implementGain.py 文件源码

def renamereads(inbamfn, outbamfn):

    inbam = pysam.Samfile(inbamfn, 'rb')
    outbam = pysam.Samfile(outbamfn, 'wb', template=inbam)

    paired = {}

    n = 0
    p = 0
    u = 0
    w = 0
    m = 0

    for read in inbam.fetch(until_eof=True):
        n += 1
        if read.is_paired:
            p += 1
            if read.qname in paired:
                uuid = paired[read.qname]
                del paired[read.qname]
                read.qname = uuid
                outbam.write(read)
                w += 1
                m += 1
            else:
                newname = str(uuid4())
                paired[read.qname] = newname
                read.qname = newname
                outbam.write(read)
                w += 1
        else:
            u += 1
            read.qname = str(uuid4())
            outbam.write(read)
            w += 1

    outbam.close()
    inbam.close()