merge_bams.py 文件源码

def merge_reads(bams, merged_output_dir):
    """
        Merge bam files, can take odd numbers of reads. 
    """
    try:
        os.mkdir(merged_output_dir)
    except OSError:
        pass

    bam_list = get_bam_pairs(bams)
    for sample_id, bams in bam_list.items():
        header = get_header(bams[0])
        bam_out = os.path.join(merged_output_dir, os.path.basename(sample_id)) + '.bam'
        out = pysam.AlignmentFile(bam_out, 'wb', header=header)
        for bam in bams:
            sam = pysam.AlignmentFile(bam, 'rb')
            for read in sam:
                out.write(read)
        out.close()
        pysam.sort(bam_out, 'tmp')
        os.rename('tmp.bam',bam_out)
        pysam.index(bam_out)