file_parse.py 文件源码

def parse_fusion_bam(bam_f):
    fusions = {}
    bam = pysam.AlignmentFile(bam_f, 'rb')
    for read in bam:
        if read.is_secondary:  # not the primary alignment
            continue
        if not read.has_tag('XF'):  # not fusion junctions
            continue
        chr1, chr2 = read.get_tag('XF').split()[1].split('-')
        if chr1 != chr2:  # not on the same chromosome
            continue
        strand = '+' if not read.is_reverse else '-'
        if read.query_name not in fusions:  # first fragment
            fusions[read.query_name] = [chr1, strand, read.reference_start,
                                        read.reference_end]
        else:  # second fragment
            if chr1 == fusions[read.query_name][0] \
               and strand == fusions[read.query_name][1]:
                yield [chr1, strand, read.reference_start, read.reference_end]
                yield fusions[read.query_name]
    bam.close()