslx": self.assertEqual( alignment.target.seq[35483340:35483365], "caaaggggctgggcgtagtggctga" ) self.assertEqual(alignment.target.seq[35483499:35483510], "cacctgtaatc") self.assertEqual( alignment.query.seq[10:46], self.queries[alignment.query.id][10:46] ) self.assertEqual( str(alignment), """\ chr19 35483340 caaaggggctgggcgtagtggctga??????????????????????????????????? 0 ||||||||||||||||.||||||.|----------------------------------- hg19_dna 10 caaaggggctgggcgtggtggctca----------------------------------- chr19 35483400 ???????????????????????????????????????????????????????????? 60 ------------------------------------------------------------ hg19_dna 35 ------------------------------------------------------------ chr19 35483460 ???????????????????????????????????????cacctgtaatc 35483510 120 ---------------------------------------||||||||||| 170 hg19_dna 35 ---------------------------------------cacctgtaatc 46 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[35483340, 35483365, 35483499, 35483510], [ 10, 35, 35, 46]]), # fmt: on ) ) self.assertEqual( format(alignment, "psl"), """\ 34 2 0 0 0 0 1 134 + hg19_dna 50 10 46 chr19 59128983 35483340 35483510 2 25,11, 10,35, 35483340,35483499, """, ) alignment = next(alignments) self.assertEqual(alignment.matches, 39) self.assertEqual(alignment.misMatches, 0) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.shape, (2, 39)) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr18") self.assertEqual(alignment.query.id, "hg19_dna") self.assertEqual(len(alignment.target.seq), 78077248) self.assertEqual(len(alignment.query.seq), 50) if fmt == "psl": self.assertEqual( str(alignment), """\ chr18 23891310 ??????????????????????????????????????? 23891349 0 ||||||||||||||||||||||||||||||||||||||| 39 hg19_dna 10 ??????????????????????????????????????? 49 """, ) elif fmt == "pslx": self.assertEqual( alignment.target.seq[23891310:23891349], "caaaggggctgggcgtggtggctcacacctgtaatccca", ) self.assertEqual( alignment.query.seq[10:49], self.queries[alignment.query.id][10:49] ) self.assertEqual( str(alignment), """\ chr18 23891310 caaaggggctgggcgtggtggctcacacctgtaatccca 23891349 0 ||||||||||||||||||||||||||||||||||||||| 39 hg19_dna 10 caaaggggctgggcgtggtggctcacacctgtaatccca 49 """, ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['c', 'a', 'a', 'a', 'g', 'g', 'g', 'g', 'c', 't', 'g', 'g', 'g', 'c', 'g', 't', 'g', 'g', 't', 'g', 'g', 'c', 't', 'c', 'a', 'c', 'a', 'c', 'c', 't', 'g', 't', 'a', 'a', 't', 'c', 'c', 'c', 'a'], ['c', 'a', 'a', 'a', 'g', 'g', 'g', 'g', 'c', 't', 'g', 'g', 'g', 'c', 'g', 't', 'g', 'g', 't', 'g', 'g', 'c', 't', 'c', 'a', 'c', 'a', 'c', 'c', 't', 'g', 't', 'a', 'a', 't', 'c', 'c', 'c', 'a']], dtype='U') # fmt: on ) ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[23891310, 23891349], [ 10, 49]]), # fmt: on ) ) self.assertEqual( format(alignment, "psl"), """\ 39 0 0 0 0 0 0 0 + hg19_dna 50 10 49 chr18 78077248 23891310 23891349 1 39, 10, 23891310, """, ) alignment = next(alignments) self.assertEqual(alignment.matches, 27) self.assertEqual(alignment.misMatches, 1) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.shape, (2, 28)) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr18") self.assertEqual(alignment.query.id, "hg19_dna") self.assertEqual(len(alignment.target.seq), 78077248) self.assertEqual(len(alignment.query.seq), 50) if fmt == "psl": self.assertEqual( str(alignment), """\ chr18 43252217 ???????????????????????????? 43252245 0 |||||||||||||||||||||||||||| 28 hg19_dna 21 ???????????????????????????? 49 """, ) elif fmt == "pslx": self.assertEqual( alignment.target.seq[43252217:43252245], "ggcgtggtggctcacgcctgtaatccca" ) self.assertEqual( alignment.query.seq[21:49], self.queries[alignment.query.id][21:49] ) self.assertEqual( str(alignment), """\ chr18 43252217 ggcgtggtggctcacgcctgtaatccca 43252245 0 |||||||||||||||.|||||||||||| 28 hg19_dna 21 ggcgtggtggctcacacctgtaatccca 49 """, ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['g', 'g', 'c', 'g', 't', 'g', 'g', 't', 'g', 'g', 'c', 't', 'c', 'a', 'c', 'g', 'c', 'c', 't', 'g', 't', 'a', 'a', 't', 'c', 'c', 'c', 'a'], ['g', 'g', 'c', 'g', 't', 'g', 'g', 't', 'g', 'g', 'c', 't', 'c', 'a', 'c', 'a', 'c', 'c', 't', 'g', 't', 'a', 'a', 't', 'c', 'c', 'c', 'a']], dtype='U') # fmt: on ) ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[43252217, 43252245], [ 21, 49]]), # fmt: on ) ) self.assertEqual( format(alignment, "psl"), """\ 27 1 0 0 0 0 0 0 + hg19_dna 50 21 49 chr18 78077248 43252217 43252245 1 28, 21, 43252217, """, ) alignment = next(alignments) self.assertEqual(alignment.matches, 44) self.assertEqual(alignment.misMatches, 1) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.shape, (2, 54)) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr13") self.assertEqual(alignment.query.id, "hg19_dna") self.assertEqual(len(alignment.target.seq), 115169878) self.assertEqual(len(alignment.query.seq), 50) if fmt == "psl": self.assertEqual( str(alignment), """\ chr13 52759147 ?????????????---?????????????????????????????????????? 0 |||||||---------|||||||||||||||||||||||||||||||||||||| hg19_dna 1 ???????------????????????????????????????????????????? chr13 52759198 54 hg19_dna 49 """, ) elif fmt == "pslx": self.assertEqual(alignment.target.seq[52759147:52759154], "aaaaatt") self.assertEqual( alignment.target.seq[52759160:52759198], "aaaggggctgggcgtggtggctcacgcctgtaatccca", ) self.assertEqual( alignment.query.seq[1:8], self.queries[alignment.query.id][1:8] ) self.assertEqual( alignment.query.seq[38:49], self.queries[alignment.query.id][38:49] ) self.assertEqual( str(alignment), """\ chr13 52759147 aaaaatt??????---aaaggggctgggcgtggtggctcacgcctgtaatccca 0 |||||||---------|||||||||||||||||||||||||.|||||||||||| hg19_dna 1 aaaaatt------???aaaggggctgggcgtggtggctcacacctgtaatccca chr13 52759198 54 hg19_dna 49 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[52759147, 52759154, 52759160, 52759160, 52759198], [ 1, 8, 8, 11, 49]]), # fmt: on ) ) self.assertEqual( format(alignment, "psl"), """\ 44 1 0 0 1 3 1 6 + hg19_dna 50 1 49 chr13 115169878 52759147 52759198 2 7,38, 1,11, 52759147,52759160, """, ) alignment = next(alignments) self.assertEqual(alignment.matches, 50) self.assertEqual(alignment.misMatches, 0) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.shape, (2, 50)) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr1") self.assertEqual(alignment.query.id, "hg19_dna") self.assertEqual(len(alignment.target.seq), 249250621) self.assertEqual(len(alignment.query.seq), 50) if fmt == "psl": self.assertEqual( str(alignment), """\ chr1 1207056 ?????????????????????????????????????????????????? 1207106 0 |||||||||||||||||||||||||||||||||||||||||||||||||| 50 hg19_dna 0 ?????????????????????????????????????????????????? 50 """, ) elif fmt == "pslx": self.assertEqual( alignment.target.seq[1207056:1207106], "caaaaattcacaaaggggctgggcgtggtggctcacacctgtaatcccaa", ) self.assertEqual(alignment.query.seq, self.queries[alignment.query.id]) self.assertEqual( str(alignment), """\ chr1 1207056 caaaaattcacaaaggggctgggcgtggtggctcacacctgtaatcccaa 1207106 0 |||||||||||||||||||||||||||||||||||||||||||||||||| 50 hg19_dna 0 caaaaattcacaaaggggctgggcgtggtggctcacacctgtaatcccaa 50 """, ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['c', 'a', 'a', 'a', 'a', 'a', 't', 't', 'c', 'a', 'c', 'a', 'a', 'a', 'g', 'g', 'g', 'g', 'c', 't', 'g', 'g', 'g', 'c', 'g', 't', 'g', 'g', 't', 'g', 'g', 'c', 't', 'c', 'a', 'c', 'a', 'c', 'c', 't', 'g', 't', 'a', 'a', 't', 'c', 'c', 'c', 'a', 'a'], ['c', 'a', 'a', 'a', 'a', 'a', 't', 't', 'c', 'a', 'c', 'a', 'a', 'a', 'g', 'g', 'g', 'g', 'c', 't', 'g', 'g', 'g', 'c', 'g', 't', 'g', 'g', 't', 'g', 'g', 'c', 't', 'c', 'a', 'c', 'a', 'c', 'c', 't', 'g', 't', 'a', 'a', 't', 'c', 'c', 'c', 'a', 'a']], dtype='U') # fmt: on ) ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[1207056, 1207106], [ 0, 50]]), # fmt: on ) ) self.assertEqual( format(alignment, "psl"), """\ 50 0 0 0 0 0 0 0 + hg19_dna 50 0 50 chr1 249250621 1207056 1207106 1 50, 0, 1207056, """, ) alignment = next(alignments) self.assertEqual(alignment.matches, 31) self.assertEqual(alignment.misMatches, 3) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.shape, (2, 34)) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr1") self.assertEqual(alignment.query.id, "hg19_dna") self.assertEqual(len(alignment.target.seq), 249250621) self.assertEqual(len(alignment.query.seq), 50) if fmt == "psl": self.assertEqual( str(alignment), """\ chr1 61700837 ?????????????????????????????????? 61700871 0 |||||||||||||||||||||||||||||||||| 34 hg19_dna 1 ?????????????????????????????????? 35 """, ) elif fmt == "pslx": self.assertEqual( alignment.target.seq[61700837:61700871], "aaaaatgaacaaaggggctgggcgcggtggctca", ) self.assertEqual( alignment.query.seq[1:35], self.queries[alignment.query.id][1:35] ) self.assertEqual( str(alignment), """\ chr1 61700837 aaaaatgaacaaaggggctgggcgcggtggctca 61700871 0 ||||||..||||||||||||||||.||||||||| 34 hg19_dna 1 aaaaattcacaaaggggctgggcgtggtggctca 35 """, ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['a', 'a', 'a', 'a', 'a', 't', 'g', 'a', 'a', 'c', 'a', 'a', 'a', 'g', 'g', 'g', 'g', 'c', 't', 'g', 'g', 'g', 'c', 'g', 'c', 'g', 'g', 't', 'g', 'g', 'c', 't', 'c', 'a'], ['a', 'a', 'a', 'a', 'a', 't', 't', 'c', 'a', 'c', 'a', 'a', 'a', 'g', 'g', 'g', 'g', 'c', 't', 'g', 'g', 'g', 'c', 'g', 't', 'g', 'g', 't', 'g', 'g', 'c', 't', 'c', 'a']], dtype='U') # fmt: on ) ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[61700837, 61700871], [ 1, 35]]), # fmt: on ) ) self.assertEqual( format(alignment, "psl"), """\ 31 3 0 0 0 0 0 0 + hg19_dna 50 1 35 chr1 249250621 61700837 61700871 1 34, 1, 61700837, """, ) alignment = next(alignments) self.assertEqual(alignment.matches, 28) self.assertEqual(alignment.misMatches, 0) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.shape, (2, 44)) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr4") self.assertEqual(alignment.query.id, "hg19_dna") self.assertEqual(len(alignment.target.seq), 191154276) self.assertEqual(len(alignment.query.seq), 50) if fmt == "psl": self.assertEqual( str(alignment), """\ chr4 37558157 ????????????????----------?????????????????? 37558191 0 ||||||||||----------------|||||||||||||||||| 44 hg19_dna 49 ??????????------???????????????????????????? 11 """, ) elif fmt == "pslx": self.assertEqual(alignment.target.seq[37558157:37558167], "tgggattaca") self.assertEqual( alignment.target.seq[37558173:37558191], "accacgcccagccccttt" ) self.assertEqual( alignment.query.seq[11:29], self.queries[alignment.query.id][11:29] ) self.assertEqual( alignment.query.seq[39:49], self.queries[alignment.query.id][39:49] ) self.assertEqual( str(alignment), """\ chr4 37558157 tgggattaca??????----------accacgcccagccccttt 37558191 0 ||||||||||----------------|||||||||||||||||| 44 hg19_dna 49 tgggattaca------??????????accacgcccagccccttt 11 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[37558157, 37558167, 37558173, 37558173, 37558191], [ 49, 39, 39, 29, 11]]), # fmt: on ) ) self.assertEqual( format(alignment, "psl"), """\ 28 0 0 0 1 10 1 6 - hg19_dna 50 11 49 chr4 191154276 37558157 37558191 2 10,18, 1,21, 37558157,37558173, """, ) alignment = next(alignments) self.assertEqual(alignment.matches, 35) self.assertEqual(alignment.misMatches, 2) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.shape, (2, 37)) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr22") self.assertEqual(alignment.query.id, "hg19_dna") self.assertEqual(len(alignment.target.seq), 51304566) self.assertEqual(len(alignment.query.seq), 50) if fmt == "psl": self.assertEqual( str(alignment), """\ chr22 48997405 ????????????????????????????????????? 48997442 0 ||||||||||||||||||||||||||||||||||||| 37 hg19_dna 49 ????????????????????????????????????? 12 """, ) elif fmt == "pslx": self.assertEqual( alignment.target.seq[48997405:48997442], "tgggattacaggcgggagccaccacgcccagcccctt", ) self.assertEqual( alignment.query.seq[12:49], self.queries[alignment.query.id][12:49] ) self.assertEqual( str(alignment), """\ chr22 48997405 tgggattacaggcgggagccaccacgcccagcccctt 48997442 0 ||||||||||||.|.|||||||||||||||||||||| 37 hg19_dna 49 tgggattacaggtgtgagccaccacgcccagcccctt 12 """, ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['t', 'g', 'g', 'g', 'a', 't', 't', 'a', 'c', 'a', 'g', 'g', 'c', 'g', 'g', 'g', 'a', 'g', 'c', 'c', 'a', 'c', 'c', 'a', 'c', 'g', 'c', 'c', 'c', 'a', 'g', 'c', 'c', 'c', 'c', 't', 't'], ['t', 'g', 'g', 'g', 'a', 't', 't', 'a', 'c', 'a', 'g', 'g', 't', 'g', 't', 'g', 'a', 'g', 'c', 'c', 'a', 'c', 'c', 'a', 'c', 'g', 'c', 'c', 'c', 'a', 'g', 'c', 'c', 'c', 'c', 't', 't']], dtype='U') # fmt: on ) ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[48997405, 48997442], [ 49, 12]]), # fmt: on ) ) self.assertEqual( format(alignment, "psl"), """\ 35 2 0 0 0 0 0 0 - hg19_dna 50 12 49 chr22 51304566 48997405 48997442 1 37, 1, 48997405, """, ) alignment = next(alignments) self.assertEqual(alignment.matches, 35) self.assertEqual(alignment.misMatches, 1) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.shape, (2, 36)) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr2") self.assertEqual(alignment.query.id, "hg19_dna") self.assertEqual(len(alignment.target.seq), 243199373) self.assertEqual(len(alignment.query.seq), 50) if fmt == "psl": self.assertEqual( str(alignment), """\ chr2 120641740 ???????????????????????????????????? 120641776 0 |||||||||||||||||||||||||||||||||||| 36 hg19_dna 49 ???????????????????????????????????? 13 """, ) elif fmt == "pslx": self.assertEqual( alignment.target.seq[120641740:120641776], "tgggattacaggcgtgagccaccacgcccagcccct", ) self.assertEqual( alignment.query.seq[13:49], self.queries[alignment.query.id][13:49] ) self.assertEqual( str(alignment), """\ chr2 120641740 tgggattacaggcgtgagccaccacgcccagcccct 120641776 0 ||||||||||||.||||||||||||||||||||||| 36 hg19_dna 49 tgggattacaggtgtgagccaccacgcccagcccct 13 """, ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['t', 'g', 'g', 'g', 'a', 't', 't', 'a', 'c', 'a', 'g', 'g', 'c', 'g', 't', 'g', 'a', 'g', 'c', 'c', 'a', 'c', 'c', 'a', 'c', 'g', 'c', 'c', 'c', 'a', 'g', 'c', 'c', 'c', 'c', 't'], ['t', 'g', 'g', 'g', 'a', 't', 't', 'a', 'c', 'a', 'g', 'g', 't', 'g', 't', 'g', 'a', 'g', 'c', 'c', 'a', 'c', 'c', 'a', 'c', 'g', 'c', 'c', 'c', 'a', 'g', 'c', 'c', 'c', 'c', 't']], dtype='U') # fmt: on ) ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[120641740, 120641776], [ 49, 13]]), # fmt: on ) ) self.assertEqual( format(alignment, "psl"), """\ 35 1 0 0 0 0 0 0 - hg19_dna 50 13 49 chr2 243199373 120641740 120641776 1 36, 1, 120641740, """, ) alignment = next(alignments) self.assertEqual(alignment.matches, 39) self.assertEqual(alignment.misMatches, 0) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.shape, (2, 39)) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr19") self.assertEqual(alignment.query.id, "hg19_dna") self.assertEqual(len(alignment.target.seq), 59128983) self.assertEqual(len(alignment.query.seq), 50) if fmt == "psl": self.assertEqual( str(alignment), """\ chr19 54017130 ??????????????????????????????????????? 54017169 0 ||||||||||||||||||||||||||||||||||||||| 39 hg19_dna 49 ??????????????????????????????????????? 10 """, ) elif fmt == "pslx": self.assertEqual( alignment.target.seq[54017130:54017169], "tgggattacaggtgtgagccaccacgcccagcccctttg", ) self.assertEqual( alignment.query.seq[10:49], self.queries[alignment.query.id][10:49] ) self.assertEqual( str(alignment), """\ chr19 54017130 tgggattacaggtgtgagccaccacgcccagcccctttg 54017169 0 ||||||||||||||||||||||||||||||||||||||| 39 hg19_dna 49 tgggattacaggtgtgagccaccacgcccagcccctttg 10 """, ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['t', 'g', 'g', 'g', 'a', 't', 't', 'a', 'c', 'a', 'g', 'g', 't', 'g', 't', 'g', 'a', 'g', 'c', 'c', 'a', 'c', 'c', 'a', 'c', 'g', 'c', 'c', 'c', 'a', 'g', 'c', 'c', 'c', 'c', 't', 't', 't', 'g'], ['t', 'g', 'g', 'g', 'a', 't', 't', 'a', 'c', 'a', 'g', 'g', 't', 'g', 't', 'g', 'a', 'g', 'c', 'c', 'a', 'c', 'c', 'a', 'c', 'g', 'c', 'c', 'c', 'a', 'g', 'c', 'c', 'c', 'c', 't', 't', 't', 'g']], dtype='U') # fmt: on ) ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[54017130, 54017169], [ 49, 10]]), # fmt: on ) ) self.assertEqual( format(alignment, "psl"), """\ 39 0 0 0 0 0 0 0 - hg19_dna 50 10 49 chr19 59128983 54017130 54017169 1 39, 1, 54017130, """, ) alignment = next(alignments) self.assertEqual(alignment.matches, 36) self.assertEqual(alignment.misMatches, 3) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.shape, (2, 39)) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr19") self.assertEqual(alignment.query.id, "hg19_dna") self.assertEqual(len(alignment.target.seq), 59128983) self.assertEqual(len(alignment.query.seq), 50) if fmt == "psl": self.assertEqual( str(alignment), """\ chr19 553742 ??????????????????????????????????????? 553781 0 ||||||||||||||||||||||||||||||||||||||| 39 hg19_dna 49 ??????????????????????????????????????? 10 """, ) elif fmt == "pslx": self.assertEqual( alignment.target.seq[553742:553781], "tgggatgacaggggtgaggcaccacgcccagcccctttg", ) self.assertEqual( alignment.query.seq[10:49], self.queries[alignment.query.id][10:49] ) self.assertEqual( str(alignment), """\ chr19 553742 tgggatgacaggggtgaggcaccacgcccagcccctttg 553781 0 ||||||.|||||.|||||.|||||||||||||||||||| 39 hg19_dna 49 tgggattacaggtgtgagccaccacgcccagcccctttg 10 """, ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['t', 'g', 'g', 'g', 'a', 't', 'g', 'a', 'c', 'a', 'g', 'g', 'g', 'g', 't', 'g', 'a', 'g', 'g', 'c', 'a', 'c', 'c', 'a', 'c', 'g', 'c', 'c', 'c', 'a', 'g', 'c', 'c', 'c', 'c', 't', 't', 't', 'g'], ['t', 'g', 'g', 'g', 'a', 't', 't', 'a', 'c', 'a', 'g', 'g', 't', 'g', 't', 'g', 'a', 'g', 'c', 'c', 'a', 'c', 'c', 'a', 'c', 'g', 'c', 'c', 'c', 'a', 'g', 'c', 'c', 'c', 'c', 't', 't', 't', 'g']], dtype='U') # fmt: on ) ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[553742, 553781], [ 49, 10]]), # fmt: on ) ) self.assertEqual( format(alignment, "psl"), """\ 36 3 0 0 0 0 0 0 - hg19_dna 50 10 49 chr19 59128983 553742 553781 1 39, 1, 553742, """, ) alignment = next(alignments) self.assertEqual(alignment.matches, 33) self.assertEqual(alignment.misMatches, 3) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.shape, (2, 36)) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr10") self.assertEqual(alignment.query.id, "hg19_dna") self.assertEqual(len(alignment.target.seq), 135534747) self.assertEqual(len(alignment.query.seq), 50) if fmt == "psl": self.assertEqual( str(alignment), """\ chr10 99388555 ???????????????????????????????????? 99388591 0 |||||||||||||||||||||||||||||||||||| 36 hg19_dna 49 ???????????????????????????????????? 13 """, ) elif fmt == "pslx": self.assertEqual( alignment.target.seq[99388555:99388591], "tgggattataggcatgagccaccacgcccagcccct", ) self.assertEqual( alignment.query.seq[13:49], self.queries[alignment.query.id][13:49] ) self.assertEqual( str(alignment), """\ chr10 99388555 tgggattataggcatgagccaccacgcccagcccct 99388591 0 ||||||||.|||..|||||||||||||||||||||| 36 hg19_dna 49 tgggattacaggtgtgagccaccacgcccagcccct 13 """, ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['t', 'g', 'g', 'g', 'a', 't', 't', 'a', 't', 'a', 'g', 'g', 'c', 'a', 't', 'g', 'a', 'g', 'c', 'c', 'a', 'c', 'c', 'a', 'c', 'g', 'c', 'c', 'c', 'a', 'g', 'c', 'c', 'c', 'c', 't'], ['t', 'g', 'g', 'g', 'a', 't', 't', 'a', 'c', 'a', 'g', 'g', 't', 'g', 't', 'g', 'a', 'g', 'c', 'c', 'a', 'c', 'c', 'a', 'c', 'g', 'c', 'c', 'c', 'a', 'g', 'c', 'c', 'c', 'c', 't']], dtype='U') # fmt: on ) ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[99388555, 99388591], [ 49, 13]]), # fmt: on ) ) self.assertEqual( format(alignment, "psl"), """\ 33 3 0 0 0 0 0 0 - hg19_dna 50 13 49 chr10 135534747 99388555 99388591 1 36, 1, 99388555, """, ) alignment = next(alignments) self.assertEqual(alignment.matches, 24) self.assertEqual(alignment.misMatches, 1) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.shape, (2, 25)) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr10") self.assertEqual(alignment.query.id, "hg19_dna") self.assertEqual(len(alignment.target.seq), 135534747) self.assertEqual(len(alignment.query.seq), 50) if fmt == "psl": self.assertEqual( str(alignment), """\ chr10 112178171 ????????????????????????? 112178196 0 ||||||||||||||||||||||||| 25 hg19_dna 35 ????????????????????????? 10 """, ) elif fmt == "pslx": self.assertEqual( alignment.target.seq[112178171:112178196], "tgagtcaccacgcccagcccctttg" ) self.assertEqual( alignment.query.seq[10:35], self.queries[alignment.query.id][10:35] ) self.assertEqual( str(alignment), """\ chr10 112178171 tgagtcaccacgcccagcccctttg 112178196 0 ||||.|||||||||||||||||||| 25 hg19_dna 35 tgagccaccacgcccagcccctttg 10 """, ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['t', 'g', 'a', 'g', 't', 'c', 'a', 'c', 'c', 'a', 'c', 'g', 'c', 'c', 'c', 'a', 'g', 'c', 'c', 'c', 'c', 't', 't', 't', 'g'], ['t', 'g', 'a', 'g', 'c', 'c', 'a', 'c', 'c', 'a', 'c', 'g', 'c', 'c', 'c', 'a', 'g', 'c', 'c', 'c', 'c', 't', 't', 't', 'g']], dtype='U') # fmt: on ) ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[112178171, 112178196], [ 35, 10]]), # fmt: on ) ) self.assertEqual( format(alignment, "psl"), """\ 24 1 0 0 0 0 0 0 - hg19_dna 50 10 35 chr10 135534747 112178171 112178196 1 25, 15, 112178171, """, ) alignment = next(alignments) self.assertEqual(alignment.matches, 35) self.assertEqual(alignment.misMatches, 1) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.shape, (2, 36)) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr1") self.assertEqual(alignment.query.id, "hg19_dna") self.assertEqual(len(alignment.target.seq), 249250621) self.assertEqual(len(alignment.query.seq), 50) if fmt == "psl": self.assertEqual( str(alignment), """\ chr1 39368490 ???????????????????????????????????? 39368526 0 |||||||||||||||||||||||||||||||||||| 36 hg19_dna 49 ???????????????????????????????????? 13 """, ) elif fmt == "pslx": self.assertEqual( alignment.target.seq[39368490:39368526], "tgggattacaggcgtgagccaccacgcccagcccct", ) self.assertEqual( alignment.query.seq[13:49], self.queries[alignment.query.id][13:49] ) self.assertEqual( str(alignment), """\ chr1 39368490 tgggattacaggcgtgagccaccacgcccagcccct 39368526 0 ||||||||||||.||||||||||||||||||||||| 36 hg19_dna 49 tgggattacaggtgtgagccaccacgcccagcccct 13 """, ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['t', 'g', 'g', 'g', 'a', 't', 't', 'a', 'c', 'a', 'g', 'g', 'c', 'g', 't', 'g', 'a', 'g', 'c', 'c', 'a', 'c', 'c', 'a', 'c', 'g', 'c', 'c', 'c', 'a', 'g', 'c', 'c', 'c', 'c', 't'], ['t', 'g', 'g', 'g', 'a', 't', 't', 'a', 'c', 'a', 'g', 'g', 't', 'g', 't', 'g', 'a', 'g', 'c', 'c', 'a', 'c', 'c', 'a', 'c', 'g', 'c', 'c', 'c', 'a', 'g', 'c', 'c', 'c', 'c', 't']], dtype='U') # fmt: on ) ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[39368490, 39368526], [ 49, 13]]), # fmt: on ) ) self.assertEqual( format(alignment, "psl"), """\ 35 1 0 0 0 0 0 0 - hg19_dna 50 13 49 chr1 249250621 39368490 39368526 1 36, 1, 39368490, """, ) alignment = next(alignments) self.assertEqual(alignment.matches, 33) self.assertEqual(alignment.misMatches, 1) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.shape, (2, 34)) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr1") self.assertEqual(alignment.query.id, "hg19_dna") self.assertEqual(len(alignment.target.seq), 249250621) self.assertEqual(len(alignment.query.seq), 50) if fmt == "psl": self.assertEqual( str(alignment), """\ chr1 220325687 ?????????????????????????????????? 220325721 0 |||||||||||||||||||||||||||||||||| 34 hg19_dna 47 ?????????????????????????????????? 13 """, ) elif fmt == "pslx": self.assertEqual( alignment.target.seq[220325687:220325721], "ggattacaggcgtgagccaccacgcccagcccct", ) self.assertEqual( alignment.query.seq[13:47], self.queries[alignment.query.id][13:47] ) self.assertEqual( str(alignment), """\ chr1 220325687 ggattacaggcgtgagccaccacgcccagcccct 220325721 0 ||||||||||.||||||||||||||||||||||| 34 hg19_dna 47 ggattacaggtgtgagccaccacgcccagcccct 13 """, ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['g', 'g', 'a', 't', 't', 'a', 'c', 'a', 'g', 'g', 'c', 'g', 't', 'g', 'a', 'g', 'c', 'c', 'a', 'c', 'c', 'a', 'c', 'g', 'c', 'c', 'c', 'a', 'g', 'c', 'c', 'c', 'c', 't'], ['g', 'g', 'a', 't', 't', 'a', 'c', 'a', 'g', 'g', 't', 'g', 't', 'g', 'a', 'g', 'c', 'c', 'a', 'c', 'c', 'a', 'c', 'g', 'c', 'c', 'c', 'a', 'g', 'c', 'c', 'c', 'c', 't']], dtype='U') # fmt: on ) ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[220325687, 220325721], [ 47, 13]]), # fmt: on ) ) self.assertEqual( format(alignment, "psl"), """\ 33 1 0 0 0 0 0 0 - hg19_dna 50 13 47 chr1 249250621 220325687 220325721 1 34, 3, 220325687, """, ) self.assertRaises(StopIteration, next, alignments) def test_writing_psl_34_004(self): """Test writing the alignments in psl_34_004.psl.""" path = "Blat/psl_34_004.psl" with open(path) as stream: original_data = stream.read() alignments = Align.parse(path, "psl") stream = StringIO() n = Align.write(alignments, stream, "psl") self.assertEqual(n, 19) stream.seek(0) written_data = stream.read() stream.close() self.assertEqual(original_data, written_data) def test_reading_psl_34_005(self): """Test parsing psl_34_005.psl and pslx_34_005.pslx.""" self.check_reading_psl_34_005("psl") self.check_reading_psl_34_005("pslx") def check_reading_psl_34_005(self, fmt): """Check parsing psl_34_005.psl or pslx_34_005.pslx.""" path = "Blat/%s_34_005.%s" % (fmt, fmt) alignments = Align.parse(path, "psl") alignment = next(alignments) self.assertEqual(alignment.matches, 16) self.assertEqual(alignment.misMatches, 0) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.shape, (2, 16)) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr4") self.assertEqual(alignment.query.id, "hg18_dna") self.assertEqual(len(alignment.target.seq), 191154276) self.assertEqual(len(alignment.query.seq), 33) if fmt == "psl": self.assertEqual( str(alignment), """\ chr4 61646095 ???????????????? 61646111 0 |||||||||||||||| 16 hg18_dna 11 ???????????????? 27 """, ) elif fmt == "pslx": self.assertEqual( alignment.target.seq[61646095:61646111], "aggtaaactgccttca" ) self.assertEqual( alignment.query.seq[11:27], self.queries[alignment.query.id][11:27] ) self.assertEqual( str(alignment), """\ chr4 61646095 aggtaaactgccttca 61646111 0 |||||||||||||||| 16 hg18_dna 11 aggtaaactgccttca 27 """, ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['a', 'g', 'g', 't', 'a', 'a', 'a', 'c', 't', 'g', 'c', 'c', 't', 't', 'c', 'a'], ['a', 'g', 'g', 't', 'a', 'a', 'a', 'c', 't', 'g', 'c', 'c', 't', 't', 'c', 'a']], dtype='U') # fmt: on ) ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[61646095, 61646111], [ 11, 27]]), # fmt: on ) ) self.assertEqual( format(alignment, "psl"), """\ 16 0 0 0 0 0 0 0 + hg18_dna 33 11 27 chr4 191154276 61646095 61646111 1 16, 11, 61646095, """, ) alignment = next(alignments) self.assertEqual(alignment.matches, 33) self.assertEqual(alignment.misMatches, 0) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.shape, (2, 33)) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr1") self.assertEqual(alignment.query.id, "hg18_dna") self.assertEqual(len(alignment.target.seq), 249250621) self.assertEqual(len(alignment.query.seq), 33) if fmt == "psl": self.assertEqual( str(alignment), """\ chr1 10271783 ????????????????????????????????? 10271816 0 ||||||||||||||||||||||||||||||||| 33 hg18_dna 0 ????????????????????????????????? 33 """, ) elif fmt == "pslx": self.assertEqual( alignment.target.seq[10271783:10271816], "atgagcttccaaggtaaactgccttcaagattc", ) self.assertEqual(alignment.query.seq, self.queries[alignment.query.id]) self.assertEqual( str(alignment), """\ chr1 10271783 atgagcttccaaggtaaactgccttcaagattc 10271816 0 ||||||||||||||||||||||||||||||||| 33 hg18_dna 0 atgagcttccaaggtaaactgccttcaagattc 33 """, ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['a', 't', 'g', 'a', 'g', 'c', 't', 't', 'c', 'c', 'a', 'a', 'g', 'g', 't', 'a', 'a', 'a', 'c', 't', 'g', 'c', 'c', 't', 't', 'c', 'a', 'a', 'g', 'a', 't', 't', 'c'], ['a', 't', 'g', 'a', 'g', 'c', 't', 't', 'c', 'c', 'a', 'a', 'g', 'g', 't', 'a', 'a', 'a', 'c', 't', 'g', 'c', 'c', 't', 't', 'c', 'a', 'a', 'g', 'a', 't', 't', 'c']], dtype='U') # fmt: on ) ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[10271783, 10271816], [ 0, 33]]), # fmt: on ) ) self.assertEqual( format(alignment, "psl"), """\ 33 0 0 0 0 0 0 0 + hg18_dna 33 0 33 chr1 249250621 10271783 10271816 1 33, 0, 10271783, """, ) alignment = next(alignments) self.assertEqual(alignment.matches, 17) self.assertEqual(alignment.misMatches, 0) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.shape, (2, 17)) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr2") self.assertEqual(alignment.query.id, "hg18_dna") self.assertEqual(len(alignment.target.seq), 243199373) self.assertEqual(len(alignment.query.seq), 33) if fmt == "psl": self.assertEqual( str(alignment), """\ chr2 53575980 ????????????????? 53575997 0 ||||||||||||||||| 17 hg18_dna 25 ????????????????? 8 """, ) elif fmt == "pslx": self.assertEqual( alignment.target.seq[53575980:53575997], "aaggcagtttaccttgg" ) self.assertEqual( alignment.query.seq[8:25], self.queries[alignment.query.id][8:25] ) self.assertEqual( str(alignment), """\ chr2 53575980 aaggcagtttaccttgg 53575997 0 ||||||||||||||||| 17 hg18_dna 25 aaggcagtttaccttgg 8 """, ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['a', 'a', 'g', 'g', 'c', 'a', 'g', 't', 't', 't', 'a', 'c', 'c', 't', 't', 'g', 'g'], ['a', 'a', 'g', 'g', 'c', 'a', 'g', 't', 't', 't', 'a', 'c', 'c', 't', 't', 'g', 'g']], dtype='U') # fmt: on ) ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[53575980, 53575997], [ 25, 8]]), # fmt: on ) ) self.assertEqual( format(alignment, "psl"), """\ 17 0 0 0 0 0 0 0 - hg18_dna 33 8 25 chr2 243199373 53575980 53575997 1 17, 8, 53575980, """, ) alignment = next(alignments) self.assertEqual(alignment.matches, 38) self.assertEqual(alignment.misMatches, 3) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.shape, (2, 41)) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr9") self.assertEqual(alignment.query.id, "hg19_dna") self.assertEqual(len(alignment.target.seq), 141213431) self.assertEqual(len(alignment.query.seq), 50) if fmt == "psl": self.assertEqual( str(alignment), """\ chr9 85737865 ????????????????????????????????????????? 85737906 0 ||||||||||||||||||||||||||||||||||||||||| 41 hg19_dna 9 ????????????????????????????????????????? 50 """, ) elif fmt == "pslx": self.assertEqual( alignment.target.seq[85737865:85737906], "acaaaggggctgggcgcagtggctcacgcctgtaatcccaa", ) self.assertEqual( alignment.query.seq[9:], self.queries[alignment.query.id][9:] ) self.assertEqual( str(alignment), """\ chr9 85737865 acaaaggggctgggcgcagtggctcacgcctgtaatcccaa 85737906 0 ||||||||||||||||..|||||||||.||||||||||||| 41 hg19_dna 9 acaaaggggctgggcgtggtggctcacacctgtaatcccaa 50 """, ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['a', 'c', 'a', 'a', 'a', 'g', 'g', 'g', 'g', 'c', 't', 'g', 'g', 'g', 'c', 'g', 'c', 'a', 'g', 't', 'g', 'g', 'c', 't', 'c', 'a', 'c', 'g', 'c', 'c', 't', 'g', 't', 'a', 'a', 't', 'c', 'c', 'c', 'a', 'a'], ['a', 'c', 'a', 'a', 'a', 'g', 'g', 'g', 'g', 'c', 't', 'g', 'g', 'g', 'c', 'g', 't', 'g', 'g', 't', 'g', 'g', 'c', 't', 'c', 'a', 'c', 'a', 'c', 'c', 't', 'g', 't', 'a', 'a', 't', 'c', 'c', 'c', 'a', 'a']], dtype='U') # fmt: on ) ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[85737865, 85737906], [ 9, 50]]), # fmt: on ) ) self.assertEqual( format(alignment, "psl"), """\ 38 3 0 0 0 0 0 0 + hg19_dna 50 9 50 chr9 141213431 85737865 85737906 1 41, 9, 85737865, """, ) alignment = next(alignments) self.assertEqual(alignment.matches, 41) self.assertEqual(alignment.misMatches, 0) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.shape, (2, 41)) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr8") self.assertEqual(alignment.query.id, "hg19_dna") self.assertEqual(len(alignment.target.seq), 146364022) self.assertEqual(len(alignment.query.seq), 50) if fmt == "psl": self.assertEqual( str(alignment), """\ chr8 95160479 ????????????????????????????????????????? 95160520 0 ||||||||||||||||||||||||||||||||||||||||| 41 hg19_dna 8 ????????????????????????????????????????? 49 """, ) elif fmt == "pslx": self.assertEqual( alignment.target.seq[95160479:95160520], "cacaaaggggctgggcgtggtggctcacacctgtaatccca", ) self.assertEqual( alignment.query.seq[8:49], self.queries[alignment.query.id][8:49] ) self.assertEqual( str(alignment), """\ chr8 95160479 cacaaaggggctgggcgtggtggctcacacctgtaatccca 95160520 0 ||||||||||||||||||||||||||||||||||||||||| 41 hg19_dna 8 cacaaaggggctgggcgtggtggctcacacctgtaatccca 49 """, ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['c', 'a', 'c', 'a', 'a', 'a', 'g', 'g', 'g', 'g', 'c', 't', 'g', 'g', 'g', 'c', 'g', 't', 'g', 'g', 't', 'g', 'g', 'c', 't', 'c', 'a', 'c', 'a', 'c', 'c', 't', 'g', 't', 'a', 'a', 't', 'c', 'c', 'c', 'a'], ['c', 'a', 'c', 'a', 'a', 'a', 'g', 'g', 'g', 'g', 'c', 't', 'g', 'g', 'g', 'c', 'g', 't', 'g', 'g', 't', 'g', 'g', 'c', 't', 'c', 'a', 'c', 'a', 'c', 'c', 't', 'g', 't', 'a', 'a', 't', 'c', 'c', 'c', 'a']], dtype='U') # fmt: on ) ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[95160479, 95160520], [ 8, 49]]), # fmt: on ) ) self.assertEqual( format(alignment, "psl"), """\ 41 0 0 0 0 0 0 0 + hg19_dna 50 8 49 chr8 146364022 95160479 95160520 1 41, 8, 95160479, """, ) alignment = next(alignments) self.assertEqual(alignment.matches, 33) self.assertEqual(alignment.misMatches, 3) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.shape, (2, 36)) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr22") self.assertEqual(alignment.query.id, "hg19_dna") self.assertEqual(len(alignment.target.seq), 51304566) self.assertEqual(len(alignment.query.seq), 50) if fmt == "psl": self.assertEqual( str(alignment), """\ chr22 42144400 ???????????????????????????????????? 42144436 0 |||||||||||||||||||||||||||||||||||| 36 hg19_dna 11 ???????????????????????????????????? 47 """, ) elif fmt == "pslx": self.assertEqual( alignment.target.seq[42144400:42144436], "aaaggggctgggcgtggtagctcatgcctgtaatcc", ) self.assertEqual( alignment.query.seq[11:47], self.queries[alignment.query.id][11:47] ) self.assertEqual( str(alignment), """\ chr22 42144400 aaaggggctgggcgtggtagctcatgcctgtaatcc 42144436 0 ||||||||||||||||||.|||||..|||||||||| 36 hg19_dna 11 aaaggggctgggcgtggtggctcacacctgtaatcc 47 """, ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['a', 'a', 'a', 'g', 'g', 'g', 'g', 'c', 't', 'g', 'g', 'g', 'c', 'g', 't', 'g', 'g', 't', 'a', 'g', 'c', 't', 'c', 'a', 't', 'g', 'c', 'c', 't', 'g', 't', 'a', 'a', 't', 'c', 'c'], ['a', 'a', 'a', 'g', 'g', 'g', 'g', 'c', 't', 'g', 'g', 'g', 'c', 'g', 't', 'g', 'g', 't', 'g', 'g', 'c', 't', 'c', 'a', 'c', 'a', 'c', 'c', 't', 'g', 't', 'a', 'a', 't', 'c', 'c']], dtype='U') # fmt: on ) ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[42144400, 42144436], [ 11, 47]]), # fmt: on ) ) self.assertEqual( format(alignment, "psl"), """\ 33 3 0 0 0 0 0 0 + hg19_dna 50 11 47 chr22 51304566 42144400 42144436 1 36, 11, 42144400, """, ) alignment = next(alignments) self.assertEqual(alignment.matches, 43) self.assertEqual(alignment.misMatches, 1) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.shape, (2, 48)) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr2") self.assertEqual(alignment.query.id, "hg19_dna") self.assertEqual(len(alignment.target.seq), 243199373) self.assertEqual(len(alignment.query.seq), 50) if fmt == "psl": self.assertEqual( str(alignment), """\ chr2 183925984 ??????----?????????????????????????????????????? 183926028 0 ||||||----|||||||||||||||||||||||||||||||||||||| 48 hg19_dna 1 ???????????????????????????????????????????????? 49 """, ) elif fmt == "pslx": self.assertEqual(alignment.target.seq[183925984:183925990], "aaaaat") self.assertEqual( alignment.target.seq[183925990:183926028], "aaaggggctgggcgtggtggctcacgcctgtaatccca", ) self.assertEqual( alignment.query.seq[1:7], self.queries[alignment.query.id][1:7] ) self.assertEqual( alignment.query.seq[11:49], self.queries[alignment.query.id][11:49] ) self.assertEqual( str(alignment), """\ chr2 183925984 aaaaat----aaaggggctgggcgtggtggctcacgcctgtaatccca 183926028 0 ||||||----|||||||||||||||||||||||||.|||||||||||| 48 hg19_dna 1 aaaaat????aaaggggctgggcgtggtggctcacacctgtaatccca 49 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[183925984, 183925990, 183925990, 183926028], [ 1, 7, 11, 49]]), # fmt: on ) ) self.assertEqual( format(alignment, "psl"), """\ 43 1 0 0 1 4 0 0 + hg19_dna 50 1 49 chr2 243199373 183925984 183926028 2 6,38, 1,11, 183925984,183925990, """, ) alignment = next(alignments) self.assertEqual(alignment.matches, 34) self.assertEqual(alignment.misMatches, 2) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.shape, (2, 170)) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr19") self.assertEqual(alignment.query.id, "hg19_dna") self.assertEqual(len(alignment.target.seq), 59128983) self.assertEqual(len(alignment.query.seq), 50) if fmt == "psl": self.assertEqual( str(alignment), """\ chr19 35483340 ???????????????????????????????????????????????????????????? 0 |||||||||||||||||||||||||----------------------------------- hg19_dna 10 ?????????????????????????----------------------------------- chr19 35483400 ???????????????????????????????????????????????????????????? 60 ------------------------------------------------------------ hg19_dna 35 ------------------------------------------------------------ chr19 35483460 ?????????????????????????????????????????????????? 35483510 120 ---------------------------------------||||||||||| 170 hg19_dna 35 ---------------------------------------??????????? 46 """, ) elif fmt == "pslx": self.assertEqual( alignment.target.seq[35483340:35483365], "caaaggggctgggcgtagtggctga" ) self.assertEqual(alignment.target.seq[35483499:35483510], "cacctgtaatc") self.assertEqual( alignment.query.seq[10:46], self.queries[alignment.query.id][10:46] ) self.assertEqual( str(alignment), """\ chr19 35483340 caaaggggctgggcgtagtggctga??????????????????????????????????? 0 ||||||||||||||||.||||||.|----------------------------------- hg19_dna 10 caaaggggctgggcgtggtggctca----------------------------------- chr19 35483400 ???????????????????????????????????????????????????????????? 60 ------------------------------------------------------------ hg19_dna 35 ------------------------------------------------------------ chr19 35483460 ???????????????????????????????????????cacctgtaatc 35483510 120 ---------------------------------------||||||||||| 170 hg19_dna 35 ---------------------------------------cacctgtaatc 46 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[35483340, 35483365, 35483499, 35483510], [ 10, 35, 35, 46]]), # fmt: on ) ) self.assertEqual( format(alignment, "psl"), """\ 34 2 0 0 0 0 1 134 + hg19_dna 50 10 46 chr19 59128983 35483340 35483510 2 25,11, 10,35, 35483340,35483499, """, ) alignment = next(alignments) self.assertEqual(alignment.matches, 39) self.assertEqual(alignment.misMatches, 0) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.shape, (2, 39)) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr18") self.assertEqual(alignment.query.id, "hg19_dna") self.assertEqual(len(alignment.target.seq), 78077248) self.assertEqual(len(alignment.query.seq), 50) if fmt == "psl": self.assertEqual( str(alignment), """\ chr18 23891310 ??????????????????????????????????????? 23891349 0 ||||||||||||||||||||||||||||||||||||||| 39 hg19_dna 10 ??????????????????????????????????????? 49 """, ) elif fmt == "pslx": self.assertEqual( alignment.target.seq[23891310:23891349], "caaaggggctgggcgtggtggctcacacctgtaatccca", ) self.assertEqual( alignment.query.seq[10:49], self.queries[alignment.query.id][10:49] ) self.assertEqual( str(alignment), """\ chr18 23891310 caaaggggctgggcgtggtggctcacacctgtaatccca 23891349 0 ||||||||||||||||||||||||||||||||||||||| 39 hg19_dna 10 caaaggggctgggcgtggtggctcacacctgtaatccca 49 """, ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['c', 'a', 'a', 'a', 'g', 'g', 'g', 'g', 'c', 't', 'g', 'g', 'g', 'c', 'g', 't', 'g', 'g', 't', 'g', 'g', 'c', 't', 'c', 'a', 'c', 'a', 'c', 'c', 't', 'g', 't', 'a', 'a', 't', 'c', 'c', 'c', 'a'], ['c', 'a', 'a', 'a', 'g', 'g', 'g', 'g', 'c', 't', 'g', 'g', 'g', 'c', 'g', 't', 'g', 'g', 't', 'g', 'g', 'c', 't', 'c', 'a', 'c', 'a', 'c', 'c', 't', 'g', 't', 'a', 'a', 't', 'c', 'c', 'c', 'a']], dtype='U') # fmt: on ) ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[23891310, 23891349], [ 10, 49]]), # fmt: on ) ) self.assertEqual( format(alignment, "psl"), """\ 39 0 0 0 0 0 0 0 + hg19_dna 50 10 49 chr18 78077248 23891310 23891349 1 39, 10, 23891310, """, ) alignment = next(alignments) self.assertEqual(alignment.matches, 27) self.assertEqual(alignment.misMatches, 1) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.shape, (2, 28)) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr18") self.assertEqual(alignment.query.id, "hg19_dna") self.assertEqual(len(alignment.target.seq), 78077248) self.assertEqual(len(alignment.query.seq), 50) if fmt == "psl": self.assertEqual( str(alignment), """\ chr18 43252217 ???????????????????????????? 43252245 0 |||||||||||||||||||||||||||| 28 hg19_dna 21 ???????????????????????????? 49 """, ) elif fmt == "pslx": self.assertEqual( alignment.target.seq[43252217:43252245], "ggcgtggtggctcacgcctgtaatccca" ) self.assertEqual( alignment.query.seq[21:49], self.queries[alignment.query.id][21:49] ) self.assertEqual( str(alignment), """\ chr18 43252217 ggcgtggtggctcacgcctgtaatccca 43252245 0 |||||||||||||||.|||||||||||| 28 hg19_dna 21 ggcgtggtggctcacacctgtaatccca 49 """, ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['g', 'g', 'c', 'g', 't', 'g', 'g', 't', 'g', 'g', 'c', 't', 'c', 'a', 'c', 'g', 'c', 'c', 't', 'g', 't', 'a', 'a', 't', 'c', 'c', 'c', 'a'], ['g', 'g', 'c', 'g', 't', 'g', 'g', 't', 'g', 'g', 'c', 't', 'c', 'a', 'c', 'a', 'c', 'c', 't', 'g', 't', 'a', 'a', 't', 'c', 'c', 'c', 'a']], dtype='U') # fmt: on ) ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[43252217, 43252245], [ 21, 49]]), # fmt: on ) ) self.assertEqual( format(alignment, "psl"), """\ 27 1 0 0 0 0 0 0 + hg19_dna 50 21 49 chr18 78077248 43252217 43252245 1 28, 21, 43252217, """, ) alignment = next(alignments) self.assertEqual(alignment.matches, 44) self.assertEqual(alignment.misMatches, 1) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.shape, (2, 54)) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr13") self.assertEqual(alignment.query.id, "hg19_dna") self.assertEqual(len(alignment.target.seq), 115169878) self.assertEqual(len(alignment.query.seq), 50) if fmt == "psl": self.assertEqual( str(alignment), """\ chr13 52759147 ?????????????---?????????????????????????????????????? 0 |||||||---------|||||||||||||||||||||||||||||||||||||| hg19_dna 1 ???????------????????????????????????????????????????? chr13 52759198 54 hg19_dna 49 """, ) elif fmt == "pslx": self.assertEqual(alignment.target.seq[52759147:52759154], "aaaaatt") self.assertEqual( alignment.target.seq[52759160:52759198], "aaaggggctgggcgtggtggctcacgcctgtaatccca", ) self.assertEqual( alignment.query.seq[1:8], self.queries[alignment.query.id][1:8] ) self.assertEqual( alignment.query.seq[38:49], self.queries[alignment.query.id][38:49] ) self.assertEqual( str(alignment), """\ chr13 52759147 aaaaatt??????---aaaggggctgggcgtggtggctcacgcctgtaatccca 0 |||||||---------|||||||||||||||||||||||||.|||||||||||| hg19_dna 1 aaaaatt------???aaaggggctgggcgtggtggctcacacctgtaatccca chr13 52759198 54 hg19_dna 49 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[52759147, 52759154, 52759160, 52759160, 52759198], [ 1, 8, 8, 11, 49]]), # fmt: on ) ) self.assertEqual( format(alignment, "psl"), """\ 44 1 0 0 1 3 1 6 + hg19_dna 50 1 49 chr13 115169878 52759147 52759198 2 7,38, 1,11, 52759147,52759160, """, ) alignment = next(alignments) self.assertEqual(alignment.matches, 50) self.assertEqual(alignment.misMatches, 0) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.shape, (2, 50)) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr1") self.assertEqual(alignment.query.id, "hg19_dna") self.assertEqual(len(alignment.target.seq), 249250621) self.assertEqual(len(alignment.query.seq), 50) if fmt == "psl": self.assertEqual( str(alignment), """\ chr1 1207056 ?????????????????????????????????????????????????? 1207106 0 |||||||||||||||||||||||||||||||||||||||||||||||||| 50 hg19_dna 0 ?????????????????????????????????????????????????? 50 """, ) if fmt == "pslx": self.assertEqual( alignment.target.seq[1207056:1207106], "caaaaattcacaaaggggctgggcgtggtggctcacacctgtaatcccaa", ) self.assertEqual(alignment.query.seq, self.queries[alignment.query.id]) self.assertEqual( str(alignment), """\ chr1 1207056 caaaaattcacaaaggggctgggcgtggtggctcacacctgtaatcccaa 1207106 0 |||||||||||||||||||||||||||||||||||||||||||||||||| 50 hg19_dna 0 caaaaattcacaaaggggctgggcgtggtggctcacacctgtaatcccaa 50 """, ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['c', 'a', 'a', 'a', 'a', 'a', 't', 't', 'c', 'a', 'c', 'a', 'a', 'a', 'g', 'g', 'g', 'g', 'c', 't', 'g', 'g', 'g', 'c', 'g', 't', 'g', 'g', 't', 'g', 'g', 'c', 't', 'c', 'a', 'c', 'a', 'c', 'c', 't', 'g', 't', 'a', 'a', 't', 'c', 'c', 'c', 'a', 'a'], ['c', 'a', 'a', 'a', 'a', 'a', 't', 't', 'c', 'a', 'c', 'a', 'a', 'a', 'g', 'g', 'g', 'g', 'c', 't', 'g', 'g', 'g', 'c', 'g', 't', 'g', 'g', 't', 'g', 'g', 'c', 't', 'c', 'a', 'c', 'a', 'c', 'c', 't', 'g', 't', 'a', 'a', 't', 'c', 'c', 'c', 'a', 'a']], dtype='U') # fmt: on ) ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[1207056, 1207106], [ 0, 50]]), # fmt: on ) ) self.assertEqual( format(alignment, "psl"), """\ 50 0 0 0 0 0 0 0 + hg19_dna 50 0 50 chr1 249250621 1207056 1207106 1 50, 0, 1207056, """, ) alignment = next(alignments) self.assertEqual(alignment.matches, 31) self.assertEqual(alignment.misMatches, 3) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.shape, (2, 34)) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr1") self.assertEqual(alignment.query.id, "hg19_dna") self.assertEqual(len(alignment.target.seq), 249250621) self.assertEqual(len(alignment.query.seq), 50) if fmt == "psl": self.assertEqual( str(alignment), """\ chr1 61700837 ?????????????????????????????????? 61700871 0 |||||||||||||||||||||||||||||||||| 34 hg19_dna 1 ?????????????????????????????????? 35 """, ) elif fmt == "pslx": self.assertEqual( alignment.target.seq[61700837:61700871], "aaaaatgaacaaaggggctgggcgcggtggctca", ) self.assertEqual( alignment.query.seq[1:35], self.queries[alignment.query.id][1:35] ) self.assertEqual( str(alignment), """\ chr1 61700837 aaaaatgaacaaaggggctgggcgcggtggctca 61700871 0 ||||||..||||||||||||||||.||||||||| 34 hg19_dna 1 aaaaattcacaaaggggctgggcgtggtggctca 35 """, ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['a', 'a', 'a', 'a', 'a', 't', 'g', 'a', 'a', 'c', 'a', 'a', 'a', 'g', 'g', 'g', 'g', 'c', 't', 'g', 'g', 'g', 'c', 'g', 'c', 'g', 'g', 't', 'g', 'g', 'c', 't', 'c', 'a'], ['a', 'a', 'a', 'a', 'a', 't', 't', 'c', 'a', 'c', 'a', 'a', 'a', 'g', 'g', 'g', 'g', 'c', 't', 'g', 'g', 'g', 'c', 'g', 't', 'g', 'g', 't', 'g', 'g', 'c', 't', 'c', 'a']], dtype='U') # fmt: on ) ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[61700837, 61700871], [ 1, 35]]), # fmt: on ) ) self.assertEqual( format(alignment, "psl"), """\ 31 3 0 0 0 0 0 0 + hg19_dna 50 1 35 chr1 249250621 61700837 61700871 1 34, 1, 61700837, """, ) alignment = next(alignments) self.assertEqual(alignment.matches, 28) self.assertEqual(alignment.misMatches, 0) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.shape, (2, 44)) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr4") self.assertEqual(alignment.query.id, "hg19_dna") self.assertEqual(len(alignment.target.seq), 191154276) self.assertEqual(len(alignment.query.seq), 50) if fmt == "psl": self.assertEqual( str(alignment), """\ chr4 37558157 ????????????????----------?????????????????? 37558191 0 ||||||||||----------------|||||||||||||||||| 44 hg19_dna 49 ??????????------???????????????????????????? 11 """, ) elif fmt == "pslx": self.assertEqual(alignment.target.seq[37558157:37558167], "tgggattaca") self.assertEqual( alignment.target.seq[37558173:37558191], "accacgcccagccccttt" ) self.assertEqual( alignment.query.seq[11:29], self.queries[alignment.query.id][11:29] ) self.assertEqual( alignment.query.seq[39:49], self.queries[alignment.query.id][39:49] ) self.assertEqual( str(alignment), """\ chr4 37558157 tgggattaca??????----------accacgcccagccccttt 37558191 0 ||||||||||----------------|||||||||||||||||| 44 hg19_dna 49 tgggattaca------??????????accacgcccagccccttt 11 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[37558157, 37558167, 37558173, 37558173, 37558191], [ 49, 39, 39, 29, 11]]), # fmt: on ) ) self.assertEqual( format(alignment, "psl"), """\ 28 0 0 0 1 10 1 6 - hg19_dna 50 11 49 chr4 191154276 37558157 37558191 2 10,18, 1,21, 37558157,37558173, """, ) alignment = next(alignments) self.assertEqual(alignment.matches, 35) self.assertEqual(alignment.misMatches, 2) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.shape, (2, 37)) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr22") self.assertEqual(alignment.query.id, "hg19_dna") self.assertEqual(len(alignment.target.seq), 51304566) self.assertEqual(len(alignment.query.seq), 50) if fmt == "psl": self.assertEqual( str(alignment), """\ chr22 48997405 ????????????????????????????????????? 48997442 0 ||||||||||||||||||||||||||||||||||||| 37 hg19_dna 49 ????????????????????????????????????? 12 """, ) elif fmt == "pslx": self.assertEqual( alignment.target.seq[48997405:48997442], "tgggattacaggcgggagccaccacgcccagcccctt", ) self.assertEqual( alignment.query.seq[12:49], self.queries[alignment.query.id][12:49] ) self.assertEqual( str(alignment), """\ chr22 48997405 tgggattacaggcgggagccaccacgcccagcccctt 48997442 0 ||||||||||||.|.|||||||||||||||||||||| 37 hg19_dna 49 tgggattacaggtgtgagccaccacgcccagcccctt 12 """, ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['t', 'g', 'g', 'g', 'a', 't', 't', 'a', 'c', 'a', 'g', 'g', 'c', 'g', 'g', 'g', 'a', 'g', 'c', 'c', 'a', 'c', 'c', 'a', 'c', 'g', 'c', 'c', 'c', 'a', 'g', 'c', 'c', 'c', 'c', 't', 't'], ['t', 'g', 'g', 'g', 'a', 't', 't', 'a', 'c', 'a', 'g', 'g', 't', 'g', 't', 'g', 'a', 'g', 'c', 'c', 'a', 'c', 'c', 'a', 'c', 'g', 'c', 'c', 'c', 'a', 'g', 'c', 'c', 'c', 'c', 't', 't']], dtype='U') # fmt: on ) ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[48997405, 48997442], [ 49, 12]]), # fmt: on ) ) self.assertEqual( format(alignment, "psl"), """\ 35 2 0 0 0 0 0 0 - hg19_dna 50 12 49 chr22 51304566 48997405 48997442 1 37, 1, 48997405, """, ) alignment = next(alignments) self.assertEqual(alignment.matches, 35) self.assertEqual(alignment.misMatches, 1) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.shape, (2, 36)) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr2") self.assertEqual(alignment.query.id, "hg19_dna") self.assertEqual(len(alignment.target.seq), 243199373) self.assertEqual(len(alignment.query.seq), 50) if fmt == "psl": self.assertEqual( str(alignment), """\ chr2 120641740 ???????????????????????????????????? 120641776 0 |||||||||||||||||||||||||||||||||||| 36 hg19_dna 49 ???????????????????????????????????? 13 """, ) elif fmt == "pslx": self.assertEqual( alignment.target.seq[120641740:120641776], "tgggattacaggcgtgagccaccacgcccagcccct", ) self.assertEqual( alignment.query.seq[13:49], self.queries[alignment.query.id][13:49] ) self.assertEqual( str(alignment), """\ chr2 120641740 tgggattacaggcgtgagccaccacgcccagcccct 120641776 0 ||||||||||||.||||||||||||||||||||||| 36 hg19_dna 49 tgggattacaggtgtgagccaccacgcccagcccct 13 """, ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['t', 'g', 'g', 'g', 'a', 't', 't', 'a', 'c', 'a', 'g', 'g', 'c', 'g', 't', 'g', 'a', 'g', 'c', 'c', 'a', 'c', 'c', 'a', 'c', 'g', 'c', 'c', 'c', 'a', 'g', 'c', 'c', 'c', 'c', 't'], ['t', 'g', 'g', 'g', 'a', 't', 't', 'a', 'c', 'a', 'g', 'g', 't', 'g', 't', 'g', 'a', 'g', 'c', 'c', 'a', 'c', 'c', 'a', 'c', 'g', 'c', 'c', 'c', 'a', 'g', 'c', 'c', 'c', 'c', 't']], dtype='U') # fmt: on ) ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[120641740, 120641776], [ 49, 13]]), # fmt: on ) ) self.assertEqual( format(alignment, "psl"), """\ 35 1 0 0 0 0 0 0 - hg19_dna 50 13 49 chr2 243199373 120641740 120641776 1 36, 1, 120641740, """, ) alignment = next(alignments) self.assertEqual(alignment.matches, 39) self.assertEqual(alignment.misMatches, 0) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.shape, (2, 39)) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr19") self.assertEqual(alignment.query.id, "hg19_dna") self.assertEqual(len(alignment.target.seq), 59128983) self.assertEqual(len(alignment.query.seq), 50) if fmt == "psl": self.assertEqual( str(alignment), """\ chr19 54017130 ??????????????????????????????????????? 54017169 0 ||||||||||||||||||||||||||||||||||||||| 39 hg19_dna 49 ??????????????????????????????????????? 10 """, ) elif fmt == "pslx": self.assertEqual( alignment.target.seq[54017130:54017169], "tgggattacaggtgtgagccaccacgcccagcccctttg", ) self.assertEqual( alignment.query.seq[10:49], self.queries[alignment.query.id][10:49] ) self.assertEqual( str(alignment), """\ chr19 54017130 tgggattacaggtgtgagccaccacgcccagcccctttg 54017169 0 ||||||||||||||||||||||||||||||||||||||| 39 hg19_dna 49 tgggattacaggtgtgagccaccacgcccagcccctttg 10 """, ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['t', 'g', 'g', 'g', 'a', 't', 't', 'a', 'c', 'a', 'g', 'g', 't', 'g', 't', 'g', 'a', 'g', 'c', 'c', 'a', 'c', 'c', 'a', 'c', 'g', 'c', 'c', 'c', 'a', 'g', 'c', 'c', 'c', 'c', 't', 't', 't', 'g'], ['t', 'g', 'g', 'g', 'a', 't', 't', 'a', 'c', 'a', 'g', 'g', 't', 'g', 't', 'g', 'a', 'g', 'c', 'c', 'a', 'c', 'c', 'a', 'c', 'g', 'c', 'c', 'c', 'a', 'g', 'c', 'c', 'c', 'c', 't', 't', 't', 'g']], dtype='U') # fmt: on ) ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[54017130, 54017169], [ 49, 10]]), # fmt: on ) ) self.assertEqual( format(alignment, "psl"), """\ 39 0 0 0 0 0 0 0 - hg19_dna 50 10 49 chr19 59128983 54017130 54017169 1 39, 1, 54017130, """, ) alignment = next(alignments) self.assertEqual(alignment.matches, 36) self.assertEqual(alignment.misMatches, 3) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.shape, (2, 39)) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr19") self.assertEqual(alignment.query.id, "hg19_dna") self.assertEqual(len(alignment.target.seq), 59128983) self.assertEqual(len(alignment.query.seq), 50) if fmt == "psl": self.assertEqual( str(alignment), """\ chr19 553742 ??????????????????????????????????????? 553781 0 ||||||||||||||||||||||||||||||||||||||| 39 hg19_dna 49 ??????????????????????????????????????? 10 """, ) elif fmt == "pslx": self.assertEqual( alignment.target.seq[553742:553781], "tgggatgacaggggtgaggcaccacgcccagcccctttg", ) self.assertEqual( alignment.query.seq[10:49], self.queries[alignment.query.id][10:49] ) self.assertEqual( str(alignment), """\ chr19 553742 tgggatgacaggggtgaggcaccacgcccagcccctttg 553781 0 ||||||.|||||.|||||.|||||||||||||||||||| 39 hg19_dna 49 tgggattacaggtgtgagccaccacgcccagcccctttg 10 """, ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['t', 'g', 'g', 'g', 'a', 't', 'g', 'a', 'c', 'a', 'g', 'g', 'g', 'g', 't', 'g', 'a', 'g', 'g', 'c', 'a', 'c', 'c', 'a', 'c', 'g', 'c', 'c', 'c', 'a', 'g', 'c', 'c', 'c', 'c', 't', 't', 't', 'g'], ['t', 'g', 'g', 'g', 'a', 't', 't', 'a', 'c', 'a', 'g', 'g', 't', 'g', 't', 'g', 'a', 'g', 'c', 'c', 'a', 'c', 'c', 'a', 'c', 'g', 'c', 'c', 'c', 'a', 'g', 'c', 'c', 'c', 'c', 't', 't', 't', 'g']], dtype='U') # fmt: on ) ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[553742, 553781], [ 49, 10]]), # fmt: on ) ) self.assertEqual( format(alignment, "psl"), """\ 36 3 0 0 0 0 0 0 - hg19_dna 50 10 49 chr19 59128983 553742 553781 1 39, 1, 553742, """, ) alignment = next(alignments) self.assertEqual(alignment.matches, 33) self.assertEqual(alignment.misMatches, 3) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.shape, (2, 36)) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr10") self.assertEqual(alignment.query.id, "hg19_dna") self.assertEqual(len(alignment.target.seq), 135534747) self.assertEqual(len(alignment.query.seq), 50) if fmt == "psl": self.assertEqual( str(alignment), """\ chr10 99388555 ???????????????????????????????????? 99388591 0 |||||||||||||||||||||||||||||||||||| 36 hg19_dna 49 ???????????????????????????????????? 13 """, ) elif fmt == "pslx": self.assertEqual( alignment.target.seq[99388555:99388591], "tgggattataggcatgagccaccacgcccagcccct", ) self.assertEqual( alignment.query.seq[13:49], self.queries[alignment.query.id][13:49] ) self.assertEqual( str(alignment), """\ chr10 99388555 tgggattataggcatgagccaccacgcccagcccct 99388591 0 ||||||||.|||..|||||||||||||||||||||| 36 hg19_dna 49 tgggattacaggtgtgagccaccacgcccagcccct 13 """, ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['t', 'g', 'g', 'g', 'a', 't', 't', 'a', 't', 'a', 'g', 'g', 'c', 'a', 't', 'g', 'a', 'g', 'c', 'c', 'a', 'c', 'c', 'a', 'c', 'g', 'c', 'c', 'c', 'a', 'g', 'c', 'c', 'c', 'c', 't'], ['t', 'g', 'g', 'g', 'a', 't', 't', 'a', 'c', 'a', 'g', 'g', 't', 'g', 't', 'g', 'a', 'g', 'c', 'c', 'a', 'c', 'c', 'a', 'c', 'g', 'c', 'c', 'c', 'a', 'g', 'c', 'c', 'c', 'c', 't']], dtype='U') # fmt: on ) ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[99388555, 99388591], [ 49, 13]]), # fmt: on ) ) self.assertEqual( format(alignment, "psl"), """\ 33 3 0 0 0 0 0 0 - hg19_dna 50 13 49 chr10 135534747 99388555 99388591 1 36, 1, 99388555, """, ) alignment = next(alignments) self.assertEqual(alignment.matches, 24) self.assertEqual(alignment.misMatches, 1) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.shape, (2, 25)) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr10") self.assertEqual(alignment.query.id, "hg19_dna") self.assertEqual(len(alignment.target.seq), 135534747) self.assertEqual(len(alignment.query.seq), 50) if fmt == "psl": self.assertEqual( str(alignment), """\ chr10 112178171 ????????????????????????? 112178196 0 ||||||||||||||||||||||||| 25 hg19_dna 35 ????????????????????????? 10 """, ) elif fmt == "pslx": self.assertEqual( alignment.target.seq[112178171:112178196], "tgagtcaccacgcccagcccctttg" ) self.assertEqual( alignment.query.seq[10:35], self.queries[alignment.query.id][10:35] ) self.assertEqual( str(alignment), """\ chr10 112178171 tgagtcaccacgcccagcccctttg 112178196 0 ||||.|||||||||||||||||||| 25 hg19_dna 35 tgagccaccacgcccagcccctttg 10 """, ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['t', 'g', 'a', 'g', 't', 'c', 'a', 'c', 'c', 'a', 'c', 'g', 'c', 'c', 'c', 'a', 'g', 'c', 'c', 'c', 'c', 't', 't', 't', 'g'], ['t', 'g', 'a', 'g', 'c', 'c', 'a', 'c', 'c', 'a', 'c', 'g', 'c', 'c', 'c', 'a', 'g', 'c', 'c', 'c', 'c', 't', 't', 't', 'g']], dtype='U') # fmt: on ) ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[112178171, 112178196], [ 35, 10]]), # fmt: on ) ) self.assertEqual( format(alignment, "psl"), """\ 24 1 0 0 0 0 0 0 - hg19_dna 50 10 35 chr10 135534747 112178171 112178196 1 25, 15, 112178171, """, ) alignment = next(alignments) self.assertEqual(alignment.matches, 35) self.assertEqual(alignment.misMatches, 1) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.shape, (2, 36)) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr1") self.assertEqual(alignment.query.id, "hg19_dna") self.assertEqual(len(alignment.target.seq), 249250621) self.assertEqual(len(alignment.query.seq), 50) if fmt == "psl": self.assertEqual( str(alignment), """\ chr1 39368490 ???????????????????????????????????? 39368526 0 |||||||||||||||||||||||||||||||||||| 36 hg19_dna 49 ???????????????????????????????????? 13 """, ) elif fmt == "pslx": self.assertEqual( alignment.target.seq[39368490:39368526], "tgggattacaggcgtgagccaccacgcccagcccct", ) self.assertEqual( alignment.query.seq[13:49], self.queries[alignment.query.id][13:49] ) self.assertEqual( str(alignment), """\ chr1 39368490 tgggattacaggcgtgagccaccacgcccagcccct 39368526 0 ||||||||||||.||||||||||||||||||||||| 36 hg19_dna 49 tgggattacaggtgtgagccaccacgcccagcccct 13 """, ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['t', 'g', 'g', 'g', 'a', 't', 't', 'a', 'c', 'a', 'g', 'g', 'c', 'g', 't', 'g', 'a', 'g', 'c', 'c', 'a', 'c', 'c', 'a', 'c', 'g', 'c', 'c', 'c', 'a', 'g', 'c', 'c', 'c', 'c', 't'], ['t', 'g', 'g', 'g', 'a', 't', 't', 'a', 'c', 'a', 'g', 'g', 't', 'g', 't', 'g', 'a', 'g', 'c', 'c', 'a', 'c', 'c', 'a', 'c', 'g', 'c', 'c', 'c', 'a', 'g', 'c', 'c', 'c', 'c', 't']], dtype='U') # fmt: on ) ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[39368490, 39368526], [ 49, 13]]), # fmt: on ) ) self.assertEqual( format(alignment, "psl"), """\ 35 1 0 0 0 0 0 0 - hg19_dna 50 13 49 chr1 249250621 39368490 39368526 1 36, 1, 39368490, """, ) alignment = next(alignments) self.assertEqual(alignment.matches, 33) self.assertEqual(alignment.misMatches, 1) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(alignment.shape, (2, 34)) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr1") self.assertEqual(alignment.query.id, "hg19_dna") self.assertEqual(len(alignment.target.seq), 249250621) self.assertEqual(len(alignment.query.seq), 50) if fmt == "psl": self.assertEqual( str(alignment), """\ chr1 220325687 ?????????????????????????????????? 220325721 0 |||||||||||||||||||||||||||||||||| 34 hg19_dna 47 ?????????????????????????????????? 13 """, ) elif fmt == "pslx": self.assertEqual( alignment.target.seq[220325687:220325721], "ggattacaggcgtgagccaccacgcccagcccct", ) self.assertEqual( alignment.query.seq[13:47], self.queries[alignment.query.id][13:47] ) self.assertEqual( str(alignment), """\ chr1 220325687 ggattacaggcgtgagccaccacgcccagcccct 220325721 0 ||||||||||.||||||||||||||||||||||| 34 hg19_dna 47 ggattacaggtgtgagccaccacgcccagcccct 13 """, ) self.assertTrue( np.array_equal( np.array(alignment, "U"), # fmt: off np.array([['g', 'g', 'a', 't', 't', 'a', 'c', 'a', 'g', 'g', 'c', 'g', 't', 'g', 'a', 'g', 'c', 'c', 'a', 'c', 'c', 'a', 'c', 'g', 'c', 'c', 'c', 'a', 'g', 'c', 'c', 'c', 'c', 't'], ['g', 'g', 'a', 't', 't', 'a', 'c', 'a', 'g', 'g', 't', 'g', 't', 'g', 'a', 'g', 'c', 'c', 'a', 'c', 'c', 'a', 'c', 'g', 'c', 'c', 'c', 'a', 'g', 'c', 'c', 'c', 'c', 't']], dtype='U') # fmt: on ) ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[220325687, 220325721], [ 47, 13]]), # fmt: on ) ) self.assertEqual( format(alignment, "psl"), """\ 33 1 0 0 0 0 0 0 - hg19_dna 50 13 47 chr1 249250621 220325687 220325721 1 34, 3, 220325687, """, ) self.assertRaises(StopIteration, next, alignments) def test_writing_psl_34_005(self): """Test writing the alignments in psl_34_005.psl.""" path = "Blat/psl_34_005.psl" with open(path) as stream: original_data = stream.read() alignments = Align.parse(path, "psl") stream = StringIO() n = Align.write(alignments, stream, "psl", header=False) self.assertEqual(n, 22) stream.seek(0) written_data = stream.read() stream.close() self.assertEqual(original_data, written_data) class TestAlign_dnax_prot(unittest.TestCase): @classmethod def read_dna(cls, assembly, sequence): path = "Blat/%s.fa" % assembly records = SeqIO.parse(path, "fasta") for record in records: name, start_end = record.id.split(":") if name == sequence.id: break else: raise Exception("Failed to find DNA sequence") start, end = start_end.split("-") start = int(start) end = int(end) length = len(sequence) sequence = str(record.seq) dna = Seq({start: sequence}, length=length) return dna def test_reading_psl_35_001(self): """Test parsing psl_35_001.psl and pslx_35_001.pslx.""" self.check_reading_psl_35_001("psl") self.check_reading_psl_35_001("pslx") def check_reading_psl_35_001(self, fmt): """Check parsing psl_35_001.psl or pslx_35_001.pslx.""" path = "Blat/%s_35_001.%s" % (fmt, fmt) alignments = Align.parse(path, "psl") self.assertEqual(alignments.metadata["psLayout version"], "3") alignment = next(alignments) self.assertEqual(alignment.matches, 52) self.assertEqual(alignment.misMatches, 0) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr13") self.assertEqual(alignment.query.id, "CAG33136.1") self.assertEqual(len(alignment.target.seq), 114364328) self.assertEqual(len(alignment.query.seq), 230) if fmt == "pslx": self.assertEqual( alignment.query.seq[61:113], "YEVFRTEEEEKIKSQGQDVTSSVYFMKQTISNACGTIGLIHAIANNKDKMHF", ) self.assertEqual(len(alignment.target.seq.defined_ranges), 0) self.assertEqual(len(alignment.target.features), 1) feature = alignment.target.features[0] self.assertEqual( feature.location, SimpleLocation( ExactPosition(75566694), ExactPosition(75566850), strand=+1 ), ) self.assertEqual(feature.type, "CDS") self.assertEqual(len(feature.qualifiers), 1) self.assertEqual(len(feature.qualifiers["translation"]), 1) self.assertEqual( feature.qualifiers["translation"][0], "YEVFRTEEEEKIKSQGQDVTSSVYFMKQTISNACGTIGLIHAIANNKDKMHF", ) alignment.target.seq = TestAlign_dnax_prot.read_dna( "hg38", alignment.target ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[75566694, 75566850], [ 61, 113]]), # fmt: on ) ) self.assertEqual( format(alignment, "psl"), """\ 52 0 0 0 0 0 0 0 ++ CAG33136.1 230 61 113 chr13 114364328 75566694 75566850 1 52, 61, 75566694, """, ) alignment = next(alignments) self.assertEqual(alignment.matches, 44) self.assertEqual(alignment.misMatches, 0) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr13") self.assertEqual(alignment.query.id, "CAG33136.1") self.assertEqual(len(alignment.target.seq), 114364328) self.assertEqual(len(alignment.query.seq), 230) if fmt == "pslx": self.assertEqual( alignment.query.seq[17:61], "QFLKQLGLHPNWQFVDVYGMDPELLSMVPRPVCAVLLLFPITEK", ) self.assertEqual(len(alignment.target.seq.defined_ranges), 0) self.assertEqual(len(alignment.target.features), 1) feature = alignment.target.features[0] self.assertEqual( feature.location, SimpleLocation( ExactPosition(75560749), ExactPosition(75560881), strand=+1 ), ) self.assertEqual(feature.type, "CDS") self.assertEqual(len(feature.qualifiers), 1) self.assertEqual(len(feature.qualifiers["translation"]), 1) self.assertEqual( feature.qualifiers["translation"][0], "QFLKQLGLHPNWQFVDVYGMDPELLSMVPRPVCAVLLLFPITEK", ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[75560749, 75560881], [ 17, 61]]), # fmt: on ) ) self.assertEqual( format(alignment, "psl"), """\ 44 0 0 0 0 0 0 0 ++ CAG33136.1 230 17 61 chr13 114364328 75560749 75560881 1 44, 17, 75560749, """, ) alignment = next(alignments) self.assertEqual(alignment.matches, 44) self.assertEqual(alignment.misMatches, 0) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr13") self.assertEqual(alignment.query.id, "CAG33136.1") self.assertEqual(len(alignment.target.seq), 114364328) self.assertEqual(len(alignment.query.seq), 230) if fmt == "pslx": self.assertEqual(alignment.query.seq[:15], "MEGQRWLPLEANPEV") self.assertEqual( alignment.query.seq[113:142], "ESGSTLKKFLEESVSMSPEERARYLENYD" ) self.assertEqual(len(alignment.target.seq.defined_ranges), 0) self.assertEqual(len(alignment.target.features), 1) feature = alignment.target.features[0] self.assertEqual( feature.location, CompoundLocation( [ SimpleLocation( ExactPosition(75549820), ExactPosition(75549865), strand=+1 ), SimpleLocation( ExactPosition(75567225), ExactPosition(75567312), strand=+1 ), ], operator="join", ), ) self.assertEqual(feature.type, "CDS") self.assertEqual(len(feature.qualifiers), 1) self.assertEqual(len(feature.qualifiers["translation"]), 1) self.assertEqual( feature.qualifiers["translation"][0], "MEGQRWLPLEANPEVESGSTLKKFLEESVSMSPEERARYLENYD", ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[75549820, 75549865, 75567225, 75567225, 75567312], [ 0, 15, 15, 113, 142]]), # fmt: on ) ) self.assertEqual( format(alignment, "psl"), """\ 44 0 0 0 1 98 1 17360 ++ CAG33136.1 230 0 142 chr13 114364328 75549820 75567312 2 15,29, 0,113, 75549820,75567225, """, ) alignment = next(alignments) self.assertEqual(alignment.matches, 47) self.assertEqual(alignment.misMatches, 0) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr13") self.assertEqual(alignment.query.id, "CAG33136.1") self.assertEqual(len(alignment.target.seq), 114364328) self.assertEqual(len(alignment.query.seq), 230) if fmt == "pslx": self.assertEqual( alignment.query.seq[183:], "DGRKPFPINHGETSDETLLEDAIEVCKKFMERDPDELRFNAIALSAA", ) self.assertEqual(len(alignment.target.seq.defined_ranges), 0) self.assertEqual(len(alignment.target.features), 1) feature = alignment.target.features[0] self.assertEqual( feature.location, CompoundLocation( [ SimpleLocation( ExactPosition(75604767), ExactPosition(75604827), strand=+1 ), SimpleLocation( ExactPosition(75605728), ExactPosition(75605809), strand=+1 ), ], operator="join", ), ) self.assertEqual(feature.type, "CDS") self.assertEqual(len(feature.qualifiers), 1) self.assertEqual(len(feature.qualifiers["translation"]), 1) self.assertEqual( feature.qualifiers["translation"][0], "DGRKPFPINHGETSDETLLEDAIEVCKKFMERDPDELRFNAIALSAA", ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[75604767, 75604827, 75605728, 75605809], [ 183, 203, 203, 230]]), # fmt: on ) ) self.assertEqual( format(alignment, "psl"), """\ 47 0 0 0 0 0 1 901 ++ CAG33136.1 230 183 230 chr13 114364328 75604767 75605809 2 20,27, 183,203, 75604767,75605728, """, ) alignment = next(alignments) self.assertEqual(alignment.matches, 25) self.assertEqual(alignment.misMatches, 0) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr13") self.assertEqual(alignment.query.id, "CAG33136.1") self.assertEqual(len(alignment.target.seq), 114364328) self.assertEqual(len(alignment.query.seq), 230) if fmt == "pslx": self.assertEqual(alignment.query.seq[158:183], "APSIDEKVDLHFIALVHVDGHLYEL") self.assertEqual(len(alignment.target.seq.defined_ranges), 0) self.assertEqual(len(alignment.target.features), 1) feature = alignment.target.features[0] self.assertEqual( feature.location, SimpleLocation( ExactPosition(75594914), ExactPosition(75594989), strand=+1 ), ) self.assertEqual(feature.type, "CDS") self.assertEqual(len(feature.qualifiers), 1) self.assertEqual(len(feature.qualifiers["translation"]), 1) self.assertEqual( feature.qualifiers["translation"][0], "APSIDEKVDLHFIALVHVDGHLYEL" ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[75594914, 75594989], [ 158, 183]]), # fmt: on ) ) self.assertEqual( format(alignment, "psl"), """\ 25 0 0 0 0 0 0 0 ++ CAG33136.1 230 158 183 chr13 114364328 75594914 75594989 1 25, 158, 75594914, """, ) alignment = next(alignments) self.assertEqual(alignment.matches, 16) self.assertEqual(alignment.misMatches, 0) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr13") self.assertEqual(alignment.query.id, "CAG33136.1") self.assertEqual(len(alignment.target.seq), 114364328) self.assertEqual(len(alignment.query.seq), 230) if fmt == "pslx": self.assertEqual(alignment.query.seq[142:158], "AIRVTHETSAHEGQTE") self.assertEqual(len(alignment.target.seq.defined_ranges), 0) self.assertEqual(len(alignment.target.features), 1) feature = alignment.target.features[0] self.assertEqual( feature.location, SimpleLocation( ExactPosition(75569459), ExactPosition(75569507), strand=+1 ), ) self.assertEqual(feature.type, "CDS") self.assertEqual(len(feature.qualifiers), 1) self.assertEqual(len(feature.qualifiers["translation"]), 1) self.assertEqual(feature.qualifiers["translation"][0], "AIRVTHETSAHEGQTE") self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[75569459, 75569507], [ 142, 158]]), # fmt: on ) ) self.assertEqual( format(alignment, "psl"), """\ 16 0 0 0 0 0 0 0 ++ CAG33136.1 230 142 158 chr13 114364328 75569459 75569507 1 16, 142, 75569459, """, ) alignment = next(alignments) self.assertEqual(alignment.matches, 26) self.assertEqual(alignment.misMatches, 8) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr4") self.assertEqual(alignment.query.id, "CAG33136.1") self.assertEqual(len(alignment.target.seq), 190214555) self.assertEqual(len(alignment.query.seq), 230) if fmt == "pslx": self.assertEqual( alignment.query.seq[76:110], "GQDVTSSVYFMKQTISNACGTIGLIHAIANNKDK" ) self.assertEqual(len(alignment.target.seq.defined_ranges), 0) self.assertEqual(len(alignment.target.features), 1) feature = alignment.target.features[0] self.assertEqual( feature.location, SimpleLocation( ExactPosition(41260685), ExactPosition(41260787), strand=+1 ), ) self.assertEqual(feature.type, "CDS") self.assertEqual(len(feature.qualifiers), 1) self.assertEqual(len(feature.qualifiers["translation"]), 1) self.assertEqual( feature.qualifiers["translation"][0], "GQEVSPKVYFMKQTIGNSCGTIGLIHAVANNQDK", ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[41260685, 41260787], [ 76, 110]]), # fmt: on ) ) self.assertEqual( format(alignment, "psl"), """\ 26 8 0 0 0 0 0 0 ++ CAG33136.1 230 76 110 chr4 190214555 41260685 41260787 1 34, 76, 41260685, """, ) alignment = next(alignments) self.assertEqual(alignment.matches, 37) self.assertEqual(alignment.misMatches, 26) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr4") self.assertEqual(alignment.query.id, "CAG33136.1") self.assertEqual(len(alignment.target.seq), 190214555) self.assertEqual(len(alignment.query.seq), 230) if fmt == "pslx": self.assertEqual( alignment.query.seq[17:59], "QFLKQLGLHPNWQFVDVYGMDPELLSMVPRPVCAVLLLFPIT" ) self.assertEqual(alignment.query.seq[162:183], "DEKVDLHFIALVHVDGHLYEL") self.assertEqual(len(alignment.target.seq.defined_ranges), 0) self.assertEqual(len(alignment.target.features), 1) feature = alignment.target.features[0] self.assertEqual( feature.location, CompoundLocation( [ SimpleLocation( ExactPosition(41257605), ExactPosition(41257731), strand=+1 ), SimpleLocation( ExactPosition(41263227), ExactPosition(41263290), strand=+1 ), ], operator="join", ), ) self.assertEqual(feature.type, "CDS") self.assertEqual(len(feature.qualifiers), 1) self.assertEqual(len(feature.qualifiers["translation"]), 1) self.assertEqual( feature.qualifiers["translation"][0], "QVLSRLGVAGQWRFVDVLGLEEESLGSVPAPACALLLLFPLTDDKVNFHFILFNNVDGHLYEL", ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[41257605, 41257731, 41263227, 41263227, 41263290], [ 17, 59, 59, 162, 183]]), # fmt: on ) ) self.assertEqual( format(alignment, "psl"), """\ 37 26 0 0 1 103 1 5496 ++ CAG33136.1 230 17 183 chr4 190214555 41257605 41263290 2 42,21, 17,162, 41257605,41263227, """, ) self.assertRaises(StopIteration, next, alignments) def test_writing_psl_35_001(self): """Test writing the alignments in psl_35_001.psl.""" path = "Blat/psl_35_001.psl" with open(path) as stream: original_data = stream.read() alignments = Align.parse(path, "psl") stream = StringIO() n = Align.write(alignments, stream, "psl") self.assertEqual(n, 8) stream.seek(0) written_data = stream.read() stream.close() self.assertEqual(original_data, written_data) # Convert the alignment to a protein alignment and insert the # appropriate sequence data. Write this alignment in a PSL file; # the writer will recalculate the values for matches, misMatches, # repMatches, and nCount from the sequence data and the alignment. # # The alignments were generated using # blat -t=dnax -q=prot hg38.2bit CAG33136.1.fasta psl_35_001.psl # # To save disk space, we extracted the necessary sequence data using # # twoBitToFa hg38.2bit:chr13:75549820-75605809 stdout # twoBitToFa hg38.2bit:chr4:41257605-41263290 stdout # # and concatenating the results into file hg38.fa. We will use this # file below, and create partially defined Seq objects. # # Load the protein sequence: protein = SeqIO.read("Blat/CAG33136.1.fasta", "fasta") protein_alignments = [] alignments = Align.parse(path, "psl") for i, alignment in enumerate(alignments): alignment.sequences[0].seq = TestAlign_dnax_prot.read_dna( "hg38", alignment.sequences[0] ) self.assertEqual(alignment.sequences[1].id, protein.id) alignment.sequences[1].seq = protein.seq # The alignment is on the forward strand of the DNA sequence: self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) # The protein alignment is also in the forward orientation: self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) # Now extract the aligned sequences: aligned_dna = "" aligned_protein = "" for start, end in alignment.aligned[0]: aligned_dna += alignment.sequences[0].seq[start:end] for start, end in alignment.aligned[1]: aligned_protein += alignment.sequences[1].seq[start:end] # Translate the aligned DNA sequence: aligned_dna = Seq(aligned_dna) aligned_dna_translated = Seq(aligned_dna.translate()) aligned_protein = Seq(aligned_protein) # Create a new alignment including the aligned sequences only: records = [ SeqRecord(aligned_dna_translated, id=alignment.sequences[0].id), SeqRecord(aligned_protein, id=alignment.sequences[1].id), ] coordinates = np.array( [[0, len(aligned_dna_translated)], [0, len(aligned_protein)]] ) protein_alignment = Alignment(records, coordinates) protein_alignments.append(protein_alignment) if i == 0: self.assertEqual( str(protein_alignment), """\ chr13 0 YEVFRTEEEEKIKSQGQDVTSSVYFMKQTISNACGTIGLIHAIANNKDKMHF 52 0 |||||||||||||||||||||||||||||||||||||||||||||||||||| 52 CAG33136. 0 YEVFRTEEEEKIKSQGQDVTSSVYFMKQTISNACGTIGLIHAIANNKDKMHF 52 """, ) elif i == 1: self.assertEqual( str(protein_alignment), """\ chr13 0 QFLKQLGLHPNWQFVDVYGMDPELLSMVPRPVCAVLLLFPITEK 44 0 |||||||||||||||||||||||||||||||||||||||||||| 44 CAG33136. 0 QFLKQLGLHPNWQFVDVYGMDPELLSMVPRPVCAVLLLFPITEK 44 """, ) elif i == 2: self.assertEqual( str(protein_alignment), """\ chr13 0 MEGQRWLPLEANPEVESGSTLKKFLEESVSMSPEERARYLENYD 44 0 |||||||||||||||||||||||||||||||||||||||||||| 44 CAG33136. 0 MEGQRWLPLEANPEVESGSTLKKFLEESVSMSPEERARYLENYD 44 """, ) elif i == 3: self.assertEqual( str(protein_alignment), """\ chr13 0 DGRKPFPINHGETSDETLLEDAIEVCKKFMERDPDELRFNAIALSAA 47 0 ||||||||||||||||||||||||||||||||||||||||||||||| 47 CAG33136. 0 DGRKPFPINHGETSDETLLEDAIEVCKKFMERDPDELRFNAIALSAA 47 """, ) elif i == 4: self.assertEqual( str(protein_alignment), """\ chr13 0 APSIDEKVDLHFIALVHVDGHLYEL 25 0 ||||||||||||||||||||||||| 25 CAG33136. 0 APSIDEKVDLHFIALVHVDGHLYEL 25 """, ) elif i == 5: self.assertEqual( str(protein_alignment), """\ chr13 0 AIRVTHETSAHEGQTE 16 0 |||||||||||||||| 16 CAG33136. 0 AIRVTHETSAHEGQTE 16 """, ) elif i == 6: self.assertEqual( str(protein_alignment), """\ chr4 0 GQEVSPKVYFMKQTIGNSCGTIGLIHAVANNQDK 34 0 ||.|...||||||||.|.|||||||||.|||.|| 34 CAG33136. 0 GQDVTSSVYFMKQTISNACGTIGLIHAIANNKDK 34 """, ) elif i == 7: self.assertEqual( str(protein_alignment), """\ chr4 0 QVLSRLGVAGQWRFVDVLGLEEESLGSVPAPACALLLLFPLTDDKVNFHFILFNNVDGHL 0 |.|..||....|.||||.|...|.|..||.|.||.|||||.||.||..|||....||||| CAG33136. 0 QFLKQLGLHPNWQFVDVYGMDPELLSMVPRPVCAVLLLFPITDEKVDLHFIALVHVDGHL chr4 60 YEL 63 60 ||| 63 CAG33136. 60 YEL 63 """, ) # Write the protein alignments to a PSL file: stream = StringIO() n = Align.write(protein_alignments, stream, "psl", wildcard="X") self.assertEqual(n, 8) # Read the alignments back in: alignments = Align.parse(path, "psl") stream.seek(0) protein_alignments = Align.parse(stream, "psl") for alignment, protein_alignment in zip(alignments, protein_alignments): # Confirm that the recalculated values for matches, misMatches, # repMatches, and nCount are correct: self.assertEqual(alignment.matches, protein_alignment.matches) self.assertEqual(alignment.misMatches, protein_alignment.misMatches) self.assertEqual(alignment.repMatches, protein_alignment.repMatches) self.assertEqual(alignment.nCount, protein_alignment.nCount) def test_reading_psl_35_002(self): """Test parsing psl_35_002.psl.""" # See below for a description of the file balAcu1.fa. # We use this file here so we can check the SeqFeatures. records = SeqIO.parse("Blat/balAcu1.fa", "fasta") self.dna = {} for record in records: name, start_end = record.id.split(":") start, end = start_end.split("-") start = int(start) end = int(end) sequence = str(record.seq) self.dna[name] = Seq({start: sequence}, length=end) self.check_reading_psl_35_002("psl") self.check_reading_psl_35_002("pslx") def check_reading_psl_35_002(self, fmt): """Check parsing psl_35_002.psl or pslx_35_002.pslx.""" path = "Blat/%s_35_002.%s" % (fmt, fmt) alignments = Align.parse(path, "psl") self.assertEqual(alignments.metadata["psLayout version"], "3") alignment = next(alignments) self.assertEqual(alignment.matches, 210) self.assertEqual(alignment.misMatches, 3) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "KI537979") self.assertEqual(alignment.query.id, "CAG33136.1") self.assertEqual(len(alignment.target.seq), 14052872) self.assertEqual(len(alignment.query.seq), 230) if fmt == "pslx": self.assertEqual( alignment.query.seq[17:], "QFLKQLGLHPNWQFVDVYGMDPELLSMVPRPVCAVLLLFPITEKYEVFRTEEEEKIKSQGQDVTSSVYFMKQTISNACGTIGLIHAIANNKDKMHFESGSTLKKFLEESVSMSPEERARYLENYDAIRVTHETSAHEGQTEAPSIDEKVDLHFIALVHVDGHLYELDGRKPFPINHGETSDETLLEDAIEVCKKFMERDPDELRFNAIALSAA", ) self.assertEqual(len(alignment.target.seq.defined_ranges), 0) self.assertEqual(len(alignment.target.features), 1) feature = alignment.target.features[0] self.assertEqual( feature.location, CompoundLocation( [ SimpleLocation( ExactPosition(9712654), ExactPosition(9712786), strand=+1 ), SimpleLocation( ExactPosition(9715941), ExactPosition(9716097), strand=+1 ), SimpleLocation( ExactPosition(9716445), ExactPosition(9716532), strand=+1 ), SimpleLocation( ExactPosition(9718374), ExactPosition(9718422), strand=+1 ), SimpleLocation( ExactPosition(9739264), ExactPosition(9739339), strand=+1 ), SimpleLocation( ExactPosition(9743706), ExactPosition(9743766), strand=+1 ), SimpleLocation( ExactPosition(9744511), ExactPosition(9744592), strand=+1 ), ], operator="join", ), ) self.assertEqual(feature.type, "CDS") self.assertEqual(len(feature.qualifiers), 1) self.assertEqual(len(feature.qualifiers["translation"]), 1) self.assertEqual( feature.qualifiers["translation"][0], "QFLKQLGLHPNWQFVDVYGMDPELLSMVPRPVCAVLLLFPITEKYEIFRTEEEEKIKSQGQDVTSSVYFMKQTISNACGTIGLIHAIANNKDKMHFESGSTLKKFLEESASMSPEERARYLENYDAIRVTHETSAHEGQTEAPNIDEKVDLHFIALVHVDGHLYELDGRKPFPINHGETSDETLLEDAIEVCKKFMERDPDELRFNAIALSAA", ) # confirm that the feature coordinates are correct by extracting # the feature sequence from the target sequence and translating it. cds = feature.extract(self.dna[alignment.target.id]).translate() self.assertEqual(feature.qualifiers["translation"][0], cds) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[9712654, 9712786, 9715941, 9716097, 9716445, 9716532, 9718374, 9718422, 9739264, 9739339, 9743706, 9743766, 9744511, 9744592], [ 17, 61, 61, 113, 113, 142, 142, 158, 158, 183, 183, 203, 203, 230]]), # fmt: on ) ) self.assertEqual( format(alignment, "psl"), """\ 210 3 0 0 0 0 6 31299 ++ CAG33136.1 230 17 230 KI537979 14052872 9712654 9744592 7 44,52,29,16,25,20,27, 17,61,113,142,158,183,203, 9712654,9715941,9716445,9718374,9739264,9743706,9744511, """, ) alignment = next(alignments) self.assertEqual(alignment.matches, 207) self.assertEqual(alignment.misMatches, 22) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "KI538594") self.assertEqual(alignment.query.id, "CAG33136.1") self.assertEqual(len(alignment.target.seq), 7819582) self.assertEqual(len(alignment.query.seq), 230) if fmt == "pslx": self.assertEqual(alignment.query.seq[:20], "MEGQRWLPLEANPEVTNQFL") self.assertEqual( alignment.query.seq[21:], "QLGLHPNWQFVDVYGMDPELLSMVPRPVCAVLLLFPITEKYEVFRTEEEEKIKSQGQDVTSSVYFMKQTISNACGTIGLIHAIANNKDKMHFESGSTLKKFLEESVSMSPEERARYLENYDAIRVTHETSAHEGQTEAPSIDEKVDLHFIALVHVDGHLYELDGRKPFPINHGETSDETLLEDAIEVCKKFMERDPDELRFNAIALSAA", ) self.assertEqual(len(alignment.target.seq.defined_ranges), 0) self.assertEqual(len(alignment.target.features), 1) feature = alignment.target.features[0] self.assertEqual( feature.location, CompoundLocation( [ SimpleLocation( ExactPosition(2103463), ExactPosition(2103523), strand=+1 ), SimpleLocation( ExactPosition(2103522), ExactPosition(2104149), strand=+1 ), ], operator="join", ), ) self.assertEqual(feature.type, "CDS") self.assertEqual(len(feature.qualifiers), 1) self.assertEqual(len(feature.qualifiers["translation"]), 1) self.assertEqual( feature.qualifiers["translation"][0], "MEGQCWLPLEANPEVTNQLLQLGLHPNWQFVDVYGMDPELLSMVPRPVCAVLLLFPITEKYEVFRTEEEEKIKSQGQNITSSGYFMRQTISSACGTIGLIHAIANNKDKMHFESGSTLKKFLEESASLSPEERAIYLENYDSIRVTHKTSDHEGQTEAQNIDEKVDLHFIALVHVDGHLYELDGWKPFPINHGETSDATLLRDAIEVFKKFRERDPDERRFNVIALSAA", ) # confirm that the feature coordinates are correct by extracting # the feature sequence from the target sequence and translating it. cds = feature.extract(self.dna[alignment.target.id]).translate() self.assertEqual(feature.qualifiers["translation"][0], cds) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[2103463, 2103523, 2103522, 2103522, 2104149], [ 0, 20, 20, 21, 230]]), # fmt: on ) ) self.assertEqual( format(alignment, "psl"), """\ 207 22 0 0 1 1 1 -1 ++ CAG33136.1 230 0 230 KI538594 7819582 2103463 2104149 2 20,209, 0,21, 2103463,2103522, """, ) alignment = next(alignments) self.assertEqual(alignment.matches, 204) self.assertEqual(alignment.misMatches, 6) self.assertEqual(alignment.repMatches, 0) self.assertEqual(alignment.nCount, 0) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "KI537194") self.assertEqual(alignment.query.id, "CAG33136.1") self.assertEqual(len(alignment.target.seq), 37111980) self.assertEqual(len(alignment.query.seq), 230) if fmt == "pslx": self.assertEqual( alignment.query.seq[:183], "MEGQRWLPLEANPEVTNQFLKQLGLHPNWQFVDVYGMDPELLSMVPRPVCAVLLLFPITEKYEVFRTEEEEKIKSQGQDVTSSVYFMKQTISNACGTIGLIHAIANNKDKMHFESGSTLKKFLEESVSMSPEERARYLENYDAIRVTHETSAHEGQTEAPSIDEKVDLHFIALVHVDGHLYEL", ) self.assertEqual(alignment.query.seq[203:], "DAIEVCKKFMERDPDELRFNAIALSAA") self.assertEqual(len(alignment.target.seq.defined_ranges), 0) self.assertEqual(len(alignment.target.features), 1) feature = alignment.target.features[0] self.assertEqual( feature.location, CompoundLocation( [ SimpleLocation( ExactPosition(20872472), ExactPosition(20873021), strand=-1 ), SimpleLocation( ExactPosition(20872390), ExactPosition(20872471), strand=-1 ), ], operator="join", ), ) self.assertEqual(feature.type, "CDS") self.assertEqual(len(feature.qualifiers), 1) self.assertEqual(len(feature.qualifiers["translation"]), 1) self.assertEqual( feature.qualifiers["translation"][0], "MESQRWLPLEANPEVTNQFLKQLGLHPNWQCVDVYGMDPELLSMVPRPVCAVLLLFPITEKYEIFRTEEEEKTKSQGQDVTSSVYFMKQTISNACGTIGLIHAIANNKDKMHFESGSTLKKFLEESASMSPEERARYLENYDAIRVTHETSAHEGQTEAPNIDEKVDLHFIALVHVDGHLYELDAIEVCKKFMERDPDELRFNAIALSAA", ) # confirm that the feature coordinates are correct by extracting # the feature sequence from the target sequence and translating it. cds = feature.extract(self.dna[alignment.target.id]).translate() self.assertEqual(feature.qualifiers["translation"][0], cds) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[20873021, 20872472, 20872471, 20872471, 20872390], [ 0, 183, 183, 203, 230]]), # fmt: on ) ) self.assertEqual( format(alignment, "psl"), """\ 204 6 0 0 1 20 1 1 +- CAG33136.1 230 0 230 KI537194 37111980 20872390 20873021 2 183,27, 0,203, 16238959,16239509, """, ) self.assertRaises(StopIteration, next, alignments) def test_writing_psl_35_002(self): """Test writing the alignments in psl_35_002.psl.""" path = "Blat/psl_35_002.psl" with open(path) as stream: original_data = stream.read() alignments = Align.parse(path, "psl") stream = StringIO() n = Align.write(alignments, stream, "psl") self.assertEqual(n, 3) stream.seek(0) written_data = stream.read() stream.close() self.assertEqual(original_data, written_data) # Convert the alignment to a protein alignment and insert the # appropriate sequence data. Write this alignment in a PSL file; # the writer will recalculate the values for matches, misMatches, # repMatches, and nCount from the sequence data and the alignment. # # The alignments were generated using # blat -t=dnax -q=prot balAcu1.2bit CAG33136.1.fasta psl_35_001.psl # # To save disk space, we extracted the necessary sequence data using # # twoBitToFa balAcu1.2bit:KI537979:9712654-9744592 stdout # twoBitToFa balAcu1.2bit:KI538594:2103463-2104149 stdout # twoBitToFa balAcu1.2bit:KI537194:20872390-20873021 stdout # # and concatenating the results into file balAcu1.fa. We will use this # file below, and create partially defined Seq objects. # # Load the protein sequence: protein = SeqIO.read("Blat/CAG33136.1.fasta", "fasta") protein_alignments = [] alignments = Align.parse(path, "psl") for i, alignment in enumerate(alignments): alignment.sequences[0].seq = TestAlign_dnax_prot.read_dna( "balAcu1", alignment.sequences[0] ) self.assertEqual(alignment.sequences[1].id, protein.id) alignment.sequences[1].seq = protein.seq if i == 0 or i == 1: # The alignment is on the forward strand of the DNA sequence: self.assertLess( alignment.coordinates[0, 0], alignment.coordinates[0, -1] ) elif i == 2: # The alignment is on the reverse strand of the DNA sequence: self.assertGreater( alignment.coordinates[0, 0], alignment.coordinates[0, -1] ) # so we take the reverse complement: alignment.coordinates[0, :] = ( len(alignment.sequences[0].seq) - alignment.coordinates[0, :] ) alignment.sequences[0].seq = alignment.sequences[ 0 ].seq.reverse_complement() # The protein alignment is always in the forward orientation: self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) # Now extract the aligned sequences: aligned_dna = "" aligned_protein = "" for start, end in alignment.aligned[0]: aligned_dna += alignment.sequences[0].seq[start:end] for start, end in alignment.aligned[1]: aligned_protein += alignment.sequences[1].seq[start:end] # Translate the aligned DNA sequence: aligned_dna = Seq(aligned_dna) aligned_dna_translated = Seq(aligned_dna.translate()) aligned_protein = Seq(aligned_protein) # Create a new alignment including the aligned sequences only: records = [ SeqRecord(aligned_dna_translated, id=alignment.sequences[0].id), SeqRecord(aligned_protein, id=alignment.sequences[1].id), ] coordinates = np.array( [[0, len(aligned_dna_translated)], [0, len(aligned_protein)]] ) protein_alignment = Alignment(records, coordinates) protein_alignments.append(protein_alignment) if i == 0: self.assertEqual( str(protein_alignment), """\ KI537979 0 QFLKQLGLHPNWQFVDVYGMDPELLSMVPRPVCAVLLLFPITEKYEIFRTEEEEKIKSQG 0 ||||||||||||||||||||||||||||||||||||||||||||||.||||||||||||| CAG33136. 0 QFLKQLGLHPNWQFVDVYGMDPELLSMVPRPVCAVLLLFPITEKYEVFRTEEEEKIKSQG KI537979 60 QDVTSSVYFMKQTISNACGTIGLIHAIANNKDKMHFESGSTLKKFLEESASMSPEERARY 60 |||||||||||||||||||||||||||||||||||||||||||||||||.|||||||||| CAG33136. 60 QDVTSSVYFMKQTISNACGTIGLIHAIANNKDKMHFESGSTLKKFLEESVSMSPEERARY KI537979 120 LENYDAIRVTHETSAHEGQTEAPNIDEKVDLHFIALVHVDGHLYELDGRKPFPINHGETS 120 |||||||||||||||||||||||.|||||||||||||||||||||||||||||||||||| CAG33136. 120 LENYDAIRVTHETSAHEGQTEAPSIDEKVDLHFIALVHVDGHLYELDGRKPFPINHGETS KI537979 180 DETLLEDAIEVCKKFMERDPDELRFNAIALSAA 213 180 ||||||||||||||||||||||||||||||||| 213 CAG33136. 180 DETLLEDAIEVCKKFMERDPDELRFNAIALSAA 213 """, ) elif i == 1: self.assertEqual( str(protein_alignment), """\ KI538594 0 MEGQCWLPLEANPEVTNQLLQLGLHPNWQFVDVYGMDPELLSMVPRPVCAVLLLFPITEK 0 ||||.|||||||||||||.||||||||||||||||||||||||||||||||||||||||| CAG33136. 0 MEGQRWLPLEANPEVTNQFLQLGLHPNWQFVDVYGMDPELLSMVPRPVCAVLLLFPITEK KI538594 60 YEVFRTEEEEKIKSQGQNITSSGYFMRQTISSACGTIGLIHAIANNKDKMHFESGSTLKK 60 |||||||||||||||||..|||.|||.||||.|||||||||||||||||||||||||||| CAG33136. 60 YEVFRTEEEEKIKSQGQDVTSSVYFMKQTISNACGTIGLIHAIANNKDKMHFESGSTLKK KI538594 120 FLEESASLSPEERAIYLENYDSIRVTHKTSDHEGQTEAQNIDEKVDLHFIALVHVDGHLY 120 |||||.|.||||||.||||||.|||||.||.|||||||..|||||||||||||||||||| CAG33136. 120 FLEESVSMSPEERARYLENYDAIRVTHETSAHEGQTEAPSIDEKVDLHFIALVHVDGHLY KI538594 180 ELDGWKPFPINHGETSDATLLRDAIEVFKKFRERDPDERRFNVIALSAA 229 180 ||||.||||||||||||.|||.|||||.|||.||||||.|||.|||||| 229 CAG33136. 180 ELDGRKPFPINHGETSDETLLEDAIEVCKKFMERDPDELRFNAIALSAA 229 """, ) elif i == 2: self.assertEqual( str(protein_alignment), """\ KI537194 0 MESQRWLPLEANPEVTNQFLKQLGLHPNWQCVDVYGMDPELLSMVPRPVCAVLLLFPITE 0 ||.|||||||||||||||||||||||||||.||||||||||||||||||||||||||||| CAG33136. 0 MEGQRWLPLEANPEVTNQFLKQLGLHPNWQFVDVYGMDPELLSMVPRPVCAVLLLFPITE KI537194 60 KYEIFRTEEEEKTKSQGQDVTSSVYFMKQTISNACGTIGLIHAIANNKDKMHFESGSTLK 60 |||.||||||||.||||||||||||||||||||||||||||||||||||||||||||||| CAG33136. 60 KYEVFRTEEEEKIKSQGQDVTSSVYFMKQTISNACGTIGLIHAIANNKDKMHFESGSTLK KI537194 120 KFLEESASMSPEERARYLENYDAIRVTHETSAHEGQTEAPNIDEKVDLHFIALVHVDGHL 120 ||||||.|||||||||||||||||||||||||||||||||.||||||||||||||||||| CAG33136. 120 KFLEESVSMSPEERARYLENYDAIRVTHETSAHEGQTEAPSIDEKVDLHFIALVHVDGHL KI537194 180 YELDAIEVCKKFMERDPDELRFNAIALSAA 210 180 |||||||||||||||||||||||||||||| 210 CAG33136. 180 YELDAIEVCKKFMERDPDELRFNAIALSAA 210 """, ) # Write the protein alignments to a PSL file: stream = StringIO() n = Align.write(protein_alignments, stream, "psl", wildcard="X") self.assertEqual(n, 3) # Read the alignments back in: alignments = Align.parse(path, "psl") stream.seek(0) protein_alignments = Align.parse(stream, "psl") for alignment, protein_alignment in zip(alignments, protein_alignments): # Confirm that the recalculated values for matches, misMatches, # repMatches, and nCount are correct: self.assertEqual(alignment.matches, protein_alignment.matches) self.assertEqual(alignment.misMatches, protein_alignment.misMatches) self.assertEqual(alignment.repMatches, protein_alignment.repMatches) self.assertEqual(alignment.nCount, protein_alignment.nCount) class TestAlign_strand(unittest.TestCase): def test_format(self): """Test alignment with the target on the opposite strand.""" sequences = ["AACAGCAGCGTGTCG", "CAGCTAGCGAA"] coordinates = np.array( [[0, 2, 2, 3, 4, 6, 6, 9, 10, 12, 15], [11, 11, 9, 8, 8, 6, 5, 2, 2, 0, 0]] ) alignment = Alignment(sequences, coordinates) alignment.score = 8 line = """\ 8 0 0 0 1 1 2 2 - query 11 0 9 target 15 2 12 4 1,2,3,2, 2,3,6,9, 2,4,6,10, """ self.assertEqual( str(alignment), """\ target 0 AA--CAGC-AGCGTGTCG 15 0 ----|-||-|||-||--- 18 query 11 --TTC-GCTAGC-TG--- 0 """, ) self.assertEqual(format(alignment, "psl"), line) alignment.coordinates = alignment.coordinates[:, ::-1] self.assertEqual( str(alignment), """\ target 15 CGACACGCT-GCTG--TT 0 0 ---||-|||-||-|---- 18 query 0 ---CA-GCTAGC-GAA-- 11 """, ) self.assertEqual(format(alignment, "psl"), line) alignment.coordinates = alignment.coordinates[:, ::-1] line = """\ 8 0 0 0 1 1 2 2 - query 11 2 11 target 15 3 13 4 2,3,2,1, 0,2,6,8, 3,6,9,12, """ alignment = alignment.reverse_complement() self.assertEqual( str(alignment), """\ target 0 CGACACGCT-GCTG--TT 15 0 ---||-|||-||-|---- 18 query 11 ---CA-GCTAGC-GAA-- 0 """, ) self.assertEqual(format(alignment, "psl"), line) alignment.coordinates = alignment.coordinates[:, ::-1] self.assertEqual( str(alignment), """\ target 15 AA--CAGC-AGCGTGTCG 0 0 ----|-||-|||-||--- 18 query 0 --TTC-GCTAGC-TG--- 11 """, ) self.assertEqual(format(alignment, "psl"), line) if __name__ == "__main__": runner = unittest.TextTestRunner(verbosity=2) unittest.main(testRunner=runner)