def test_process_reads_read_obs_paired_end_overlap_1bad_base_qual(self): aln1b = pysam.AlignedSegment() aln1b.reference_start = 20 aln1b.query_name = 'read1' aln1b.mapping_quality = 20 aln1b.query_sequence = "AAAAATAAAACAAAAC" qqual = [30] * 16 qqual[0] = 5 aln1b.query_qualities = qqual aln1b.cigarstring = '16M' self.alns.append(aln1b) var_pos = [15, 20, 25, 35] res = preprocess.process_reads(self.alns, var_pos, 20, 10) exp = { 'read1': { 15: 'T', 20: 'T', 25: 'T', 35: 'C' }, 'read2': { 15: 'G', 20: 'G', 25: 'G' } } self.assertEqual(res, exp)
def test_process_reads_read_obs_min_base_quality(self): res = preprocess.process_reads(self.alns, [15, 20, 25], 20, 30) exp = { 'read1': { 15: 'T', 20: 'T', 25: 'T' }, 'read2': { 20: 'G', 25: 'G' } } self.assertEqual(res, exp)
def test_process_reads_read_obs_simple(self): res = preprocess.process_reads(self.alns, [15, 20, 25], 20, 10) exp = { 'read1': { 15: 'T', 20: 'T', 25: 'T' }, 'read2': { 15: 'G', 20: 'G', 25: 'G' } } self.assertEqual(res, exp)
def test_process_reads_read_obs_min_map_quality(self): res = preprocess.process_reads(self.alns, [15, 20, 25], 25, 10) exp = {'read1': {15: 'T', 20: 'T', 25: 'T'}} self.assertEqual(res, exp)