peakcaller.py 文件源码

def make_bam_handler_dict(ip_bam_list, con_bam_list):
    """DOCSTRING
    Args
    Returns
    """
    bam_dict = defaultdict(list)
    try:
        ubam_ip, mbam_ip = ip_bam_list
    except:
        ubam_ip = ip_bam_list[0]
        mbam_ip = None
    for bam_fn in ubam_ip.split(','):
        if not os.path.isfile(bam_fn):
            raise Exception('%s not found'%bam_fn)
        bam_dict['ubam.ip'].append( pysam.Samfile(bam_fn, 'rb') )
    if mbam_ip is not None:
        for bam_fn in mbam_ip.split(','):
            if not os.path.isfile(bam_fn):
                raise Exception('%s not found'%bam_fn)
            bam_dict['mbam.ip'].append( pysam.Samfile(bam_fn, 'rb') )

    if con_bam_list is None:
        return bam_dict
    try:
        ubam_con, mbam_con = con_bam_list
    except:
        ubam_con = con_bam_list[0]
        mbam_con = None
    for bam_fn in ubam_con.split(','):
        if not os.path.isfile(bam_fn):
            raise Exception('%s not found'%bam_fn)
        bam_dict['ubam.con'].append( pysam.Samfile(bam_fn, 'rb') )
    if mbam_con is not None:
        for bam_fn in mbam_con.split(','):
            if not os.path.isfile(bam_fn):
                raise Exception('%s not found'%bam_fn)
            bam_dict['mbam.con'].append( pysam.Samfile(bam_fn, 'rb') )
    return bam_dict