# Copyright 2022 by Michiel de Hoon. All rights reserved. # This code is part of the Biopython distribution and governed by its # license. Please see the LICENSE file that should have been included # as part of this package. """Tests for Align.bed module.""" import os import tempfile import unittest from io import StringIO import numpy as np from Bio import Align from Bio import SeqIO from Bio.Align import Alignment from Bio.Seq import Seq from Bio.SeqRecord import SeqRecord class TestAlign_dna_rna(unittest.TestCase): # The BED file dna_rna.bed was generated using this command: # pslToBed dna_rna.psl dna_rna.bed 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 = Seq(data, length=198295559) # hg38 chr3 records = SeqIO.parse("Blat/rna.fa", "fasta") self.rna = {record.id: record.seq for record in records} def check_alignments(self, alignments): alignment = next(alignments) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.shape, (2, 1711)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr3") self.assertEqual(alignment.query.id, "NR_046654.1") self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[42530895, 42530958, 42532020, 42532095, 42532563, 42532606], [ 181, 118, 118, 43, 43, 0]]) # fmt: on ) ) alignment.target.seq = self.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.], ]) ) ) 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, "bed"), """\ chr3 42530895 42532606 NR_046654.1 1000 - 42530895 42532606 0 3 63,75,43, 0,1125,1668, """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 181: identities = 175, mismatches = 6. gaps = 1530: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 1530: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 1530: open_internal_deletions = 2, extend_internal_deletions = 1528; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 1530) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 1530) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 1530) self.assertEqual(counts.gaps, 1530) self.assertEqual(counts.aligned, 181) self.assertEqual(counts.identities, 175) self.assertEqual(counts.mismatches, 6) alignment = next(alignments) self.assertEqual(alignment.score, 978) self.assertEqual(alignment.shape, (2, 1711)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) 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.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[42530895, 42530922, 42530958, 42532020, 42532037, 42532039, 42532095, 42532563, 42532606], [ 179, 152, 116, 116, 99, 99, 43, 43, 0]]) # fmt: on ) ) self.assertEqual( str(alignment), """\ chr3 42530895 ???????????????????????????????????????????????????????????? 0 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| NR_046654 179 ???????????????????????????????????????????????????????????? chr3 42530955 ???????????????????????????????????????????????????????????? 60 |||--------------------------------------------------------- NR_046654 119 ???--------------------------------------------------------- chr3 42531015 ???????????????????????????????????????????????????????????? 120 ------------------------------------------------------------ NR_046654 116 ------------------------------------------------------------ chr3 42531075 ???????????????????????????????????????????????????????????? 180 ------------------------------------------------------------ NR_046654 116 ------------------------------------------------------------ chr3 42531135 ???????????????????????????????????????????????????????????? 240 ------------------------------------------------------------ NR_046654 116 ------------------------------------------------------------ chr3 42531195 ???????????????????????????????????????????????????????????? 300 ------------------------------------------------------------ NR_046654 116 ------------------------------------------------------------ chr3 42531255 ???????????????????????????????????????????????????????????? 360 ------------------------------------------------------------ NR_046654 116 ------------------------------------------------------------ chr3 42531315 ???????????????????????????????????????????????????????????? 420 ------------------------------------------------------------ NR_046654 116 ------------------------------------------------------------ chr3 42531375 ???????????????????????????????????????????????????????????? 480 ------------------------------------------------------------ NR_046654 116 ------------------------------------------------------------ chr3 42531435 ???????????????????????????????????????????????????????????? 540 ------------------------------------------------------------ NR_046654 116 ------------------------------------------------------------ chr3 42531495 ???????????????????????????????????????????????????????????? 600 ------------------------------------------------------------ NR_046654 116 ------------------------------------------------------------ chr3 42531555 ???????????????????????????????????????????????????????????? 660 ------------------------------------------------------------ NR_046654 116 ------------------------------------------------------------ chr3 42531615 ???????????????????????????????????????????????????????????? 720 ------------------------------------------------------------ NR_046654 116 ------------------------------------------------------------ chr3 42531675 ???????????????????????????????????????????????????????????? 780 ------------------------------------------------------------ NR_046654 116 ------------------------------------------------------------ chr3 42531735 ???????????????????????????????????????????????????????????? 840 ------------------------------------------------------------ NR_046654 116 ------------------------------------------------------------ chr3 42531795 ???????????????????????????????????????????????????????????? 900 ------------------------------------------------------------ NR_046654 116 ------------------------------------------------------------ chr3 42531855 ???????????????????????????????????????????????????????????? 960 ------------------------------------------------------------ NR_046654 116 ------------------------------------------------------------ chr3 42531915 ???????????????????????????????????????????????????????????? 1020 ------------------------------------------------------------ NR_046654 116 ------------------------------------------------------------ chr3 42531975 ???????????????????????????????????????????????????????????? 1080 ---------------------------------------------||||||||||||||| NR_046654 116 ---------------------------------------------??????????????? chr3 42532035 ???????????????????????????????????????????????????????????? 1140 ||--|||||||||||||||||||||||||||||||||||||||||||||||||||||||| NR_046654 101 ??--???????????????????????????????????????????????????????? chr3 42532095 ???????????????????????????????????????????????????????????? 1200 ------------------------------------------------------------ NR_046654 43 ------------------------------------------------------------ chr3 42532155 ???????????????????????????????????????????????????????????? 1260 ------------------------------------------------------------ NR_046654 43 ------------------------------------------------------------ chr3 42532215 ???????????????????????????????????????????????????????????? 1320 ------------------------------------------------------------ NR_046654 43 ------------------------------------------------------------ chr3 42532275 ???????????????????????????????????????????????????????????? 1380 ------------------------------------------------------------ NR_046654 43 ------------------------------------------------------------ chr3 42532335 ???????????????????????????????????????????????????????????? 1440 ------------------------------------------------------------ NR_046654 43 ------------------------------------------------------------ chr3 42532395 ???????????????????????????????????????????????????????????? 1500 ------------------------------------------------------------ NR_046654 43 ------------------------------------------------------------ chr3 42532455 ???????????????????????????????????????????????????????????? 1560 ------------------------------------------------------------ NR_046654 43 ------------------------------------------------------------ chr3 42532515 ???????????????????????????????????????????????????????????? 1620 ------------------------------------------------|||||||||||| NR_046654 43 ------------------------------------------------???????????? chr3 42532575 ??????????????????????????????? 42532606 1680 ||||||||||||||||||||||||||||||| 1711 NR_046654 31 ??????????????????????????????? 0 """, ) self.assertEqual( format(alignment, "bed"), """\ chr3 42530895 42532606 NR_046654.1_modified 978 - 42530895 42532606 0 5 27,36,17,56,43, 0,27,1125,1144,1668, """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 179: identities = 0, mismatches = 0. gaps = 1532: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 1532: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 1532: open_internal_deletions = 3, extend_internal_deletions = 1529; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 1532) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 1532) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 1532) self.assertEqual(counts.gaps, 1532) self.assertEqual(counts.aligned, 179) alignment = next(alignments) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.shape, (2, 5407)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) 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.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[48663767, 48663813, 48665640, 48665722, 48669098, 48669174], [ 0, 46, 46, 128, 128, 204]]) # fmt: on ) ) alignment.target.seq = self.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.], ]) ) ) 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, "bed"), """\ chr3 48663767 48669174 NR_111921.1 1000 + 48663767 48669174 0 3 46,82,76, 0,1873,5331, """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 204: identities = 165, mismatches = 39. gaps = 5203: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 5203: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 5203: open_internal_deletions = 2, extend_internal_deletions = 5201; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 5203) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 5203) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 5203) self.assertEqual(counts.gaps, 5203) self.assertEqual(counts.aligned, 204) self.assertEqual(counts.identities, 165) self.assertEqual(counts.mismatches, 39) alignment = next(alignments) self.assertEqual(alignment.score, 972) self.assertEqual(alignment.shape, (2, 5407)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) 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.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[48663767, 48663795, 48663796, 48663813, 48665640, 48665716, 48665722, 48669098, 48669174], [ 0, 28, 28, 45, 45, 121, 127, 127, 203]]) # fmt: on ) ) # The modified RNAs have gaps in their sequence. As this information is # not stored in a BED file, we cannot calculate the substitution matrix. self.assertEqual( str(alignment), """\ chr3 48663767 ???????????????????????????????????????????????????????????? 0 ||||||||||||||||||||||||||||-|||||||||||||||||-------------- NR_111921 0 ????????????????????????????-?????????????????-------------- chr3 48663827 ???????????????????????????????????????????????????????????? 60 ------------------------------------------------------------ NR_111921 45 ------------------------------------------------------------ chr3 48663887 ???????????????????????????????????????????????????????????? 120 ------------------------------------------------------------ NR_111921 45 ------------------------------------------------------------ chr3 48663947 ???????????????????????????????????????????????????????????? 180 ------------------------------------------------------------ NR_111921 45 ------------------------------------------------------------ chr3 48664007 ???????????????????????????????????????????????????????????? 240 ------------------------------------------------------------ NR_111921 45 ------------------------------------------------------------ chr3 48664067 ???????????????????????????????????????????????????????????? 300 ------------------------------------------------------------ NR_111921 45 ------------------------------------------------------------ chr3 48664127 ???????????????????????????????????????????????????????????? 360 ------------------------------------------------------------ NR_111921 45 ------------------------------------------------------------ chr3 48664187 ???????????????????????????????????????????????????????????? 420 ------------------------------------------------------------ NR_111921 45 ------------------------------------------------------------ chr3 48664247 ???????????????????????????????????????????????????????????? 480 ------------------------------------------------------------ NR_111921 45 ------------------------------------------------------------ chr3 48664307 ???????????????????????????????????????????????????????????? 540 ------------------------------------------------------------ NR_111921 45 ------------------------------------------------------------ chr3 48664367 ???????????????????????????????????????????????????????????? 600 ------------------------------------------------------------ NR_111921 45 ------------------------------------------------------------ chr3 48664427 ???????????????????????????????????????????????????????????? 660 ------------------------------------------------------------ NR_111921 45 ------------------------------------------------------------ chr3 48664487 ???????????????????????????????????????????????????????????? 720 ------------------------------------------------------------ NR_111921 45 ------------------------------------------------------------ chr3 48664547 ???????????????????????????????????????????????????????????? 780 ------------------------------------------------------------ NR_111921 45 ------------------------------------------------------------ chr3 48664607 ???????????????????????????????????????????????????????????? 840 ------------------------------------------------------------ NR_111921 45 ------------------------------------------------------------ chr3 48664667 ???????????????????????????????????????????????????????????? 900 ------------------------------------------------------------ NR_111921 45 ------------------------------------------------------------ chr3 48664727 ???????????????????????????????????????????????????????????? 960 ------------------------------------------------------------ NR_111921 45 ------------------------------------------------------------ chr3 48664787 ???????????????????????????????????????????????????????????? 1020 ------------------------------------------------------------ NR_111921 45 ------------------------------------------------------------ chr3 48664847 ???????????????????????????????????????????????????????????? 1080 ------------------------------------------------------------ NR_111921 45 ------------------------------------------------------------ chr3 48664907 ???????????????????????????????????????????????????????????? 1140 ------------------------------------------------------------ NR_111921 45 ------------------------------------------------------------ chr3 48664967 ???????????????????????????????????????????????????????????? 1200 ------------------------------------------------------------ NR_111921 45 ------------------------------------------------------------ chr3 48665027 ???????????????????????????????????????????????????????????? 1260 ------------------------------------------------------------ NR_111921 45 ------------------------------------------------------------ chr3 48665087 ???????????????????????????????????????????????????????????? 1320 ------------------------------------------------------------ NR_111921 45 ------------------------------------------------------------ chr3 48665147 ???????????????????????????????????????????????????????????? 1380 ------------------------------------------------------------ NR_111921 45 ------------------------------------------------------------ chr3 48665207 ???????????????????????????????????????????????????????????? 1440 ------------------------------------------------------------ NR_111921 45 ------------------------------------------------------------ chr3 48665267 ???????????????????????????????????????????????????????????? 1500 ------------------------------------------------------------ NR_111921 45 ------------------------------------------------------------ chr3 48665327 ???????????????????????????????????????????????????????????? 1560 ------------------------------------------------------------ NR_111921 45 ------------------------------------------------------------ chr3 48665387 ???????????????????????????????????????????????????????????? 1620 ------------------------------------------------------------ NR_111921 45 ------------------------------------------------------------ chr3 48665447 ???????????????????????????????????????????????????????????? 1680 ------------------------------------------------------------ NR_111921 45 ------------------------------------------------------------ chr3 48665507 ???????????????????????????????????????????????????????????? 1740 ------------------------------------------------------------ NR_111921 45 ------------------------------------------------------------ chr3 48665567 ???????????????????????????????????????????????????????????? 1800 ------------------------------------------------------------ NR_111921 45 ------------------------------------------------------------ chr3 48665627 ???????????????????????????????????????????????????????????? 1860 -------------||||||||||||||||||||||||||||||||||||||||||||||| NR_111921 45 -------------??????????????????????????????????????????????? chr3 48665687 ???????????????????????????????????????????????????????????? 1920 |||||||||||||||||||||||||||||||||||------------------------- NR_111921 92 ???????????????????????????????????------------------------- chr3 48665747 ???????????????????????????????????????????????????????????? 1980 ------------------------------------------------------------ NR_111921 127 ------------------------------------------------------------ chr3 48665807 ???????????????????????????????????????????????????????????? 2040 ------------------------------------------------------------ NR_111921 127 ------------------------------------------------------------ chr3 48665867 ???????????????????????????????????????????????????????????? 2100 ------------------------------------------------------------ NR_111921 127 ------------------------------------------------------------ chr3 48665927 ???????????????????????????????????????????????????????????? 2160 ------------------------------------------------------------ NR_111921 127 ------------------------------------------------------------ chr3 48665987 ???????????????????????????????????????????????????????????? 2220 ------------------------------------------------------------ NR_111921 127 ------------------------------------------------------------ chr3 48666047 ???????????????????????????????????????????????????????????? 2280 ------------------------------------------------------------ NR_111921 127 ------------------------------------------------------------ chr3 48666107 ???????????????????????????????????????????????????????????? 2340 ------------------------------------------------------------ NR_111921 127 ------------------------------------------------------------ chr3 48666167 ???????????????????????????????????????????????????????????? 2400 ------------------------------------------------------------ NR_111921 127 ------------------------------------------------------------ chr3 48666227 ???????????????????????????????????????????????????????????? 2460 ------------------------------------------------------------ NR_111921 127 ------------------------------------------------------------ chr3 48666287 ???????????????????????????????????????????????????????????? 2520 ------------------------------------------------------------ NR_111921 127 ------------------------------------------------------------ chr3 48666347 ???????????????????????????????????????????????????????????? 2580 ------------------------------------------------------------ NR_111921 127 ------------------------------------------------------------ chr3 48666407 ???????????????????????????????????????????????????????????? 2640 ------------------------------------------------------------ NR_111921 127 ------------------------------------------------------------ chr3 48666467 ???????????????????????????????????????????????????????????? 2700 ------------------------------------------------------------ NR_111921 127 ------------------------------------------------------------ chr3 48666527 ???????????????????????????????????????????????????????????? 2760 ------------------------------------------------------------ NR_111921 127 ------------------------------------------------------------ chr3 48666587 ???????????????????????????????????????????????????????????? 2820 ------------------------------------------------------------ NR_111921 127 ------------------------------------------------------------ chr3 48666647 ???????????????????????????????????????????????????????????? 2880 ------------------------------------------------------------ NR_111921 127 ------------------------------------------------------------ chr3 48666707 ???????????????????????????????????????????????????????????? 2940 ------------------------------------------------------------ NR_111921 127 ------------------------------------------------------------ chr3 48666767 ???????????????????????????????????????????????????????????? 3000 ------------------------------------------------------------ NR_111921 127 ------------------------------------------------------------ chr3 48666827 ???????????????????????????????????????????????????????????? 3060 ------------------------------------------------------------ NR_111921 127 ------------------------------------------------------------ chr3 48666887 ???????????????????????????????????????????????????????????? 3120 ------------------------------------------------------------ NR_111921 127 ------------------------------------------------------------ chr3 48666947 ???????????????????????????????????????????????????????????? 3180 ------------------------------------------------------------ NR_111921 127 ------------------------------------------------------------ chr3 48667007 ???????????????????????????????????????????????????????????? 3240 ------------------------------------------------------------ NR_111921 127 ------------------------------------------------------------ chr3 48667067 ???????????????????????????????????????????????????????????? 3300 ------------------------------------------------------------ NR_111921 127 ------------------------------------------------------------ chr3 48667127 ???????????????????????????????????????????????????????????? 3360 ------------------------------------------------------------ NR_111921 127 ------------------------------------------------------------ chr3 48667187 ???????????????????????????????????????????????????????????? 3420 ------------------------------------------------------------ NR_111921 127 ------------------------------------------------------------ chr3 48667247 ???????????????????????????????????????????????????????????? 3480 ------------------------------------------------------------ NR_111921 127 ------------------------------------------------------------ chr3 48667307 ???????????????????????????????????????????????????????????? 3540 ------------------------------------------------------------ NR_111921 127 ------------------------------------------------------------ chr3 48667367 ???????????????????????????????????????????????????????????? 3600 ------------------------------------------------------------ NR_111921 127 ------------------------------------------------------------ chr3 48667427 ???????????????????????????????????????????????????????????? 3660 ------------------------------------------------------------ NR_111921 127 ------------------------------------------------------------ chr3 48667487 ???????????????????????????????????????????????????????????? 3720 ------------------------------------------------------------ NR_111921 127 ------------------------------------------------------------ chr3 48667547 ???????????????????????????????????????????????????????????? 3780 ------------------------------------------------------------ NR_111921 127 ------------------------------------------------------------ chr3 48667607 ???????????????????????????????????????????????????????????? 3840 ------------------------------------------------------------ NR_111921 127 ------------------------------------------------------------ chr3 48667667 ???????????????????????????????????????????????????????????? 3900 ------------------------------------------------------------ NR_111921 127 ------------------------------------------------------------ chr3 48667727 ???????????????????????????????????????????????????????????? 3960 ------------------------------------------------------------ NR_111921 127 ------------------------------------------------------------ chr3 48667787 ???????????????????????????????????????????????????????????? 4020 ------------------------------------------------------------ NR_111921 127 ------------------------------------------------------------ chr3 48667847 ???????????????????????????????????????????????????????????? 4080 ------------------------------------------------------------ NR_111921 127 ------------------------------------------------------------ chr3 48667907 ???????????????????????????????????????????????????????????? 4140 ------------------------------------------------------------ NR_111921 127 ------------------------------------------------------------ chr3 48667967 ???????????????????????????????????????????????????????????? 4200 ------------------------------------------------------------ NR_111921 127 ------------------------------------------------------------ chr3 48668027 ???????????????????????????????????????????????????????????? 4260 ------------------------------------------------------------ NR_111921 127 ------------------------------------------------------------ chr3 48668087 ???????????????????????????????????????????????????????????? 4320 ------------------------------------------------------------ NR_111921 127 ------------------------------------------------------------ chr3 48668147 ???????????????????????????????????????????????????????????? 4380 ------------------------------------------------------------ NR_111921 127 ------------------------------------------------------------ chr3 48668207 ???????????????????????????????????????????????????????????? 4440 ------------------------------------------------------------ NR_111921 127 ------------------------------------------------------------ chr3 48668267 ???????????????????????????????????????????????????????????? 4500 ------------------------------------------------------------ NR_111921 127 ------------------------------------------------------------ chr3 48668327 ???????????????????????????????????????????????????????????? 4560 ------------------------------------------------------------ NR_111921 127 ------------------------------------------------------------ chr3 48668387 ???????????????????????????????????????????????????????????? 4620 ------------------------------------------------------------ NR_111921 127 ------------------------------------------------------------ chr3 48668447 ???????????????????????????????????????????????????????????? 4680 ------------------------------------------------------------ NR_111921 127 ------------------------------------------------------------ chr3 48668507 ???????????????????????????????????????????????????????????? 4740 ------------------------------------------------------------ NR_111921 127 ------------------------------------------------------------ chr3 48668567 ???????????????????????????????????????????????????????????? 4800 ------------------------------------------------------------ NR_111921 127 ------------------------------------------------------------ chr3 48668627 ???????????????????????????????????????????????????????????? 4860 ------------------------------------------------------------ NR_111921 127 ------------------------------------------------------------ chr3 48668687 ???????????????????????????????????????????????????????????? 4920 ------------------------------------------------------------ NR_111921 127 ------------------------------------------------------------ chr3 48668747 ???????????????????????????????????????????????????????????? 4980 ------------------------------------------------------------ NR_111921 127 ------------------------------------------------------------ chr3 48668807 ???????????????????????????????????????????????????????????? 5040 ------------------------------------------------------------ NR_111921 127 ------------------------------------------------------------ chr3 48668867 ???????????????????????????????????????????????????????????? 5100 ------------------------------------------------------------ NR_111921 127 ------------------------------------------------------------ chr3 48668927 ???????????????????????????????????????????????????????????? 5160 ------------------------------------------------------------ NR_111921 127 ------------------------------------------------------------ chr3 48668987 ???????????????????????????????????????????????????????????? 5220 ------------------------------------------------------------ NR_111921 127 ------------------------------------------------------------ chr3 48669047 ???????????????????????????????????????????????????????????? 5280 ---------------------------------------------------||||||||| NR_111921 127 ---------------------------------------------------????????? chr3 48669107 ???????????????????????????????????????????????????????????? 5340 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| NR_111921 136 ???????????????????????????????????????????????????????????? chr3 48669167 ??????? 48669174 5400 ||||||| 5407 NR_111921 196 ??????? 203 """, ) self.assertEqual( format(alignment, "bed"), """\ chr3 48663767 48669174 NR_111921.1_modified 972 + 48663767 48669174 0 5 28,17,76,6,76, 0,29,1873,1949,5331, """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 203: identities = 0, mismatches = 0. gaps = 5204: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 5204: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 5204: open_internal_deletions = 3, extend_internal_deletions = 5201; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 5204) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 5204) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 5204) self.assertEqual(counts.gaps, 5204) self.assertEqual(counts.aligned, 203) self.assertRaises(StopIteration, next, alignments) def test_reading(self): """Test parsing dna_rna.bed.""" path = "Blat/dna_rna.bed" alignments = Align.parse(path, "bed") self.check_alignments(alignments) alignments = iter(alignments) self.check_alignments(alignments) with Align.parse(path, "bed") as alignments: self.check_alignments(alignments) with self.assertRaises(AttributeError): alignments._stream with Align.parse(path, "bed") as alignments: pass with self.assertRaises(AttributeError): alignments._stream def test_writing(self): """Test writing the alignments in dna_rna.bed.""" path = "Blat/dna_rna.bed" with open(path) as stream: original_data = stream.read() alignments = Align.parse(path, "bed") stream = StringIO() n = Align.write(alignments, stream, "bed") self.assertEqual(n, 4) stream.seek(0) written_data = stream.read() stream.close() self.assertEqual(original_data, written_data) class TestAlign_dna(unittest.TestCase): def test_reading_psl_34_001(self): """Test parsing psl_34_001.bed.""" path = "Blat/psl_34_001.bed" alignments = Align.parse(path, "bed") alignment = next(alignments) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.shape, (2, 16)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) 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.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[61646095, 61646111], [ 0, 16]]), # fmt: on ) ) self.assertEqual( str(alignment), """\ chr4 61646095 ???????????????? 61646111 0 |||||||||||||||| 16 hg19_dna 0 ???????????????? 16 """, ) self.assertEqual( format(alignment, "bed"), """\ chr4 61646095 61646111 hg19_dna 1000 + 61646095 61646111 0 1 16, 0, """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 16: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 16) alignment = next(alignments) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.shape, (2, 33)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) 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.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[10271783, 10271816], [ 0, 33]]), # fmt: on ) ) self.assertEqual( str(alignment), """\ chr1 10271783 ????????????????????????????????? 10271816 0 ||||||||||||||||||||||||||||||||| 33 hg19_dna 0 ????????????????????????????????? 33 """, ) self.assertEqual( format(alignment, "bed"), """\ chr1 10271783 10271816 hg19_dna 1000 + 10271783 10271816 0 1 33, 0, """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 33: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 33) alignment = next(alignments) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.shape, (2, 17)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) 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.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[53575980, 53575997], [ 17, 0]]), # fmt: on ) ) self.assertEqual( str(alignment), """\ chr2 53575980 ????????????????? 53575997 0 ||||||||||||||||| 17 hg19_dna 17 ????????????????? 0 """, ) self.assertEqual( format(alignment, "bed"), """\ chr2 53575980 53575997 hg19_dna 1000 - 53575980 53575997 0 1 17, 0, """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 17: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 17) alignment = next(alignments) self.assertEqual(alignment.score, 854) self.assertEqual(alignment.shape, (2, 41)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) 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.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[85737865, 85737906], [ 0, 41]]), # fmt: on ) ) self.assertEqual( str(alignment), """\ chr9 85737865 ????????????????????????????????????????? 85737906 0 ||||||||||||||||||||||||||||||||||||||||| 41 hg19_dna 0 ????????????????????????????????????????? 41 """, ) self.assertEqual( format(alignment, "bed"), """\ chr9 85737865 85737906 hg19_dna 854 + 85737865 85737906 0 1 41, 0, """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 41: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 41) alignment = next(alignments) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.shape, (2, 41)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) 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.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[95160479, 95160520], [ 0, 41]]), # fmt: on ) ) self.assertEqual( str(alignment), """\ chr8 95160479 ????????????????????????????????????????? 95160520 0 ||||||||||||||||||||||||||||||||||||||||| 41 hg19_dna 0 ????????????????????????????????????????? 41 """, ) self.assertEqual( format(alignment, "bed"), """\ chr8 95160479 95160520 hg19_dna 1000 + 95160479 95160520 0 1 41, 0, """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 41: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 41) alignment = next(alignments) self.assertEqual(alignment.score, 834) self.assertEqual(alignment.shape, (2, 36)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) 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.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[42144400, 42144436], [ 0, 36]]), # fmt: on ) ) self.assertEqual( str(alignment), """\ chr22 42144400 ???????????????????????????????????? 42144436 0 |||||||||||||||||||||||||||||||||||| 36 hg19_dna 0 ???????????????????????????????????? 36 """, ) self.assertEqual( format(alignment, "bed"), """\ chr22 42144400 42144436 hg19_dna 834 + 42144400 42144436 0 1 36, 0, """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 36: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 36) alignment = next(alignments) self.assertEqual(alignment.score, 682) self.assertEqual(alignment.shape, (2, 44)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) 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.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[183925984, 183925990, 183926028], [ 0, 6, 44]]), # fmt: on ) ) self.assertEqual( str(alignment), """\ chr2 183925984 ???????????????????????????????????????????? 183926028 0 |||||||||||||||||||||||||||||||||||||||||||| 44 hg19_dna 0 ???????????????????????????????????????????? 44 """, ) self.assertEqual( format(alignment, "bed"), """\ chr2 183925984 183926028 hg19_dna 682 + 183925984 183926028 0 2 6,38, 0,6, """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 44: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 44) alignment = next(alignments) self.assertEqual(alignment.score, 890) self.assertEqual(alignment.shape, (2, 170)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) 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.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[35483340, 35483365, 35483499, 35483510], [ 0, 25, 25, 36]]), # fmt: on ) ) self.assertEqual( str(alignment), """\ chr19 35483340 ???????????????????????????????????????????????????????????? 0 |||||||||||||||||||||||||----------------------------------- hg19_dna 0 ?????????????????????????----------------------------------- chr19 35483400 ???????????????????????????????????????????????????????????? 60 ------------------------------------------------------------ hg19_dna 25 ------------------------------------------------------------ chr19 35483460 ?????????????????????????????????????????????????? 35483510 120 ---------------------------------------||||||||||| 170 hg19_dna 25 ---------------------------------------??????????? 36 """, ) self.assertEqual( format(alignment, "bed"), """\ chr19 35483340 35483510 hg19_dna 890 + 35483340 35483510 0 2 25,11, 0,159, """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 36: identities = 0, mismatches = 0. gaps = 134: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 134: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 134: open_internal_deletions = 1, extend_internal_deletions = 133; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 134) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 134) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 134) self.assertEqual(counts.gaps, 134) self.assertEqual(counts.aligned, 36) alignment = next(alignments) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.shape, (2, 39)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) 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.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[23891310, 23891349], [ 0, 39]]), # fmt: on ) ) self.assertEqual( str(alignment), """\ chr18 23891310 ??????????????????????????????????????? 23891349 0 ||||||||||||||||||||||||||||||||||||||| 39 hg19_dna 0 ??????????????????????????????????????? 39 """, ) self.assertEqual( format(alignment, "bed"), """\ chr18 23891310 23891349 hg19_dna 1000 + 23891310 23891349 0 1 39, 0, """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 39: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 39) alignment = next(alignments) self.assertEqual(alignment.score, 930) self.assertEqual(alignment.shape, (2, 28)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) 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.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[43252217, 43252245], [ 0, 28]]), # fmt: on ) ) self.assertEqual( str(alignment), """\ chr18 43252217 ???????????????????????????? 43252245 0 |||||||||||||||||||||||||||| 28 hg19_dna 0 ???????????????????????????? 28 """, ) self.assertEqual( format(alignment, "bed"), """\ chr18 43252217 43252245 hg19_dna 930 + 43252217 43252245 0 1 28, 0, """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 28: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 28) alignment = next(alignments) self.assertEqual(alignment.score, 912) self.assertEqual(alignment.shape, (2, 51)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) 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.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[52759147, 52759154, 52759160, 52759198], [ 0, 7, 7, 45]]), # fmt: on ) ) self.assertEqual( str(alignment), """\ chr13 52759147 ??????????????????????????????????????????????????? 52759198 0 |||||||------|||||||||||||||||||||||||||||||||||||| 51 hg19_dna 0 ???????------?????????????????????????????????????? 45 """, ) self.assertEqual( format(alignment, "bed"), """\ chr13 52759147 52759198 hg19_dna 912 + 52759147 52759198 0 2 7,38, 0,13, """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 45: identities = 0, mismatches = 0. gaps = 6: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 6: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 6: open_internal_deletions = 1, extend_internal_deletions = 5; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 6) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 6) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 6) self.assertEqual(counts.gaps, 6) self.assertEqual(counts.aligned, 45) alignment = next(alignments) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.shape, (2, 50)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) 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.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[1207056, 1207106], [ 0, 50]]), # fmt: on ) ) self.assertEqual( str(alignment), """\ chr1 1207056 ?????????????????????????????????????????????????? 1207106 0 |||||||||||||||||||||||||||||||||||||||||||||||||| 50 hg19_dna 0 ?????????????????????????????????????????????????? 50 """, ) self.assertEqual( format(alignment, "bed"), """\ chr1 1207056 1207106 hg19_dna 1000 + 1207056 1207106 0 1 50, 0, """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 50: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 50) alignment = next(alignments) self.assertEqual(alignment.score, 824) self.assertEqual(alignment.shape, (2, 34)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) 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.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[61700837, 61700871], [ 0, 34]]), # fmt: on ) ) self.assertEqual( str(alignment), """\ chr1 61700837 ?????????????????????????????????? 61700871 0 |||||||||||||||||||||||||||||||||| 34 hg19_dna 0 ?????????????????????????????????? 34 """, ) self.assertEqual( format(alignment, "bed"), """\ chr1 61700837 61700871 hg19_dna 824 + 61700837 61700871 0 1 34, 0, """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 34: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 34) alignment = next(alignments) self.assertEqual(alignment.score, 572) self.assertEqual(alignment.shape, (2, 34)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) 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.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[37558157, 37558167, 37558173, 37558191], [ 28, 18, 18, 0]]), # fmt: on ) ) self.assertEqual( str(alignment), """\ chr4 37558157 ?????????????????????????????????? 37558191 0 ||||||||||------|||||||||||||||||| 34 hg19_dna 28 ??????????------?????????????????? 0 """, ) self.assertEqual( format(alignment, "bed"), """\ chr4 37558157 37558191 hg19_dna 572 - 37558157 37558191 0 2 10,18, 0,16, """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 28: identities = 0, mismatches = 0. gaps = 6: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 6: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 6: open_internal_deletions = 1, extend_internal_deletions = 5; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 6) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 6) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 6) self.assertEqual(counts.gaps, 6) self.assertEqual(counts.aligned, 28) alignment = next(alignments) self.assertEqual(alignment.score, 892) self.assertEqual(alignment.shape, (2, 37)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) 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.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[48997405, 48997442], [ 37, 0]]), # fmt: on ) ) self.assertEqual( str(alignment), """\ chr22 48997405 ????????????????????????????????????? 48997442 0 ||||||||||||||||||||||||||||||||||||| 37 hg19_dna 37 ????????????????????????????????????? 0 """, ) self.assertEqual( format(alignment, "bed"), """\ chr22 48997405 48997442 hg19_dna 892 - 48997405 48997442 0 1 37, 0, """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 37: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 37) alignment = next(alignments) self.assertEqual(alignment.score, 946) self.assertEqual(alignment.shape, (2, 36)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) 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.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[120641740, 120641776], [ 36, 0]]), # fmt: on ) ) self.assertEqual( str(alignment), """\ chr2 120641740 ???????????????????????????????????? 120641776 0 |||||||||||||||||||||||||||||||||||| 36 hg19_dna 36 ???????????????????????????????????? 0 """, ) self.assertEqual( format(alignment, "bed"), """\ chr2 120641740 120641776 hg19_dna 946 - 120641740 120641776 0 1 36, 0, """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 36: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 36) alignment = next(alignments) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.shape, (2, 39)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) 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.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[54017130, 54017169], [ 39, 0]]), # fmt: on ) ) self.assertEqual( str(alignment), """\ chr19 54017130 ??????????????????????????????????????? 54017169 0 ||||||||||||||||||||||||||||||||||||||| 39 hg19_dna 39 ??????????????????????????????????????? 0 """, ) self.assertEqual( format(alignment, "bed"), """\ chr19 54017130 54017169 hg19_dna 1000 - 54017130 54017169 0 1 39, 0, """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 39: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 39) alignment = next(alignments) self.assertEqual(alignment.score, 848) self.assertEqual(alignment.shape, (2, 39)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) 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.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[553742, 553781], [ 39, 0]]), # fmt: on ) ) self.assertEqual( str(alignment), """\ chr19 553742 ??????????????????????????????????????? 553781 0 ||||||||||||||||||||||||||||||||||||||| 39 hg19_dna 39 ??????????????????????????????????????? 0 """, ) self.assertEqual( format(alignment, "bed"), """\ chr19 553742 553781 hg19_dna 848 - 553742 553781 0 1 39, 0, """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 39: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 39) alignment = next(alignments) self.assertEqual(alignment.score, 834) self.assertEqual(alignment.shape, (2, 36)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) 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.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[99388555, 99388591], [ 36, 0]]), # fmt: on ) ) self.assertEqual( str(alignment), """\ chr10 99388555 ???????????????????????????????????? 99388591 0 |||||||||||||||||||||||||||||||||||| 36 hg19_dna 36 ???????????????????????????????????? 0 """, ) self.assertEqual( format(alignment, "bed"), """\ chr10 99388555 99388591 hg19_dna 834 - 99388555 99388591 0 1 36, 0, """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 36: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 36) alignment = next(alignments) self.assertEqual(alignment.score, 920) self.assertEqual(alignment.shape, (2, 25)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) 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.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[112178171, 112178196], [ 25, 0]]), # fmt: on ) ) self.assertEqual( str(alignment), """\ chr10 112178171 ????????????????????????? 112178196 0 ||||||||||||||||||||||||| 25 hg19_dna 25 ????????????????????????? 0 """, ) self.assertEqual( format(alignment, "bed"), """\ chr10 112178171 112178196 hg19_dna 920 - 112178171 112178196 0 1 25, 0, """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 25: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 25) alignment = next(alignments) self.assertEqual(alignment.score, 946) self.assertEqual(alignment.shape, (2, 36)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) 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.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[39368490, 39368526], [ 36, 0]]), # fmt: on ) ) self.assertEqual( str(alignment), """\ chr1 39368490 ???????????????????????????????????? 39368526 0 |||||||||||||||||||||||||||||||||||| 36 hg19_dna 36 ???????????????????????????????????? 0 """, ) self.assertEqual( format(alignment, "bed"), """\ chr1 39368490 39368526 hg19_dna 946 - 39368490 39368526 0 1 36, 0, """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 36: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 36) alignment = next(alignments) self.assertEqual(alignment.score, 942) self.assertEqual(alignment.shape, (2, 34)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) 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.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[220325687, 220325721], [ 34, 0]]), # fmt: on ) ) self.assertEqual( str(alignment), """\ chr1 220325687 ?????????????????????????????????? 220325721 0 |||||||||||||||||||||||||||||||||| 34 hg19_dna 34 ?????????????????????????????????? 0 """, ) self.assertEqual( format(alignment, "bed"), """\ chr1 220325687 220325721 hg19_dna 942 - 220325687 220325721 0 1 34, 0, """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 34: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 34) self.assertRaises(StopIteration, next, alignments) def test_writing_psl_34_001(self): """Test writing the alignments in psl_34_001.bed.""" path = "Blat/psl_34_001.bed" with open(path) as stream: original_data = stream.read() alignments = Align.parse(path, "bed") stream = StringIO() n = Align.write(alignments, stream, "bed") self.assertEqual(n, 22) stream.seek(0) written_data = stream.read() stream.close() self.assertEqual(original_data, written_data) def test_reading_psl_34_003(self): """Test parsing psl_34_003.bed.""" path = "Blat/psl_34_003.bed" alignments = Align.parse(path, "bed") alignment = next(alignments) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.shape, (2, 16)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) 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.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[61646095, 61646111], [ 0, 16]]), # fmt: on ) ) self.assertEqual( str(alignment), """\ chr4 61646095 ???????????????? 61646111 0 |||||||||||||||| 16 hg18_dna 0 ???????????????? 16 """, ) self.assertEqual( format(alignment, "bed"), """\ chr4 61646095 61646111 hg18_dna 1000 + 61646095 61646111 0 1 16, 0, """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 16: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 16) alignment = next(alignments) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.shape, (2, 33)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) 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.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[10271783, 10271816], [ 0, 33]]), # fmt: on ) ) self.assertEqual( str(alignment), """\ chr1 10271783 ????????????????????????????????? 10271816 0 ||||||||||||||||||||||||||||||||| 33 hg18_dna 0 ????????????????????????????????? 33 """, ) self.assertEqual( format(alignment, "bed"), """\ chr1 10271783 10271816 hg18_dna 1000 + 10271783 10271816 0 1 33, 0, """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 33: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 33) alignment = next(alignments) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.shape, (2, 17)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) 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.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[53575980, 53575997], [ 17, 0]]), # fmt: on ) ) self.assertEqual( str(alignment), """\ chr2 53575980 ????????????????? 53575997 0 ||||||||||||||||| 17 hg18_dna 17 ????????????????? 0 """, ) self.assertEqual( format(alignment, "bed"), """\ chr2 53575980 53575997 hg18_dna 1000 - 53575980 53575997 0 1 17, 0, """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 17: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 17) self.assertRaises(StopIteration, next, alignments) def test_writing_psl_34_003(self): """Test writing the alignments in psl_34_003.bed.""" path = "Blat/psl_34_003.bed" with open(path) as stream: original_data = stream.read() alignments = Align.parse(path, "bed") stream = StringIO() n = Align.write(alignments, stream, "bed") self.assertEqual(n, 3) stream.seek(0) written_data = stream.read() stream.close() self.assertEqual(original_data, written_data) def test_reading_psl_34_004(self): """Test parsing psl_34_004.bed.""" path = "Blat/psl_34_004.bed" alignments = Align.parse(path, "bed") alignment = next(alignments) self.assertEqual(alignment.score, 854) self.assertEqual(alignment.shape, (2, 41)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) 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.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[85737865, 85737906], [ 0, 41]]), # fmt: on ) ) self.assertEqual( str(alignment), """\ chr9 85737865 ????????????????????????????????????????? 85737906 0 ||||||||||||||||||||||||||||||||||||||||| 41 hg19_dna 0 ????????????????????????????????????????? 41 """, ) self.assertEqual( format(alignment, "bed"), """\ chr9 85737865 85737906 hg19_dna 854 + 85737865 85737906 0 1 41, 0, """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 41: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 41) alignment = next(alignments) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.shape, (2, 41)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) 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.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[95160479, 95160520], [ 0, 41]]), # fmt: on ) ) self.assertEqual( str(alignment), """\ chr8 95160479 ????????????????????????????????????????? 95160520 0 ||||||||||||||||||||||||||||||||||||||||| 41 hg19_dna 0 ????????????????????????????????????????? 41 """, ) self.assertEqual( format(alignment, "bed"), """\ chr8 95160479 95160520 hg19_dna 1000 + 95160479 95160520 0 1 41, 0, """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 41: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 41) alignment = next(alignments) self.assertEqual(alignment.score, 834) self.assertEqual(alignment.shape, (2, 36)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) 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.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[42144400, 42144436], [ 0, 36]]), # fmt: on ) ) self.assertEqual( str(alignment), """\ chr22 42144400 ???????????????????????????????????? 42144436 0 |||||||||||||||||||||||||||||||||||| 36 hg19_dna 0 ???????????????????????????????????? 36 """, ) self.assertEqual( format(alignment, "bed"), """\ chr22 42144400 42144436 hg19_dna 834 + 42144400 42144436 0 1 36, 0, """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 36: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 36) alignment = next(alignments) self.assertEqual(alignment.score, 682) self.assertEqual(alignment.shape, (2, 44)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) 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.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[183925984, 183925990, 183926028], [ 0, 6, 44]]), # fmt: on ) ) self.assertEqual( str(alignment), """\ chr2 183925984 ???????????????????????????????????????????? 183926028 0 |||||||||||||||||||||||||||||||||||||||||||| 44 hg19_dna 0 ???????????????????????????????????????????? 44 """, ) self.assertEqual( format(alignment, "bed"), """\ chr2 183925984 183926028 hg19_dna 682 + 183925984 183926028 0 2 6,38, 0,6, """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 44: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 44) alignment = next(alignments) self.assertEqual(alignment.score, 890) self.assertEqual(alignment.shape, (2, 170)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) 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.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[35483340, 35483365, 35483499, 35483510], [ 0, 25, 25, 36]]), # fmt: on ) ) self.assertEqual( str(alignment), """\ chr19 35483340 ???????????????????????????????????????????????????????????? 0 |||||||||||||||||||||||||----------------------------------- hg19_dna 0 ?????????????????????????----------------------------------- chr19 35483400 ???????????????????????????????????????????????????????????? 60 ------------------------------------------------------------ hg19_dna 25 ------------------------------------------------------------ chr19 35483460 ?????????????????????????????????????????????????? 35483510 120 ---------------------------------------||||||||||| 170 hg19_dna 25 ---------------------------------------??????????? 36 """, ) self.assertEqual( format(alignment, "bed"), """\ chr19 35483340 35483510 hg19_dna 890 + 35483340 35483510 0 2 25,11, 0,159, """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 36: identities = 0, mismatches = 0. gaps = 134: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 134: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 134: open_internal_deletions = 1, extend_internal_deletions = 133; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 134) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 134) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 134) self.assertEqual(counts.gaps, 134) self.assertEqual(counts.aligned, 36) alignment = next(alignments) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.shape, (2, 39)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) 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.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[23891310, 23891349], [ 0, 39]]), # fmt: on ) ) self.assertEqual( str(alignment), """\ chr18 23891310 ??????????????????????????????????????? 23891349 0 ||||||||||||||||||||||||||||||||||||||| 39 hg19_dna 0 ??????????????????????????????????????? 39 """, ) self.assertEqual( format(alignment, "bed"), """\ chr18 23891310 23891349 hg19_dna 1000 + 23891310 23891349 0 1 39, 0, """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 39: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 39) alignment = next(alignments) self.assertEqual(alignment.score, 930) self.assertEqual(alignment.shape, (2, 28)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) 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.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[43252217, 43252245], [ 0, 28]]), # fmt: on ) ) self.assertEqual( str(alignment), """\ chr18 43252217 ???????????????????????????? 43252245 0 |||||||||||||||||||||||||||| 28 hg19_dna 0 ???????????????????????????? 28 """, ) self.assertEqual( format(alignment, "bed"), """\ chr18 43252217 43252245 hg19_dna 930 + 43252217 43252245 0 1 28, 0, """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 28: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 28) alignment = next(alignments) self.assertEqual(alignment.score, 912) self.assertEqual(alignment.shape, (2, 51)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) 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.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[52759147, 52759154, 52759160, 52759198], [ 0, 7, 7, 45]]), # fmt: on ) ) self.assertEqual( str(alignment), """\ chr13 52759147 ??????????????????????????????????????????????????? 52759198 0 |||||||------|||||||||||||||||||||||||||||||||||||| 51 hg19_dna 0 ???????------?????????????????????????????????????? 45 """, ) self.assertEqual( format(alignment, "bed"), """\ chr13 52759147 52759198 hg19_dna 912 + 52759147 52759198 0 2 7,38, 0,13, """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 45: identities = 0, mismatches = 0. gaps = 6: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 6: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 6: open_internal_deletions = 1, extend_internal_deletions = 5; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 6) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 6) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 6) self.assertEqual(counts.gaps, 6) self.assertEqual(counts.aligned, 45) alignment = next(alignments) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.shape, (2, 50)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) 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.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[1207056, 1207106], [ 0, 50]]), # fmt: on ) ) self.assertEqual( str(alignment), """\ chr1 1207056 ?????????????????????????????????????????????????? 1207106 0 |||||||||||||||||||||||||||||||||||||||||||||||||| 50 hg19_dna 0 ?????????????????????????????????????????????????? 50 """, ) self.assertEqual( format(alignment, "bed"), """\ chr1 1207056 1207106 hg19_dna 1000 + 1207056 1207106 0 1 50, 0, """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 50: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 50) alignment = next(alignments) self.assertEqual(alignment.score, 824) self.assertEqual(alignment.shape, (2, 34)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) 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.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[61700837, 61700871], [ 0, 34]]), # fmt: on ) ) self.assertEqual( str(alignment), """\ chr1 61700837 ?????????????????????????????????? 61700871 0 |||||||||||||||||||||||||||||||||| 34 hg19_dna 0 ?????????????????????????????????? 34 """, ) self.assertEqual( format(alignment, "bed"), """\ chr1 61700837 61700871 hg19_dna 824 + 61700837 61700871 0 1 34, 0, """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 34: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 34) alignment = next(alignments) self.assertEqual(alignment.score, 572) self.assertEqual(alignment.shape, (2, 34)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) 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.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[37558157, 37558167, 37558173, 37558191], [ 28, 18, 18, 0]]), # fmt: on ) ) self.assertEqual( str(alignment), """\ chr4 37558157 ?????????????????????????????????? 37558191 0 ||||||||||------|||||||||||||||||| 34 hg19_dna 28 ??????????------?????????????????? 0 """, ) self.assertEqual( format(alignment, "bed"), """\ chr4 37558157 37558191 hg19_dna 572 - 37558157 37558191 0 2 10,18, 0,16, """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 28: identities = 0, mismatches = 0. gaps = 6: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 6: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 6: open_internal_deletions = 1, extend_internal_deletions = 5; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 6) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 6) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 6) self.assertEqual(counts.gaps, 6) self.assertEqual(counts.aligned, 28) alignment = next(alignments) self.assertEqual(alignment.score, 892) self.assertEqual(alignment.shape, (2, 37)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) 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.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[48997405, 48997442], [ 37, 0]]), # fmt: on ) ) self.assertEqual( str(alignment), """\ chr22 48997405 ????????????????????????????????????? 48997442 0 ||||||||||||||||||||||||||||||||||||| 37 hg19_dna 37 ????????????????????????????????????? 0 """, ) self.assertEqual( format(alignment, "bed"), """\ chr22 48997405 48997442 hg19_dna 892 - 48997405 48997442 0 1 37, 0, """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 37: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 37) alignment = next(alignments) self.assertEqual(alignment.score, 946) self.assertEqual(alignment.shape, (2, 36)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) 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.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[120641740, 120641776], [ 36, 0]]), # fmt: on ) ) self.assertEqual( str(alignment), """\ chr2 120641740 ???????????????????????????????????? 120641776 0 |||||||||||||||||||||||||||||||||||| 36 hg19_dna 36 ???????????????????????????????????? 0 """, ) self.assertEqual( format(alignment, "bed"), """\ chr2 120641740 120641776 hg19_dna 946 - 120641740 120641776 0 1 36, 0, """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 36: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 36) alignment = next(alignments) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.shape, (2, 39)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) 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.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[54017130, 54017169], [ 39, 0]]), # fmt: on ) ) self.assertEqual( str(alignment), """\ chr19 54017130 ??????????????????????????????????????? 54017169 0 ||||||||||||||||||||||||||||||||||||||| 39 hg19_dna 39 ??????????????????????????????????????? 0 """, ) self.assertEqual( format(alignment, "bed"), """\ chr19 54017130 54017169 hg19_dna 1000 - 54017130 54017169 0 1 39, 0, """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 39: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 39) alignment = next(alignments) self.assertEqual(alignment.score, 848) self.assertEqual(alignment.shape, (2, 39)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) 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.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[553742, 553781], [ 39, 0]]), # fmt: on ) ) self.assertEqual( str(alignment), """\ chr19 553742 ??????????????????????????????????????? 553781 0 ||||||||||||||||||||||||||||||||||||||| 39 hg19_dna 39 ??????????????????????????????????????? 0 """, ) self.assertEqual( format(alignment, "bed"), """\ chr19 553742 553781 hg19_dna 848 - 553742 553781 0 1 39, 0, """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 39: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 39) alignment = next(alignments) self.assertEqual(alignment.score, 834) self.assertEqual(alignment.shape, (2, 36)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) 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.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[99388555, 99388591], [ 36, 0]]), # fmt: on ) ) self.assertEqual( str(alignment), """\ chr10 99388555 ???????????????????????????????????? 99388591 0 |||||||||||||||||||||||||||||||||||| 36 hg19_dna 36 ???????????????????????????????????? 0 """, ) self.assertEqual( format(alignment, "bed"), """\ chr10 99388555 99388591 hg19_dna 834 - 99388555 99388591 0 1 36, 0, """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 36: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 36) alignment = next(alignments) self.assertEqual(alignment.score, 920) self.assertEqual(alignment.shape, (2, 25)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) 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.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[112178171, 112178196], [ 25, 0]]), # fmt: on ) ) self.assertEqual( str(alignment), """\ chr10 112178171 ????????????????????????? 112178196 0 ||||||||||||||||||||||||| 25 hg19_dna 25 ????????????????????????? 0 """, ) self.assertEqual( format(alignment, "bed"), """\ chr10 112178171 112178196 hg19_dna 920 - 112178171 112178196 0 1 25, 0, """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 25: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 25) alignment = next(alignments) self.assertEqual(alignment.score, 946) self.assertEqual(alignment.shape, (2, 36)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) 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.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[39368490, 39368526], [ 36, 0]]), # fmt: on ) ) self.assertEqual( str(alignment), """\ chr1 39368490 ???????????????????????????????????? 39368526 0 |||||||||||||||||||||||||||||||||||| 36 hg19_dna 36 ???????????????????????????????????? 0 """, ) self.assertEqual( format(alignment, "bed"), """\ chr1 39368490 39368526 hg19_dna 946 - 39368490 39368526 0 1 36, 0, """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 36: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 36) alignment = next(alignments) self.assertEqual(alignment.score, 942) self.assertEqual(alignment.shape, (2, 34)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) 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.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[220325687, 220325721], [ 34, 0]]), # fmt: on ) ) self.assertEqual( str(alignment), """\ chr1 220325687 ?????????????????????????????????? 220325721 0 |||||||||||||||||||||||||||||||||| 34 hg19_dna 34 ?????????????????????????????????? 0 """, ) self.assertEqual( format(alignment, "bed"), """\ chr1 220325687 220325721 hg19_dna 942 - 220325687 220325721 0 1 34, 0, """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 34: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 34) self.assertRaises(StopIteration, next, alignments) def test_writing_psl_34_004(self): """Test writing the alignments in psl_34_004.bed.""" path = "Blat/psl_34_004.bed" with open(path) as stream: original_data = stream.read() alignments = Align.parse(path, "bed") stream = StringIO() n = Align.write(alignments, stream, "bed") self.assertEqual(n, 19) stream.seek(0) written_data = stream.read() stream.close() self.assertEqual(original_data, written_data) def test_reading_psl_34_005(self): """Test parsing psl_34_005.bed.""" path = "Blat/psl_34_005.bed" alignments = Align.parse(path, "bed") alignment = next(alignments) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.shape, (2, 16)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) 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.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[61646095, 61646111], [ 0, 16]]), # fmt: on ) ) self.assertEqual( str(alignment), """\ chr4 61646095 ???????????????? 61646111 0 |||||||||||||||| 16 hg19_dna 0 ???????????????? 16 """, ) self.assertEqual( format(alignment, "bed"), """\ chr4 61646095 61646111 hg19_dna 1000 + 61646095 61646111 0 1 16, 0, """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 16: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 16) alignment = next(alignments) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.shape, (2, 33)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) 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.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[10271783, 10271816], [ 0, 33]]), # fmt: on ) ) self.assertEqual( str(alignment), """\ chr1 10271783 ????????????????????????????????? 10271816 0 ||||||||||||||||||||||||||||||||| 33 hg19_dna 0 ????????????????????????????????? 33 """, ) self.assertEqual( format(alignment, "bed"), """\ chr1 10271783 10271816 hg19_dna 1000 + 10271783 10271816 0 1 33, 0, """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 33: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 33) alignment = next(alignments) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.shape, (2, 17)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) 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.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[53575980, 53575997], [ 17, 0]]), # fmt: on ) ) self.assertEqual( str(alignment), """\ chr2 53575980 ????????????????? 53575997 0 ||||||||||||||||| 17 hg19_dna 17 ????????????????? 0 """, ) self.assertEqual( format(alignment, "bed"), """\ chr2 53575980 53575997 hg19_dna 1000 - 53575980 53575997 0 1 17, 0, """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 17: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 17) alignment = next(alignments) self.assertEqual(alignment.score, 854) self.assertEqual(alignment.shape, (2, 41)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) 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.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[85737865, 85737906], [ 0, 41]]), # fmt: on ) ) self.assertEqual( str(alignment), """\ chr9 85737865 ????????????????????????????????????????? 85737906 0 ||||||||||||||||||||||||||||||||||||||||| 41 hg19_dna 0 ????????????????????????????????????????? 41 """, ) self.assertEqual( format(alignment, "bed"), """\ chr9 85737865 85737906 hg19_dna 854 + 85737865 85737906 0 1 41, 0, """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 41: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 41) alignment = next(alignments) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.shape, (2, 41)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) 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.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[95160479, 95160520], [ 0, 41]]), # fmt: on ) ) self.assertEqual( str(alignment), """\ chr8 95160479 ????????????????????????????????????????? 95160520 0 ||||||||||||||||||||||||||||||||||||||||| 41 hg19_dna 0 ????????????????????????????????????????? 41 """, ) self.assertEqual( format(alignment, "bed"), """\ chr8 95160479 95160520 hg19_dna 1000 + 95160479 95160520 0 1 41, 0, """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 41: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 41) alignment = next(alignments) self.assertEqual(alignment.score, 834) self.assertEqual(alignment.shape, (2, 36)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) 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.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[42144400, 42144436], [ 0, 36]]), # fmt: on ) ) self.assertEqual( str(alignment), """\ chr22 42144400 ???????????????????????????????????? 42144436 0 |||||||||||||||||||||||||||||||||||| 36 hg19_dna 0 ???????????????????????????????????? 36 """, ) self.assertEqual( format(alignment, "bed"), """\ chr22 42144400 42144436 hg19_dna 834 + 42144400 42144436 0 1 36, 0, """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 36: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 36) alignment = next(alignments) self.assertEqual(alignment.score, 682) self.assertEqual(alignment.shape, (2, 44)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) 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.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[183925984, 183925990, 183926028], [ 0, 6, 44]]), # fmt: on ) ) self.assertEqual( str(alignment), """\ chr2 183925984 ???????????????????????????????????????????? 183926028 0 |||||||||||||||||||||||||||||||||||||||||||| 44 hg19_dna 0 ???????????????????????????????????????????? 44 """, ) self.assertEqual( format(alignment, "bed"), """\ chr2 183925984 183926028 hg19_dna 682 + 183925984 183926028 0 2 6,38, 0,6, """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 44: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 44) alignment = next(alignments) self.assertEqual(alignment.score, 890) self.assertEqual(alignment.shape, (2, 170)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) 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.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[35483340, 35483365, 35483499, 35483510], [ 0, 25, 25, 36]]), # fmt: on ) ) self.assertEqual( str(alignment), """\ chr19 35483340 ???????????????????????????????????????????????????????????? 0 |||||||||||||||||||||||||----------------------------------- hg19_dna 0 ?????????????????????????----------------------------------- chr19 35483400 ???????????????????????????????????????????????????????????? 60 ------------------------------------------------------------ hg19_dna 25 ------------------------------------------------------------ chr19 35483460 ?????????????????????????????????????????????????? 35483510 120 ---------------------------------------||||||||||| 170 hg19_dna 25 ---------------------------------------??????????? 36 """, ) self.assertEqual( format(alignment, "bed"), """\ chr19 35483340 35483510 hg19_dna 890 + 35483340 35483510 0 2 25,11, 0,159, """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 36: identities = 0, mismatches = 0. gaps = 134: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 134: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 134: open_internal_deletions = 1, extend_internal_deletions = 133; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 134) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 134) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 134) self.assertEqual(counts.gaps, 134) self.assertEqual(counts.aligned, 36) alignment = next(alignments) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.shape, (2, 39)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) 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.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[23891310, 23891349], [ 0, 39]]), # fmt: on ) ) self.assertEqual( str(alignment), """\ chr18 23891310 ??????????????????????????????????????? 23891349 0 ||||||||||||||||||||||||||||||||||||||| 39 hg19_dna 0 ??????????????????????????????????????? 39 """, ) self.assertEqual( format(alignment, "bed"), """\ chr18 23891310 23891349 hg19_dna 1000 + 23891310 23891349 0 1 39, 0, """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 39: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 39) alignment = next(alignments) self.assertEqual(alignment.score, 930) self.assertEqual(alignment.shape, (2, 28)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) 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.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[43252217, 43252245], [ 0, 28]]), # fmt: on ) ) self.assertEqual( str(alignment), """\ chr18 43252217 ???????????????????????????? 43252245 0 |||||||||||||||||||||||||||| 28 hg19_dna 0 ???????????????????????????? 28 """, ) self.assertEqual( format(alignment, "bed"), """\ chr18 43252217 43252245 hg19_dna 930 + 43252217 43252245 0 1 28, 0, """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 28: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 28) alignment = next(alignments) self.assertEqual(alignment.score, 912) self.assertEqual(alignment.shape, (2, 51)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) 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.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[52759147, 52759154, 52759160, 52759198], [ 0, 7, 7, 45]]), # fmt: on ) ) self.assertEqual( str(alignment), """\ chr13 52759147 ??????????????????????????????????????????????????? 52759198 0 |||||||------|||||||||||||||||||||||||||||||||||||| 51 hg19_dna 0 ???????------?????????????????????????????????????? 45 """, ) self.assertEqual( format(alignment, "bed"), """\ chr13 52759147 52759198 hg19_dna 912 + 52759147 52759198 0 2 7,38, 0,13, """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 45: identities = 0, mismatches = 0. gaps = 6: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 6: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 6: open_internal_deletions = 1, extend_internal_deletions = 5; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 6) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 6) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 6) self.assertEqual(counts.gaps, 6) self.assertEqual(counts.aligned, 45) alignment = next(alignments) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.shape, (2, 50)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) 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.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[1207056, 1207106], [ 0, 50]]), # fmt: on ) ) self.assertEqual( str(alignment), """\ chr1 1207056 ?????????????????????????????????????????????????? 1207106 0 |||||||||||||||||||||||||||||||||||||||||||||||||| 50 hg19_dna 0 ?????????????????????????????????????????????????? 50 """, ) self.assertEqual( format(alignment, "bed"), """\ chr1 1207056 1207106 hg19_dna 1000 + 1207056 1207106 0 1 50, 0, """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 50: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 50) alignment = next(alignments) self.assertEqual(alignment.score, 824) self.assertEqual(alignment.shape, (2, 34)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) 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.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[61700837, 61700871], [ 0, 34]]), # fmt: on ) ) self.assertEqual( str(alignment), """\ chr1 61700837 ?????????????????????????????????? 61700871 0 |||||||||||||||||||||||||||||||||| 34 hg19_dna 0 ?????????????????????????????????? 34 """, ) self.assertEqual( format(alignment, "bed"), """\ chr1 61700837 61700871 hg19_dna 824 + 61700837 61700871 0 1 34, 0, """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 34: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 34) alignment = next(alignments) self.assertEqual(alignment.score, 572) self.assertEqual(alignment.shape, (2, 34)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) 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.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[37558157, 37558167, 37558173, 37558191], [ 28, 18, 18, 0]]), # fmt: on ) ) self.assertEqual( str(alignment), """\ chr4 37558157 ?????????????????????????????????? 37558191 0 ||||||||||------|||||||||||||||||| 34 hg19_dna 28 ??????????------?????????????????? 0 """, ) self.assertEqual( format(alignment, "bed"), """\ chr4 37558157 37558191 hg19_dna 572 - 37558157 37558191 0 2 10,18, 0,16, """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 28: identities = 0, mismatches = 0. gaps = 6: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 6: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 6: open_internal_deletions = 1, extend_internal_deletions = 5; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 6) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 6) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 6) self.assertEqual(counts.gaps, 6) self.assertEqual(counts.aligned, 28) alignment = next(alignments) self.assertEqual(alignment.score, 892) self.assertEqual(alignment.shape, (2, 37)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) 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.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[48997405, 48997442], [ 37, 0]]), # fmt: on ) ) self.assertEqual( str(alignment), """\ chr22 48997405 ????????????????????????????????????? 48997442 0 ||||||||||||||||||||||||||||||||||||| 37 hg19_dna 37 ????????????????????????????????????? 0 """, ) self.assertEqual( format(alignment, "bed"), """\ chr22 48997405 48997442 hg19_dna 892 - 48997405 48997442 0 1 37, 0, """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 37: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 37) alignment = next(alignments) self.assertEqual(alignment.score, 946) self.assertEqual(alignment.shape, (2, 36)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) 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.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[120641740, 120641776], [ 36, 0]]), # fmt: on ) ) self.assertEqual( str(alignment), """\ chr2 120641740 ???????????????????????????????????? 120641776 0 |||||||||||||||||||||||||||||||||||| 36 hg19_dna 36 ???????????????????????????????????? 0 """, ) self.assertEqual( format(alignment, "bed"), """\ chr2 120641740 120641776 hg19_dna 946 - 120641740 120641776 0 1 36, 0, """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 36: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 36) alignment = next(alignments) self.assertEqual(alignment.score, 1000) self.assertEqual(alignment.shape, (2, 39)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) 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.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[54017130, 54017169], [ 39, 0]]), # fmt: on ) ) self.assertEqual( str(alignment), """\ chr19 54017130 ??????????????????????????????????????? 54017169 0 ||||||||||||||||||||||||||||||||||||||| 39 hg19_dna 39 ??????????????????????????????????????? 0 """, ) self.assertEqual( format(alignment, "bed"), """\ chr19 54017130 54017169 hg19_dna 1000 - 54017130 54017169 0 1 39, 0, """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 39: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 39) alignment = next(alignments) self.assertEqual(alignment.score, 848) self.assertEqual(alignment.shape, (2, 39)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) 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.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[553742, 553781], [ 39, 0]]), # fmt: on ) ) self.assertEqual( str(alignment), """\ chr19 553742 ??????????????????????????????????????? 553781 0 ||||||||||||||||||||||||||||||||||||||| 39 hg19_dna 39 ??????????????????????????????????????? 0 """, ) self.assertEqual( format(alignment, "bed"), """\ chr19 553742 553781 hg19_dna 848 - 553742 553781 0 1 39, 0, """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 39: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 39) alignment = next(alignments) self.assertEqual(alignment.score, 834) self.assertEqual(alignment.shape, (2, 36)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) 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.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[99388555, 99388591], [ 36, 0]]), # fmt: on ) ) self.assertEqual( str(alignment), """\ chr10 99388555 ???????????????????????????????????? 99388591 0 |||||||||||||||||||||||||||||||||||| 36 hg19_dna 36 ???????????????????????????????????? 0 """, ) self.assertEqual( format(alignment, "bed"), """\ chr10 99388555 99388591 hg19_dna 834 - 99388555 99388591 0 1 36, 0, """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 36: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 36) alignment = next(alignments) self.assertEqual(alignment.score, 920) self.assertEqual(alignment.shape, (2, 25)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) 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.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[112178171, 112178196], [ 25, 0]]), # fmt: on ) ) self.assertEqual( str(alignment), """\ chr10 112178171 ????????????????????????? 112178196 0 ||||||||||||||||||||||||| 25 hg19_dna 25 ????????????????????????? 0 """, ) self.assertEqual( format(alignment, "bed"), """\ chr10 112178171 112178196 hg19_dna 920 - 112178171 112178196 0 1 25, 0, """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 25: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 25) alignment = next(alignments) self.assertEqual(alignment.score, 946) self.assertEqual(alignment.shape, (2, 36)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) 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.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[39368490, 39368526], [ 36, 0]]), # fmt: on ) ) self.assertEqual( str(alignment), """\ chr1 39368490 ???????????????????????????????????? 39368526 0 |||||||||||||||||||||||||||||||||||| 36 hg19_dna 36 ???????????????????????????????????? 0 """, ) self.assertEqual( format(alignment, "bed"), """\ chr1 39368490 39368526 hg19_dna 946 - 39368490 39368526 0 1 36, 0, """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 36: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 36) alignment = next(alignments) self.assertEqual(alignment.score, 942) self.assertEqual(alignment.shape, (2, 34)) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) 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.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[220325687, 220325721], [ 34, 0]]), # fmt: on ) ) self.assertEqual( str(alignment), """\ chr1 220325687 ?????????????????????????????????? 220325721 0 |||||||||||||||||||||||||||||||||| 34 hg19_dna 34 ?????????????????????????????????? 0 """, ) self.assertEqual( format(alignment, "bed"), """\ chr1 220325687 220325721 hg19_dna 942 - 220325687 220325721 0 1 34, 0, """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 34: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 34) self.assertRaises(StopIteration, next, alignments) def test_writing_psl_34_005(self): """Test writing the alignments in psl_34_005.bed.""" path = "Blat/psl_34_005.bed" with open(path) as stream: original_data = stream.read() alignments = Align.parse(path, "bed") stream = StringIO() n = Align.write(alignments, stream, "bed") self.assertEqual(n, 22) stream.seek(0) written_data = stream.read() stream.close() self.assertEqual(original_data, written_data) class TestAlign_dnax_prot(unittest.TestCase): def test_reading_psl_35_001(self): """Test parsing psl_35_001.bed.""" path = "Blat/psl_35_001.bed" alignments = Align.parse(path, "bed") alignment = next(alignments) self.assertEqual(alignment.score, 1000) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr13") self.assertEqual(alignment.query.id, "CAG33136.1") self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[75566694, 75566850], [ 0, 156]]), # fmt: on ) ) self.assertEqual( str(alignment), """\ chr13 75566694 ???????????????????????????????????????????????????????????? 0 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| CAG33136. 0 ???????????????????????????????????????????????????????????? chr13 75566754 ???????????????????????????????????????????????????????????? 60 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| CAG33136. 60 ???????????????????????????????????????????????????????????? chr13 75566814 ???????????????????????????????????? 75566850 120 |||||||||||||||||||||||||||||||||||| 156 CAG33136. 120 ???????????????????????????????????? 156 """, ) self.assertEqual( format(alignment, "bed"), """\ chr13 75566694 75566850 CAG33136.1 1000 + 75566694 75566850 0 1 156, 0, """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 156: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 156) alignment = next(alignments) self.assertEqual(alignment.score, 1000) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr13") self.assertEqual(alignment.query.id, "CAG33136.1") self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[75560749, 75560881], [ 0, 132]]), # fmt: on ) ) self.assertEqual( str(alignment), """\ chr13 75560749 ???????????????????????????????????????????????????????????? 0 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| CAG33136. 0 ???????????????????????????????????????????????????????????? chr13 75560809 ???????????????????????????????????????????????????????????? 60 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| CAG33136. 60 ???????????????????????????????????????????????????????????? chr13 75560869 ???????????? 75560881 120 |||||||||||| 132 CAG33136. 120 ???????????? 132 """, ) self.assertEqual( format(alignment, "bed"), """\ chr13 75560749 75560881 CAG33136.1 1000 + 75560749 75560881 0 1 132, 0, """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 132: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 132) alignment = next(alignments) self.assertEqual(alignment.score, 986) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr13") self.assertEqual(alignment.query.id, "CAG33136.1") self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[75549820, 75549865, 75567225, 75567312], [ 0, 45, 45, 132]]), # fmt: on ) ) self.assertEqual( str(alignment), """\ chr13 75549820 ???????????????????????????????????????????????????????????? 0 |||||||||||||||||||||||||||||||||||||||||||||--------------- CAG33136. 0 ?????????????????????????????????????????????--------------- chr13 75549880 ???????????????????????????????????????????????????????????? 60 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75549940 ???????????????????????????????????????????????????????????? 120 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75550000 ???????????????????????????????????????????????????????????? 180 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75550060 ???????????????????????????????????????????????????????????? 240 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75550120 ???????????????????????????????????????????????????????????? 300 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75550180 ???????????????????????????????????????????????????????????? 360 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75550240 ???????????????????????????????????????????????????????????? 420 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75550300 ???????????????????????????????????????????????????????????? 480 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75550360 ???????????????????????????????????????????????????????????? 540 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75550420 ???????????????????????????????????????????????????????????? 600 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75550480 ???????????????????????????????????????????????????????????? 660 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75550540 ???????????????????????????????????????????????????????????? 720 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75550600 ???????????????????????????????????????????????????????????? 780 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75550660 ???????????????????????????????????????????????????????????? 840 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75550720 ???????????????????????????????????????????????????????????? 900 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75550780 ???????????????????????????????????????????????????????????? 960 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75550840 ???????????????????????????????????????????????????????????? 1020 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75550900 ???????????????????????????????????????????????????????????? 1080 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75550960 ???????????????????????????????????????????????????????????? 1140 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75551020 ???????????????????????????????????????????????????????????? 1200 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75551080 ???????????????????????????????????????????????????????????? 1260 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75551140 ???????????????????????????????????????????????????????????? 1320 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75551200 ???????????????????????????????????????????????????????????? 1380 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75551260 ???????????????????????????????????????????????????????????? 1440 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75551320 ???????????????????????????????????????????????????????????? 1500 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75551380 ???????????????????????????????????????????????????????????? 1560 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75551440 ???????????????????????????????????????????????????????????? 1620 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75551500 ???????????????????????????????????????????????????????????? 1680 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75551560 ???????????????????????????????????????????????????????????? 1740 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75551620 ???????????????????????????????????????????????????????????? 1800 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75551680 ???????????????????????????????????????????????????????????? 1860 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75551740 ???????????????????????????????????????????????????????????? 1920 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75551800 ???????????????????????????????????????????????????????????? 1980 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75551860 ???????????????????????????????????????????????????????????? 2040 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75551920 ???????????????????????????????????????????????????????????? 2100 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75551980 ???????????????????????????????????????????????????????????? 2160 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75552040 ???????????????????????????????????????????????????????????? 2220 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75552100 ???????????????????????????????????????????????????????????? 2280 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75552160 ???????????????????????????????????????????????????????????? 2340 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75552220 ???????????????????????????????????????????????????????????? 2400 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75552280 ???????????????????????????????????????????????????????????? 2460 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75552340 ???????????????????????????????????????????????????????????? 2520 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75552400 ???????????????????????????????????????????????????????????? 2580 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75552460 ???????????????????????????????????????????????????????????? 2640 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75552520 ???????????????????????????????????????????????????????????? 2700 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75552580 ???????????????????????????????????????????????????????????? 2760 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75552640 ???????????????????????????????????????????????????????????? 2820 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75552700 ???????????????????????????????????????????????????????????? 2880 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75552760 ???????????????????????????????????????????????????????????? 2940 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75552820 ???????????????????????????????????????????????????????????? 3000 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75552880 ???????????????????????????????????????????????????????????? 3060 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75552940 ???????????????????????????????????????????????????????????? 3120 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75553000 ???????????????????????????????????????????????????????????? 3180 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75553060 ???????????????????????????????????????????????????????????? 3240 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75553120 ???????????????????????????????????????????????????????????? 3300 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75553180 ???????????????????????????????????????????????????????????? 3360 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75553240 ???????????????????????????????????????????????????????????? 3420 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75553300 ???????????????????????????????????????????????????????????? 3480 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75553360 ???????????????????????????????????????????????????????????? 3540 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75553420 ???????????????????????????????????????????????????????????? 3600 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75553480 ???????????????????????????????????????????????????????????? 3660 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75553540 ???????????????????????????????????????????????????????????? 3720 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75553600 ???????????????????????????????????????????????????????????? 3780 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75553660 ???????????????????????????????????????????????????????????? 3840 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75553720 ???????????????????????????????????????????????????????????? 3900 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75553780 ???????????????????????????????????????????????????????????? 3960 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75553840 ???????????????????????????????????????????????????????????? 4020 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75553900 ???????????????????????????????????????????????????????????? 4080 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75553960 ???????????????????????????????????????????????????????????? 4140 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75554020 ???????????????????????????????????????????????????????????? 4200 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75554080 ???????????????????????????????????????????????????????????? 4260 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75554140 ???????????????????????????????????????????????????????????? 4320 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75554200 ???????????????????????????????????????????????????????????? 4380 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75554260 ???????????????????????????????????????????????????????????? 4440 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75554320 ???????????????????????????????????????????????????????????? 4500 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75554380 ???????????????????????????????????????????????????????????? 4560 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75554440 ???????????????????????????????????????????????????????????? 4620 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75554500 ???????????????????????????????????????????????????????????? 4680 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75554560 ???????????????????????????????????????????????????????????? 4740 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75554620 ???????????????????????????????????????????????????????????? 4800 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75554680 ???????????????????????????????????????????????????????????? 4860 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75554740 ???????????????????????????????????????????????????????????? 4920 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75554800 ???????????????????????????????????????????????????????????? 4980 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75554860 ???????????????????????????????????????????????????????????? 5040 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75554920 ???????????????????????????????????????????????????????????? 5100 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75554980 ???????????????????????????????????????????????????????????? 5160 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75555040 ???????????????????????????????????????????????????????????? 5220 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75555100 ???????????????????????????????????????????????????????????? 5280 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75555160 ???????????????????????????????????????????????????????????? 5340 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75555220 ???????????????????????????????????????????????????????????? 5400 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75555280 ???????????????????????????????????????????????????????????? 5460 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75555340 ???????????????????????????????????????????????????????????? 5520 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75555400 ???????????????????????????????????????????????????????????? 5580 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75555460 ???????????????????????????????????????????????????????????? 5640 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75555520 ???????????????????????????????????????????????????????????? 5700 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75555580 ???????????????????????????????????????????????????????????? 5760 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75555640 ???????????????????????????????????????????????????????????? 5820 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75555700 ???????????????????????????????????????????????????????????? 5880 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75555760 ???????????????????????????????????????????????????????????? 5940 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75555820 ???????????????????????????????????????????????????????????? 6000 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75555880 ???????????????????????????????????????????????????????????? 6060 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75555940 ???????????????????????????????????????????????????????????? 6120 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75556000 ???????????????????????????????????????????????????????????? 6180 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75556060 ???????????????????????????????????????????????????????????? 6240 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75556120 ???????????????????????????????????????????????????????????? 6300 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75556180 ???????????????????????????????????????????????????????????? 6360 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75556240 ???????????????????????????????????????????????????????????? 6420 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75556300 ???????????????????????????????????????????????????????????? 6480 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75556360 ???????????????????????????????????????????????????????????? 6540 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75556420 ???????????????????????????????????????????????????????????? 6600 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75556480 ???????????????????????????????????????????????????????????? 6660 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75556540 ???????????????????????????????????????????????????????????? 6720 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75556600 ???????????????????????????????????????????????????????????? 6780 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75556660 ???????????????????????????????????????????????????????????? 6840 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75556720 ???????????????????????????????????????????????????????????? 6900 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75556780 ???????????????????????????????????????????????????????????? 6960 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75556840 ???????????????????????????????????????????????????????????? 7020 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75556900 ???????????????????????????????????????????????????????????? 7080 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75556960 ???????????????????????????????????????????????????????????? 7140 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75557020 ???????????????????????????????????????????????????????????? 7200 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75557080 ???????????????????????????????????????????????????????????? 7260 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75557140 ???????????????????????????????????????????????????????????? 7320 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75557200 ???????????????????????????????????????????????????????????? 7380 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75557260 ???????????????????????????????????????????????????????????? 7440 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75557320 ???????????????????????????????????????????????????????????? 7500 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75557380 ???????????????????????????????????????????????????????????? 7560 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75557440 ???????????????????????????????????????????????????????????? 7620 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75557500 ???????????????????????????????????????????????????????????? 7680 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75557560 ???????????????????????????????????????????????????????????? 7740 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75557620 ???????????????????????????????????????????????????????????? 7800 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75557680 ???????????????????????????????????????????????????????????? 7860 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75557740 ???????????????????????????????????????????????????????????? 7920 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75557800 ???????????????????????????????????????????????????????????? 7980 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75557860 ???????????????????????????????????????????????????????????? 8040 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75557920 ???????????????????????????????????????????????????????????? 8100 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75557980 ???????????????????????????????????????????????????????????? 8160 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75558040 ???????????????????????????????????????????????????????????? 8220 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75558100 ???????????????????????????????????????????????????????????? 8280 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75558160 ???????????????????????????????????????????????????????????? 8340 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75558220 ???????????????????????????????????????????????????????????? 8400 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75558280 ???????????????????????????????????????????????????????????? 8460 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75558340 ???????????????????????????????????????????????????????????? 8520 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75558400 ???????????????????????????????????????????????????????????? 8580 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75558460 ???????????????????????????????????????????????????????????? 8640 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75558520 ???????????????????????????????????????????????????????????? 8700 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75558580 ???????????????????????????????????????????????????????????? 8760 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75558640 ???????????????????????????????????????????????????????????? 8820 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75558700 ???????????????????????????????????????????????????????????? 8880 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75558760 ???????????????????????????????????????????????????????????? 8940 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75558820 ???????????????????????????????????????????????????????????? 9000 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75558880 ???????????????????????????????????????????????????????????? 9060 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75558940 ???????????????????????????????????????????????????????????? 9120 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75559000 ???????????????????????????????????????????????????????????? 9180 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75559060 ???????????????????????????????????????????????????????????? 9240 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75559120 ???????????????????????????????????????????????????????????? 9300 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75559180 ???????????????????????????????????????????????????????????? 9360 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75559240 ???????????????????????????????????????????????????????????? 9420 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75559300 ???????????????????????????????????????????????????????????? 9480 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75559360 ???????????????????????????????????????????????????????????? 9540 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75559420 ???????????????????????????????????????????????????????????? 9600 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75559480 ???????????????????????????????????????????????????????????? 9660 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75559540 ???????????????????????????????????????????????????????????? 9720 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75559600 ???????????????????????????????????????????????????????????? 9780 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75559660 ???????????????????????????????????????????????????????????? 9840 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75559720 ???????????????????????????????????????????????????????????? 9900 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75559780 ???????????????????????????????????????????????????????????? 9960 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75559840 ???????????????????????????????????????????????????????????? 10020 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75559900 ???????????????????????????????????????????????????????????? 10080 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75559960 ???????????????????????????????????????????????????????????? 10140 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75560020 ???????????????????????????????????????????????????????????? 10200 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75560080 ???????????????????????????????????????????????????????????? 10260 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75560140 ???????????????????????????????????????????????????????????? 10320 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75560200 ???????????????????????????????????????????????????????????? 10380 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75560260 ???????????????????????????????????????????????????????????? 10440 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75560320 ???????????????????????????????????????????????????????????? 10500 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75560380 ???????????????????????????????????????????????????????????? 10560 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75560440 ???????????????????????????????????????????????????????????? 10620 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75560500 ???????????????????????????????????????????????????????????? 10680 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75560560 ???????????????????????????????????????????????????????????? 10740 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75560620 ???????????????????????????????????????????????????????????? 10800 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75560680 ???????????????????????????????????????????????????????????? 10860 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75560740 ???????????????????????????????????????????????????????????? 10920 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75560800 ???????????????????????????????????????????????????????????? 10980 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75560860 ???????????????????????????????????????????????????????????? 11040 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75560920 ???????????????????????????????????????????????????????????? 11100 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75560980 ???????????????????????????????????????????????????????????? 11160 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75561040 ???????????????????????????????????????????????????????????? 11220 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75561100 ???????????????????????????????????????????????????????????? 11280 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75561160 ???????????????????????????????????????????????????????????? 11340 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75561220 ???????????????????????????????????????????????????????????? 11400 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75561280 ???????????????????????????????????????????????????????????? 11460 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75561340 ???????????????????????????????????????????????????????????? 11520 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75561400 ???????????????????????????????????????????????????????????? 11580 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75561460 ???????????????????????????????????????????????????????????? 11640 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75561520 ???????????????????????????????????????????????????????????? 11700 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75561580 ???????????????????????????????????????????????????????????? 11760 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75561640 ???????????????????????????????????????????????????????????? 11820 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75561700 ???????????????????????????????????????????????????????????? 11880 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75561760 ???????????????????????????????????????????????????????????? 11940 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75561820 ???????????????????????????????????????????????????????????? 12000 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75561880 ???????????????????????????????????????????????????????????? 12060 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75561940 ???????????????????????????????????????????????????????????? 12120 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75562000 ???????????????????????????????????????????????????????????? 12180 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75562060 ???????????????????????????????????????????????????????????? 12240 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75562120 ???????????????????????????????????????????????????????????? 12300 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75562180 ???????????????????????????????????????????????????????????? 12360 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75562240 ???????????????????????????????????????????????????????????? 12420 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75562300 ???????????????????????????????????????????????????????????? 12480 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75562360 ???????????????????????????????????????????????????????????? 12540 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75562420 ???????????????????????????????????????????????????????????? 12600 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75562480 ???????????????????????????????????????????????????????????? 12660 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75562540 ???????????????????????????????????????????????????????????? 12720 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75562600 ???????????????????????????????????????????????????????????? 12780 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75562660 ???????????????????????????????????????????????????????????? 12840 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75562720 ???????????????????????????????????????????????????????????? 12900 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75562780 ???????????????????????????????????????????????????????????? 12960 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75562840 ???????????????????????????????????????????????????????????? 13020 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75562900 ???????????????????????????????????????????????????????????? 13080 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75562960 ???????????????????????????????????????????????????????????? 13140 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75563020 ???????????????????????????????????????????????????????????? 13200 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75563080 ???????????????????????????????????????????????????????????? 13260 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75563140 ???????????????????????????????????????????????????????????? 13320 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75563200 ???????????????????????????????????????????????????????????? 13380 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75563260 ???????????????????????????????????????????????????????????? 13440 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75563320 ???????????????????????????????????????????????????????????? 13500 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75563380 ???????????????????????????????????????????????????????????? 13560 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75563440 ???????????????????????????????????????????????????????????? 13620 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75563500 ???????????????????????????????????????????????????????????? 13680 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75563560 ???????????????????????????????????????????????????????????? 13740 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75563620 ???????????????????????????????????????????????????????????? 13800 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75563680 ???????????????????????????????????????????????????????????? 13860 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75563740 ???????????????????????????????????????????????????????????? 13920 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75563800 ???????????????????????????????????????????????????????????? 13980 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75563860 ???????????????????????????????????????????????????????????? 14040 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75563920 ???????????????????????????????????????????????????????????? 14100 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75563980 ???????????????????????????????????????????????????????????? 14160 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75564040 ???????????????????????????????????????????????????????????? 14220 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75564100 ???????????????????????????????????????????????????????????? 14280 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75564160 ???????????????????????????????????????????????????????????? 14340 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75564220 ???????????????????????????????????????????????????????????? 14400 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75564280 ???????????????????????????????????????????????????????????? 14460 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75564340 ???????????????????????????????????????????????????????????? 14520 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75564400 ???????????????????????????????????????????????????????????? 14580 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75564460 ???????????????????????????????????????????????????????????? 14640 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75564520 ???????????????????????????????????????????????????????????? 14700 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75564580 ???????????????????????????????????????????????????????????? 14760 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75564640 ???????????????????????????????????????????????????????????? 14820 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75564700 ???????????????????????????????????????????????????????????? 14880 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75564760 ???????????????????????????????????????????????????????????? 14940 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75564820 ???????????????????????????????????????????????????????????? 15000 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75564880 ???????????????????????????????????????????????????????????? 15060 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75564940 ???????????????????????????????????????????????????????????? 15120 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75565000 ???????????????????????????????????????????????????????????? 15180 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75565060 ???????????????????????????????????????????????????????????? 15240 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75565120 ???????????????????????????????????????????????????????????? 15300 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75565180 ???????????????????????????????????????????????????????????? 15360 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75565240 ???????????????????????????????????????????????????????????? 15420 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75565300 ???????????????????????????????????????????????????????????? 15480 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75565360 ???????????????????????????????????????????????????????????? 15540 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75565420 ???????????????????????????????????????????????????????????? 15600 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75565480 ???????????????????????????????????????????????????????????? 15660 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75565540 ???????????????????????????????????????????????????????????? 15720 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75565600 ???????????????????????????????????????????????????????????? 15780 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75565660 ???????????????????????????????????????????????????????????? 15840 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75565720 ???????????????????????????????????????????????????????????? 15900 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75565780 ???????????????????????????????????????????????????????????? 15960 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75565840 ???????????????????????????????????????????????????????????? 16020 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75565900 ???????????????????????????????????????????????????????????? 16080 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75565960 ???????????????????????????????????????????????????????????? 16140 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75566020 ???????????????????????????????????????????????????????????? 16200 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75566080 ???????????????????????????????????????????????????????????? 16260 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75566140 ???????????????????????????????????????????????????????????? 16320 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75566200 ???????????????????????????????????????????????????????????? 16380 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75566260 ???????????????????????????????????????????????????????????? 16440 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75566320 ???????????????????????????????????????????????????????????? 16500 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75566380 ???????????????????????????????????????????????????????????? 16560 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75566440 ???????????????????????????????????????????????????????????? 16620 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75566500 ???????????????????????????????????????????????????????????? 16680 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75566560 ???????????????????????????????????????????????????????????? 16740 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75566620 ???????????????????????????????????????????????????????????? 16800 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75566680 ???????????????????????????????????????????????????????????? 16860 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75566740 ???????????????????????????????????????????????????????????? 16920 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75566800 ???????????????????????????????????????????????????????????? 16980 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75566860 ???????????????????????????????????????????????????????????? 17040 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75566920 ???????????????????????????????????????????????????????????? 17100 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75566980 ???????????????????????????????????????????????????????????? 17160 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75567040 ???????????????????????????????????????????????????????????? 17220 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75567100 ???????????????????????????????????????????????????????????? 17280 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75567160 ???????????????????????????????????????????????????????????? 17340 ------------------------------------------------------------ CAG33136. 45 ------------------------------------------------------------ chr13 75567220 ???????????????????????????????????????????????????????????? 17400 -----||||||||||||||||||||||||||||||||||||||||||||||||||||||| CAG33136. 45 -----??????????????????????????????????????????????????????? chr13 75567280 ???????????????????????????????? 75567312 17460 |||||||||||||||||||||||||||||||| 17492 CAG33136. 100 ???????????????????????????????? 132 """, ) self.assertEqual( format(alignment, "bed"), """\ chr13 75549820 75567312 CAG33136.1 986 + 75549820 75567312 0 2 45,87, 0,17405, """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 132: identities = 0, mismatches = 0. gaps = 17360: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 17360: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 17360: open_internal_deletions = 1, extend_internal_deletions = 17359; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 17360) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 17360) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 17360) self.assertEqual(counts.gaps, 17360) self.assertEqual(counts.aligned, 132) alignment = next(alignments) self.assertEqual(alignment.score, 1000) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr13") self.assertEqual(alignment.query.id, "CAG33136.1") self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[75604767, 75604827, 75605728, 75605809], [ 0, 60, 60, 141]]), # fmt: on ) ) self.assertEqual( str(alignment), """\ chr13 75604767 ???????????????????????????????????????????????????????????? 0 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| CAG33136. 0 ???????????????????????????????????????????????????????????? chr13 75604827 ???????????????????????????????????????????????????????????? 60 ------------------------------------------------------------ CAG33136. 60 ------------------------------------------------------------ chr13 75604887 ???????????????????????????????????????????????????????????? 120 ------------------------------------------------------------ CAG33136. 60 ------------------------------------------------------------ chr13 75604947 ???????????????????????????????????????????????????????????? 180 ------------------------------------------------------------ CAG33136. 60 ------------------------------------------------------------ chr13 75605007 ???????????????????????????????????????????????????????????? 240 ------------------------------------------------------------ CAG33136. 60 ------------------------------------------------------------ chr13 75605067 ???????????????????????????????????????????????????????????? 300 ------------------------------------------------------------ CAG33136. 60 ------------------------------------------------------------ chr13 75605127 ???????????????????????????????????????????????????????????? 360 ------------------------------------------------------------ CAG33136. 60 ------------------------------------------------------------ chr13 75605187 ???????????????????????????????????????????????????????????? 420 ------------------------------------------------------------ CAG33136. 60 ------------------------------------------------------------ chr13 75605247 ???????????????????????????????????????????????????????????? 480 ------------------------------------------------------------ CAG33136. 60 ------------------------------------------------------------ chr13 75605307 ???????????????????????????????????????????????????????????? 540 ------------------------------------------------------------ CAG33136. 60 ------------------------------------------------------------ chr13 75605367 ???????????????????????????????????????????????????????????? 600 ------------------------------------------------------------ CAG33136. 60 ------------------------------------------------------------ chr13 75605427 ???????????????????????????????????????????????????????????? 660 ------------------------------------------------------------ CAG33136. 60 ------------------------------------------------------------ chr13 75605487 ???????????????????????????????????????????????????????????? 720 ------------------------------------------------------------ CAG33136. 60 ------------------------------------------------------------ chr13 75605547 ???????????????????????????????????????????????????????????? 780 ------------------------------------------------------------ CAG33136. 60 ------------------------------------------------------------ chr13 75605607 ???????????????????????????????????????????????????????????? 840 ------------------------------------------------------------ CAG33136. 60 ------------------------------------------------------------ chr13 75605667 ???????????????????????????????????????????????????????????? 900 ------------------------------------------------------------ CAG33136. 60 ------------------------------------------------------------ chr13 75605727 ???????????????????????????????????????????????????????????? 960 -||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| CAG33136. 60 -??????????????????????????????????????????????????????????? chr13 75605787 ?????????????????????? 75605809 1020 |||||||||||||||||||||| 1042 CAG33136. 119 ?????????????????????? 141 """, ) self.assertEqual( format(alignment, "bed"), """\ chr13 75604767 75605809 CAG33136.1 1000 + 75604767 75605809 0 2 60,81, 0,961, """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 141: identities = 0, mismatches = 0. gaps = 901: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 901: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 901: open_internal_deletions = 1, extend_internal_deletions = 900; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 901) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 901) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 901) self.assertEqual(counts.gaps, 901) self.assertEqual(counts.aligned, 141) alignment = next(alignments) self.assertEqual(alignment.score, 1000) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr13") self.assertEqual(alignment.query.id, "CAG33136.1") self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[75594914, 75594989], [ 0, 75]]), # fmt: on ) ) self.assertEqual( str(alignment), """\ chr13 75594914 ???????????????????????????????????????????????????????????? 0 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| CAG33136. 0 ???????????????????????????????????????????????????????????? chr13 75594974 ??????????????? 75594989 60 ||||||||||||||| 75 CAG33136. 60 ??????????????? 75 """, ) self.assertEqual( format(alignment, "bed"), """\ chr13 75594914 75594989 CAG33136.1 1000 + 75594914 75594989 0 1 75, 0, """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 75: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 75) alignment = next(alignments) self.assertEqual(alignment.score, 1000) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr13") self.assertEqual(alignment.query.id, "CAG33136.1") self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[75569459, 75569507], [ 0, 48]]), # fmt: on ) ) self.assertEqual( str(alignment), """\ chr13 75569459 ???????????????????????????????????????????????? 75569507 0 |||||||||||||||||||||||||||||||||||||||||||||||| 48 CAG33136. 0 ???????????????????????????????????????????????? 48 """, ) self.assertEqual( format(alignment, "bed"), """\ chr13 75569459 75569507 CAG33136.1 1000 + 75569459 75569507 0 1 48, 0, """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 48: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 48) alignment = next(alignments) self.assertEqual(alignment.score, 530) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr4") self.assertEqual(alignment.query.id, "CAG33136.1") self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[41260685, 41260787], [ 0, 102]]), # fmt: on ) ) self.assertEqual( str(alignment), """\ chr4 41260685 ???????????????????????????????????????????????????????????? 0 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| CAG33136. 0 ???????????????????????????????????????????????????????????? chr4 41260745 ?????????????????????????????????????????? 41260787 60 |||||||||||||||||||||||||||||||||||||||||| 102 CAG33136. 60 ?????????????????????????????????????????? 102 """, ) self.assertEqual( format(alignment, "bed"), """\ chr4 41260685 41260787 CAG33136.1 530 + 41260685 41260787 0 1 102, 0, """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 102: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 102) alignment = next(alignments) self.assertEqual(alignment.score, 166) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr4") self.assertEqual(alignment.query.id, "CAG33136.1") self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[41257605, 41257731, 41263227, 41263290], [ 0, 126, 126, 189]]), # fmt: on ) ) self.assertEqual( str(alignment), """\ chr4 41257605 ???????????????????????????????????????????????????????????? 0 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| CAG33136. 0 ???????????????????????????????????????????????????????????? chr4 41257665 ???????????????????????????????????????????????????????????? 60 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| CAG33136. 60 ???????????????????????????????????????????????????????????? chr4 41257725 ???????????????????????????????????????????????????????????? 120 ||||||------------------------------------------------------ CAG33136. 120 ??????------------------------------------------------------ chr4 41257785 ???????????????????????????????????????????????????????????? 180 ------------------------------------------------------------ CAG33136. 126 ------------------------------------------------------------ chr4 41257845 ???????????????????????????????????????????????????????????? 240 ------------------------------------------------------------ CAG33136. 126 ------------------------------------------------------------ chr4 41257905 ???????????????????????????????????????????????????????????? 300 ------------------------------------------------------------ CAG33136. 126 ------------------------------------------------------------ chr4 41257965 ???????????????????????????????????????????????????????????? 360 ------------------------------------------------------------ CAG33136. 126 ------------------------------------------------------------ chr4 41258025 ???????????????????????????????????????????????????????????? 420 ------------------------------------------------------------ CAG33136. 126 ------------------------------------------------------------ chr4 41258085 ???????????????????????????????????????????????????????????? 480 ------------------------------------------------------------ CAG33136. 126 ------------------------------------------------------------ chr4 41258145 ???????????????????????????????????????????????????????????? 540 ------------------------------------------------------------ CAG33136. 126 ------------------------------------------------------------ chr4 41258205 ???????????????????????????????????????????????????????????? 600 ------------------------------------------------------------ CAG33136. 126 ------------------------------------------------------------ chr4 41258265 ???????????????????????????????????????????????????????????? 660 ------------------------------------------------------------ CAG33136. 126 ------------------------------------------------------------ chr4 41258325 ???????????????????????????????????????????????????????????? 720 ------------------------------------------------------------ CAG33136. 126 ------------------------------------------------------------ chr4 41258385 ???????????????????????????????????????????????????????????? 780 ------------------------------------------------------------ CAG33136. 126 ------------------------------------------------------------ chr4 41258445 ???????????????????????????????????????????????????????????? 840 ------------------------------------------------------------ CAG33136. 126 ------------------------------------------------------------ chr4 41258505 ???????????????????????????????????????????????????????????? 900 ------------------------------------------------------------ CAG33136. 126 ------------------------------------------------------------ chr4 41258565 ???????????????????????????????????????????????????????????? 960 ------------------------------------------------------------ CAG33136. 126 ------------------------------------------------------------ chr4 41258625 ???????????????????????????????????????????????????????????? 1020 ------------------------------------------------------------ CAG33136. 126 ------------------------------------------------------------ chr4 41258685 ???????????????????????????????????????????????????????????? 1080 ------------------------------------------------------------ CAG33136. 126 ------------------------------------------------------------ chr4 41258745 ???????????????????????????????????????????????????????????? 1140 ------------------------------------------------------------ CAG33136. 126 ------------------------------------------------------------ chr4 41258805 ???????????????????????????????????????????????????????????? 1200 ------------------------------------------------------------ CAG33136. 126 ------------------------------------------------------------ chr4 41258865 ???????????????????????????????????????????????????????????? 1260 ------------------------------------------------------------ CAG33136. 126 ------------------------------------------------------------ chr4 41258925 ???????????????????????????????????????????????????????????? 1320 ------------------------------------------------------------ CAG33136. 126 ------------------------------------------------------------ chr4 41258985 ???????????????????????????????????????????????????????????? 1380 ------------------------------------------------------------ CAG33136. 126 ------------------------------------------------------------ chr4 41259045 ???????????????????????????????????????????????????????????? 1440 ------------------------------------------------------------ CAG33136. 126 ------------------------------------------------------------ chr4 41259105 ???????????????????????????????????????????????????????????? 1500 ------------------------------------------------------------ CAG33136. 126 ------------------------------------------------------------ chr4 41259165 ???????????????????????????????????????????????????????????? 1560 ------------------------------------------------------------ CAG33136. 126 ------------------------------------------------------------ chr4 41259225 ???????????????????????????????????????????????????????????? 1620 ------------------------------------------------------------ CAG33136. 126 ------------------------------------------------------------ chr4 41259285 ???????????????????????????????????????????????????????????? 1680 ------------------------------------------------------------ CAG33136. 126 ------------------------------------------------------------ chr4 41259345 ???????????????????????????????????????????????????????????? 1740 ------------------------------------------------------------ CAG33136. 126 ------------------------------------------------------------ chr4 41259405 ???????????????????????????????????????????????????????????? 1800 ------------------------------------------------------------ CAG33136. 126 ------------------------------------------------------------ chr4 41259465 ???????????????????????????????????????????????????????????? 1860 ------------------------------------------------------------ CAG33136. 126 ------------------------------------------------------------ chr4 41259525 ???????????????????????????????????????????????????????????? 1920 ------------------------------------------------------------ CAG33136. 126 ------------------------------------------------------------ chr4 41259585 ???????????????????????????????????????????????????????????? 1980 ------------------------------------------------------------ CAG33136. 126 ------------------------------------------------------------ chr4 41259645 ???????????????????????????????????????????????????????????? 2040 ------------------------------------------------------------ CAG33136. 126 ------------------------------------------------------------ chr4 41259705 ???????????????????????????????????????????????????????????? 2100 ------------------------------------------------------------ CAG33136. 126 ------------------------------------------------------------ chr4 41259765 ???????????????????????????????????????????????????????????? 2160 ------------------------------------------------------------ CAG33136. 126 ------------------------------------------------------------ chr4 41259825 ???????????????????????????????????????????????????????????? 2220 ------------------------------------------------------------ CAG33136. 126 ------------------------------------------------------------ chr4 41259885 ???????????????????????????????????????????????????????????? 2280 ------------------------------------------------------------ CAG33136. 126 ------------------------------------------------------------ chr4 41259945 ???????????????????????????????????????????????????????????? 2340 ------------------------------------------------------------ CAG33136. 126 ------------------------------------------------------------ chr4 41260005 ???????????????????????????????????????????????????????????? 2400 ------------------------------------------------------------ CAG33136. 126 ------------------------------------------------------------ chr4 41260065 ???????????????????????????????????????????????????????????? 2460 ------------------------------------------------------------ CAG33136. 126 ------------------------------------------------------------ chr4 41260125 ???????????????????????????????????????????????????????????? 2520 ------------------------------------------------------------ CAG33136. 126 ------------------------------------------------------------ chr4 41260185 ???????????????????????????????????????????????????????????? 2580 ------------------------------------------------------------ CAG33136. 126 ------------------------------------------------------------ chr4 41260245 ???????????????????????????????????????????????????????????? 2640 ------------------------------------------------------------ CAG33136. 126 ------------------------------------------------------------ chr4 41260305 ???????????????????????????????????????????????????????????? 2700 ------------------------------------------------------------ CAG33136. 126 ------------------------------------------------------------ chr4 41260365 ???????????????????????????????????????????????????????????? 2760 ------------------------------------------------------------ CAG33136. 126 ------------------------------------------------------------ chr4 41260425 ???????????????????????????????????????????????????????????? 2820 ------------------------------------------------------------ CAG33136. 126 ------------------------------------------------------------ chr4 41260485 ???????????????????????????????????????????????????????????? 2880 ------------------------------------------------------------ CAG33136. 126 ------------------------------------------------------------ chr4 41260545 ???????????????????????????????????????????????????????????? 2940 ------------------------------------------------------------ CAG33136. 126 ------------------------------------------------------------ chr4 41260605 ???????????????????????????????????????????????????????????? 3000 ------------------------------------------------------------ CAG33136. 126 ------------------------------------------------------------ chr4 41260665 ???????????????????????????????????????????????????????????? 3060 ------------------------------------------------------------ CAG33136. 126 ------------------------------------------------------------ chr4 41260725 ???????????????????????????????????????????????????????????? 3120 ------------------------------------------------------------ CAG33136. 126 ------------------------------------------------------------ chr4 41260785 ???????????????????????????????????????????????????????????? 3180 ------------------------------------------------------------ CAG33136. 126 ------------------------------------------------------------ chr4 41260845 ???????????????????????????????????????????????????????????? 3240 ------------------------------------------------------------ CAG33136. 126 ------------------------------------------------------------ chr4 41260905 ???????????????????????????????????????????????????????????? 3300 ------------------------------------------------------------ CAG33136. 126 ------------------------------------------------------------ chr4 41260965 ???????????????????????????????????????????????????????????? 3360 ------------------------------------------------------------ CAG33136. 126 ------------------------------------------------------------ chr4 41261025 ???????????????????????????????????????????????????????????? 3420 ------------------------------------------------------------ CAG33136. 126 ------------------------------------------------------------ chr4 41261085 ???????????????????????????????????????????????????????????? 3480 ------------------------------------------------------------ CAG33136. 126 ------------------------------------------------------------ chr4 41261145 ???????????????????????????????????????????????????????????? 3540 ------------------------------------------------------------ CAG33136. 126 ------------------------------------------------------------ chr4 41261205 ???????????????????????????????????????????????????????????? 3600 ------------------------------------------------------------ CAG33136. 126 ------------------------------------------------------------ chr4 41261265 ???????????????????????????????????????????????????????????? 3660 ------------------------------------------------------------ CAG33136. 126 ------------------------------------------------------------ chr4 41261325 ???????????????????????????????????????????????????????????? 3720 ------------------------------------------------------------ CAG33136. 126 ------------------------------------------------------------ chr4 41261385 ???????????????????????????????????????????????????????????? 3780 ------------------------------------------------------------ CAG33136. 126 ------------------------------------------------------------ chr4 41261445 ???????????????????????????????????????????????????????????? 3840 ------------------------------------------------------------ CAG33136. 126 ------------------------------------------------------------ chr4 41261505 ???????????????????????????????????????????????????????????? 3900 ------------------------------------------------------------ CAG33136. 126 ------------------------------------------------------------ chr4 41261565 ???????????????????????????????????????????????????????????? 3960 ------------------------------------------------------------ CAG33136. 126 ------------------------------------------------------------ chr4 41261625 ???????????????????????????????????????????????????????????? 4020 ------------------------------------------------------------ CAG33136. 126 ------------------------------------------------------------ chr4 41261685 ???????????????????????????????????????????????????????????? 4080 ------------------------------------------------------------ CAG33136. 126 ------------------------------------------------------------ chr4 41261745 ???????????????????????????????????????????????????????????? 4140 ------------------------------------------------------------ CAG33136. 126 ------------------------------------------------------------ chr4 41261805 ???????????????????????????????????????????????????????????? 4200 ------------------------------------------------------------ CAG33136. 126 ------------------------------------------------------------ chr4 41261865 ???????????????????????????????????????????????????????????? 4260 ------------------------------------------------------------ CAG33136. 126 ------------------------------------------------------------ chr4 41261925 ???????????????????????????????????????????????????????????? 4320 ------------------------------------------------------------ CAG33136. 126 ------------------------------------------------------------ chr4 41261985 ???????????????????????????????????????????????????????????? 4380 ------------------------------------------------------------ CAG33136. 126 ------------------------------------------------------------ chr4 41262045 ???????????????????????????????????????????????????????????? 4440 ------------------------------------------------------------ CAG33136. 126 ------------------------------------------------------------ chr4 41262105 ???????????????????????????????????????????????????????????? 4500 ------------------------------------------------------------ CAG33136. 126 ------------------------------------------------------------ chr4 41262165 ???????????????????????????????????????????????????????????? 4560 ------------------------------------------------------------ CAG33136. 126 ------------------------------------------------------------ chr4 41262225 ???????????????????????????????????????????????????????????? 4620 ------------------------------------------------------------ CAG33136. 126 ------------------------------------------------------------ chr4 41262285 ???????????????????????????????????????????????????????????? 4680 ------------------------------------------------------------ CAG33136. 126 ------------------------------------------------------------ chr4 41262345 ???????????????????????????????????????????????????????????? 4740 ------------------------------------------------------------ CAG33136. 126 ------------------------------------------------------------ chr4 41262405 ???????????????????????????????????????????????????????????? 4800 ------------------------------------------------------------ CAG33136. 126 ------------------------------------------------------------ chr4 41262465 ???????????????????????????????????????????????????????????? 4860 ------------------------------------------------------------ CAG33136. 126 ------------------------------------------------------------ chr4 41262525 ???????????????????????????????????????????????????????????? 4920 ------------------------------------------------------------ CAG33136. 126 ------------------------------------------------------------ chr4 41262585 ???????????????????????????????????????????????????????????? 4980 ------------------------------------------------------------ CAG33136. 126 ------------------------------------------------------------ chr4 41262645 ???????????????????????????????????????????????????????????? 5040 ------------------------------------------------------------ CAG33136. 126 ------------------------------------------------------------ chr4 41262705 ???????????????????????????????????????????????????????????? 5100 ------------------------------------------------------------ CAG33136. 126 ------------------------------------------------------------ chr4 41262765 ???????????????????????????????????????????????????????????? 5160 ------------------------------------------------------------ CAG33136. 126 ------------------------------------------------------------ chr4 41262825 ???????????????????????????????????????????????????????????? 5220 ------------------------------------------------------------ CAG33136. 126 ------------------------------------------------------------ chr4 41262885 ???????????????????????????????????????????????????????????? 5280 ------------------------------------------------------------ CAG33136. 126 ------------------------------------------------------------ chr4 41262945 ???????????????????????????????????????????????????????????? 5340 ------------------------------------------------------------ CAG33136. 126 ------------------------------------------------------------ chr4 41263005 ???????????????????????????????????????????????????????????? 5400 ------------------------------------------------------------ CAG33136. 126 ------------------------------------------------------------ chr4 41263065 ???????????????????????????????????????????????????????????? 5460 ------------------------------------------------------------ CAG33136. 126 ------------------------------------------------------------ chr4 41263125 ???????????????????????????????????????????????????????????? 5520 ------------------------------------------------------------ CAG33136. 126 ------------------------------------------------------------ chr4 41263185 ???????????????????????????????????????????????????????????? 5580 ------------------------------------------|||||||||||||||||| CAG33136. 126 ------------------------------------------?????????????????? chr4 41263245 ????????????????????????????????????????????? 41263290 5640 ||||||||||||||||||||||||||||||||||||||||||||| 5685 CAG33136. 144 ????????????????????????????????????????????? 189 """, ) self.assertEqual( format(alignment, "bed"), """\ chr4 41257605 41263290 CAG33136.1 166 + 41257605 41263290 0 2 126,63, 0,5622, """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 189: identities = 0, mismatches = 0. gaps = 5496: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 5496: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 5496: open_internal_deletions = 1, extend_internal_deletions = 5495; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 5496) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 5496) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 5496) self.assertEqual(counts.gaps, 5496) self.assertEqual(counts.aligned, 189) self.assertRaises(StopIteration, next, alignments) def test_writing_psl_35_001(self): """Test writing the alignments in psl_35_001.bed.""" path = "Blat/psl_35_001.bed" with open(path) as stream: original_data = stream.read() alignments = Align.parse(path, "bed") stream = StringIO() n = Align.write(alignments, stream, "bed") self.assertEqual(n, 8) stream.seek(0) written_data = stream.read() stream.close() self.assertEqual(original_data, written_data) def test_reading_psl_35_002(self): """Test parsing psl_35_002.bed.""" path = "Blat/psl_35_002.bed" alignments = Align.parse(path, "bed") alignment = next(alignments) self.assertEqual(alignment.score, 972) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "KI537979") self.assertEqual(alignment.query.id, "CAG33136.1") self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[9712654, 9712786, 9715941, 9716097, 9716445, 9716532, 9718374, 9718422, 9739264, 9739339, 9743706, 9743766, 9744511, 9744592], [ 0, 132, 132, 288, 288, 375, 375, 423, 423, 498, 498, 558, 558, 639]]), # fmt: on ) ) self.assertEqual( str(alignment), """\ KI537979 9712654 ???????????????????????????????????????????????????????????? 0 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| CAG33136. 0 ???????????????????????????????????????????????????????????? KI537979 9712714 ???????????????????????????????????????????????????????????? 60 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| CAG33136. 60 ???????????????????????????????????????????????????????????? KI537979 9712774 ???????????????????????????????????????????????????????????? 120 ||||||||||||------------------------------------------------ CAG33136. 120 ????????????------------------------------------------------ KI537979 9712834 ???????????????????????????????????????????????????????????? 180 ------------------------------------------------------------ CAG33136. 132 ------------------------------------------------------------ KI537979 9712894 ???????????????????????????????????????????????????????????? 240 ------------------------------------------------------------ CAG33136. 132 ------------------------------------------------------------ KI537979 9712954 ???????????????????????????????????????????????????????????? 300 ------------------------------------------------------------ CAG33136. 132 ------------------------------------------------------------ KI537979 9713014 ???????????????????????????????????????????????????????????? 360 ------------------------------------------------------------ CAG33136. 132 ------------------------------------------------------------ KI537979 9713074 ???????????????????????????????????????????????????????????? 420 ------------------------------------------------------------ CAG33136. 132 ------------------------------------------------------------ KI537979 9713134 ???????????????????????????????????????????????????????????? 480 ------------------------------------------------------------ CAG33136. 132 ------------------------------------------------------------ KI537979 9713194 ???????????????????????????????????????????????????????????? 540 ------------------------------------------------------------ CAG33136. 132 ------------------------------------------------------------ KI537979 9713254 ???????????????????????????????????????????????????????????? 600 ------------------------------------------------------------ CAG33136. 132 ------------------------------------------------------------ KI537979 9713314 ???????????????????????????????????????????????????????????? 660 ------------------------------------------------------------ CAG33136. 132 ------------------------------------------------------------ KI537979 9713374 ???????????????????????????????????????????????????????????? 720 ------------------------------------------------------------ CAG33136. 132 ------------------------------------------------------------ KI537979 9713434 ???????????????????????????????????????????????????????????? 780 ------------------------------------------------------------ CAG33136. 132 ------------------------------------------------------------ KI537979 9713494 ???????????????????????????????????????????????????????????? 840 ------------------------------------------------------------ CAG33136. 132 ------------------------------------------------------------ KI537979 9713554 ???????????????????????????????????????????????????????????? 900 ------------------------------------------------------------ CAG33136. 132 ------------------------------------------------------------ KI537979 9713614 ???????????????????????????????????????????????????????????? 960 ------------------------------------------------------------ CAG33136. 132 ------------------------------------------------------------ KI537979 9713674 ???????????????????????????????????????????????????????????? 1020 ------------------------------------------------------------ CAG33136. 132 ------------------------------------------------------------ KI537979 9713734 ???????????????????????????????????????????????????????????? 1080 ------------------------------------------------------------ CAG33136. 132 ------------------------------------------------------------ KI537979 9713794 ???????????????????????????????????????????????????????????? 1140 ------------------------------------------------------------ CAG33136. 132 ------------------------------------------------------------ KI537979 9713854 ???????????????????????????????????????????????????????????? 1200 ------------------------------------------------------------ CAG33136. 132 ------------------------------------------------------------ KI537979 9713914 ???????????????????????????????????????????????????????????? 1260 ------------------------------------------------------------ CAG33136. 132 ------------------------------------------------------------ KI537979 9713974 ???????????????????????????????????????????????????????????? 1320 ------------------------------------------------------------ CAG33136. 132 ------------------------------------------------------------ KI537979 9714034 ???????????????????????????????????????????????????????????? 1380 ------------------------------------------------------------ CAG33136. 132 ------------------------------------------------------------ KI537979 9714094 ???????????????????????????????????????????????????????????? 1440 ------------------------------------------------------------ CAG33136. 132 ------------------------------------------------------------ KI537979 9714154 ???????????????????????????????????????????????????????????? 1500 ------------------------------------------------------------ CAG33136. 132 ------------------------------------------------------------ KI537979 9714214 ???????????????????????????????????????????????????????????? 1560 ------------------------------------------------------------ CAG33136. 132 ------------------------------------------------------------ KI537979 9714274 ???????????????????????????????????????????????????????????? 1620 ------------------------------------------------------------ CAG33136. 132 ------------------------------------------------------------ KI537979 9714334 ???????????????????????????????????????????????????????????? 1680 ------------------------------------------------------------ CAG33136. 132 ------------------------------------------------------------ KI537979 9714394 ???????????????????????????????????????????????????????????? 1740 ------------------------------------------------------------ CAG33136. 132 ------------------------------------------------------------ KI537979 9714454 ???????????????????????????????????????????????????????????? 1800 ------------------------------------------------------------ CAG33136. 132 ------------------------------------------------------------ KI537979 9714514 ???????????????????????????????????????????????????????????? 1860 ------------------------------------------------------------ CAG33136. 132 ------------------------------------------------------------ KI537979 9714574 ???????????????????????????????????????????????????????????? 1920 ------------------------------------------------------------ CAG33136. 132 ------------------------------------------------------------ KI537979 9714634 ???????????????????????????????????????????????????????????? 1980 ------------------------------------------------------------ CAG33136. 132 ------------------------------------------------------------ KI537979 9714694 ???????????????????????????????????????????????????????????? 2040 ------------------------------------------------------------ CAG33136. 132 ------------------------------------------------------------ KI537979 9714754 ???????????????????????????????????????????????????????????? 2100 ------------------------------------------------------------ CAG33136. 132 ------------------------------------------------------------ KI537979 9714814 ???????????????????????????????????????????????????????????? 2160 ------------------------------------------------------------ CAG33136. 132 ------------------------------------------------------------ KI537979 9714874 ???????????????????????????????????????????????????????????? 2220 ------------------------------------------------------------ CAG33136. 132 ------------------------------------------------------------ KI537979 9714934 ???????????????????????????????????????????????????????????? 2280 ------------------------------------------------------------ CAG33136. 132 ------------------------------------------------------------ KI537979 9714994 ???????????????????????????????????????????????????????????? 2340 ------------------------------------------------------------ CAG33136. 132 ------------------------------------------------------------ KI537979 9715054 ???????????????????????????????????????????????????????????? 2400 ------------------------------------------------------------ CAG33136. 132 ------------------------------------------------------------ KI537979 9715114 ???????????????????????????????????????????????????????????? 2460 ------------------------------------------------------------ CAG33136. 132 ------------------------------------------------------------ KI537979 9715174 ???????????????????????????????????????????????????????????? 2520 ------------------------------------------------------------ CAG33136. 132 ------------------------------------------------------------ KI537979 9715234 ???????????????????????????????????????????????????????????? 2580 ------------------------------------------------------------ CAG33136. 132 ------------------------------------------------------------ KI537979 9715294 ???????????????????????????????????????????????????????????? 2640 ------------------------------------------------------------ CAG33136. 132 ------------------------------------------------------------ KI537979 9715354 ???????????????????????????????????????????????????????????? 2700 ------------------------------------------------------------ CAG33136. 132 ------------------------------------------------------------ KI537979 9715414 ???????????????????????????????????????????????????????????? 2760 ------------------------------------------------------------ CAG33136. 132 ------------------------------------------------------------ KI537979 9715474 ???????????????????????????????????????????????????????????? 2820 ------------------------------------------------------------ CAG33136. 132 ------------------------------------------------------------ KI537979 9715534 ???????????????????????????????????????????????????????????? 2880 ------------------------------------------------------------ CAG33136. 132 ------------------------------------------------------------ KI537979 9715594 ???????????????????????????????????????????????????????????? 2940 ------------------------------------------------------------ CAG33136. 132 ------------------------------------------------------------ KI537979 9715654 ???????????????????????????????????????????????????????????? 3000 ------------------------------------------------------------ CAG33136. 132 ------------------------------------------------------------ KI537979 9715714 ???????????????????????????????????????????????????????????? 3060 ------------------------------------------------------------ CAG33136. 132 ------------------------------------------------------------ KI537979 9715774 ???????????????????????????????????????????????????????????? 3120 ------------------------------------------------------------ CAG33136. 132 ------------------------------------------------------------ KI537979 9715834 ???????????????????????????????????????????????????????????? 3180 ------------------------------------------------------------ CAG33136. 132 ------------------------------------------------------------ KI537979 9715894 ???????????????????????????????????????????????????????????? 3240 -----------------------------------------------||||||||||||| CAG33136. 132 -----------------------------------------------????????????? KI537979 9715954 ???????????????????????????????????????????????????????????? 3300 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| CAG33136. 145 ???????????????????????????????????????????????????????????? KI537979 9716014 ???????????????????????????????????????????????????????????? 3360 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| CAG33136. 205 ???????????????????????????????????????????????????????????? KI537979 9716074 ???????????????????????????????????????????????????????????? 3420 |||||||||||||||||||||||------------------------------------- CAG33136. 265 ???????????????????????------------------------------------- KI537979 9716134 ???????????????????????????????????????????????????????????? 3480 ------------------------------------------------------------ CAG33136. 288 ------------------------------------------------------------ KI537979 9716194 ???????????????????????????????????????????????????????????? 3540 ------------------------------------------------------------ CAG33136. 288 ------------------------------------------------------------ KI537979 9716254 ???????????????????????????????????????????????????????????? 3600 ------------------------------------------------------------ CAG33136. 288 ------------------------------------------------------------ KI537979 9716314 ???????????????????????????????????????????????????????????? 3660 ------------------------------------------------------------ CAG33136. 288 ------------------------------------------------------------ KI537979 9716374 ???????????????????????????????????????????????????????????? 3720 ------------------------------------------------------------ CAG33136. 288 ------------------------------------------------------------ KI537979 9716434 ???????????????????????????????????????????????????????????? 3780 -----------||||||||||||||||||||||||||||||||||||||||||||||||| CAG33136. 288 -----------????????????????????????????????????????????????? KI537979 9716494 ???????????????????????????????????????????????????????????? 3840 ||||||||||||||||||||||||||||||||||||||---------------------- CAG33136. 337 ??????????????????????????????????????---------------------- KI537979 9716554 ???????????????????????????????????????????????????????????? 3900 ------------------------------------------------------------ CAG33136. 375 ------------------------------------------------------------ KI537979 9716614 ???????????????????????????????????????????????????????????? 3960 ------------------------------------------------------------ CAG33136. 375 ------------------------------------------------------------ KI537979 9716674 ???????????????????????????????????????????????????????????? 4020 ------------------------------------------------------------ CAG33136. 375 ------------------------------------------------------------ KI537979 9716734 ???????????????????????????????????????????????????????????? 4080 ------------------------------------------------------------ CAG33136. 375 ------------------------------------------------------------ KI537979 9716794 ???????????????????????????????????????????????????????????? 4140 ------------------------------------------------------------ CAG33136. 375 ------------------------------------------------------------ KI537979 9716854 ???????????????????????????????????????????????????????????? 4200 ------------------------------------------------------------ CAG33136. 375 ------------------------------------------------------------ KI537979 9716914 ???????????????????????????????????????????????????????????? 4260 ------------------------------------------------------------ CAG33136. 375 ------------------------------------------------------------ KI537979 9716974 ???????????????????????????????????????????????????????????? 4320 ------------------------------------------------------------ CAG33136. 375 ------------------------------------------------------------ KI537979 9717034 ???????????????????????????????????????????????????????????? 4380 ------------------------------------------------------------ CAG33136. 375 ------------------------------------------------------------ KI537979 9717094 ???????????????????????????????????????????????????????????? 4440 ------------------------------------------------------------ CAG33136. 375 ------------------------------------------------------------ KI537979 9717154 ???????????????????????????????????????????????????????????? 4500 ------------------------------------------------------------ CAG33136. 375 ------------------------------------------------------------ KI537979 9717214 ???????????????????????????????????????????????????????????? 4560 ------------------------------------------------------------ CAG33136. 375 ------------------------------------------------------------ KI537979 9717274 ???????????????????????????????????????????????????????????? 4620 ------------------------------------------------------------ CAG33136. 375 ------------------------------------------------------------ KI537979 9717334 ???????????????????????????????????????????????????????????? 4680 ------------------------------------------------------------ CAG33136. 375 ------------------------------------------------------------ KI537979 9717394 ???????????????????????????????????????????????????????????? 4740 ------------------------------------------------------------ CAG33136. 375 ------------------------------------------------------------ KI537979 9717454 ???????????????????????????????????????????????????????????? 4800 ------------------------------------------------------------ CAG33136. 375 ------------------------------------------------------------ KI537979 9717514 ???????????????????????????????????????????????????????????? 4860 ------------------------------------------------------------ CAG33136. 375 ------------------------------------------------------------ KI537979 9717574 ???????????????????????????????????????????????????????????? 4920 ------------------------------------------------------------ CAG33136. 375 ------------------------------------------------------------ KI537979 9717634 ???????????????????????????????????????????????????????????? 4980 ------------------------------------------------------------ CAG33136. 375 ------------------------------------------------------------ KI537979 9717694 ???????????????????????????????????????????????????????????? 5040 ------------------------------------------------------------ CAG33136. 375 ------------------------------------------------------------ KI537979 9717754 ???????????????????????????????????????????????????????????? 5100 ------------------------------------------------------------ CAG33136. 375 ------------------------------------------------------------ KI537979 9717814 ???????????????????????????????????????????????????????????? 5160 ------------------------------------------------------------ CAG33136. 375 ------------------------------------------------------------ KI537979 9717874 ???????????????????????????????????????????????????????????? 5220 ------------------------------------------------------------ CAG33136. 375 ------------------------------------------------------------ KI537979 9717934 ???????????????????????????????????????????????????????????? 5280 ------------------------------------------------------------ CAG33136. 375 ------------------------------------------------------------ KI537979 9717994 ???????????????????????????????????????????????????????????? 5340 ------------------------------------------------------------ CAG33136. 375 ------------------------------------------------------------ KI537979 9718054 ???????????????????????????????????????????????????????????? 5400 ------------------------------------------------------------ CAG33136. 375 ------------------------------------------------------------ KI537979 9718114 ???????????????????????????????????????????????????????????? 5460 ------------------------------------------------------------ CAG33136. 375 ------------------------------------------------------------ KI537979 9718174 ???????????????????????????????????????????????????????????? 5520 ------------------------------------------------------------ CAG33136. 375 ------------------------------------------------------------ KI537979 9718234 ???????????????????????????????????????????????????????????? 5580 ------------------------------------------------------------ CAG33136. 375 ------------------------------------------------------------ KI537979 9718294 ???????????????????????????????????????????????????????????? 5640 ------------------------------------------------------------ CAG33136. 375 ------------------------------------------------------------ KI537979 9718354 ???????????????????????????????????????????????????????????? 5700 --------------------|||||||||||||||||||||||||||||||||||||||| CAG33136. 375 --------------------???????????????????????????????????????? KI537979 9718414 ???????????????????????????????????????????????????????????? 5760 ||||||||---------------------------------------------------- CAG33136. 415 ????????---------------------------------------------------- KI537979 9718474 ???????????????????????????????????????????????????????????? 5820 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9718534 ???????????????????????????????????????????????????????????? 5880 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9718594 ???????????????????????????????????????????????????????????? 5940 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9718654 ???????????????????????????????????????????????????????????? 6000 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9718714 ???????????????????????????????????????????????????????????? 6060 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9718774 ???????????????????????????????????????????????????????????? 6120 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9718834 ???????????????????????????????????????????????????????????? 6180 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9718894 ???????????????????????????????????????????????????????????? 6240 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9718954 ???????????????????????????????????????????????????????????? 6300 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9719014 ???????????????????????????????????????????????????????????? 6360 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9719074 ???????????????????????????????????????????????????????????? 6420 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9719134 ???????????????????????????????????????????????????????????? 6480 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9719194 ???????????????????????????????????????????????????????????? 6540 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9719254 ???????????????????????????????????????????????????????????? 6600 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9719314 ???????????????????????????????????????????????????????????? 6660 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9719374 ???????????????????????????????????????????????????????????? 6720 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9719434 ???????????????????????????????????????????????????????????? 6780 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9719494 ???????????????????????????????????????????????????????????? 6840 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9719554 ???????????????????????????????????????????????????????????? 6900 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9719614 ???????????????????????????????????????????????????????????? 6960 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9719674 ???????????????????????????????????????????????????????????? 7020 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9719734 ???????????????????????????????????????????????????????????? 7080 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9719794 ???????????????????????????????????????????????????????????? 7140 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9719854 ???????????????????????????????????????????????????????????? 7200 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9719914 ???????????????????????????????????????????????????????????? 7260 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9719974 ???????????????????????????????????????????????????????????? 7320 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9720034 ???????????????????????????????????????????????????????????? 7380 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9720094 ???????????????????????????????????????????????????????????? 7440 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9720154 ???????????????????????????????????????????????????????????? 7500 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9720214 ???????????????????????????????????????????????????????????? 7560 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9720274 ???????????????????????????????????????????????????????????? 7620 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9720334 ???????????????????????????????????????????????????????????? 7680 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9720394 ???????????????????????????????????????????????????????????? 7740 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9720454 ???????????????????????????????????????????????????????????? 7800 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9720514 ???????????????????????????????????????????????????????????? 7860 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9720574 ???????????????????????????????????????????????????????????? 7920 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9720634 ???????????????????????????????????????????????????????????? 7980 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9720694 ???????????????????????????????????????????????????????????? 8040 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9720754 ???????????????????????????????????????????????????????????? 8100 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9720814 ???????????????????????????????????????????????????????????? 8160 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9720874 ???????????????????????????????????????????????????????????? 8220 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9720934 ???????????????????????????????????????????????????????????? 8280 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9720994 ???????????????????????????????????????????????????????????? 8340 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9721054 ???????????????????????????????????????????????????????????? 8400 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9721114 ???????????????????????????????????????????????????????????? 8460 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9721174 ???????????????????????????????????????????????????????????? 8520 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9721234 ???????????????????????????????????????????????????????????? 8580 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9721294 ???????????????????????????????????????????????????????????? 8640 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9721354 ???????????????????????????????????????????????????????????? 8700 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9721414 ???????????????????????????????????????????????????????????? 8760 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9721474 ???????????????????????????????????????????????????????????? 8820 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9721534 ???????????????????????????????????????????????????????????? 8880 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9721594 ???????????????????????????????????????????????????????????? 8940 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9721654 ???????????????????????????????????????????????????????????? 9000 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9721714 ???????????????????????????????????????????????????????????? 9060 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9721774 ???????????????????????????????????????????????????????????? 9120 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9721834 ???????????????????????????????????????????????????????????? 9180 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9721894 ???????????????????????????????????????????????????????????? 9240 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9721954 ???????????????????????????????????????????????????????????? 9300 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9722014 ???????????????????????????????????????????????????????????? 9360 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9722074 ???????????????????????????????????????????????????????????? 9420 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9722134 ???????????????????????????????????????????????????????????? 9480 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9722194 ???????????????????????????????????????????????????????????? 9540 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9722254 ???????????????????????????????????????????????????????????? 9600 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9722314 ???????????????????????????????????????????????????????????? 9660 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9722374 ???????????????????????????????????????????????????????????? 9720 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9722434 ???????????????????????????????????????????????????????????? 9780 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9722494 ???????????????????????????????????????????????????????????? 9840 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9722554 ???????????????????????????????????????????????????????????? 9900 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9722614 ???????????????????????????????????????????????????????????? 9960 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9722674 ???????????????????????????????????????????????????????????? 10020 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9722734 ???????????????????????????????????????????????????????????? 10080 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9722794 ???????????????????????????????????????????????????????????? 10140 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9722854 ???????????????????????????????????????????????????????????? 10200 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9722914 ???????????????????????????????????????????????????????????? 10260 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9722974 ???????????????????????????????????????????????????????????? 10320 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9723034 ???????????????????????????????????????????????????????????? 10380 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9723094 ???????????????????????????????????????????????????????????? 10440 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9723154 ???????????????????????????????????????????????????????????? 10500 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9723214 ???????????????????????????????????????????????????????????? 10560 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9723274 ???????????????????????????????????????????????????????????? 10620 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9723334 ???????????????????????????????????????????????????????????? 10680 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9723394 ???????????????????????????????????????????????????????????? 10740 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9723454 ???????????????????????????????????????????????????????????? 10800 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9723514 ???????????????????????????????????????????????????????????? 10860 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9723574 ???????????????????????????????????????????????????????????? 10920 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9723634 ???????????????????????????????????????????????????????????? 10980 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9723694 ???????????????????????????????????????????????????????????? 11040 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9723754 ???????????????????????????????????????????????????????????? 11100 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9723814 ???????????????????????????????????????????????????????????? 11160 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9723874 ???????????????????????????????????????????????????????????? 11220 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9723934 ???????????????????????????????????????????????????????????? 11280 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9723994 ???????????????????????????????????????????????????????????? 11340 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9724054 ???????????????????????????????????????????????????????????? 11400 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9724114 ???????????????????????????????????????????????????????????? 11460 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9724174 ???????????????????????????????????????????????????????????? 11520 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9724234 ???????????????????????????????????????????????????????????? 11580 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9724294 ???????????????????????????????????????????????????????????? 11640 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9724354 ???????????????????????????????????????????????????????????? 11700 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9724414 ???????????????????????????????????????????????????????????? 11760 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9724474 ???????????????????????????????????????????????????????????? 11820 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9724534 ???????????????????????????????????????????????????????????? 11880 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9724594 ???????????????????????????????????????????????????????????? 11940 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9724654 ???????????????????????????????????????????????????????????? 12000 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9724714 ???????????????????????????????????????????????????????????? 12060 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9724774 ???????????????????????????????????????????????????????????? 12120 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9724834 ???????????????????????????????????????????????????????????? 12180 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9724894 ???????????????????????????????????????????????????????????? 12240 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9724954 ???????????????????????????????????????????????????????????? 12300 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9725014 ???????????????????????????????????????????????????????????? 12360 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9725074 ???????????????????????????????????????????????????????????? 12420 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9725134 ???????????????????????????????????????????????????????????? 12480 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9725194 ???????????????????????????????????????????????????????????? 12540 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9725254 ???????????????????????????????????????????????????????????? 12600 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9725314 ???????????????????????????????????????????????????????????? 12660 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9725374 ???????????????????????????????????????????????????????????? 12720 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9725434 ???????????????????????????????????????????????????????????? 12780 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9725494 ???????????????????????????????????????????????????????????? 12840 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9725554 ???????????????????????????????????????????????????????????? 12900 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9725614 ???????????????????????????????????????????????????????????? 12960 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9725674 ???????????????????????????????????????????????????????????? 13020 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9725734 ???????????????????????????????????????????????????????????? 13080 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9725794 ???????????????????????????????????????????????????????????? 13140 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9725854 ???????????????????????????????????????????????????????????? 13200 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9725914 ???????????????????????????????????????????????????????????? 13260 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9725974 ???????????????????????????????????????????????????????????? 13320 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9726034 ???????????????????????????????????????????????????????????? 13380 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9726094 ???????????????????????????????????????????????????????????? 13440 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9726154 ???????????????????????????????????????????????????????????? 13500 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9726214 ???????????????????????????????????????????????????????????? 13560 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9726274 ???????????????????????????????????????????????????????????? 13620 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9726334 ???????????????????????????????????????????????????????????? 13680 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9726394 ???????????????????????????????????????????????????????????? 13740 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9726454 ???????????????????????????????????????????????????????????? 13800 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9726514 ???????????????????????????????????????????????????????????? 13860 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9726574 ???????????????????????????????????????????????????????????? 13920 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9726634 ???????????????????????????????????????????????????????????? 13980 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9726694 ???????????????????????????????????????????????????????????? 14040 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9726754 ???????????????????????????????????????????????????????????? 14100 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9726814 ???????????????????????????????????????????????????????????? 14160 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9726874 ???????????????????????????????????????????????????????????? 14220 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9726934 ???????????????????????????????????????????????????????????? 14280 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9726994 ???????????????????????????????????????????????????????????? 14340 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9727054 ???????????????????????????????????????????????????????????? 14400 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9727114 ???????????????????????????????????????????????????????????? 14460 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9727174 ???????????????????????????????????????????????????????????? 14520 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9727234 ???????????????????????????????????????????????????????????? 14580 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9727294 ???????????????????????????????????????????????????????????? 14640 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9727354 ???????????????????????????????????????????????????????????? 14700 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9727414 ???????????????????????????????????????????????????????????? 14760 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9727474 ???????????????????????????????????????????????????????????? 14820 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9727534 ???????????????????????????????????????????????????????????? 14880 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9727594 ???????????????????????????????????????????????????????????? 14940 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9727654 ???????????????????????????????????????????????????????????? 15000 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9727714 ???????????????????????????????????????????????????????????? 15060 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9727774 ???????????????????????????????????????????????????????????? 15120 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9727834 ???????????????????????????????????????????????????????????? 15180 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9727894 ???????????????????????????????????????????????????????????? 15240 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9727954 ???????????????????????????????????????????????????????????? 15300 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9728014 ???????????????????????????????????????????????????????????? 15360 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9728074 ???????????????????????????????????????????????????????????? 15420 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9728134 ???????????????????????????????????????????????????????????? 15480 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9728194 ???????????????????????????????????????????????????????????? 15540 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9728254 ???????????????????????????????????????????????????????????? 15600 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9728314 ???????????????????????????????????????????????????????????? 15660 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9728374 ???????????????????????????????????????????????????????????? 15720 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9728434 ???????????????????????????????????????????????????????????? 15780 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9728494 ???????????????????????????????????????????????????????????? 15840 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9728554 ???????????????????????????????????????????????????????????? 15900 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9728614 ???????????????????????????????????????????????????????????? 15960 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9728674 ???????????????????????????????????????????????????????????? 16020 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9728734 ???????????????????????????????????????????????????????????? 16080 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9728794 ???????????????????????????????????????????????????????????? 16140 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9728854 ???????????????????????????????????????????????????????????? 16200 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9728914 ???????????????????????????????????????????????????????????? 16260 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9728974 ???????????????????????????????????????????????????????????? 16320 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9729034 ???????????????????????????????????????????????????????????? 16380 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9729094 ???????????????????????????????????????????????????????????? 16440 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9729154 ???????????????????????????????????????????????????????????? 16500 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9729214 ???????????????????????????????????????????????????????????? 16560 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9729274 ???????????????????????????????????????????????????????????? 16620 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9729334 ???????????????????????????????????????????????????????????? 16680 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9729394 ???????????????????????????????????????????????????????????? 16740 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9729454 ???????????????????????????????????????????????????????????? 16800 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9729514 ???????????????????????????????????????????????????????????? 16860 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9729574 ???????????????????????????????????????????????????????????? 16920 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9729634 ???????????????????????????????????????????????????????????? 16980 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9729694 ???????????????????????????????????????????????????????????? 17040 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9729754 ???????????????????????????????????????????????????????????? 17100 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9729814 ???????????????????????????????????????????????????????????? 17160 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9729874 ???????????????????????????????????????????????????????????? 17220 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9729934 ???????????????????????????????????????????????????????????? 17280 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9729994 ???????????????????????????????????????????????????????????? 17340 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9730054 ???????????????????????????????????????????????????????????? 17400 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9730114 ???????????????????????????????????????????????????????????? 17460 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9730174 ???????????????????????????????????????????????????????????? 17520 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9730234 ???????????????????????????????????????????????????????????? 17580 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9730294 ???????????????????????????????????????????????????????????? 17640 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9730354 ???????????????????????????????????????????????????????????? 17700 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9730414 ???????????????????????????????????????????????????????????? 17760 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9730474 ???????????????????????????????????????????????????????????? 17820 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9730534 ???????????????????????????????????????????????????????????? 17880 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9730594 ???????????????????????????????????????????????????????????? 17940 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9730654 ???????????????????????????????????????????????????????????? 18000 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9730714 ???????????????????????????????????????????????????????????? 18060 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9730774 ???????????????????????????????????????????????????????????? 18120 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9730834 ???????????????????????????????????????????????????????????? 18180 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9730894 ???????????????????????????????????????????????????????????? 18240 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9730954 ???????????????????????????????????????????????????????????? 18300 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9731014 ???????????????????????????????????????????????????????????? 18360 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9731074 ???????????????????????????????????????????????????????????? 18420 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9731134 ???????????????????????????????????????????????????????????? 18480 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9731194 ???????????????????????????????????????????????????????????? 18540 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9731254 ???????????????????????????????????????????????????????????? 18600 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9731314 ???????????????????????????????????????????????????????????? 18660 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9731374 ???????????????????????????????????????????????????????????? 18720 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9731434 ???????????????????????????????????????????????????????????? 18780 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9731494 ???????????????????????????????????????????????????????????? 18840 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9731554 ???????????????????????????????????????????????????????????? 18900 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9731614 ???????????????????????????????????????????????????????????? 18960 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9731674 ???????????????????????????????????????????????????????????? 19020 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9731734 ???????????????????????????????????????????????????????????? 19080 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9731794 ???????????????????????????????????????????????????????????? 19140 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9731854 ???????????????????????????????????????????????????????????? 19200 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9731914 ???????????????????????????????????????????????????????????? 19260 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9731974 ???????????????????????????????????????????????????????????? 19320 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9732034 ???????????????????????????????????????????????????????????? 19380 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9732094 ???????????????????????????????????????????????????????????? 19440 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9732154 ???????????????????????????????????????????????????????????? 19500 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9732214 ???????????????????????????????????????????????????????????? 19560 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9732274 ???????????????????????????????????????????????????????????? 19620 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9732334 ???????????????????????????????????????????????????????????? 19680 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9732394 ???????????????????????????????????????????????????????????? 19740 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9732454 ???????????????????????????????????????????????????????????? 19800 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9732514 ???????????????????????????????????????????????????????????? 19860 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9732574 ???????????????????????????????????????????????????????????? 19920 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9732634 ???????????????????????????????????????????????????????????? 19980 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9732694 ???????????????????????????????????????????????????????????? 20040 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9732754 ???????????????????????????????????????????????????????????? 20100 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9732814 ???????????????????????????????????????????????????????????? 20160 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9732874 ???????????????????????????????????????????????????????????? 20220 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9732934 ???????????????????????????????????????????????????????????? 20280 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9732994 ???????????????????????????????????????????????????????????? 20340 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9733054 ???????????????????????????????????????????????????????????? 20400 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9733114 ???????????????????????????????????????????????????????????? 20460 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9733174 ???????????????????????????????????????????????????????????? 20520 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9733234 ???????????????????????????????????????????????????????????? 20580 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9733294 ???????????????????????????????????????????????????????????? 20640 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9733354 ???????????????????????????????????????????????????????????? 20700 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9733414 ???????????????????????????????????????????????????????????? 20760 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9733474 ???????????????????????????????????????????????????????????? 20820 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9733534 ???????????????????????????????????????????????????????????? 20880 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9733594 ???????????????????????????????????????????????????????????? 20940 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9733654 ???????????????????????????????????????????????????????????? 21000 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9733714 ???????????????????????????????????????????????????????????? 21060 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9733774 ???????????????????????????????????????????????????????????? 21120 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9733834 ???????????????????????????????????????????????????????????? 21180 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9733894 ???????????????????????????????????????????????????????????? 21240 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9733954 ???????????????????????????????????????????????????????????? 21300 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9734014 ???????????????????????????????????????????????????????????? 21360 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9734074 ???????????????????????????????????????????????????????????? 21420 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9734134 ???????????????????????????????????????????????????????????? 21480 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9734194 ???????????????????????????????????????????????????????????? 21540 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9734254 ???????????????????????????????????????????????????????????? 21600 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9734314 ???????????????????????????????????????????????????????????? 21660 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9734374 ???????????????????????????????????????????????????????????? 21720 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9734434 ???????????????????????????????????????????????????????????? 21780 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9734494 ???????????????????????????????????????????????????????????? 21840 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9734554 ???????????????????????????????????????????????????????????? 21900 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9734614 ???????????????????????????????????????????????????????????? 21960 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9734674 ???????????????????????????????????????????????????????????? 22020 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9734734 ???????????????????????????????????????????????????????????? 22080 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9734794 ???????????????????????????????????????????????????????????? 22140 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9734854 ???????????????????????????????????????????????????????????? 22200 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9734914 ???????????????????????????????????????????????????????????? 22260 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9734974 ???????????????????????????????????????????????????????????? 22320 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9735034 ???????????????????????????????????????????????????????????? 22380 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9735094 ???????????????????????????????????????????????????????????? 22440 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9735154 ???????????????????????????????????????????????????????????? 22500 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9735214 ???????????????????????????????????????????????????????????? 22560 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9735274 ???????????????????????????????????????????????????????????? 22620 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9735334 ???????????????????????????????????????????????????????????? 22680 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9735394 ???????????????????????????????????????????????????????????? 22740 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9735454 ???????????????????????????????????????????????????????????? 22800 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9735514 ???????????????????????????????????????????????????????????? 22860 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9735574 ???????????????????????????????????????????????????????????? 22920 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9735634 ???????????????????????????????????????????????????????????? 22980 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9735694 ???????????????????????????????????????????????????????????? 23040 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9735754 ???????????????????????????????????????????????????????????? 23100 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9735814 ???????????????????????????????????????????????????????????? 23160 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9735874 ???????????????????????????????????????????????????????????? 23220 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9735934 ???????????????????????????????????????????????????????????? 23280 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9735994 ???????????????????????????????????????????????????????????? 23340 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9736054 ???????????????????????????????????????????????????????????? 23400 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9736114 ???????????????????????????????????????????????????????????? 23460 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9736174 ???????????????????????????????????????????????????????????? 23520 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9736234 ???????????????????????????????????????????????????????????? 23580 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9736294 ???????????????????????????????????????????????????????????? 23640 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9736354 ???????????????????????????????????????????????????????????? 23700 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9736414 ???????????????????????????????????????????????????????????? 23760 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9736474 ???????????????????????????????????????????????????????????? 23820 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9736534 ???????????????????????????????????????????????????????????? 23880 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9736594 ???????????????????????????????????????????????????????????? 23940 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9736654 ???????????????????????????????????????????????????????????? 24000 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9736714 ???????????????????????????????????????????????????????????? 24060 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9736774 ???????????????????????????????????????????????????????????? 24120 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9736834 ???????????????????????????????????????????????????????????? 24180 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9736894 ???????????????????????????????????????????????????????????? 24240 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9736954 ???????????????????????????????????????????????????????????? 24300 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9737014 ???????????????????????????????????????????????????????????? 24360 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9737074 ???????????????????????????????????????????????????????????? 24420 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9737134 ???????????????????????????????????????????????????????????? 24480 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9737194 ???????????????????????????????????????????????????????????? 24540 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9737254 ???????????????????????????????????????????????????????????? 24600 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9737314 ???????????????????????????????????????????????????????????? 24660 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9737374 ???????????????????????????????????????????????????????????? 24720 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9737434 ???????????????????????????????????????????????????????????? 24780 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9737494 ???????????????????????????????????????????????????????????? 24840 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9737554 ???????????????????????????????????????????????????????????? 24900 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9737614 ???????????????????????????????????????????????????????????? 24960 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9737674 ???????????????????????????????????????????????????????????? 25020 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9737734 ???????????????????????????????????????????????????????????? 25080 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9737794 ???????????????????????????????????????????????????????????? 25140 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9737854 ???????????????????????????????????????????????????????????? 25200 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9737914 ???????????????????????????????????????????????????????????? 25260 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9737974 ???????????????????????????????????????????????????????????? 25320 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9738034 ???????????????????????????????????????????????????????????? 25380 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9738094 ???????????????????????????????????????????????????????????? 25440 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9738154 ???????????????????????????????????????????????????????????? 25500 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9738214 ???????????????????????????????????????????????????????????? 25560 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9738274 ???????????????????????????????????????????????????????????? 25620 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9738334 ???????????????????????????????????????????????????????????? 25680 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9738394 ???????????????????????????????????????????????????????????? 25740 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9738454 ???????????????????????????????????????????????????????????? 25800 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9738514 ???????????????????????????????????????????????????????????? 25860 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9738574 ???????????????????????????????????????????????????????????? 25920 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9738634 ???????????????????????????????????????????????????????????? 25980 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9738694 ???????????????????????????????????????????????????????????? 26040 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9738754 ???????????????????????????????????????????????????????????? 26100 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9738814 ???????????????????????????????????????????????????????????? 26160 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9738874 ???????????????????????????????????????????????????????????? 26220 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9738934 ???????????????????????????????????????????????????????????? 26280 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9738994 ???????????????????????????????????????????????????????????? 26340 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9739054 ???????????????????????????????????????????????????????????? 26400 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9739114 ???????????????????????????????????????????????????????????? 26460 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9739174 ???????????????????????????????????????????????????????????? 26520 ------------------------------------------------------------ CAG33136. 423 ------------------------------------------------------------ KI537979 9739234 ???????????????????????????????????????????????????????????? 26580 ------------------------------|||||||||||||||||||||||||||||| CAG33136. 423 ------------------------------?????????????????????????????? KI537979 9739294 ???????????????????????????????????????????????????????????? 26640 |||||||||||||||||||||||||||||||||||||||||||||--------------- CAG33136. 453 ?????????????????????????????????????????????--------------- KI537979 9739354 ???????????????????????????????????????????????????????????? 26700 ------------------------------------------------------------ CAG33136. 498 ------------------------------------------------------------ KI537979 9739414 ???????????????????????????????????????????????????????????? 26760 ------------------------------------------------------------ CAG33136. 498 ------------------------------------------------------------ KI537979 9739474 ???????????????????????????????????????????????????????????? 26820 ------------------------------------------------------------ CAG33136. 498 ------------------------------------------------------------ KI537979 9739534 ???????????????????????????????????????????????????????????? 26880 ------------------------------------------------------------ CAG33136. 498 ------------------------------------------------------------ KI537979 9739594 ???????????????????????????????????????????????????????????? 26940 ------------------------------------------------------------ CAG33136. 498 ------------------------------------------------------------ KI537979 9739654 ???????????????????????????????????????????????????????????? 27000 ------------------------------------------------------------ CAG33136. 498 ------------------------------------------------------------ KI537979 9739714 ???????????????????????????????????????????????????????????? 27060 ------------------------------------------------------------ CAG33136. 498 ------------------------------------------------------------ KI537979 9739774 ???????????????????????????????????????????????????????????? 27120 ------------------------------------------------------------ CAG33136. 498 ------------------------------------------------------------ KI537979 9739834 ???????????????????????????????????????????????????????????? 27180 ------------------------------------------------------------ CAG33136. 498 ------------------------------------------------------------ KI537979 9739894 ???????????????????????????????????????????????????????????? 27240 ------------------------------------------------------------ CAG33136. 498 ------------------------------------------------------------ KI537979 9739954 ???????????????????????????????????????????????????????????? 27300 ------------------------------------------------------------ CAG33136. 498 ------------------------------------------------------------ KI537979 9740014 ???????????????????????????????????????????????????????????? 27360 ------------------------------------------------------------ CAG33136. 498 ------------------------------------------------------------ KI537979 9740074 ???????????????????????????????????????????????????????????? 27420 ------------------------------------------------------------ CAG33136. 498 ------------------------------------------------------------ KI537979 9740134 ???????????????????????????????????????????????????????????? 27480 ------------------------------------------------------------ CAG33136. 498 ------------------------------------------------------------ KI537979 9740194 ???????????????????????????????????????????????????????????? 27540 ------------------------------------------------------------ CAG33136. 498 ------------------------------------------------------------ KI537979 9740254 ???????????????????????????????????????????????????????????? 27600 ------------------------------------------------------------ CAG33136. 498 ------------------------------------------------------------ KI537979 9740314 ???????????????????????????????????????????????????????????? 27660 ------------------------------------------------------------ CAG33136. 498 ------------------------------------------------------------ KI537979 9740374 ???????????????????????????????????????????????????????????? 27720 ------------------------------------------------------------ CAG33136. 498 ------------------------------------------------------------ KI537979 9740434 ???????????????????????????????????????????????????????????? 27780 ------------------------------------------------------------ CAG33136. 498 ------------------------------------------------------------ KI537979 9740494 ???????????????????????????????????????????????????????????? 27840 ------------------------------------------------------------ CAG33136. 498 ------------------------------------------------------------ KI537979 9740554 ???????????????????????????????????????????????????????????? 27900 ------------------------------------------------------------ CAG33136. 498 ------------------------------------------------------------ KI537979 9740614 ???????????????????????????????????????????????????????????? 27960 ------------------------------------------------------------ CAG33136. 498 ------------------------------------------------------------ KI537979 9740674 ???????????????????????????????????????????????????????????? 28020 ------------------------------------------------------------ CAG33136. 498 ------------------------------------------------------------ KI537979 9740734 ???????????????????????????????????????????????????????????? 28080 ------------------------------------------------------------ CAG33136. 498 ------------------------------------------------------------ KI537979 9740794 ???????????????????????????????????????????????????????????? 28140 ------------------------------------------------------------ CAG33136. 498 ------------------------------------------------------------ KI537979 9740854 ???????????????????????????????????????????????????????????? 28200 ------------------------------------------------------------ CAG33136. 498 ------------------------------------------------------------ KI537979 9740914 ???????????????????????????????????????????????????????????? 28260 ------------------------------------------------------------ CAG33136. 498 ------------------------------------------------------------ KI537979 9740974 ???????????????????????????????????????????????????????????? 28320 ------------------------------------------------------------ CAG33136. 498 ------------------------------------------------------------ KI537979 9741034 ???????????????????????????????????????????????????????????? 28380 ------------------------------------------------------------ CAG33136. 498 ------------------------------------------------------------ KI537979 9741094 ???????????????????????????????????????????????????????????? 28440 ------------------------------------------------------------ CAG33136. 498 ------------------------------------------------------------ KI537979 9741154 ???????????????????????????????????????????????????????????? 28500 ------------------------------------------------------------ CAG33136. 498 ------------------------------------------------------------ KI537979 9741214 ???????????????????????????????????????????????????????????? 28560 ------------------------------------------------------------ CAG33136. 498 ------------------------------------------------------------ KI537979 9741274 ???????????????????????????????????????????????????????????? 28620 ------------------------------------------------------------ CAG33136. 498 ------------------------------------------------------------ KI537979 9741334 ???????????????????????????????????????????????????????????? 28680 ------------------------------------------------------------ CAG33136. 498 ------------------------------------------------------------ KI537979 9741394 ???????????????????????????????????????????????????????????? 28740 ------------------------------------------------------------ CAG33136. 498 ------------------------------------------------------------ KI537979 9741454 ???????????????????????????????????????????????????????????? 28800 ------------------------------------------------------------ CAG33136. 498 ------------------------------------------------------------ KI537979 9741514 ???????????????????????????????????????????????????????????? 28860 ------------------------------------------------------------ CAG33136. 498 ------------------------------------------------------------ KI537979 9741574 ???????????????????????????????????????????????????????????? 28920 ------------------------------------------------------------ CAG33136. 498 ------------------------------------------------------------ KI537979 9741634 ???????????????????????????????????????????????????????????? 28980 ------------------------------------------------------------ CAG33136. 498 ------------------------------------------------------------ KI537979 9741694 ???????????????????????????????????????????????????????????? 29040 ------------------------------------------------------------ CAG33136. 498 ------------------------------------------------------------ KI537979 9741754 ???????????????????????????????????????????????????????????? 29100 ------------------------------------------------------------ CAG33136. 498 ------------------------------------------------------------ KI537979 9741814 ???????????????????????????????????????????????????????????? 29160 ------------------------------------------------------------ CAG33136. 498 ------------------------------------------------------------ KI537979 9741874 ???????????????????????????????????????????????????????????? 29220 ------------------------------------------------------------ CAG33136. 498 ------------------------------------------------------------ KI537979 9741934 ???????????????????????????????????????????????????????????? 29280 ------------------------------------------------------------ CAG33136. 498 ------------------------------------------------------------ KI537979 9741994 ???????????????????????????????????????????????????????????? 29340 ------------------------------------------------------------ CAG33136. 498 ------------------------------------------------------------ KI537979 9742054 ???????????????????????????????????????????????????????????? 29400 ------------------------------------------------------------ CAG33136. 498 ------------------------------------------------------------ KI537979 9742114 ???????????????????????????????????????????????????????????? 29460 ------------------------------------------------------------ CAG33136. 498 ------------------------------------------------------------ KI537979 9742174 ???????????????????????????????????????????????????????????? 29520 ------------------------------------------------------------ CAG33136. 498 ------------------------------------------------------------ KI537979 9742234 ???????????????????????????????????????????????????????????? 29580 ------------------------------------------------------------ CAG33136. 498 ------------------------------------------------------------ KI537979 9742294 ???????????????????????????????????????????????????????????? 29640 ------------------------------------------------------------ CAG33136. 498 ------------------------------------------------------------ KI537979 9742354 ???????????????????????????????????????????????????????????? 29700 ------------------------------------------------------------ CAG33136. 498 ------------------------------------------------------------ KI537979 9742414 ???????????????????????????????????????????????????????????? 29760 ------------------------------------------------------------ CAG33136. 498 ------------------------------------------------------------ KI537979 9742474 ???????????????????????????????????????????????????????????? 29820 ------------------------------------------------------------ CAG33136. 498 ------------------------------------------------------------ KI537979 9742534 ???????????????????????????????????????????????????????????? 29880 ------------------------------------------------------------ CAG33136. 498 ------------------------------------------------------------ KI537979 9742594 ???????????????????????????????????????????????????????????? 29940 ------------------------------------------------------------ CAG33136. 498 ------------------------------------------------------------ KI537979 9742654 ???????????????????????????????????????????????????????????? 30000 ------------------------------------------------------------ CAG33136. 498 ------------------------------------------------------------ KI537979 9742714 ???????????????????????????????????????????????????????????? 30060 ------------------------------------------------------------ CAG33136. 498 ------------------------------------------------------------ KI537979 9742774 ???????????????????????????????????????????????????????????? 30120 ------------------------------------------------------------ CAG33136. 498 ------------------------------------------------------------ KI537979 9742834 ???????????????????????????????????????????????????????????? 30180 ------------------------------------------------------------ CAG33136. 498 ------------------------------------------------------------ KI537979 9742894 ???????????????????????????????????????????????????????????? 30240 ------------------------------------------------------------ CAG33136. 498 ------------------------------------------------------------ KI537979 9742954 ???????????????????????????????????????????????????????????? 30300 ------------------------------------------------------------ CAG33136. 498 ------------------------------------------------------------ KI537979 9743014 ???????????????????????????????????????????????????????????? 30360 ------------------------------------------------------------ CAG33136. 498 ------------------------------------------------------------ KI537979 9743074 ???????????????????????????????????????????????????????????? 30420 ------------------------------------------------------------ CAG33136. 498 ------------------------------------------------------------ KI537979 9743134 ???????????????????????????????????????????????????????????? 30480 ------------------------------------------------------------ CAG33136. 498 ------------------------------------------------------------ KI537979 9743194 ???????????????????????????????????????????????????????????? 30540 ------------------------------------------------------------ CAG33136. 498 ------------------------------------------------------------ KI537979 9743254 ???????????????????????????????????????????????????????????? 30600 ------------------------------------------------------------ CAG33136. 498 ------------------------------------------------------------ KI537979 9743314 ???????????????????????????????????????????????????????????? 30660 ------------------------------------------------------------ CAG33136. 498 ------------------------------------------------------------ KI537979 9743374 ???????????????????????????????????????????????????????????? 30720 ------------------------------------------------------------ CAG33136. 498 ------------------------------------------------------------ KI537979 9743434 ???????????????????????????????????????????????????????????? 30780 ------------------------------------------------------------ CAG33136. 498 ------------------------------------------------------------ KI537979 9743494 ???????????????????????????????????????????????????????????? 30840 ------------------------------------------------------------ CAG33136. 498 ------------------------------------------------------------ KI537979 9743554 ???????????????????????????????????????????????????????????? 30900 ------------------------------------------------------------ CAG33136. 498 ------------------------------------------------------------ KI537979 9743614 ???????????????????????????????????????????????????????????? 30960 ------------------------------------------------------------ CAG33136. 498 ------------------------------------------------------------ KI537979 9743674 ???????????????????????????????????????????????????????????? 31020 --------------------------------|||||||||||||||||||||||||||| CAG33136. 498 --------------------------------???????????????????????????? KI537979 9743734 ???????????????????????????????????????????????????????????? 31080 ||||||||||||||||||||||||||||||||---------------------------- CAG33136. 526 ????????????????????????????????---------------------------- KI537979 9743794 ???????????????????????????????????????????????????????????? 31140 ------------------------------------------------------------ CAG33136. 558 ------------------------------------------------------------ KI537979 9743854 ???????????????????????????????????????????????????????????? 31200 ------------------------------------------------------------ CAG33136. 558 ------------------------------------------------------------ KI537979 9743914 ???????????????????????????????????????????????????????????? 31260 ------------------------------------------------------------ CAG33136. 558 ------------------------------------------------------------ KI537979 9743974 ???????????????????????????????????????????????????????????? 31320 ------------------------------------------------------------ CAG33136. 558 ------------------------------------------------------------ KI537979 9744034 ???????????????????????????????????????????????????????????? 31380 ------------------------------------------------------------ CAG33136. 558 ------------------------------------------------------------ KI537979 9744094 ???????????????????????????????????????????????????????????? 31440 ------------------------------------------------------------ CAG33136. 558 ------------------------------------------------------------ KI537979 9744154 ???????????????????????????????????????????????????????????? 31500 ------------------------------------------------------------ CAG33136. 558 ------------------------------------------------------------ KI537979 9744214 ???????????????????????????????????????????????????????????? 31560 ------------------------------------------------------------ CAG33136. 558 ------------------------------------------------------------ KI537979 9744274 ???????????????????????????????????????????????????????????? 31620 ------------------------------------------------------------ CAG33136. 558 ------------------------------------------------------------ KI537979 9744334 ???????????????????????????????????????????????????????????? 31680 ------------------------------------------------------------ CAG33136. 558 ------------------------------------------------------------ KI537979 9744394 ???????????????????????????????????????????????????????????? 31740 ------------------------------------------------------------ CAG33136. 558 ------------------------------------------------------------ KI537979 9744454 ???????????????????????????????????????????????????????????? 31800 ---------------------------------------------------------||| CAG33136. 558 ---------------------------------------------------------??? KI537979 9744514 ???????????????????????????????????????????????????????????? 31860 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| CAG33136. 561 ???????????????????????????????????????????????????????????? KI537979 9744574 ?????????????????? 9744592 31920 |||||||||||||||||| 31938 CAG33136. 621 ?????????????????? 639 """, ) self.assertEqual( format(alignment, "bed"), """\ KI537979 9712654 9744592 CAG33136.1 972 + 9712654 9744592 0 7 132,156,87,48,75,60,81, 0,3287,3791,5720,26610,31052,31857, """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 639: identities = 0, mismatches = 0. gaps = 31299: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 31299: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 31299: open_internal_deletions = 6, extend_internal_deletions = 31293; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 31299) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 31299) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 31299) self.assertEqual(counts.gaps, 31299) self.assertEqual(counts.aligned, 639) alignment = next(alignments) self.assertEqual(alignment.score, 792) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "KI538594") self.assertEqual(alignment.query.id, "CAG33136.1") self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[2103463, 2103523, 2103522, 2104149], [ 0, 60, 60, 687]]), # fmt: on ) ) self.assertEqual( str(alignment), """\ KI538594 2103463 ???????????????????????????????????????????????????????????? 0 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| CAG33136. 0 ???????????????????????????????????????????????????????????? KI538594 2103523 60 CAG33136. 60 KI538594 2103522 ???????????????????????????????????????????????????????????? 60 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| CAG33136. 60 ???????????????????????????????????????????????????????????? KI538594 2103582 ???????????????????????????????????????????????????????????? 120 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| CAG33136. 120 ???????????????????????????????????????????????????????????? KI538594 2103642 ???????????????????????????????????????????????????????????? 180 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| CAG33136. 180 ???????????????????????????????????????????????????????????? KI538594 2103702 ???????????????????????????????????????????????????????????? 240 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| CAG33136. 240 ???????????????????????????????????????????????????????????? KI538594 2103762 ???????????????????????????????????????????????????????????? 300 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| CAG33136. 300 ???????????????????????????????????????????????????????????? KI538594 2103822 ???????????????????????????????????????????????????????????? 360 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| CAG33136. 360 ???????????????????????????????????????????????????????????? KI538594 2103882 ???????????????????????????????????????????????????????????? 420 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| CAG33136. 420 ???????????????????????????????????????????????????????????? KI538594 2103942 ???????????????????????????????????????????????????????????? 480 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| CAG33136. 480 ???????????????????????????????????????????????????????????? KI538594 2104002 ???????????????????????????????????????????????????????????? 540 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| CAG33136. 540 ???????????????????????????????????????????????????????????? KI538594 2104062 ???????????????????????????????????????????????????????????? 600 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| CAG33136. 600 ???????????????????????????????????????????????????????????? KI538594 2104122 ??????????????????????????? 2104149 660 ||||||||||||||||||||||||||| 687 CAG33136. 660 ??????????????????????????? 687 """, ) self.assertEqual( format(alignment, "bed"), """\ KI538594 2103463 2104149 CAG33136.1 792 + 2103463 2104149 0 2 60,627, 0,59, """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 687: identities = 0, mismatches = 0. gaps = -1: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = -1: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = -1: open_internal_deletions = 1, extend_internal_deletions = -2; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, -1) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, -1) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, -1) self.assertEqual(counts.gaps, -1) self.assertEqual(counts.aligned, 687) alignment = next(alignments) self.assertEqual(alignment.score, 902) self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1]) self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1]) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "KI537194") self.assertEqual(alignment.query.id, "CAG33136.1") self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[20872390, 20872471, 20872472, 20873021], [ 630, 549, 549, 0]]), # fmt: on ) ) self.assertEqual( str(alignment), """\ KI537194 20872390 ???????????????????????????????????????????????????????????? 0 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| CAG33136. 630 ???????????????????????????????????????????????????????????? KI537194 20872450 ???????????????????????????????????????????????????????????? 60 |||||||||||||||||||||-|||||||||||||||||||||||||||||||||||||| CAG33136. 570 ?????????????????????-?????????????????????????????????????? KI537194 20872510 ???????????????????????????????????????????????????????????? 120 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| CAG33136. 511 ???????????????????????????????????????????????????????????? KI537194 20872570 ???????????????????????????????????????????????????????????? 180 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| CAG33136. 451 ???????????????????????????????????????????????????????????? KI537194 20872630 ???????????????????????????????????????????????????????????? 240 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| CAG33136. 391 ???????????????????????????????????????????????????????????? KI537194 20872690 ???????????????????????????????????????????????????????????? 300 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| CAG33136. 331 ???????????????????????????????????????????????????????????? KI537194 20872750 ???????????????????????????????????????????????????????????? 360 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| CAG33136. 271 ???????????????????????????????????????????????????????????? KI537194 20872810 ???????????????????????????????????????????????????????????? 420 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| CAG33136. 211 ???????????????????????????????????????????????????????????? KI537194 20872870 ???????????????????????????????????????????????????????????? 480 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| CAG33136. 151 ???????????????????????????????????????????????????????????? KI537194 20872930 ???????????????????????????????????????????????????????????? 540 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| CAG33136. 91 ???????????????????????????????????????????????????????????? KI537194 20872990 ??????????????????????????????? 20873021 600 ||||||||||||||||||||||||||||||| 631 CAG33136. 31 ??????????????????????????????? 0 """, ) self.assertEqual( format(alignment, "bed"), """\ KI537194 20872390 20873021 CAG33136.1 902 - 20872390 20873021 0 2 81,549, 0,82, """, ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 630: identities = 0, mismatches = 0. gaps = 1: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 1: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 1: open_internal_deletions = 1, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 1) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 1) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 1) self.assertEqual(counts.gaps, 1) self.assertEqual(counts.aligned, 630) self.assertRaises(StopIteration, next, alignments) def test_writing_psl_35_002(self): """Test writing the alignments in psl_35_002.bed.""" path = "Blat/psl_35_002.bed" with open(path) as stream: original_data = stream.read() alignments = Align.parse(path, "bed") stream = StringIO() n = Align.write(alignments, stream, "bed") self.assertEqual(n, 3) stream.seek(0) written_data = stream.read() stream.close() self.assertEqual(original_data, written_data) class TestAlign_bed12(unittest.TestCase): def test_reading(self): """Test parsing alignments in file formats BED3 through BED12.""" for bedN in (3, 4, 5, 6, 7, 8, 9, 12): filename = "bed%d.bed" % bedN path = os.path.join("Blat", filename) alignments = Align.parse(path, "bed") alignment = next(alignments) if bedN >= 5: self.assertEqual(alignment.score, 960, msg=filename) self.assertEqual(alignment.shape, (2, 4000), msg=filename) self.assertLess( alignment.coordinates[0, 0], alignment.coordinates[0, -1], msg=filename ) self.assertLess( alignment.coordinates[1, 0], alignment.coordinates[1, -1], msg=filename ) self.assertEqual(len(alignment), 2, msg=filename) self.assertIs(alignment.sequences[0], alignment.target, msg=filename) self.assertIs(alignment.sequences[1], alignment.query, msg=filename) self.assertEqual(alignment.target.id, "chr22", msg=filename) if bedN >= 4: self.assertEqual(alignment.query.id, "mRNA1", msg=filename) else: self.assertIsNone(alignment.query.id, msg=filename) if bedN == 12: self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[1000, 1567, 4512, 5000], [ 0, 567, 567, 1055]]), # fmt: on ), msg=filename, ) else: self.assertTrue( np.array_equal( alignment.coordinates, np.array([[1000, 5000], [0, 4000]]), ), msg=filename, ) if bedN >= 7: self.assertEqual(alignment.thickStart, 1200, msg=filename) if bedN >= 8: self.assertEqual(alignment.thickEnd, 4900, msg=filename) if bedN >= 9: self.assertEqual(alignment.itemRgb, "255,0,0", msg=filename) words = [ "chr22", "1000", "5000", "mRNA1", "960", "+", "1200", "4900", "255,0,0", "2", "567,488,", "0,3512,", ] self.assertEqual( alignment.format("bed", bedN), "\t".join(words[:bedN]) + "\n" ) counts = alignment.counts() if bedN <= 9: self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 4000: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) else: # bedN == 12 self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 1055: identities = 0, mismatches = 0. gaps = 2945: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 2945: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 2945: open_internal_deletions = 1, extend_internal_deletions = 2944; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) if bedN == 12: self.assertEqual(counts.internal_deletions, 2945) self.assertEqual(counts.internal_gaps, 2945) self.assertEqual(counts.deletions, 2945) self.assertEqual(counts.gaps, 2945) self.assertEqual(counts.aligned, 1055) else: self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 4000) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.insertions, 0) alignment = next(alignments) if bedN >= 5: self.assertEqual(alignment.score, 900, msg=filename) self.assertEqual(alignment.shape, (2, 4000), msg=filename) self.assertLess( alignment.coordinates[0, 0], alignment.coordinates[0, -1], msg=filename ) if bedN >= 6: self.assertGreater( alignment.coordinates[1, 0], alignment.coordinates[1, -1], msg=filename, ) else: self.assertLess( alignment.coordinates[1, 0], alignment.coordinates[1, -1], msg=filename, ) self.assertEqual(len(alignment), 2, msg=filename) self.assertIs(alignment.sequences[0], alignment.target, msg=filename) self.assertIs(alignment.sequences[1], alignment.query, msg=filename) self.assertEqual(alignment.target.id, "chr22", msg=filename) if bedN >= 4: self.assertEqual(alignment.query.id, "mRNA2", msg=filename) else: self.assertIsNone(alignment.query.id, msg=filename) if bedN == 12: self.assertTrue( np.array_equal( alignment.coordinates, # fmt: off np.array([[2000, 2433, 5601, 6000], [ 832, 399, 399, 0]]) # fmt: on ), msg=filename, ) elif bedN >= 6: self.assertTrue( np.array_equal( alignment.coordinates, np.array([[2000, 6000], [4000, 0]]), ), msg=filename, ) else: self.assertTrue( np.array_equal( alignment.coordinates, np.array([[2000, 6000], [0, 4000]]), ), msg=filename, ) if bedN >= 7: self.assertEqual(alignment.thickStart, 2300, msg=filename) if bedN >= 8: self.assertEqual(alignment.thickEnd, 5960, msg=filename) if bedN >= 9: self.assertEqual(alignment.itemRgb, "0,255,0", msg=filename) words = [ "chr22", "2000", "6000", "mRNA2", "900", "-", "2300", "5960", "0,255,0", "2", "433,399,", "0,3601,", ] self.assertEqual( alignment.format("bed", bedN), "\t".join(words[:bedN]) + "\n" ) counts = alignment.counts() if bedN <= 9: self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 4000: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) else: # bedN == 12 self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 832: identities = 0, mismatches = 0. gaps = 3168: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 3168: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 3168: open_internal_deletions = 1, extend_internal_deletions = 3167; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) if bedN == 12: self.assertEqual(counts.internal_deletions, 3168) self.assertEqual(counts.deletions, 3168) self.assertEqual(counts.internal_gaps, 3168) self.assertEqual(counts.gaps, 3168) self.assertEqual(counts.aligned, 832) else: self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 4000) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.insertions, 0) with self.assertRaises(StopIteration) as cm: next(alignments) self.fail(f"More than two alignments reported in {filename}") def test_writing(self): """Test writing the alignments in bed12.bed as BED3 through BED12.""" for bedN in (3, 4, 5, 6, 7, 8, 9, 12): filename = "bed%d.bed" % bedN path = os.path.join("Blat", filename) with open(path) as stream: original_data = stream.read() alignments = Align.parse(path, "bed") stream = StringIO() n = Align.write(alignments, stream, "bed", bedN=bedN) self.assertEqual(n, 2, msg=filename) stream.seek(0) written_data = stream.read() stream.close() self.assertEqual(original_data, written_data, msg=filename) class TestAlign_strand(unittest.TestCase): def test_format(self): """Test alignment with the target on the opposite strand.""" sequences = ["AACAGCAGCGTGTCG", "CAGCTAGCGAA"] coordinates = np.array( [[0, 2, 2, 3, 4, 6, 6, 9, 10, 12, 15], [11, 11, 9, 8, 8, 6, 5, 2, 2, 0, 0]] ) alignment = Alignment(sequences, coordinates) alignment.score = 8 line = """\ target 2 12 query 8 - 2 12 0 4 1,2,3,2, 0,2,4,8, """ self.assertEqual( str(alignment), """\ target 0 AA--CAGC-AGCGTGTCG 15 0 ----|-||-|||-||--- 18 query 11 --TTC-GCTAGC-TG--- 0 """, ) self.assertEqual(format(alignment, "bed"), line) alignment.coordinates = alignment.coordinates[:, ::-1] self.assertEqual( str(alignment), """\ target 15 CGACACGCT-GCTG--TT 0 0 ---||-|||-||-|---- 18 query 0 ---CA-GCTAGC-GAA-- 11 """, ) self.assertEqual(format(alignment, "bed"), line) alignment.coordinates = alignment.coordinates[:, ::-1] line = """\ target 3 13 query 0 - 3 13 0 4 2,3,2,1, 0,3,6,9, """ alignment = alignment.reverse_complement() self.assertEqual( str(alignment), """\ target 0 CGACACGCT-GCTG--TT 15 0 ---||-|||-||-|---- 18 query 11 ---CA-GCTAGC-GAA-- 0 """, ) self.assertEqual(format(alignment, "bed"), line) alignment.coordinates = alignment.coordinates[:, ::-1] self.assertEqual( str(alignment), """\ target 15 AA--CAGC-AGCGTGTCG 0 0 ----|-||-|||-||--- 18 query 0 --TTC-GCTAGC-TG--- 11 """, ) self.assertEqual(format(alignment, "bed"), line) class TestAlign_searching(unittest.TestCase): path = "Blat/bigbedtest.bed" def check_alignments(self, alignments): alignment = next(alignments) self.assertEqual(alignment.score, 1) self.assertEqual(alignment.shape, (2, 90)) 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, "name1") self.assertTrue( np.array_equal(alignment.coordinates, np.array([[10, 100], [0, 90]])) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 90: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 90) alignment = next(alignments) self.assertEqual(alignment.score, 2) self.assertEqual(alignment.shape, (2, 10)) 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, "name2") self.assertTrue( np.array_equal(alignment.coordinates, np.array([[29, 39], [10, 0]])) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 10: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 10) alignment = next(alignments) self.assertEqual(alignment.score, 3) self.assertEqual(alignment.shape, (2, 100)) 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, "name3") self.assertTrue( np.array_equal(alignment.coordinates, np.array([[200, 300], [0, 100]])) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 100: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 100) alignment = next(alignments) self.assertEqual(alignment.score, 6) self.assertEqual(alignment.shape, (2, 0)) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr2") self.assertEqual(alignment.query.id, "name4") self.assertTrue( np.array_equal(alignment.coordinates, np.array([[50, 50], [0, 0]])) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 0: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 0) self.assertEqual(counts.identities, 0) self.assertEqual(counts.mismatches, 0) alignment = next(alignments) self.assertEqual(alignment.score, 4) self.assertEqual(alignment.shape, (2, 10)) 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, "name5") self.assertTrue( np.array_equal(alignment.coordinates, np.array([[100, 110], [0, 10]])) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 10: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 10) alignment = next(alignments) self.assertEqual(alignment.score, 5) self.assertEqual(alignment.shape, (2, 10)) 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, "name6") self.assertTrue( np.array_equal(alignment.coordinates, np.array([[200, 210], [0, 10]])) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 10: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 10) alignment = next(alignments) self.assertEqual(alignment.score, 6) self.assertEqual(alignment.shape, (2, 0)) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr2") self.assertEqual(alignment.query.id, "name7") self.assertTrue( np.array_equal(alignment.coordinates, np.array([[220, 220], [0, 0]])) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 0: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 0) self.assertEqual(counts.identities, 0) self.assertEqual(counts.mismatches, 0) alignment = next(alignments) self.assertEqual(alignment.score, 7) self.assertEqual(alignment.shape, (2, 0)) self.assertEqual(len(alignment), 2) self.assertIs(alignment.sequences[0], alignment.target) self.assertIs(alignment.sequences[1], alignment.query) self.assertEqual(alignment.target.id, "chr3") self.assertEqual(alignment.query.id, "name8") self.assertTrue( np.array_equal(alignment.coordinates, np.array([[0, 0], [0, 0]])) ) counts = alignment.counts() self.assertEqual( repr(counts), "" % id(counts), ) self.assertEqual( str(counts), """\ AlignmentCounts object with aligned = 0: identities = 0, mismatches = 0. gaps = 0: left_gaps = 0: left_insertions = 0: open_left_insertions = 0, extend_left_insertions = 0; left_deletions = 0: open_left_deletions = 0, extend_left_deletions = 0; internal_gaps = 0: internal_insertions = 0: open_internal_insertions = 0, extend_internal_insertions = 0; internal_deletions = 0: open_internal_deletions = 0, extend_internal_deletions = 0; right_gaps = 0: right_insertions = 0: open_right_insertions = 0, extend_right_insertions = 0; right_deletions = 0: open_right_deletions = 0, extend_right_deletions = 0. """, ) self.assertEqual(counts.left_insertions, 0) self.assertEqual(counts.left_deletions, 0) self.assertEqual(counts.right_insertions, 0) self.assertEqual(counts.right_deletions, 0) self.assertEqual(counts.internal_insertions, 0) self.assertEqual(counts.internal_deletions, 0) self.assertEqual(counts.left_gaps, 0) self.assertEqual(counts.right_gaps, 0) self.assertEqual(counts.internal_gaps, 0) self.assertEqual(counts.insertions, 0) self.assertEqual(counts.deletions, 0) self.assertEqual(counts.gaps, 0) self.assertEqual(counts.aligned, 0) self.assertEqual(counts.identities, 0) self.assertEqual(counts.mismatches, 0) def test_reading(self): """Test reading bigbedtest.bed.""" alignments = Align.parse(self.path, "bed") self.check_alignments(alignments) def test_writing(self): """Test writing bigbedtest.bed.""" alignments = Align.parse(self.path, "bed") with tempfile.TemporaryFile("w+t") as output: Align.write(alignments, output, "bed", bedN=6) output.seek(0) alignments = Align.parse(output, "bed") self.check_alignments(alignments) if __name__ == "__main__": runner = unittest.TextTestRunner(verbosity=2) unittest.main(testRunner=runner)