preprocess_test.py 文件源码

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)