# Copyright 2012 by Wibowo Arindrarto. 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 SearchIO BlatIO parsers.""" import os import unittest from Bio import BiopythonExperimentalWarning import warnings with warnings.catch_warnings(): warnings.simplefilter('ignore', BiopythonExperimentalWarning) from Bio.SearchIO import parse # test case files are in the Blast directory TEST_DIR = 'Blat' FMT = 'blat-psl' def get_file(filename): """Returns the path of a test file.""" return os.path.join(TEST_DIR, filename) class BlatPslCases(unittest.TestCase): def test_psl_34_001(self, testf='psl_34_001.psl', pslx=False): """Test parsing blat output (psl_34_001.psl)""" blat_file = get_file(testf) self.qresults = list(parse(blat_file, FMT, pslx=pslx)) self.assertEqual(2, len(self.qresults)) # check common attributes for qresult in self.qresults: for hit in qresult: self.assertEqual(qresult.id, hit.query_id) for hsp in hit: self.assertEqual(hit.id, hsp.hit_id) self.assertEqual(qresult.id, hsp.query_id) # test first qresult qresult = self.qresults[0] self.assertEqual('hg18_dna', qresult.id) self.assertEqual('blat', qresult.program) self.assertEqual(33, qresult.seq_len) self.assertEqual(3, len(qresult)) # first qresult, first hit hit = qresult[0] self.assertEqual('chr4', hit.id) self.assertEqual(191154276, hit.seq_len) self.assertEqual(1, len(hit.hsps)) # first qresult, first hit, first hsp hsp = qresult[0].hsps[0] self.assertEqual(16, hsp.match_num) self.assertEqual(0, hsp.match_rep_num) self.assertEqual(0, hsp.mismatch_num) self.assertEqual(0, hsp.n_num) self.assertEqual(0, hsp.query_gapopen_num) self.assertEqual(0, hsp.query_gap_num) self.assertEqual(0, hsp.hit_gapopen_num) self.assertEqual(0, hsp.hit_gap_num) self.assertEqual(1, hsp[0].query_strand) self.assertEqual(11, hsp.query_start) self.assertEqual(61646095, hsp.hit_start) self.assertEqual(27, hsp.query_end) self.assertEqual(61646111, hsp.hit_end) self.assertEqual(1, len(hsp)) self.assertEqual([16], hsp.query_span_all) self.assertEqual([16], hsp.hit_span_all) self.assertEqual([(11, 27)], hsp.query_range_all) self.assertEqual([(61646095, 61646111)], hsp.hit_range_all) # first qresult, second hit hit = qresult[1] self.assertEqual('chr1', hit.id) self.assertEqual(249250621, hit.seq_len) self.assertEqual(1, len(hit.hsps)) # first qresult, second hit, first hsp hsp = qresult[1].hsps[0] self.assertEqual(33, hsp.match_num) self.assertEqual(0, hsp.match_rep_num) self.assertEqual(0, hsp.mismatch_num) self.assertEqual(0, hsp.n_num) self.assertEqual(0, hsp.query_gapopen_num) self.assertEqual(0, hsp.query_gap_num) self.assertEqual(0, hsp.hit_gapopen_num) self.assertEqual(0, hsp.hit_gap_num) self.assertEqual(1, hsp[0].query_strand) self.assertEqual(0, hsp.query_start) self.assertEqual(10271783, hsp.hit_start) self.assertEqual(33, hsp.query_end) self.assertEqual(10271816, hsp.hit_end) self.assertEqual(1, len(hsp)) self.assertEqual([33], hsp.query_span_all) self.assertEqual([33], hsp.hit_span_all) self.assertEqual([(0, 33)], hsp.query_range_all) self.assertEqual([(10271783, 10271816)], hsp.hit_range_all) # first qresult, third hit hit = qresult[2] self.assertEqual('chr2', hit.id) self.assertEqual(243199373, hit.seq_len) self.assertEqual(1, len(hit.hsps)) # first qresult, third hit, first hsp hsp = qresult[2].hsps[0] self.assertEqual(17, hsp.match_num) self.assertEqual(0, hsp.match_rep_num) self.assertEqual(0, hsp.mismatch_num) self.assertEqual(0, hsp.n_num) self.assertEqual(0, hsp.query_gapopen_num) self.assertEqual(0, hsp.query_gap_num) self.assertEqual(0, hsp.hit_gapopen_num) self.assertEqual(0, hsp.hit_gap_num) self.assertEqual(-1, hsp[0].query_strand) self.assertEqual(8, hsp.query_start) self.assertEqual(53575980, hsp.hit_start) self.assertEqual(25, hsp.query_end) self.assertEqual(53575997, hsp.hit_end) self.assertEqual(1, len(hsp)) self.assertEqual([17], hsp.query_span_all) self.assertEqual([17], hsp.hit_span_all) self.assertEqual([(8, 25)], hsp.query_range_all) self.assertEqual([(53575980, 53575997)], hsp.hit_range_all) # test second qresult qresult = self.qresults[1] self.assertEqual('hg19_dna', qresult.id) self.assertEqual('blat', qresult.program) self.assertEqual(50, qresult.seq_len) self.assertEqual(10, len(qresult)) # second qresult, first hit hit = qresult[0] self.assertEqual('chr9', hit.id) self.assertEqual(141213431, hit.seq_len) self.assertEqual(1, len(hit.hsps)) # second qresult, first hit, first hsp hsp = qresult[0].hsps[0] self.assertEqual(38, hsp.match_num) self.assertEqual(0, hsp.match_rep_num) self.assertEqual(3, hsp.mismatch_num) self.assertEqual(0, hsp.n_num) self.assertEqual(0, hsp.query_gapopen_num) self.assertEqual(0, hsp.query_gap_num) self.assertEqual(0, hsp.hit_gapopen_num) self.assertEqual(0, hsp.hit_gap_num) self.assertEqual(1, hsp[0].query_strand) self.assertEqual(9, hsp.query_start) self.assertEqual(85737865, hsp.hit_start) self.assertEqual(50, hsp.query_end) self.assertEqual(85737906, hsp.hit_end) self.assertEqual(1, len(hsp)) self.assertEqual([41], hsp.query_span_all) self.assertEqual([41], hsp.hit_span_all) self.assertEqual([(9, 50)], hsp.query_range_all) self.assertEqual([(85737865, 85737906)], hsp.hit_range_all) # second qresult, second hit hit = qresult[1] self.assertEqual('chr8', hit.id) self.assertEqual(146364022, hit.seq_len) self.assertEqual(1, len(hit.hsps)) # second qresult, second hit, first hsp hsp = qresult[1].hsps[0] self.assertEqual(41, hsp.match_num) self.assertEqual(0, hsp.match_rep_num) self.assertEqual(0, hsp.mismatch_num) self.assertEqual(0, hsp.n_num) self.assertEqual(0, hsp.query_gapopen_num) self.assertEqual(0, hsp.query_gap_num) self.assertEqual(0, hsp.hit_gapopen_num) self.assertEqual(0, hsp.hit_gap_num) self.assertEqual(1, hsp[0].query_strand) self.assertEqual(8, hsp.query_start) self.assertEqual(95160479, hsp.hit_start) self.assertEqual(49, hsp.query_end) self.assertEqual(95160520, hsp.hit_end) self.assertEqual(1, len(hsp)) self.assertEqual([41], hsp.query_span_all) self.assertEqual([41], hsp.hit_span_all) self.assertEqual([(8, 49)], hsp.query_range_all) self.assertEqual([(95160479, 95160520)], hsp.hit_range_all) # second qresult, third hit hit = qresult[2] self.assertEqual('chr22', hit.id) self.assertEqual(51304566, hit.seq_len) self.assertEqual(2, len(hit.hsps)) # second qresult, third hit, first hsp hsp = qresult[2].hsps[0] self.assertEqual(33, hsp.match_num) self.assertEqual(0, hsp.match_rep_num) self.assertEqual(3, hsp.mismatch_num) self.assertEqual(0, hsp.n_num) self.assertEqual(0, hsp.query_gapopen_num) self.assertEqual(0, hsp.query_gap_num) self.assertEqual(0, hsp.hit_gapopen_num) self.assertEqual(0, hsp.hit_gap_num) self.assertEqual(1, hsp[0].query_strand) self.assertEqual(11, hsp.query_start) self.assertEqual(42144400, hsp.hit_start) self.assertEqual(47, hsp.query_end) self.assertEqual(42144436, hsp.hit_end) self.assertEqual(1, len(hsp)) self.assertEqual([36], hsp.query_span_all) self.assertEqual([36], hsp.hit_span_all) self.assertEqual([(11, 47)], hsp.query_range_all) self.assertEqual([(42144400, 42144436)], hsp.hit_range_all) # second qresult, third hit, second hsp hsp = qresult[2].hsps[1] self.assertEqual(35, hsp.match_num) self.assertEqual(0, hsp.match_rep_num) self.assertEqual(2, hsp.mismatch_num) self.assertEqual(0, hsp.n_num) self.assertEqual(0, hsp.query_gapopen_num) self.assertEqual(0, hsp.query_gap_num) self.assertEqual(0, hsp.hit_gapopen_num) self.assertEqual(0, hsp.hit_gap_num) self.assertEqual(-1, hsp[0].query_strand) self.assertEqual(12, hsp.query_start) self.assertEqual(48997405, hsp.hit_start) self.assertEqual(49, hsp.query_end) self.assertEqual(48997442, hsp.hit_end) self.assertEqual(1, len(hsp)) self.assertEqual([37], hsp.query_span_all) self.assertEqual([37], hsp.hit_span_all) self.assertEqual([(12, 49)], hsp.query_range_all) self.assertEqual([(48997405, 48997442)], hsp.hit_range_all) # second qresult, fourth hit hit = qresult[3] self.assertEqual('chr2', hit.id) self.assertEqual(243199373, hit.seq_len) self.assertEqual(2, len(hit.hsps)) # second qresult, fourth hit, first hsp hsp = qresult[3].hsps[0] self.assertEqual(43, hsp.match_num) self.assertEqual(0, hsp.match_rep_num) self.assertEqual(1, hsp.mismatch_num) self.assertEqual(0, hsp.n_num) self.assertEqual(1, hsp.query_gapopen_num) self.assertEqual(4, hsp.query_gap_num) self.assertEqual(0, hsp.hit_gapopen_num) self.assertEqual(0, hsp.hit_gap_num) self.assertEqual(1, hsp[0].query_strand) self.assertEqual(1, hsp.query_start) self.assertEqual(183925984, hsp.hit_start) self.assertEqual(49, hsp.query_end) self.assertEqual(183926028, hsp.hit_end) self.assertEqual(2, len(hsp)) self.assertEqual([6, 38], hsp.query_span_all) self.assertEqual([6, 38], hsp.hit_span_all) self.assertEqual([(1, 7), (11, 49)], hsp.query_range_all) self.assertEqual([1, 11], hsp.query_start_all) self.assertEqual([7, 49], hsp.query_end_all) self.assertEqual([(183925984, 183925990), (183925990, 183926028)], hsp.hit_range_all) self.assertEqual([183925984, 183925990], hsp.hit_start_all) self.assertEqual([183925990, 183926028], hsp.hit_end_all) # second qresult, fourth hit, second hsp hsp = qresult[3].hsps[1] self.assertEqual(35, hsp.match_num) self.assertEqual(0, hsp.match_rep_num) self.assertEqual(1, hsp.mismatch_num) self.assertEqual(0, hsp.n_num) self.assertEqual(0, hsp.query_gapopen_num) self.assertEqual(0, hsp.query_gap_num) self.assertEqual(0, hsp.hit_gapopen_num) self.assertEqual(0, hsp.hit_gap_num) self.assertEqual(-1, hsp[0].query_strand) self.assertEqual(13, hsp.query_start) self.assertEqual(120641740, hsp.hit_start) self.assertEqual(49, hsp.query_end) self.assertEqual(120641776, hsp.hit_end) self.assertEqual(1, len(hsp)) self.assertEqual([36], hsp.query_span_all) self.assertEqual([36], hsp.hit_span_all) self.assertEqual([(13, 49)], hsp.query_range_all) self.assertEqual([(120641740, 120641776)], hsp.hit_range_all) # second qresult, fifth hit hit = qresult[4] self.assertEqual('chr19', hit.id) self.assertEqual(59128983, hit.seq_len) self.assertEqual(3, len(hit.hsps)) # second qresult, fifth hit, first hsp hsp = qresult[4].hsps[0] self.assertEqual(34, hsp.match_num) self.assertEqual(0, hsp.match_rep_num) self.assertEqual(2, hsp.mismatch_num) self.assertEqual(0, hsp.n_num) self.assertEqual(0, hsp.query_gapopen_num) self.assertEqual(0, hsp.query_gap_num) self.assertEqual(1, hsp.hit_gapopen_num) self.assertEqual(134, hsp.hit_gap_num) self.assertEqual(1, hsp[0].query_strand) self.assertEqual(10, hsp.query_start) self.assertEqual(35483340, hsp.hit_start) self.assertEqual(46, hsp.query_end) self.assertEqual(35483510, hsp.hit_end) self.assertEqual(2, len(hsp)) self.assertEqual([25, 11], hsp.query_span_all) self.assertEqual([25, 11], hsp.hit_span_all) self.assertEqual([(10, 35), (35, 46)], hsp.query_range_all) self.assertEqual([(35483340, 35483365), (35483499, 35483510)], hsp.hit_range_all) # second qresult, fifth hit, second hsp hsp = qresult[4].hsps[1] self.assertEqual(39, hsp.match_num) self.assertEqual(0, hsp.match_rep_num) self.assertEqual(0, hsp.mismatch_num) self.assertEqual(0, hsp.n_num) self.assertEqual(0, hsp.query_gapopen_num) self.assertEqual(0, hsp.query_gap_num) self.assertEqual(0, hsp.hit_gapopen_num) self.assertEqual(0, hsp.hit_gap_num) self.assertEqual(-1, hsp[0].query_strand) self.assertEqual(10, hsp.query_start) self.assertEqual(54017130, hsp.hit_start) self.assertEqual(49, hsp.query_end) self.assertEqual(54017169, hsp.hit_end) self.assertEqual(1, len(hsp)) self.assertEqual([39], hsp.query_span_all) self.assertEqual([39], hsp.hit_span_all) self.assertEqual([(10, 49)], hsp.query_range_all) self.assertEqual([(54017130, 54017169)], hsp.hit_range_all) # second qresult, fifth hit, third hsp hsp = qresult[4].hsps[2] self.assertEqual(36, hsp.match_num) self.assertEqual(0, hsp.match_rep_num) self.assertEqual(3, hsp.mismatch_num) self.assertEqual(0, hsp.n_num) self.assertEqual(0, hsp.query_gapopen_num) self.assertEqual(0, hsp.query_gap_num) self.assertEqual(0, hsp.hit_gapopen_num) self.assertEqual(0, hsp.hit_gap_num) self.assertEqual(-1, hsp[0].query_strand) self.assertEqual(10, hsp.query_start) self.assertEqual(553742, hsp.hit_start) self.assertEqual(49, hsp.query_end) self.assertEqual(553781, hsp.hit_end) self.assertEqual(1, len(hsp)) self.assertEqual([39], hsp.query_span_all) self.assertEqual([39], hsp.hit_span_all) self.assertEqual([(10, 49)], hsp.query_range_all) self.assertEqual([(553742, 553781)], hsp.hit_range_all) def test_psl_34_002(self, testf='psl_34_002.psl', pslx=False): """Test parsing blat output (psl_34_001.psl)""" blat_file = get_file(testf) self.qresults = list(parse(blat_file, FMT, pslx=pslx)) self.assertEqual(0, len(self.qresults)) def test_psl_34_003(self, testf='psl_34_003.psl', pslx=False): """Test parsing blat output (psl_34_003.psl)""" blat_file = get_file(testf) self.qresults = list(parse(blat_file, FMT, pslx=pslx)) self.assertEqual(1, len(self.qresults)) # check common attributes for qresult in self.qresults: for hit in qresult: self.assertEqual(qresult.id, hit.query_id) for hsp in hit: self.assertEqual(hit.id, hsp.hit_id) self.assertEqual(qresult.id, hsp.query_id) # test first qresult qresult = self.qresults[0] self.assertEqual('hg18_dna', qresult.id) self.assertEqual('blat', qresult.program) self.assertEqual(33, qresult.seq_len) self.assertEqual(3, len(qresult)) # first qresult, first hit hit = qresult[0] self.assertEqual('chr4', hit.id) self.assertEqual(191154276, hit.seq_len) self.assertEqual(1, len(hit.hsps)) # first qresult, first hit, first hsp hsp = qresult[0].hsps[0] self.assertEqual(16, hsp.match_num) self.assertEqual(0, hsp.match_rep_num) self.assertEqual(0, hsp.mismatch_num) self.assertEqual(0, hsp.n_num) self.assertEqual(0, hsp.query_gapopen_num) self.assertEqual(0, hsp.query_gap_num) self.assertEqual(0, hsp.hit_gapopen_num) self.assertEqual(0, hsp.hit_gap_num) self.assertEqual(1, hsp[0].query_strand) self.assertEqual(11, hsp.query_start) self.assertEqual(61646095, hsp.hit_start) self.assertEqual(27, hsp.query_end) self.assertEqual(61646111, hsp.hit_end) self.assertEqual(1, len(hsp)) self.assertEqual([16], hsp.query_span_all) self.assertEqual([16], hsp.hit_span_all) self.assertEqual([(11, 27)], hsp.query_range_all) self.assertEqual([(61646095, 61646111)], hsp.hit_range_all) # first qresult, second hit hit = qresult[1] self.assertEqual('chr1', hit.id) self.assertEqual(249250621, hit.seq_len) self.assertEqual(1, len(hit.hsps)) # first qresult, second hit, first hsp hsp = qresult[1].hsps[0] self.assertEqual(33, hsp.match_num) self.assertEqual(0, hsp.match_rep_num) self.assertEqual(0, hsp.mismatch_num) self.assertEqual(0, hsp.n_num) self.assertEqual(0, hsp.query_gapopen_num) self.assertEqual(0, hsp.query_gap_num) self.assertEqual(0, hsp.hit_gapopen_num) self.assertEqual(0, hsp.hit_gap_num) self.assertEqual(1, hsp[0].query_strand) self.assertEqual(0, hsp.query_start) self.assertEqual(10271783, hsp.hit_start) self.assertEqual(33, hsp.query_end) self.assertEqual(10271816, hsp.hit_end) self.assertEqual(1, len(hsp)) self.assertEqual([33], hsp.query_span_all) self.assertEqual([33], hsp.hit_span_all) self.assertEqual([(0, 33)], hsp.query_range_all) self.assertEqual([(10271783, 10271816)], hsp.hit_range_all) # first qresult, third hit hit = qresult[2] self.assertEqual('chr2', hit.id) self.assertEqual(243199373, hit.seq_len) self.assertEqual(1, len(hit.hsps)) # first qresult, third hit, first hsp hsp = qresult[2].hsps[0] self.assertEqual(17, hsp.match_num) self.assertEqual(0, hsp.match_rep_num) self.assertEqual(0, hsp.mismatch_num) self.assertEqual(0, hsp.n_num) self.assertEqual(0, hsp.query_gapopen_num) self.assertEqual(0, hsp.query_gap_num) self.assertEqual(0, hsp.hit_gapopen_num) self.assertEqual(0, hsp.hit_gap_num) self.assertEqual(-1, hsp[0].query_strand) self.assertEqual(8, hsp.query_start) self.assertEqual(53575980, hsp.hit_start) self.assertEqual(25, hsp.query_end) self.assertEqual(53575997, hsp.hit_end) self.assertEqual(1, len(hsp)) self.assertEqual([17], hsp.query_span_all) self.assertEqual([17], hsp.hit_span_all) self.assertEqual([(8, 25)], hsp.query_range_all) self.assertEqual([(53575980, 53575997)], hsp.hit_range_all) def test_psl_34_004(self, testf='psl_34_004.psl', pslx=False): """Test parsing blat output (psl_34_004.psl)""" blat_file = get_file(testf) self.qresults = list(parse(blat_file, FMT, pslx=pslx)) self.assertEqual(1, len(self.qresults)) # check common attributes for qresult in self.qresults: for hit in qresult: self.assertEqual(qresult.id, hit.query_id) for hsp in hit: self.assertEqual(hit.id, hsp.hit_id) self.assertEqual(qresult.id, hsp.query_id) # test first qresult qresult = self.qresults[0] self.assertEqual('hg19_dna', qresult.id) self.assertEqual('blat', qresult.program) self.assertEqual(50, qresult.seq_len) self.assertEqual(10, len(qresult)) # first qresult, first hit hit = qresult[0] self.assertEqual('chr9', hit.id) self.assertEqual(141213431, hit.seq_len) self.assertEqual(1, len(hit.hsps)) # first qresult, first hit, first hsp hsp = qresult[0].hsps[0] self.assertEqual(38, hsp.match_num) self.assertEqual(0, hsp.match_rep_num) self.assertEqual(3, hsp.mismatch_num) self.assertEqual(0, hsp.n_num) self.assertEqual(0, hsp.query_gapopen_num) self.assertEqual(0, hsp.query_gap_num) self.assertEqual(0, hsp.hit_gapopen_num) self.assertEqual(0, hsp.hit_gap_num) self.assertEqual(1, hsp[0].query_strand) self.assertEqual(9, hsp.query_start) self.assertEqual(85737865, hsp.hit_start) self.assertEqual(50, hsp.query_end) self.assertEqual(85737906, hsp.hit_end) self.assertEqual(1, len(hsp)) self.assertEqual([41], hsp.query_span_all) self.assertEqual([41], hsp.hit_span_all) self.assertEqual([(9, 50)], hsp.query_range_all) self.assertEqual([(85737865, 85737906)], hsp.hit_range_all) # first qresult, second hit hit = qresult[1] self.assertEqual('chr8', hit.id) self.assertEqual(146364022, hit.seq_len) self.assertEqual(1, len(hit.hsps)) # first qresult, second hit, first hsp hsp = qresult[1].hsps[0] self.assertEqual(41, hsp.match_num) self.assertEqual(0, hsp.match_rep_num) self.assertEqual(0, hsp.mismatch_num) self.assertEqual(0, hsp.n_num) self.assertEqual(0, hsp.query_gapopen_num) self.assertEqual(0, hsp.query_gap_num) self.assertEqual(0, hsp.hit_gapopen_num) self.assertEqual(0, hsp.hit_gap_num) self.assertEqual(1, hsp[0].query_strand) self.assertEqual(8, hsp.query_start) self.assertEqual(95160479, hsp.hit_start) self.assertEqual(49, hsp.query_end) self.assertEqual(95160520, hsp.hit_end) self.assertEqual(1, len(hsp)) self.assertEqual([41], hsp.query_span_all) self.assertEqual([41], hsp.hit_span_all) self.assertEqual([(8, 49)], hsp.query_range_all) self.assertEqual([(95160479, 95160520)], hsp.hit_range_all) # first qresult, third hit hit = qresult[2] self.assertEqual('chr22', hit.id) self.assertEqual(51304566, hit.seq_len) self.assertEqual(2, len(hit.hsps)) # first qresult, third hit, first hsp hsp = qresult[2].hsps[0] self.assertEqual(33, hsp.match_num) self.assertEqual(0, hsp.match_rep_num) self.assertEqual(3, hsp.mismatch_num) self.assertEqual(0, hsp.n_num) self.assertEqual(0, hsp.query_gapopen_num) self.assertEqual(0, hsp.query_gap_num) self.assertEqual(0, hsp.hit_gapopen_num) self.assertEqual(0, hsp.hit_gap_num) self.assertEqual(1, hsp[0].query_strand) self.assertEqual(11, hsp.query_start) self.assertEqual(42144400, hsp.hit_start) self.assertEqual(47, hsp.query_end) self.assertEqual(42144436, hsp.hit_end) self.assertEqual(1, len(hsp)) self.assertEqual([36], hsp.query_span_all) self.assertEqual([36], hsp.hit_span_all) self.assertEqual([(11, 47)], hsp.query_range_all) self.assertEqual([(42144400, 42144436)], hsp.hit_range_all) # first qresult, third hit, second hsp hsp = qresult[2].hsps[1] self.assertEqual(35, hsp.match_num) self.assertEqual(0, hsp.match_rep_num) self.assertEqual(2, hsp.mismatch_num) self.assertEqual(0, hsp.n_num) self.assertEqual(0, hsp.query_gapopen_num) self.assertEqual(0, hsp.query_gap_num) self.assertEqual(0, hsp.hit_gapopen_num) self.assertEqual(0, hsp.hit_gap_num) self.assertEqual(-1, hsp[0].query_strand) self.assertEqual(12, hsp.query_start) self.assertEqual(48997405, hsp.hit_start) self.assertEqual(49, hsp.query_end) self.assertEqual(48997442, hsp.hit_end) self.assertEqual(1, len(hsp)) self.assertEqual([37], hsp.query_span_all) self.assertEqual([37], hsp.hit_span_all) self.assertEqual([(12, 49)], hsp.query_range_all) self.assertEqual([(48997405, 48997442)], hsp.hit_range_all) # first qresult, fourth hit hit = qresult[3] self.assertEqual('chr2', hit.id) self.assertEqual(243199373, hit.seq_len) self.assertEqual(2, len(hit.hsps)) # first qresult, fourth hit, first hsp hsp = qresult[3].hsps[0] self.assertEqual(43, hsp.match_num) self.assertEqual(0, hsp.match_rep_num) self.assertEqual(1, hsp.mismatch_num) self.assertEqual(0, hsp.n_num) self.assertEqual(1, hsp.query_gapopen_num) self.assertEqual(4, hsp.query_gap_num) self.assertEqual(0, hsp.hit_gapopen_num) self.assertEqual(0, hsp.hit_gap_num) self.assertEqual(1, hsp[0].query_strand) self.assertEqual(1, hsp.query_start) self.assertEqual(183925984, hsp.hit_start) self.assertEqual(49, hsp.query_end) self.assertEqual(183926028, hsp.hit_end) self.assertEqual(2, len(hsp)) self.assertEqual([6, 38], hsp.query_span_all) self.assertEqual([6, 38], hsp.hit_span_all) self.assertEqual([(1, 7), (11, 49)], hsp.query_range_all) self.assertEqual([(183925984, 183925990), (183925990, 183926028)], hsp.hit_range_all) # first qresult, fourth hit, second hsp hsp = qresult[3].hsps[1] self.assertEqual(35, hsp.match_num) self.assertEqual(0, hsp.match_rep_num) self.assertEqual(1, hsp.mismatch_num) self.assertEqual(0, hsp.n_num) self.assertEqual(0, hsp.query_gapopen_num) self.assertEqual(0, hsp.query_gap_num) self.assertEqual(0, hsp.hit_gapopen_num) self.assertEqual(0, hsp.hit_gap_num) self.assertEqual(-1, hsp[0].query_strand) self.assertEqual(13, hsp.query_start) self.assertEqual(120641740, hsp.hit_start) self.assertEqual(49, hsp.query_end) self.assertEqual(120641776, hsp.hit_end) self.assertEqual(1, len(hsp)) self.assertEqual([36], hsp.query_span_all) self.assertEqual([36], hsp.hit_span_all) self.assertEqual([(13, 49)], hsp.query_range_all) self.assertEqual([(120641740, 120641776)], hsp.hit_range_all) # first qresult, fifth hit hit = qresult[4] self.assertEqual('chr19', hit.id) self.assertEqual(59128983, hit.seq_len) self.assertEqual(3, len(hit.hsps)) # first qresult, fifth hit, first hsp hsp = qresult[4].hsps[0] self.assertEqual(34, hsp.match_num) self.assertEqual(0, hsp.match_rep_num) self.assertEqual(2, hsp.mismatch_num) self.assertEqual(0, hsp.n_num) self.assertEqual(0, hsp.query_gapopen_num) self.assertEqual(0, hsp.query_gap_num) self.assertEqual(1, hsp.hit_gapopen_num) self.assertEqual(134, hsp.hit_gap_num) self.assertEqual(1, hsp[0].query_strand) self.assertEqual(10, hsp.query_start) self.assertEqual(35483340, hsp.hit_start) self.assertEqual(46, hsp.query_end) self.assertEqual(35483510, hsp.hit_end) self.assertEqual(2, len(hsp)) self.assertEqual([25, 11], hsp.query_span_all) self.assertEqual([25, 11], hsp.hit_span_all) self.assertEqual([(10, 35), (35, 46)], hsp.query_range_all) self.assertEqual([(35483340, 35483365), (35483499, 35483510)], hsp.hit_range_all) # first qresult, fifth hit, second hsp hsp = qresult[4].hsps[1] self.assertEqual(39, hsp.match_num) self.assertEqual(0, hsp.match_rep_num) self.assertEqual(0, hsp.mismatch_num) self.assertEqual(0, hsp.n_num) self.assertEqual(0, hsp.query_gapopen_num) self.assertEqual(0, hsp.query_gap_num) self.assertEqual(0, hsp.hit_gapopen_num) self.assertEqual(0, hsp.hit_gap_num) self.assertEqual(-1, hsp[0].query_strand) self.assertEqual(10, hsp.query_start) self.assertEqual(54017130, hsp.hit_start) self.assertEqual(49, hsp.query_end) self.assertEqual(54017169, hsp.hit_end) self.assertEqual(1, len(hsp)) self.assertEqual([39], hsp.query_span_all) self.assertEqual([39], hsp.hit_span_all) self.assertEqual([(10, 49)], hsp.query_range_all) self.assertEqual([(54017130, 54017169)], hsp.hit_range_all) # first qresult, fifth hit, third hsp hsp = qresult[4].hsps[2] self.assertEqual(36, hsp.match_num) self.assertEqual(0, hsp.match_rep_num) self.assertEqual(3, hsp.mismatch_num) self.assertEqual(0, hsp.n_num) self.assertEqual(0, hsp.query_gapopen_num) self.assertEqual(0, hsp.query_gap_num) self.assertEqual(0, hsp.hit_gapopen_num) self.assertEqual(0, hsp.hit_gap_num) self.assertEqual(-1, hsp[0].query_strand) self.assertEqual(10, hsp.query_start) self.assertEqual(553742, hsp.hit_start) self.assertEqual(49, hsp.query_end) self.assertEqual(553781, hsp.hit_end) self.assertEqual(1, len(hsp)) self.assertEqual([39], hsp.query_span_all) self.assertEqual([39], hsp.hit_span_all) self.assertEqual([(10, 49)], hsp.query_range_all) self.assertEqual([(553742, 553781)], hsp.hit_range_all) def test_psl_34_005(self, testf='psl_34_005.psl', pslx=False): """Test parsing blat output (psl_34_005.psl)""" blat_file = get_file(testf) self.qresults = list(parse(blat_file, FMT, pslx=pslx)) self.assertEqual(2, len(self.qresults)) # check common attributes for qresult in self.qresults: for hit in qresult: self.assertEqual(qresult.id, hit.query_id) for hsp in hit: self.assertEqual(hit.id, hsp.hit_id) self.assertEqual(qresult.id, hsp.query_id) # test first qresult qresult = self.qresults[0] self.assertEqual('hg18_dna', qresult.id) self.assertEqual('blat', qresult.program) self.assertEqual(33, qresult.seq_len) self.assertEqual(3, len(qresult)) # first qresult, first hit hit = qresult[0] self.assertEqual('chr4', hit.id) self.assertEqual(191154276, hit.seq_len) self.assertEqual(1, len(hit.hsps)) # first qresult, first hit, first hsp hsp = qresult[0].hsps[0] self.assertEqual(16, hsp.match_num) self.assertEqual(0, hsp.match_rep_num) self.assertEqual(0, hsp.mismatch_num) self.assertEqual(0, hsp.n_num) self.assertEqual(0, hsp.query_gapopen_num) self.assertEqual(0, hsp.query_gap_num) self.assertEqual(0, hsp.hit_gapopen_num) self.assertEqual(0, hsp.hit_gap_num) self.assertEqual(1, hsp[0].query_strand) self.assertEqual(11, hsp.query_start) self.assertEqual(61646095, hsp.hit_start) self.assertEqual(27, hsp.query_end) self.assertEqual(61646111, hsp.hit_end) self.assertEqual(1, len(hsp)) self.assertEqual([16], hsp.query_span_all) self.assertEqual([16], hsp.hit_span_all) self.assertEqual([(11, 27)], hsp.query_range_all) self.assertEqual([(61646095, 61646111)], hsp.hit_range_all) # first qresult, second hit hit = qresult[1] self.assertEqual('chr1', hit.id) self.assertEqual(249250621, hit.seq_len) self.assertEqual(1, len(hit.hsps)) # first qresult, second hit, first hsp hsp = qresult[1].hsps[0] self.assertEqual(33, hsp.match_num) self.assertEqual(0, hsp.match_rep_num) self.assertEqual(0, hsp.mismatch_num) self.assertEqual(0, hsp.n_num) self.assertEqual(0, hsp.query_gapopen_num) self.assertEqual(0, hsp.query_gap_num) self.assertEqual(0, hsp.hit_gapopen_num) self.assertEqual(0, hsp.hit_gap_num) self.assertEqual(1, hsp[0].query_strand) self.assertEqual(0, hsp.query_start) self.assertEqual(10271783, hsp.hit_start) self.assertEqual(33, hsp.query_end) self.assertEqual(10271816, hsp.hit_end) self.assertEqual(1, len(hsp)) self.assertEqual([33], hsp.query_span_all) self.assertEqual([33], hsp.hit_span_all) self.assertEqual([(0, 33)], hsp.query_range_all) self.assertEqual([(10271783, 10271816)], hsp.hit_range_all) # first qresult, third hit hit = qresult[2] self.assertEqual('chr2', hit.id) self.assertEqual(243199373, hit.seq_len) self.assertEqual(1, len(hit.hsps)) # first qresult, third hit, first hsp hsp = qresult[2].hsps[0] self.assertEqual(17, hsp.match_num) self.assertEqual(0, hsp.match_rep_num) self.assertEqual(0, hsp.mismatch_num) self.assertEqual(0, hsp.n_num) self.assertEqual(0, hsp.query_gapopen_num) self.assertEqual(0, hsp.query_gap_num) self.assertEqual(0, hsp.hit_gapopen_num) self.assertEqual(0, hsp.hit_gap_num) self.assertEqual(-1, hsp[0].query_strand) self.assertEqual(8, hsp.query_start) self.assertEqual(53575980, hsp.hit_start) self.assertEqual(25, hsp.query_end) self.assertEqual(53575997, hsp.hit_end) self.assertEqual(1, len(hsp)) self.assertEqual([17], hsp.query_span_all) self.assertEqual([17], hsp.hit_span_all) self.assertEqual([(8, 25)], hsp.query_range_all) self.assertEqual([(53575980, 53575997)], hsp.hit_range_all) # test second qresult qresult = self.qresults[1] self.assertEqual('hg19_dna', qresult.id) self.assertEqual('blat', qresult.program) self.assertEqual(50, qresult.seq_len) self.assertEqual(10, len(qresult)) # second qresult, first hit hit = qresult[0] self.assertEqual('chr9', hit.id) self.assertEqual(141213431, hit.seq_len) self.assertEqual(1, len(hit.hsps)) # second qresult, first hit, first hsp hsp = qresult[0].hsps[0] self.assertEqual(38, hsp.match_num) self.assertEqual(0, hsp.match_rep_num) self.assertEqual(3, hsp.mismatch_num) self.assertEqual(0, hsp.n_num) self.assertEqual(0, hsp.query_gapopen_num) self.assertEqual(0, hsp.query_gap_num) self.assertEqual(0, hsp.hit_gapopen_num) self.assertEqual(0, hsp.hit_gap_num) self.assertEqual(1, hsp[0].query_strand) self.assertEqual(9, hsp.query_start) self.assertEqual(85737865, hsp.hit_start) self.assertEqual(50, hsp.query_end) self.assertEqual(85737906, hsp.hit_end) self.assertEqual(1, len(hsp)) self.assertEqual([41], hsp.query_span_all) self.assertEqual([41], hsp.hit_span_all) self.assertEqual([(9, 50)], hsp.query_range_all) self.assertEqual([(85737865, 85737906)], hsp.hit_range_all) # second qresult, second hit hit = qresult[1] self.assertEqual('chr8', hit.id) self.assertEqual(146364022, hit.seq_len) self.assertEqual(1, len(hit.hsps)) # second qresult, second hit, first hsp hsp = qresult[1].hsps[0] self.assertEqual(41, hsp.match_num) self.assertEqual(0, hsp.match_rep_num) self.assertEqual(0, hsp.mismatch_num) self.assertEqual(0, hsp.n_num) self.assertEqual(0, hsp.query_gapopen_num) self.assertEqual(0, hsp.query_gap_num) self.assertEqual(0, hsp.hit_gapopen_num) self.assertEqual(0, hsp.hit_gap_num) self.assertEqual(1, hsp[0].query_strand) self.assertEqual(8, hsp.query_start) self.assertEqual(95160479, hsp.hit_start) self.assertEqual(49, hsp.query_end) self.assertEqual(95160520, hsp.hit_end) self.assertEqual(1, len(hsp)) self.assertEqual([41], hsp.query_span_all) self.assertEqual([41], hsp.hit_span_all) self.assertEqual([(8, 49)], hsp.query_range_all) self.assertEqual([(95160479, 95160520)], hsp.hit_range_all) # second qresult, third hit hit = qresult[2] self.assertEqual('chr22', hit.id) self.assertEqual(51304566, hit.seq_len) self.assertEqual(2, len(hit.hsps)) # second qresult, third hit, first hsp hsp = qresult[2].hsps[0] self.assertEqual(33, hsp.match_num) self.assertEqual(0, hsp.match_rep_num) self.assertEqual(3, hsp.mismatch_num) self.assertEqual(0, hsp.n_num) self.assertEqual(0, hsp.query_gapopen_num) self.assertEqual(0, hsp.query_gap_num) self.assertEqual(0, hsp.hit_gapopen_num) self.assertEqual(0, hsp.hit_gap_num) self.assertEqual(1, hsp[0].query_strand) self.assertEqual(11, hsp.query_start) self.assertEqual(42144400, hsp.hit_start) self.assertEqual(47, hsp.query_end) self.assertEqual(42144436, hsp.hit_end) self.assertEqual(1, len(hsp)) self.assertEqual([36], hsp.query_span_all) self.assertEqual([36], hsp.hit_span_all) self.assertEqual([(11, 47)], hsp.query_range_all) self.assertEqual([(42144400, 42144436)], hsp.hit_range_all) # second qresult, third hit, second hsp hsp = qresult[2].hsps[1] self.assertEqual(35, hsp.match_num) self.assertEqual(0, hsp.match_rep_num) self.assertEqual(2, hsp.mismatch_num) self.assertEqual(0, hsp.n_num) self.assertEqual(0, hsp.query_gapopen_num) self.assertEqual(0, hsp.query_gap_num) self.assertEqual(0, hsp.hit_gapopen_num) self.assertEqual(0, hsp.hit_gap_num) self.assertEqual(-1, hsp[0].query_strand) self.assertEqual(12, hsp.query_start) self.assertEqual(48997405, hsp.hit_start) self.assertEqual(49, hsp.query_end) self.assertEqual(48997442, hsp.hit_end) self.assertEqual(1, len(hsp)) self.assertEqual([37], hsp.query_span_all) self.assertEqual([37], hsp.hit_span_all) self.assertEqual([(12, 49)], hsp.query_range_all) self.assertEqual([(48997405, 48997442)], hsp.hit_range_all) # second qresult, fourth hit hit = qresult[3] self.assertEqual('chr2', hit.id) self.assertEqual(243199373, hit.seq_len) self.assertEqual(2, len(hit.hsps)) # second qresult, fourth hit, first hsp hsp = qresult[3].hsps[0] self.assertEqual(43, hsp.match_num) self.assertEqual(0, hsp.match_rep_num) self.assertEqual(1, hsp.mismatch_num) self.assertEqual(0, hsp.n_num) self.assertEqual(1, hsp.query_gapopen_num) self.assertEqual(4, hsp.query_gap_num) self.assertEqual(0, hsp.hit_gapopen_num) self.assertEqual(0, hsp.hit_gap_num) self.assertEqual(1, hsp[0].query_strand) self.assertEqual(1, hsp.query_start) self.assertEqual(183925984, hsp.hit_start) self.assertEqual(49, hsp.query_end) self.assertEqual(183926028, hsp.hit_end) self.assertEqual(2, len(hsp)) self.assertEqual([6, 38], hsp.query_span_all) self.assertEqual([6, 38], hsp.hit_span_all) self.assertEqual([(1, 7), (11, 49)], hsp.query_range_all) self.assertEqual([(183925984, 183925990), (183925990, 183926028)], hsp.hit_range_all) # second qresult, fourth hit, second hsp hsp = qresult[3].hsps[1] self.assertEqual(35, hsp.match_num) self.assertEqual(0, hsp.match_rep_num) self.assertEqual(1, hsp.mismatch_num) self.assertEqual(0, hsp.n_num) self.assertEqual(0, hsp.query_gapopen_num) self.assertEqual(0, hsp.query_gap_num) self.assertEqual(0, hsp.hit_gapopen_num) self.assertEqual(0, hsp.hit_gap_num) self.assertEqual(-1, hsp[0].query_strand) self.assertEqual(13, hsp.query_start) self.assertEqual(120641740, hsp.hit_start) self.assertEqual(49, hsp.query_end) self.assertEqual(120641776, hsp.hit_end) self.assertEqual(1, len(hsp)) self.assertEqual([36], hsp.query_span_all) self.assertEqual([36], hsp.hit_span_all) self.assertEqual([(13, 49)], hsp.query_range_all) self.assertEqual([(120641740, 120641776)], hsp.hit_range_all) # second qresult, fifth hit hit = qresult[4] self.assertEqual('chr19', hit.id) self.assertEqual(59128983, hit.seq_len) self.assertEqual(3, len(hit.hsps)) # second qresult, fifth hit, first hsp hsp = qresult[4].hsps[0] self.assertEqual(34, hsp.match_num) self.assertEqual(0, hsp.match_rep_num) self.assertEqual(2, hsp.mismatch_num) self.assertEqual(0, hsp.n_num) self.assertEqual(0, hsp.query_gapopen_num) self.assertEqual(0, hsp.query_gap_num) self.assertEqual(1, hsp.hit_gapopen_num) self.assertEqual(134, hsp.hit_gap_num) self.assertEqual(1, hsp[0].query_strand) self.assertEqual(10, hsp.query_start) self.assertEqual(35483340, hsp.hit_start) self.assertEqual(46, hsp.query_end) self.assertEqual(35483510, hsp.hit_end) self.assertEqual(2, len(hsp)) self.assertEqual([25, 11], hsp.query_span_all) self.assertEqual([25, 11], hsp.hit_span_all) self.assertEqual([(10, 35), (35, 46)], hsp.query_range_all) self.assertEqual([(35483340, 35483365), (35483499, 35483510)], hsp.hit_range_all) # second qresult, fifth hit, second hsp hsp = qresult[4].hsps[1] self.assertEqual(39, hsp.match_num) self.assertEqual(0, hsp.match_rep_num) self.assertEqual(0, hsp.mismatch_num) self.assertEqual(0, hsp.n_num) self.assertEqual(0, hsp.query_gapopen_num) self.assertEqual(0, hsp.query_gap_num) self.assertEqual(0, hsp.hit_gapopen_num) self.assertEqual(0, hsp.hit_gap_num) self.assertEqual(-1, hsp[0].query_strand) self.assertEqual(10, hsp.query_start) self.assertEqual(54017130, hsp.hit_start) self.assertEqual(49, hsp.query_end) self.assertEqual(54017169, hsp.hit_end) self.assertEqual(1, len(hsp)) self.assertEqual([39], hsp.query_span_all) self.assertEqual([39], hsp.hit_span_all) self.assertEqual([(10, 49)], hsp.query_range_all) self.assertEqual([(54017130, 54017169)], hsp.hit_range_all) # second qresult, fifth hit, third hsp hsp = qresult[4].hsps[2] self.assertEqual(36, hsp.match_num) self.assertEqual(0, hsp.match_rep_num) self.assertEqual(3, hsp.mismatch_num) self.assertEqual(0, hsp.n_num) self.assertEqual(0, hsp.query_gapopen_num) self.assertEqual(0, hsp.query_gap_num) self.assertEqual(0, hsp.hit_gapopen_num) self.assertEqual(0, hsp.hit_gap_num) self.assertEqual(-1, hsp[0].query_strand) self.assertEqual(10, hsp.query_start) self.assertEqual(553742, hsp.hit_start) self.assertEqual(49, hsp.query_end) self.assertEqual(553781, hsp.hit_end) self.assertEqual(1, len(hsp)) self.assertEqual([39], hsp.query_span_all) self.assertEqual([39], hsp.hit_span_all) self.assertEqual([(10, 49)], hsp.query_range_all) self.assertEqual([(553742, 553781)], hsp.hit_range_all) class BlatPslxCases(BlatPslCases): def test_pslx_34_001(self, testf='pslx_34_001.pslx'): """Test parsing blat output (pslx_34_001.pslx)""" BlatPslCases.test_psl_34_001(self, 'pslx_34_001.pslx', pslx=True) # test first qresult qresult = self.qresults[0] # first qresult, first hit, first hsp hsp = qresult[0].hsps[0] self.assertEqual('aggtaaactgccttca', str(hsp.query_all[0].seq)) self.assertEqual('aggtaaactgccttca', str(hsp.hit_all[0].seq)) # first qresult, second hit, first hsp hsp = qresult[1].hsps[0] self.assertEqual('atgagcttccaaggtaaactgccttcaagattc', str(hsp.query_all[0].seq)) self.assertEqual('atgagcttccaaggtaaactgccttcaagattc', str(hsp.hit_all[0].seq)) # first qresult, third hit, first hsp hsp = qresult[2].hsps[0] self.assertEqual('aaggcagtttaccttgg', str(hsp.query_all[0].seq)) self.assertEqual('aaggcagtttaccttgg', str(hsp.hit_all[0].seq)) # test second qresult qresult = self.qresults[1] # second qresult, first hit, first hsp hsp = qresult[0].hsps[0] self.assertEqual('acaaaggggctgggcgtggtggctcacacctgtaatcccaa', str(hsp.query_all[0].seq)) self.assertEqual('acaaaggggctgggcgcagtggctcacgcctgtaatcccaa', str(hsp.hit_all[0].seq)) # second qresult, second hit, first hsp hsp = qresult[1].hsps[0] self.assertEqual('cacaaaggggctgggcgtggtggctcacacctgtaatccca', str(hsp.query_all[0].seq)) self.assertEqual('cacaaaggggctgggcgtggtggctcacacctgtaatccca', str(hsp.hit_all[0].seq)) # second qresult, third hit, first hsp hsp = qresult[2].hsps[0] self.assertEqual('aaaggggctgggcgtggtggctcacacctgtaatcc', str(hsp.query_all[0].seq)) self.assertEqual('aaaggggctgggcgtggtagctcatgcctgtaatcc', str(hsp.hit_all[0].seq)) # second qresult, third hit, second hsp hsp = qresult[2].hsps[1] self.assertEqual('tgggattacaggtgtgagccaccacgcccagcccctt', str(hsp.query_all[0].seq)) self.assertEqual('tgggattacaggcgggagccaccacgcccagcccctt', str(hsp.hit_all[0].seq)) # second qresult, fourth hit, first hsp hsp = qresult[3].hsps[0] self.assertEqual('aaaaat', str(hsp.query_all[0].seq)) self.assertEqual('aaaaat', str(hsp.hit_all[0].seq)) self.assertEqual('aaaggggctgggcgtggtggctcacacctgtaatccca', str(hsp.query_all[1].seq)) self.assertEqual('aaaggggctgggcgtggtggctcacgcctgtaatccca', str(hsp.hit_all[1].seq)) # second qresult, fourth hit, second hsp hsp = qresult[3].hsps[1] self.assertEqual('tgggattacaggtgtgagccaccacgcccagcccct', str(hsp.query_all[0].seq)) self.assertEqual('tgggattacaggcgtgagccaccacgcccagcccct', str(hsp.hit_all[0].seq)) # second qresult, fifth hit, first hsp hsp = qresult[4].hsps[0] self.assertEqual('caaaggggctgggcgtggtggctca', str(hsp.query_all[0].seq)) self.assertEqual('caaaggggctgggcgtagtggctga', str(hsp.hit_all[0].seq)) self.assertEqual('cacctgtaatc', str(hsp.query_all[1].seq)) self.assertEqual('cacctgtaatc', str(hsp.hit_all[1].seq)) # second qresult, fifth hit, second hsp hsp = qresult[4].hsps[1] self.assertEqual('tgggattacaggtgtgagccaccacgcccagcccctttg', str(hsp.query_all[0].seq)) self.assertEqual('tgggattacaggtgtgagccaccacgcccagcccctttg', str(hsp.hit_all[0].seq)) # second qresult, fifth hit, third hsp hsp = qresult[4].hsps[2] self.assertEqual('tgggattacaggtgtgagccaccacgcccagcccctttg', str(hsp.query_all[0].seq)) self.assertEqual('tgggatgacaggggtgaggcaccacgcccagcccctttg', str(hsp.hit_all[0].seq)) def test_pslx_34_002(self, testf='pslx_34_002.pslx'): """Test parsing blat output (pslx_34_002.pslx)""" BlatPslCases.test_psl_34_002(self, 'pslx_34_002.pslx', pslx=True) def test_pslx_34_003(self, testf='pslx_34_003.pslx'): """Test parsing blat output (pslx_34_003.pslx)""" BlatPslCases.test_psl_34_003(self, 'pslx_34_003.pslx', pslx=True) # test first qresult qresult = self.qresults[0] # first qresult, first hit, first hsp hsp = qresult[0].hsps[0] self.assertEqual('aggtaaactgccttca', str(hsp.query_all[0].seq)) self.assertEqual('aggtaaactgccttca', str(hsp.hit_all[0].seq)) # first qresult, second hit, first hsp hsp = qresult[1].hsps[0] self.assertEqual('atgagcttccaaggtaaactgccttcaagattc', str(hsp.query_all[0].seq)) self.assertEqual('atgagcttccaaggtaaactgccttcaagattc', str(hsp.hit_all[0].seq)) # first qresult, third hit, first hsp hsp = qresult[2].hsps[0] self.assertEqual('aaggcagtttaccttgg', str(hsp.query_all[0].seq)) self.assertEqual('aaggcagtttaccttgg', str(hsp.hit_all[0].seq)) def test_pslx_34_004(self, testf='pslx_34_004.pslx'): """Test parsing blat output (pslx_34_004.pslx)""" BlatPslCases.test_psl_34_004(self, 'pslx_34_004.pslx', pslx=True) # test first qresult qresult = self.qresults[0] # first qresult, first hit, first hsp hsp = qresult[0].hsps[0] self.assertEqual('acaaaggggctgggcgtggtggctcacacctgtaatcccaa', str(hsp.query_all[0].seq)) self.assertEqual('acaaaggggctgggcgcagtggctcacgcctgtaatcccaa', str(hsp.hit_all[0].seq)) # first qresult, second hit, first hsp hsp = qresult[1].hsps[0] self.assertEqual('cacaaaggggctgggcgtggtggctcacacctgtaatccca', str(hsp.query_all[0].seq)) self.assertEqual('cacaaaggggctgggcgtggtggctcacacctgtaatccca', str(hsp.hit_all[0].seq)) # first qresult, third hit, first hsp hsp = qresult[2].hsps[0] self.assertEqual('aaaggggctgggcgtggtggctcacacctgtaatcc', str(hsp.query_all[0].seq)) self.assertEqual('aaaggggctgggcgtggtagctcatgcctgtaatcc', str(hsp.hit_all[0].seq)) # first qresult, third hit, second hsp hsp = qresult[2].hsps[1] self.assertEqual('tgggattacaggtgtgagccaccacgcccagcccctt', str(hsp.query_all[0].seq)) self.assertEqual('tgggattacaggcgggagccaccacgcccagcccctt', str(hsp.hit_all[0].seq)) # first qresult, fourth hit, first hsp hsp = qresult[3].hsps[0] self.assertEqual('aaaaat', str(hsp.query_all[0].seq)) self.assertEqual('aaaaat', str(hsp.hit_all[0].seq)) self.assertEqual('aaaggggctgggcgtggtggctcacacctgtaatccca', str(hsp.query_all[1].seq)) self.assertEqual('aaaggggctgggcgtggtggctcacgcctgtaatccca', str(hsp.hit_all[1].seq)) # first qresult, fourth hit, second hsp hsp = qresult[3].hsps[1] self.assertEqual('tgggattacaggtgtgagccaccacgcccagcccct', str(hsp.query_all[0].seq)) self.assertEqual('tgggattacaggcgtgagccaccacgcccagcccct', str(hsp.hit_all[0].seq)) # first qresult, fifth hit, first hsp hsp = qresult[4].hsps[0] self.assertEqual('caaaggggctgggcgtggtggctca', str(hsp.query_all[0].seq)) self.assertEqual('caaaggggctgggcgtagtggctga', str(hsp.hit_all[0].seq)) self.assertEqual('cacctgtaatc', str(hsp.query_all[1].seq)) self.assertEqual('cacctgtaatc', str(hsp.hit_all[1].seq)) # first qresult, fifth hit, second hsp hsp = qresult[4].hsps[1] self.assertEqual('tgggattacaggtgtgagccaccacgcccagcccctttg', str(hsp.query_all[0].seq)) self.assertEqual('tgggattacaggtgtgagccaccacgcccagcccctttg', str(hsp.hit_all[0].seq)) # first qresult, fifth hit, third hsp hsp = qresult[4].hsps[2] self.assertEqual('tgggattacaggtgtgagccaccacgcccagcccctttg', str(hsp.query_all[0].seq)) self.assertEqual('tgggatgacaggggtgaggcaccacgcccagcccctttg', str(hsp.hit_all[0].seq)) def test_pslx_34_005(self, testf='pslx_34_005.pslx'): """Test parsing blat output (pslx_34_005.pslx)""" BlatPslCases.test_psl_34_005(self, 'pslx_34_005.pslx', pslx=True) # test first qresult qresult = self.qresults[0] # first qresult, first hit, first hsp hsp = qresult[0].hsps[0] self.assertEqual('aggtaaactgccttca', str(hsp.query_all[0].seq)) self.assertEqual('aggtaaactgccttca', str(hsp.hit_all[0].seq)) # first qresult, second hit, first hsp hsp = qresult[1].hsps[0] self.assertEqual('atgagcttccaaggtaaactgccttcaagattc', str(hsp.query_all[0].seq)) self.assertEqual('atgagcttccaaggtaaactgccttcaagattc', str(hsp.hit_all[0].seq)) # first qresult, third hit, first hsp hsp = qresult[2].hsps[0] self.assertEqual('aaggcagtttaccttgg', str(hsp.query_all[0].seq)) self.assertEqual('aaggcagtttaccttgg', str(hsp.hit_all[0].seq)) # test second qresult qresult = self.qresults[1] # second qresult, first hit, first hsp hsp = qresult[0].hsps[0] self.assertEqual('acaaaggggctgggcgtggtggctcacacctgtaatcccaa', str(hsp.query_all[0].seq)) self.assertEqual('acaaaggggctgggcgcagtggctcacgcctgtaatcccaa', str(hsp.hit_all[0].seq)) # second qresult, second hit, first hsp hsp = qresult[1].hsps[0] self.assertEqual('cacaaaggggctgggcgtggtggctcacacctgtaatccca', str(hsp.query_all[0].seq)) self.assertEqual('cacaaaggggctgggcgtggtggctcacacctgtaatccca', str(hsp.hit_all[0].seq)) # second qresult, third hit, first hsp hsp = qresult[2].hsps[0] self.assertEqual('aaaggggctgggcgtggtggctcacacctgtaatcc', str(hsp.query_all[0].seq)) self.assertEqual('aaaggggctgggcgtggtagctcatgcctgtaatcc', str(hsp.hit_all[0].seq)) # second qresult, third hit, second hsp hsp = qresult[2].hsps[1] self.assertEqual('tgggattacaggtgtgagccaccacgcccagcccctt', str(hsp.query_all[0].seq)) self.assertEqual('tgggattacaggcgggagccaccacgcccagcccctt', str(hsp.hit_all[0].seq)) # second qresult, fourth hit, first hsp hsp = qresult[3].hsps[0] self.assertEqual('aaaaat', str(hsp.query_all[0].seq)) self.assertEqual('aaaaat', str(hsp.hit_all[0].seq)) self.assertEqual('aaaggggctgggcgtggtggctcacacctgtaatccca', str(hsp.query_all[1].seq)) self.assertEqual('aaaggggctgggcgtggtggctcacgcctgtaatccca', str(hsp.hit_all[1].seq)) # second qresult, fourth hit, second hsp hsp = qresult[3].hsps[1] self.assertEqual('tgggattacaggtgtgagccaccacgcccagcccct', str(hsp.query_all[0].seq)) self.assertEqual('tgggattacaggcgtgagccaccacgcccagcccct', str(hsp.hit_all[0].seq)) # second qresult, fifth hit, first hsp hsp = qresult[4].hsps[0] self.assertEqual('caaaggggctgggcgtggtggctca', str(hsp.query_all[0].seq)) self.assertEqual('caaaggggctgggcgtagtggctga', str(hsp.hit_all[0].seq)) self.assertEqual('cacctgtaatc', str(hsp.query_all[1].seq)) self.assertEqual('cacctgtaatc', str(hsp.hit_all[1].seq)) # second qresult, fifth hit, second hsp hsp = qresult[4].hsps[1] self.assertEqual('tgggattacaggtgtgagccaccacgcccagcccctttg', str(hsp.query_all[0].seq)) self.assertEqual('tgggattacaggtgtgagccaccacgcccagcccctttg', str(hsp.hit_all[0].seq)) # second qresult, fifth hit, third hsp hsp = qresult[4].hsps[2] self.assertEqual('tgggattacaggtgtgagccaccacgcccagcccctttg', str(hsp.query_all[0].seq)) self.assertEqual('tgggatgacaggggtgaggcaccacgcccagcccctttg', str(hsp.hit_all[0].seq)) if __name__ == "__main__": runner = unittest.TextTestRunner(verbosity=2) unittest.main(testRunner=runner)