# 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, """, ) 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, """, ) 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, """, ) 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, """, ) 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, """, ) 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, """, ) 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, """, ) 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, """, ) 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, """, ) 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, """, ) 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, """, ) 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, """, ) 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, """, ) 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, """, ) 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, """, ) 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, """, ) 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, """, ) 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, """, ) 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, """, ) 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, """, ) 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, """, ) 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, """, ) 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, """, ) 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, """, ) 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, """, ) 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, """, ) 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, """, ) 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, """, ) 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, """, ) 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, """, ) 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, """, ) 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, """, ) 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, """, ) 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, """, ) 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, """, ) 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, """, ) 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, """, ) 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, """, ) 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, """, ) 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, """, ) 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, """, ) 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, """, ) 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, """, ) 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, """, ) 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, """, ) 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, """, ) 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, """, ) 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, """, ) 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, """, ) 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, """, ) 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, """, ) 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, """, ) 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, """, ) 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, """, ) 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, """, ) 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, """, ) 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, """, ) 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, """, ) 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, """, ) 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, """, ) 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, """, ) 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, """, ) 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, """, ) 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, """, ) 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, """, ) 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, """, ) 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, """, ) 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, """, ) 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, """, ) 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, """, ) 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, """, ) 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, """, ) 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, """, ) 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, """, ) 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, """, ) 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, """, ) 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, """, ) 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, """, ) 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, """, ) 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, """, ) 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, """, ) 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" ) 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" ) 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]])) ) 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]])) ) 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]])) ) 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]])) ) 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]])) ) 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]])) ) 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]])) ) 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]])) ) 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)