# 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 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 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 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 """, ) 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 """, ) 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 """, ) 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 """, ) self.assertRaises(StopIteration, next, 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 """, ) 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 """, ) 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 """, ) 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 """, ) 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 """, ) 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 """, ) 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 """, ) 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 """, ) 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 """, ) 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 """, ) 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 """, ) 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 """, ) 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 """, ) 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, """, ) 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 """, ) 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 """, ) 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 """, ) 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 """, ) 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 """, ) 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 """, ) 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 """, ) 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 """, ) 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 """, ) 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 """, ) 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 """, ) 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 """, ) 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 """, ) 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 """, ) 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 """, ) 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 """, ) 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 """, ) 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 """, ) 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 """, ) 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 """, ) 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 """, ) 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 """, ) 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 """, ) 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 """, ) 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 """, ) 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 """, ) 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 """, ) 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 """, ) 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 """, ) 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 """, ) 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 """, ) 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 """, ) 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 """, ) 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 """, ) 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 """, ) 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 """, ) 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 """, ) 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 """, ) 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 """, ) 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 """, ) 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 """, ) 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 """, ) 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 """, ) 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 """, ) 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 """, ) 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 """, ) 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 """, ) 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 """, ) 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 """, ) 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 """, ) 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 """, ) 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 """, ) 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)