# Copyright 2023 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.chain module.""" import unittest from io import StringIO from tempfile import NamedTemporaryFile 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.chain." ) from None class TestAlign_dna_rna(unittest.TestCase): # The chain file dna_rna.chain was generated from the PSL file using: # pslToChain dna_rna.psl dna_rna.chain 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 check_alignments(self, alignments): alignment = next(alignments) self.assertEqual(alignment.shape, (2, 1711)) self.assertEqual(len(alignment), 2) self.assertEqual(alignment.score, 176) 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") 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, "chain"), """\ chain 176 chr3 198295559 + 42530895 42532606 NR_046654.1 181 - 0 181 1 63 1062 0 75 468 0 43 """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 181: identities = 175, mismatches = 6. gaps = 1530: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 1530: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 1530: open_internal_deletions = 2, extend_internal_deletions = 1528; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 1530) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 1530) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 1530) self.assertEqual(counts.gaps, 1530) self.assertEqual(counts.aligned, 181) self.assertEqual(counts.identities, 175) self.assertEqual(counts.mismatches, 6) alignment = next(alignments) 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") 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, "chain"), """\ chain 170 chr3 198295559 + 42530895 42532606 NR_046654.1_modified 190 - 5 187 2 27 0 3 36 1062 0 17 2 0 56 468 0 43 """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 179: identities = 172, mismatches = 7. gaps = 1535: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 1535: internal_insertions = 3: open_internal_insertions = 1, extend_internal_insertions = 2; internal_deletions = 1532: open_internal_deletions = 3, extend_internal_deletions = 1529; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 3) self.assertEqual(counts.internal_deletions, 1532) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 1535) self.assertEqual(counts.insertions, 3) self.assertEqual(counts.deletions, 1532) self.assertEqual(counts.gaps, 1535) self.assertEqual(counts.aligned, 179) self.assertEqual(counts.identities, 172) self.assertEqual(counts.mismatches, 7) alignment = next(alignments) 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") 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, "chain"), """\ chain 182 chr3 198295559 + 48663767 48669174 NR_111921.1 216 + 0 204 3 46 1827 0 82 3376 0 76 """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 204: identities = 165, mismatches = 39. gaps = 5203: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 5203: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 5203: open_internal_deletions = 2, extend_internal_deletions = 5201; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 5203) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 5203) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 5203) self.assertEqual(counts.gaps, 5203) self.assertEqual(counts.aligned, 204) self.assertEqual(counts.identities, 165) self.assertEqual(counts.mismatches, 39) alignment = next(alignments) 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") 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, "chain"), """\ chain 175 chr3 198295559 + 48663767 48669174 NR_111921.1_modified 220 + 3 208 4 28 1 0 17 1827 0 76 0 2 6 3376 0 76 """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 203: identities = 162, mismatches = 41. gaps = 5206: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 5206: internal_insertions = 2: open_internal_insertions = 1, extend_internal_insertions = 1; internal_deletions = 5204: open_internal_deletions = 3, extend_internal_deletions = 5201; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 2) self.assertEqual(counts.internal_deletions, 5204) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 5206) self.assertEqual(counts.insertions, 2) self.assertEqual(counts.deletions, 5204) self.assertEqual(counts.gaps, 5206) self.assertEqual(counts.aligned, 203) self.assertEqual(counts.identities, 162) self.assertEqual(counts.mismatches, 41) self.assertRaises(StopIteration, next, alignments) def test_reading(self): """Test parsing dna_rna.chain.""" path = "Blat/dna_rna.chain" alignments = Align.parse(path, "chain") self.check_alignments(alignments) alignments = iter(alignments) self.check_alignments(alignments) with Align.parse(path, "chain") as alignments: self.check_alignments(alignments) with self.assertRaises(AttributeError): alignments._stream with Align.parse(path, "chain") as alignments: pass with self.assertRaises(AttributeError): alignments._stream with open(path) as stream: data = stream.read() stream = NamedTemporaryFile("w+t") stream.write(data) stream.seek(0) alignments = Align.parse(stream, "chain") self.check_alignments(alignments) def test_writing(self): """Test writing the alignments in dna_rna.chain.""" path = "Blat/dna_rna.chain" alignments = Align.parse(path, "chain") stream = StringIO() n = Align.write(alignments, stream, "chain") self.assertEqual(n, 4) stream.seek(0) alignments = Align.parse(stream, "chain") self.check_alignments(alignments) 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.chain.""" # The chain file psl_34_001.chain was generated from the PSL file using: # pslToChain psl_34_001.psl psl_34_001.chain path = "Blat/psl_34_001.chain" alignments = Align.parse(path, "chain") self.check_reading_psl_34_001(alignments) def check_reading_psl_34_001(self, alignments): """Check parsing psl_34_001.chain.""" alignment = next(alignments) 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) self.assertEqual( str(alignment), """\ chr4 61646095 ???????????????? 61646111 0 |||||||||||||||| 16 hg18_dna 11 ???????????????? 27 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[61646095, 61646111], [ 11, 27]]), # fmt: on ) ) self.assertEqual( format(alignment, "chain"), """\ chain 16 chr4 191154276 + 61646095 61646111 hg18_dna 33 + 11 27 1 16 """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 16: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 16) alignment = next(alignments) 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) self.assertEqual( str(alignment), """\ chr1 10271783 ????????????????????????????????? 10271816 0 ||||||||||||||||||||||||||||||||| 33 hg18_dna 0 ????????????????????????????????? 33 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[10271783, 10271816], [ 0, 33]]), # fmt: on ) ) self.assertEqual( format(alignment, "chain"), """\ chain 33 chr1 249250621 + 10271783 10271816 hg18_dna 33 + 0 33 2 33 """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 33: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 33) alignment = next(alignments) 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) self.assertEqual( str(alignment), """\ chr2 53575980 ????????????????? 53575997 0 ||||||||||||||||| 17 hg18_dna 25 ????????????????? 8 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[53575980, 53575997], [ 25, 8]]), # fmt: on ) ) self.assertEqual( format(alignment, "chain"), """\ chain 17 chr2 243199373 + 53575980 53575997 hg18_dna 33 - 8 25 3 17 """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 17: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 17) alignment = next(alignments) 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) self.assertEqual( str(alignment), """\ chr9 85737865 ????????????????????????????????????????? 85737906 0 ||||||||||||||||||||||||||||||||||||||||| 41 hg19_dna 9 ????????????????????????????????????????? 50 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[85737865, 85737906], [ 9, 50]]), # fmt: on ) ) self.assertEqual( format(alignment, "chain"), """\ chain 35 chr9 141213431 + 85737865 85737906 hg19_dna 50 + 9 50 4 41 """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 41: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 41) alignment = next(alignments) 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) self.assertEqual( str(alignment), """\ chr8 95160479 ????????????????????????????????????????? 95160520 0 ||||||||||||||||||||||||||||||||||||||||| 41 hg19_dna 8 ????????????????????????????????????????? 49 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[95160479, 95160520], [ 8, 49]]), # fmt: on ) ) self.assertEqual( format(alignment, "chain"), """\ chain 41 chr8 146364022 + 95160479 95160520 hg19_dna 50 + 8 49 5 41 """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 41: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 41) alignment = next(alignments) 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) self.assertEqual( str(alignment), """\ chr22 42144400 ???????????????????????????????????? 42144436 0 |||||||||||||||||||||||||||||||||||| 36 hg19_dna 11 ???????????????????????????????????? 47 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[42144400, 42144436], [ 11, 47]]), # fmt: on ) ) self.assertEqual( format(alignment, "chain"), """\ chain 30 chr22 51304566 + 42144400 42144436 hg19_dna 50 + 11 47 6 36 """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 36: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 36) alignment = next(alignments) 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) self.assertEqual( str(alignment), """\ chr2 183925984 ??????----?????????????????????????????????????? 183926028 0 ||||||----|||||||||||||||||||||||||||||||||||||| 48 hg19_dna 1 ???????????????????????????????????????????????? 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, "chain"), """\ chain 41 chr2 243199373 + 183925984 183926028 hg19_dna 50 + 1 49 7 6 0 4 38 """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 44: identities = 0, mismatches = 0. gaps = 4: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 4: internal_insertions = 4: open_internal_insertions = 1, extend_internal_insertions = 3; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 4) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 4) self.assertEqual(counts.insertions, 4) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 4) self.assertEqual(counts.aligned, 44) alignment = next(alignments) 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) 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 """, ) 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, "chain"), """\ chain 31 chr19 59128983 + 35483340 35483510 hg19_dna 50 + 10 46 8 25 134 0 11 """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 36: identities = 0, mismatches = 0. gaps = 134: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 134: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 134: open_internal_deletions = 1, extend_internal_deletions = 133; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 134) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 134) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 134) self.assertEqual(counts.gaps, 134) self.assertEqual(counts.aligned, 36) alignment = next(alignments) 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) self.assertEqual( str(alignment), """\ chr18 23891310 ??????????????????????????????????????? 23891349 0 ||||||||||||||||||||||||||||||||||||||| 39 hg19_dna 10 ??????????????????????????????????????? 49 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[23891310, 23891349], [ 10, 49]]), # fmt: on ) ) self.assertEqual( format(alignment, "chain"), """\ chain 39 chr18 78077248 + 23891310 23891349 hg19_dna 50 + 10 49 9 39 """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 39: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 39) alignment = next(alignments) 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) self.assertEqual( str(alignment), """\ chr18 43252217 ???????????????????????????? 43252245 0 |||||||||||||||||||||||||||| 28 hg19_dna 21 ???????????????????????????? 49 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[43252217, 43252245], [ 21, 49]]), # fmt: on ) ) self.assertEqual( format(alignment, "chain"), """\ chain 26 chr18 78077248 + 43252217 43252245 hg19_dna 50 + 21 49 10 28 """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 28: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 28) alignment = next(alignments) 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) self.assertEqual( str(alignment), """\ chr13 52759147 ?????????????---?????????????????????????????????????? 0 |||||||---------|||||||||||||||||||||||||||||||||||||| hg19_dna 1 ???????------????????????????????????????????????????? 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, "chain"), """\ chain 41 chr13 115169878 + 52759147 52759198 hg19_dna 50 + 1 49 11 7 6 3 38 """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 45: identities = 0, mismatches = 0. gaps = 9: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 9: internal_insertions = 3: open_internal_insertions = 1, extend_internal_insertions = 2; internal_deletions = 6: open_internal_deletions = 1, extend_internal_deletions = 5; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 3) self.assertEqual(counts.internal_deletions, 6) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 9) self.assertEqual(counts.insertions, 3) self.assertEqual(counts.deletions, 6) self.assertEqual(counts.gaps, 9) self.assertEqual(counts.aligned, 45) alignment = next(alignments) 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) self.assertEqual( str(alignment), """\ chr1 1207056 ?????????????????????????????????????????????????? 1207106 0 |||||||||||||||||||||||||||||||||||||||||||||||||| 50 hg19_dna 0 ?????????????????????????????????????????????????? 50 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[1207056, 1207106], [ 0, 50]]), # fmt: on ) ) self.assertEqual( format(alignment, "chain"), """\ chain 50 chr1 249250621 + 1207056 1207106 hg19_dna 50 + 0 50 12 50 """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 50: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 50) alignment = next(alignments) 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) self.assertEqual( str(alignment), """\ chr1 61700837 ?????????????????????????????????? 61700871 0 |||||||||||||||||||||||||||||||||| 34 hg19_dna 1 ?????????????????????????????????? 35 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[61700837, 61700871], [ 1, 35]]), # fmt: on ) ) self.assertEqual( format(alignment, "chain"), """\ chain 28 chr1 249250621 + 61700837 61700871 hg19_dna 50 + 1 35 13 34 """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 34: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 34) alignment = next(alignments) 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) self.assertEqual( str(alignment), """\ chr4 37558157 ????????????????----------?????????????????? 37558191 0 ||||||||||----------------|||||||||||||||||| 44 hg19_dna 49 ??????????------???????????????????????????? 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, """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 28: identities = 0, mismatches = 0. gaps = 16: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 16: internal_insertions = 10: open_internal_insertions = 1, extend_internal_insertions = 9; internal_deletions = 6: open_internal_deletions = 1, extend_internal_deletions = 5; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 10) self.assertEqual(counts.internal_deletions, 6) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 16) self.assertEqual(counts.insertions, 10) self.assertEqual(counts.deletions, 6) self.assertEqual(counts.gaps, 16) self.assertEqual(counts.aligned, 28) alignment = next(alignments) 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) self.assertEqual( str(alignment), """\ chr22 48997405 ????????????????????????????????????? 48997442 0 ||||||||||||||||||||||||||||||||||||| 37 hg19_dna 49 ????????????????????????????????????? 12 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[48997405, 48997442], [ 49, 12]]), # fmt: on ) ) self.assertEqual( format(alignment, "chain"), """\ chain 33 chr22 51304566 + 48997405 48997442 hg19_dna 50 - 1 38 15 37 """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 37: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 37) alignment = next(alignments) 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) self.assertEqual( str(alignment), """\ chr2 120641740 ???????????????????????????????????? 120641776 0 |||||||||||||||||||||||||||||||||||| 36 hg19_dna 49 ???????????????????????????????????? 13 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[120641740, 120641776], [ 49, 13]]), # fmt: on ) ) self.assertEqual( format(alignment, "chain"), """\ chain 34 chr2 243199373 + 120641740 120641776 hg19_dna 50 - 1 37 16 36 """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 36: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 36) alignment = next(alignments) 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) self.assertEqual( str(alignment), """\ chr19 54017130 ??????????????????????????????????????? 54017169 0 ||||||||||||||||||||||||||||||||||||||| 39 hg19_dna 49 ??????????????????????????????????????? 10 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[54017130, 54017169], [ 49, 10]]), # fmt: on ) ) self.assertEqual( format(alignment, "chain"), """\ chain 39 chr19 59128983 + 54017130 54017169 hg19_dna 50 - 1 40 17 39 """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 39: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 39) alignment = next(alignments) 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) self.assertEqual( str(alignment), """\ chr19 553742 ??????????????????????????????????????? 553781 0 ||||||||||||||||||||||||||||||||||||||| 39 hg19_dna 49 ??????????????????????????????????????? 10 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[553742, 553781], [ 49, 10]]), # fmt: on ) ) self.assertEqual( format(alignment, "chain"), """\ chain 33 chr19 59128983 + 553742 553781 hg19_dna 50 - 1 40 18 39 """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 39: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 39) alignment = next(alignments) 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) self.assertEqual( str(alignment), """\ chr10 99388555 ???????????????????????????????????? 99388591 0 |||||||||||||||||||||||||||||||||||| 36 hg19_dna 49 ???????????????????????????????????? 13 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[99388555, 99388591], [ 49, 13]]), # fmt: on ) ) self.assertEqual( format(alignment, "chain"), """\ chain 30 chr10 135534747 + 99388555 99388591 hg19_dna 50 - 1 37 19 36 """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 36: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 36) alignment = next(alignments) 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) self.assertEqual( str(alignment), """\ chr10 112178171 ????????????????????????? 112178196 0 ||||||||||||||||||||||||| 25 hg19_dna 35 ????????????????????????? 10 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[112178171, 112178196], [ 35, 10]]), # fmt: on ) ) self.assertEqual( format(alignment, "chain"), """\ chain 23 chr10 135534747 + 112178171 112178196 hg19_dna 50 - 15 40 20 25 """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 25: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 25) alignment = next(alignments) 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) self.assertEqual( str(alignment), """\ chr1 39368490 ???????????????????????????????????? 39368526 0 |||||||||||||||||||||||||||||||||||| 36 hg19_dna 49 ???????????????????????????????????? 13 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[39368490, 39368526], [ 49, 13]]), # fmt: on ) ) self.assertEqual( format(alignment, "chain"), """\ chain 34 chr1 249250621 + 39368490 39368526 hg19_dna 50 - 1 37 21 36 """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 36: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 36) alignment = next(alignments) 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) self.assertEqual( str(alignment), """\ chr1 220325687 ?????????????????????????????????? 220325721 0 |||||||||||||||||||||||||||||||||| 34 hg19_dna 47 ?????????????????????????????????? 13 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[220325687, 220325721], [ 47, 13]]), # fmt: on ) ) self.assertEqual( format(alignment, "chain"), """\ chain 32 chr1 249250621 + 220325687 220325721 hg19_dna 50 - 3 37 22 34 """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 34: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 34) self.assertRaises(StopIteration, next, alignments) def test_writing_chain_34_001(self): """Test writing the alignments in psl_34_001.chain.""" path = "Blat/psl_34_001.chain" with open(path) as stream: original_data = stream.read() alignments = Align.parse(path, "chain") stream = StringIO() n = Align.write(alignments, stream, "chain") self.assertEqual(n, 22) stream.seek(0) alignments = Align.parse(stream, "chain") self.check_reading_psl_34_001(alignments) def test_reading_chain_34_002(self): """Test parsing psl_34_002.chain.""" # The chain file psl_34_002.chain was generated from the PSL file using: # pslToChain psl_34_002.psl psl_34_002.chain path = "Blat/psl_34_002.chain" alignments = Align.parse(path, "chain") self.assertRaises(StopIteration, next, alignments) def test_writing_psl_34_002(self): """Test writing the alignments in psl_34_002.chain.""" path = "Blat/psl_34_002.chain" alignments = Align.parse(path, "chain") stream = StringIO() n = Align.write(alignments, stream, "chain") self.assertEqual(n, 0) stream.seek(0) alignments = Align.parse(stream, "chain") self.assertRaises(StopIteration, next, alignments) def test_reading_psl_34_003(self): """Test parsing psl_34_003.chain.""" # The chain file psl_34_003.chain was generated from the PSL file using: # pslToChain psl_34_003.psl psl_34_003.chain path = "Blat/psl_34_003.chain" alignments = Align.parse(path, "chain") self.check_reading_psl_34_003(alignments) def check_reading_psl_34_003(self, alignments): """Check parsing psl_34_003.chain.""" alignment = next(alignments) 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) self.assertEqual( str(alignment), """\ chr4 61646095 ???????????????? 61646111 0 |||||||||||||||| 16 hg18_dna 11 ???????????????? 27 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[61646095, 61646111], [ 11, 27]]), # fmt: on ) ) self.assertEqual( format(alignment, "chain"), """\ chain 16 chr4 191154276 + 61646095 61646111 hg18_dna 33 + 11 27 1 16 """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 16: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 16) alignment = next(alignments) 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) self.assertEqual( str(alignment), """\ chr1 10271783 ????????????????????????????????? 10271816 0 ||||||||||||||||||||||||||||||||| 33 hg18_dna 0 ????????????????????????????????? 33 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[10271783, 10271816], [ 0, 33]]), # fmt: on ) ) self.assertEqual( format(alignment, "chain"), """\ chain 33 chr1 249250621 + 10271783 10271816 hg18_dna 33 + 0 33 2 33 """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 33: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 33) alignment = next(alignments) 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) self.assertEqual( str(alignment), """\ chr2 53575980 ????????????????? 53575997 0 ||||||||||||||||| 17 hg18_dna 25 ????????????????? 8 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[53575980, 53575997], [ 25, 8]]), # fmt: on ) ) self.assertEqual( format(alignment, "chain"), """\ chain 17 chr2 243199373 + 53575980 53575997 hg18_dna 33 - 8 25 3 17 """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 17: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 17) self.assertRaises(StopIteration, next, alignments) def test_writing_psl_34_003(self): """Test writing the alignments in psl_34_003.chain.""" path = "Blat/psl_34_003.chain" alignments = Align.parse(path, "chain") stream = StringIO() n = Align.write(alignments, stream, "chain") self.assertEqual(n, 3) stream.seek(0) alignments = Align.parse(stream, "chain") self.check_reading_psl_34_003(alignments) def test_reading_psl_34_004(self): """Test parsing psl_34_004.chain.""" # The chain file psl_34_004.chain was generated from the PSL file using: # pslToChain psl_34_004.psl psl_34_004.chain path = "Blat/psl_34_004.chain" alignments = Align.parse(path, "chain") self.check_reading_psl_34_004(alignments) def check_reading_psl_34_004(self, alignments): """Check parsing psl_34_004.chain.""" alignment = next(alignments) 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) self.assertEqual( str(alignment), """\ chr9 85737865 ????????????????????????????????????????? 85737906 0 ||||||||||||||||||||||||||||||||||||||||| 41 hg19_dna 9 ????????????????????????????????????????? 50 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[85737865, 85737906], [ 9, 50]]), # fmt: on ) ) self.assertEqual( format(alignment, "chain"), """\ chain 35 chr9 141213431 + 85737865 85737906 hg19_dna 50 + 9 50 1 41 """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 41: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 41) alignment = next(alignments) 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) self.assertEqual( str(alignment), """\ chr8 95160479 ????????????????????????????????????????? 95160520 0 ||||||||||||||||||||||||||||||||||||||||| 41 hg19_dna 8 ????????????????????????????????????????? 49 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[95160479, 95160520], [ 8, 49]]), # fmt: on ) ) self.assertEqual( format(alignment, "chain"), """\ chain 41 chr8 146364022 + 95160479 95160520 hg19_dna 50 + 8 49 2 41 """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 41: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 41) alignment = next(alignments) 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) self.assertEqual( str(alignment), """\ chr22 42144400 ???????????????????????????????????? 42144436 0 |||||||||||||||||||||||||||||||||||| 36 hg19_dna 11 ???????????????????????????????????? 47 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[42144400, 42144436], [ 11, 47]]), # fmt: on ) ) self.assertEqual( format(alignment, "chain"), """\ chain 30 chr22 51304566 + 42144400 42144436 hg19_dna 50 + 11 47 3 36 """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 36: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 36) alignment = next(alignments) 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) self.assertEqual( str(alignment), """\ chr2 183925984 ??????----?????????????????????????????????????? 183926028 0 ||||||----|||||||||||||||||||||||||||||||||||||| 48 hg19_dna 1 ???????????????????????????????????????????????? 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, "chain"), """\ chain 41 chr2 243199373 + 183925984 183926028 hg19_dna 50 + 1 49 4 6 0 4 38 """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 44: identities = 0, mismatches = 0. gaps = 4: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 4: internal_insertions = 4: open_internal_insertions = 1, extend_internal_insertions = 3; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 4) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 4) self.assertEqual(counts.insertions, 4) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 4) self.assertEqual(counts.aligned, 44) alignment = next(alignments) 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) 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 """, ) 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, "chain"), """\ chain 31 chr19 59128983 + 35483340 35483510 hg19_dna 50 + 10 46 5 25 134 0 11 """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 36: identities = 0, mismatches = 0. gaps = 134: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 134: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 134: open_internal_deletions = 1, extend_internal_deletions = 133; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 134) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 134) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 134) self.assertEqual(counts.gaps, 134) self.assertEqual(counts.aligned, 36) alignment = next(alignments) 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) self.assertEqual( str(alignment), """\ chr18 23891310 ??????????????????????????????????????? 23891349 0 ||||||||||||||||||||||||||||||||||||||| 39 hg19_dna 10 ??????????????????????????????????????? 49 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[23891310, 23891349], [ 10, 49]]), # fmt: on ) ) self.assertEqual( format(alignment, "chain"), """\ chain 39 chr18 78077248 + 23891310 23891349 hg19_dna 50 + 10 49 6 39 """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 39: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 39) alignment = next(alignments) 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) self.assertEqual( str(alignment), """\ chr18 43252217 ???????????????????????????? 43252245 0 |||||||||||||||||||||||||||| 28 hg19_dna 21 ???????????????????????????? 49 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[43252217, 43252245], [ 21, 49]]), # fmt: on ) ) self.assertEqual( format(alignment, "chain"), """\ chain 26 chr18 78077248 + 43252217 43252245 hg19_dna 50 + 21 49 7 28 """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 28: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 28) alignment = next(alignments) 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) self.assertEqual( str(alignment), """\ chr13 52759147 ?????????????---?????????????????????????????????????? 0 |||||||---------|||||||||||||||||||||||||||||||||||||| hg19_dna 1 ???????------????????????????????????????????????????? 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, "chain"), """\ chain 41 chr13 115169878 + 52759147 52759198 hg19_dna 50 + 1 49 8 7 6 3 38 """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 45: identities = 0, mismatches = 0. gaps = 9: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 9: internal_insertions = 3: open_internal_insertions = 1, extend_internal_insertions = 2; internal_deletions = 6: open_internal_deletions = 1, extend_internal_deletions = 5; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 3) self.assertEqual(counts.internal_deletions, 6) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 9) self.assertEqual(counts.insertions, 3) self.assertEqual(counts.deletions, 6) self.assertEqual(counts.gaps, 9) self.assertEqual(counts.aligned, 45) alignment = next(alignments) 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) self.assertEqual( str(alignment), """\ chr1 1207056 ?????????????????????????????????????????????????? 1207106 0 |||||||||||||||||||||||||||||||||||||||||||||||||| 50 hg19_dna 0 ?????????????????????????????????????????????????? 50 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[1207056, 1207106], [ 0, 50]]), # fmt: on ) ) self.assertEqual( format(alignment, "chain"), """\ chain 50 chr1 249250621 + 1207056 1207106 hg19_dna 50 + 0 50 9 50 """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 50: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 50) alignment = next(alignments) 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) self.assertEqual( str(alignment), """\ chr1 61700837 ?????????????????????????????????? 61700871 0 |||||||||||||||||||||||||||||||||| 34 hg19_dna 1 ?????????????????????????????????? 35 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[61700837, 61700871], [ 1, 35]]), # fmt: on ) ) self.assertEqual( format(alignment, "chain"), """\ chain 28 chr1 249250621 + 61700837 61700871 hg19_dna 50 + 1 35 10 34 """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 34: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 34) alignment = next(alignments) 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) self.assertEqual( str(alignment), """\ chr4 37558157 ????????????????----------?????????????????? 37558191 0 ||||||||||----------------|||||||||||||||||| 44 hg19_dna 49 ??????????------???????????????????????????? 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, "chain"), """\ chain 26 chr4 191154276 + 37558157 37558191 hg19_dna 50 - 1 39 11 10 6 10 18 """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 28: identities = 0, mismatches = 0. gaps = 16: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 16: internal_insertions = 10: open_internal_insertions = 1, extend_internal_insertions = 9; internal_deletions = 6: open_internal_deletions = 1, extend_internal_deletions = 5; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 10) self.assertEqual(counts.internal_deletions, 6) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 16) self.assertEqual(counts.insertions, 10) self.assertEqual(counts.deletions, 6) self.assertEqual(counts.gaps, 16) self.assertEqual(counts.aligned, 28) alignment = next(alignments) 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) self.assertEqual( str(alignment), """\ chr22 48997405 ????????????????????????????????????? 48997442 0 ||||||||||||||||||||||||||||||||||||| 37 hg19_dna 49 ????????????????????????????????????? 12 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[48997405, 48997442], [ 49, 12]]), # fmt: on ) ) self.assertEqual( format(alignment, "chain"), """\ chain 33 chr22 51304566 + 48997405 48997442 hg19_dna 50 - 1 38 12 37 """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 37: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 37) alignment = next(alignments) 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) self.assertEqual( str(alignment), """\ chr2 120641740 ???????????????????????????????????? 120641776 0 |||||||||||||||||||||||||||||||||||| 36 hg19_dna 49 ???????????????????????????????????? 13 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[120641740, 120641776], [ 49, 13]]), # fmt: on ) ) self.assertEqual( format(alignment, "chain"), """\ chain 34 chr2 243199373 + 120641740 120641776 hg19_dna 50 - 1 37 13 36 """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 36: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 36) alignment = next(alignments) 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) self.assertEqual( str(alignment), """\ chr19 54017130 ??????????????????????????????????????? 54017169 0 ||||||||||||||||||||||||||||||||||||||| 39 hg19_dna 49 ??????????????????????????????????????? 10 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[54017130, 54017169], [ 49, 10]]), # fmt: on ) ) self.assertEqual( format(alignment, "chain"), """\ chain 39 chr19 59128983 + 54017130 54017169 hg19_dna 50 - 1 40 14 39 """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 39: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 39) alignment = next(alignments) 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) self.assertEqual( str(alignment), """\ chr19 553742 ??????????????????????????????????????? 553781 0 ||||||||||||||||||||||||||||||||||||||| 39 hg19_dna 49 ??????????????????????????????????????? 10 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[553742, 553781], [ 49, 10]]), # fmt: on ) ) self.assertEqual( format(alignment, "chain"), """\ chain 33 chr19 59128983 + 553742 553781 hg19_dna 50 - 1 40 15 39 """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 39: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 39) alignment = next(alignments) 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) self.assertEqual( str(alignment), """\ chr10 99388555 ???????????????????????????????????? 99388591 0 |||||||||||||||||||||||||||||||||||| 36 hg19_dna 49 ???????????????????????????????????? 13 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[99388555, 99388591], [ 49, 13]]), # fmt: on ) ) self.assertEqual( format(alignment, "chain"), """\ chain 30 chr10 135534747 + 99388555 99388591 hg19_dna 50 - 1 37 16 36 """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 36: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 36) alignment = next(alignments) 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) self.assertEqual( str(alignment), """\ chr10 112178171 ????????????????????????? 112178196 0 ||||||||||||||||||||||||| 25 hg19_dna 35 ????????????????????????? 10 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[112178171, 112178196], [ 35, 10]]), # fmt: on ) ) self.assertEqual( format(alignment, "chain"), """\ chain 23 chr10 135534747 + 112178171 112178196 hg19_dna 50 - 15 40 17 25 """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 25: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 25) alignment = next(alignments) 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) self.assertEqual( str(alignment), """\ chr1 39368490 ???????????????????????????????????? 39368526 0 |||||||||||||||||||||||||||||||||||| 36 hg19_dna 49 ???????????????????????????????????? 13 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[39368490, 39368526], [ 49, 13]]), # fmt: on ) ) self.assertEqual( format(alignment, "chain"), """\ chain 34 chr1 249250621 + 39368490 39368526 hg19_dna 50 - 1 37 18 36 """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 36: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 36) alignment = next(alignments) 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) self.assertEqual( str(alignment), """\ chr1 220325687 ?????????????????????????????????? 220325721 0 |||||||||||||||||||||||||||||||||| 34 hg19_dna 47 ?????????????????????????????????? 13 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[220325687, 220325721], [ 47, 13]]), # fmt: on ) ) self.assertEqual( format(alignment, "chain"), """\ chain 32 chr1 249250621 + 220325687 220325721 hg19_dna 50 - 3 37 19 34 """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 34: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 34) self.assertRaises(StopIteration, next, alignments) def test_writing_psl_34_004(self): """Test writing the alignments in psl_34_004.chain.""" path = "Blat/psl_34_004.chain" with open(path) as stream: original_data = stream.read() alignments = Align.parse(path, "chain") stream = StringIO() n = Align.write(alignments, stream, "chain") self.assertEqual(n, 19) stream.seek(0) alignments = Align.parse(stream, "chain") self.check_reading_psl_34_004(alignments) def test_reading_psl_34_005(self): """Test parsing psl_34_005.chain.""" # The chain file psl_34_005.chain was generated from the PSL file using: # pslToChain psl_34_005.psl psl_34_005.chain path = "Blat/psl_34_005.chain" alignments = Align.parse(path, "chain") self.check_reading_psl_34_005(alignments) def check_reading_psl_34_005(self, alignments): """Check parsing psl_34_005.chain.""" alignment = next(alignments) 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) self.assertEqual( str(alignment), """\ chr4 61646095 ???????????????? 61646111 0 |||||||||||||||| 16 hg18_dna 11 ???????????????? 27 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[61646095, 61646111], [ 11, 27]]), # fmt: on ) ) self.assertEqual( format(alignment, "chain"), """\ chain 16 chr4 191154276 + 61646095 61646111 hg18_dna 33 + 11 27 1 16 """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 16: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 16) alignment = next(alignments) 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) self.assertEqual( str(alignment), """\ chr1 10271783 ????????????????????????????????? 10271816 0 ||||||||||||||||||||||||||||||||| 33 hg18_dna 0 ????????????????????????????????? 33 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[10271783, 10271816], [ 0, 33]]), # fmt: on ) ) self.assertEqual( format(alignment, "chain"), """\ chain 33 chr1 249250621 + 10271783 10271816 hg18_dna 33 + 0 33 2 33 """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 33: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 33) alignment = next(alignments) 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) self.assertEqual( str(alignment), """\ chr2 53575980 ????????????????? 53575997 0 ||||||||||||||||| 17 hg18_dna 25 ????????????????? 8 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[53575980, 53575997], [ 25, 8]]), # fmt: on ) ) self.assertEqual( format(alignment, "chain"), """\ chain 17 chr2 243199373 + 53575980 53575997 hg18_dna 33 - 8 25 3 17 """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 17: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 17) alignment = next(alignments) 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) self.assertEqual( str(alignment), """\ chr9 85737865 ????????????????????????????????????????? 85737906 0 ||||||||||||||||||||||||||||||||||||||||| 41 hg19_dna 9 ????????????????????????????????????????? 50 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[85737865, 85737906], [ 9, 50]]), # fmt: on ) ) self.assertEqual( format(alignment, "chain"), """\ chain 35 chr9 141213431 + 85737865 85737906 hg19_dna 50 + 9 50 4 41 """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 41: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 41) alignment = next(alignments) 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) self.assertEqual( str(alignment), """\ chr8 95160479 ????????????????????????????????????????? 95160520 0 ||||||||||||||||||||||||||||||||||||||||| 41 hg19_dna 8 ????????????????????????????????????????? 49 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[95160479, 95160520], [ 8, 49]]), # fmt: on ) ) self.assertEqual( format(alignment, "chain"), """\ chain 41 chr8 146364022 + 95160479 95160520 hg19_dna 50 + 8 49 5 41 """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 41: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 41) alignment = next(alignments) 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) self.assertEqual( str(alignment), """\ chr22 42144400 ???????????????????????????????????? 42144436 0 |||||||||||||||||||||||||||||||||||| 36 hg19_dna 11 ???????????????????????????????????? 47 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[42144400, 42144436], [ 11, 47]]), # fmt: on ) ) self.assertEqual( format(alignment, "chain"), """\ chain 30 chr22 51304566 + 42144400 42144436 hg19_dna 50 + 11 47 6 36 """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 36: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 36) alignment = next(alignments) 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) self.assertEqual( str(alignment), """\ chr2 183925984 ??????----?????????????????????????????????????? 183926028 0 ||||||----|||||||||||||||||||||||||||||||||||||| 48 hg19_dna 1 ???????????????????????????????????????????????? 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, "chain"), """\ chain 41 chr2 243199373 + 183925984 183926028 hg19_dna 50 + 1 49 7 6 0 4 38 """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 44: identities = 0, mismatches = 0. gaps = 4: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 4: internal_insertions = 4: open_internal_insertions = 1, extend_internal_insertions = 3; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 4) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 4) self.assertEqual(counts.insertions, 4) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 4) self.assertEqual(counts.aligned, 44) alignment = next(alignments) 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) 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 """, ) 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, "chain"), """\ chain 31 chr19 59128983 + 35483340 35483510 hg19_dna 50 + 10 46 8 25 134 0 11 """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 36: identities = 0, mismatches = 0. gaps = 134: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 134: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 134: open_internal_deletions = 1, extend_internal_deletions = 133; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 134) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 134) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 134) self.assertEqual(counts.gaps, 134) self.assertEqual(counts.aligned, 36) alignment = next(alignments) 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) self.assertEqual( str(alignment), """\ chr18 23891310 ??????????????????????????????????????? 23891349 0 ||||||||||||||||||||||||||||||||||||||| 39 hg19_dna 10 ??????????????????????????????????????? 49 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[23891310, 23891349], [ 10, 49]]), # fmt: on ) ) self.assertEqual( format(alignment, "chain"), """\ chain 39 chr18 78077248 + 23891310 23891349 hg19_dna 50 + 10 49 9 39 """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 39: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 39) alignment = next(alignments) 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) self.assertEqual( str(alignment), """\ chr18 43252217 ???????????????????????????? 43252245 0 |||||||||||||||||||||||||||| 28 hg19_dna 21 ???????????????????????????? 49 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[43252217, 43252245], [ 21, 49]]), # fmt: on ) ) self.assertEqual( format(alignment, "chain"), """\ chain 26 chr18 78077248 + 43252217 43252245 hg19_dna 50 + 21 49 10 28 """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 28: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 28) alignment = next(alignments) 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) self.assertEqual( str(alignment), """\ chr13 52759147 ?????????????---?????????????????????????????????????? 0 |||||||---------|||||||||||||||||||||||||||||||||||||| hg19_dna 1 ???????------????????????????????????????????????????? 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, "chain"), """\ chain 41 chr13 115169878 + 52759147 52759198 hg19_dna 50 + 1 49 11 7 6 3 38 """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 45: identities = 0, mismatches = 0. gaps = 9: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 9: internal_insertions = 3: open_internal_insertions = 1, extend_internal_insertions = 2; internal_deletions = 6: open_internal_deletions = 1, extend_internal_deletions = 5; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 3) self.assertEqual(counts.internal_deletions, 6) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 9) self.assertEqual(counts.insertions, 3) self.assertEqual(counts.deletions, 6) self.assertEqual(counts.gaps, 9) self.assertEqual(counts.aligned, 45) alignment = next(alignments) 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) self.assertEqual( str(alignment), """\ chr1 1207056 ?????????????????????????????????????????????????? 1207106 0 |||||||||||||||||||||||||||||||||||||||||||||||||| 50 hg19_dna 0 ?????????????????????????????????????????????????? 50 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[1207056, 1207106], [ 0, 50]]), # fmt: on ) ) self.assertEqual( format(alignment, "chain"), """\ chain 50 chr1 249250621 + 1207056 1207106 hg19_dna 50 + 0 50 12 50 """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 50: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 50) alignment = next(alignments) 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) self.assertEqual( str(alignment), """\ chr1 61700837 ?????????????????????????????????? 61700871 0 |||||||||||||||||||||||||||||||||| 34 hg19_dna 1 ?????????????????????????????????? 35 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[61700837, 61700871], [ 1, 35]]), # fmt: on ) ) self.assertEqual( format(alignment, "chain"), """\ chain 28 chr1 249250621 + 61700837 61700871 hg19_dna 50 + 1 35 13 34 """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 34: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 34) alignment = next(alignments) 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) self.assertEqual( str(alignment), """\ chr4 37558157 ????????????????----------?????????????????? 37558191 0 ||||||||||----------------|||||||||||||||||| 44 hg19_dna 49 ??????????------???????????????????????????? 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, "chain"), """\ chain 26 chr4 191154276 + 37558157 37558191 hg19_dna 50 - 1 39 14 10 6 10 18 """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 28: identities = 0, mismatches = 0. gaps = 16: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 16: internal_insertions = 10: open_internal_insertions = 1, extend_internal_insertions = 9; internal_deletions = 6: open_internal_deletions = 1, extend_internal_deletions = 5; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 10) self.assertEqual(counts.internal_deletions, 6) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 16) self.assertEqual(counts.insertions, 10) self.assertEqual(counts.deletions, 6) self.assertEqual(counts.gaps, 16) self.assertEqual(counts.aligned, 28) alignment = next(alignments) 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) self.assertEqual( str(alignment), """\ chr22 48997405 ????????????????????????????????????? 48997442 0 ||||||||||||||||||||||||||||||||||||| 37 hg19_dna 49 ????????????????????????????????????? 12 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[48997405, 48997442], [ 49, 12]]), # fmt: on ) ) self.assertEqual( format(alignment, "chain"), """\ chain 33 chr22 51304566 + 48997405 48997442 hg19_dna 50 - 1 38 15 37 """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 37: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 37) alignment = next(alignments) 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) self.assertEqual( str(alignment), """\ chr2 120641740 ???????????????????????????????????? 120641776 0 |||||||||||||||||||||||||||||||||||| 36 hg19_dna 49 ???????????????????????????????????? 13 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[120641740, 120641776], [ 49, 13]]), # fmt: on ) ) self.assertEqual( format(alignment, "chain"), """\ chain 34 chr2 243199373 + 120641740 120641776 hg19_dna 50 - 1 37 16 36 """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 36: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 36) alignment = next(alignments) 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) self.assertEqual( str(alignment), """\ chr19 54017130 ??????????????????????????????????????? 54017169 0 ||||||||||||||||||||||||||||||||||||||| 39 hg19_dna 49 ??????????????????????????????????????? 10 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[54017130, 54017169], [ 49, 10]]), # fmt: on ) ) self.assertEqual( format(alignment, "chain"), """\ chain 39 chr19 59128983 + 54017130 54017169 hg19_dna 50 - 1 40 17 39 """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 39: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 39) alignment = next(alignments) 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) self.assertEqual( str(alignment), """\ chr19 553742 ??????????????????????????????????????? 553781 0 ||||||||||||||||||||||||||||||||||||||| 39 hg19_dna 49 ??????????????????????????????????????? 10 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[553742, 553781], [ 49, 10]]), # fmt: on ) ) self.assertEqual( format(alignment, "chain"), """\ chain 33 chr19 59128983 + 553742 553781 hg19_dna 50 - 1 40 18 39 """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 39: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 39) alignment = next(alignments) 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) self.assertEqual( str(alignment), """\ chr10 99388555 ???????????????????????????????????? 99388591 0 |||||||||||||||||||||||||||||||||||| 36 hg19_dna 49 ???????????????????????????????????? 13 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[99388555, 99388591], [ 49, 13]]), # fmt: on ) ) self.assertEqual( format(alignment, "chain"), """\ chain 30 chr10 135534747 + 99388555 99388591 hg19_dna 50 - 1 37 19 36 """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 36: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 36) alignment = next(alignments) 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) self.assertEqual( str(alignment), """\ chr10 112178171 ????????????????????????? 112178196 0 ||||||||||||||||||||||||| 25 hg19_dna 35 ????????????????????????? 10 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[112178171, 112178196], [ 35, 10]]), # fmt: on ) ) self.assertEqual( format(alignment, "chain"), """\ chain 23 chr10 135534747 + 112178171 112178196 hg19_dna 50 - 15 40 20 25 """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 25: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 25) alignment = next(alignments) 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) self.assertEqual( str(alignment), """\ chr1 39368490 ???????????????????????????????????? 39368526 0 |||||||||||||||||||||||||||||||||||| 36 hg19_dna 49 ???????????????????????????????????? 13 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[39368490, 39368526], [ 49, 13]]), # fmt: on ) ) self.assertEqual( format(alignment, "chain"), """\ chain 34 chr1 249250621 + 39368490 39368526 hg19_dna 50 - 1 37 21 36 """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 36: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 36) alignment = next(alignments) 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) self.assertEqual( str(alignment), """\ chr1 220325687 ?????????????????????????????????? 220325721 0 |||||||||||||||||||||||||||||||||| 34 hg19_dna 47 ?????????????????????????????????? 13 """, ) self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[220325687, 220325721], [ 47, 13]]), # fmt: on ) ) self.assertEqual( format(alignment, "chain"), """\ chain 32 chr1 249250621 + 220325687 220325721 hg19_dna 50 - 3 37 22 34 """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 34: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 34) self.assertRaises(StopIteration, next, alignments) def test_writing_psl_34_005(self): """Test writing the alignments in psl_34_005.chain.""" path = "Blat/psl_34_005.chain" alignments = Align.parse(path, "chain") stream = StringIO() n = Align.write(alignments, stream, "chain") self.assertEqual(n, 22) stream.seek(0) alignments = Align.parse(stream, "chain") self.check_reading_psl_34_005(alignments) 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]] ) score = 8 alignment = Alignment(sequences, coordinates) alignment.score = score chain1 = """\ chain 8 target 15 + 0 15 query 11 - 0 11 0 2 2 1 1 0 2 0 1 3 1 0 0 3 0 2 """ chain2 = """\ chain 8 target 15 - 0 15 query 11 + 0 11 2 3 0 3 1 0 2 0 1 1 1 0 0 2 2 0 """ chain3 = """\ chain 8 target 15 + 0 15 query 11 - 0 11 2 3 0 3 1 0 2 0 1 1 1 0 0 2 2 0 """ chain4 = """\ chain 8 target 15 - 0 15 query 11 + 0 11 0 2 2 1 1 0 2 0 1 3 1 0 0 3 0 2 """ self.assertEqual( str(alignment), """\ target 0 AA--CAGC-AGCGTGTCG 15 0 ----|-||-|||-||--- 18 query 11 --TTC-GCTAGC-TG--- 0 """, ) self.assertEqual(format(alignment, "chain"), chain1) 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, "chain"), chain2) alignment.coordinates = alignment.coordinates[:, ::-1] alignment = alignment.reverse_complement() alignment.score = score self.assertEqual( str(alignment), """\ target 0 CGACACGCT-GCTG--TT 15 0 ---||-|||-||-|---- 18 query 11 ---CA-GCTAGC-GAA-- 0 """, ) self.assertEqual(format(alignment, "chain"), chain3) 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, "chain"), chain4) if __name__ == "__main__": runner = unittest.TextTestRunner(verbosity=2) unittest.main(testRunner=runner)