def bedpe(args):
    """
    %prog bedpe bedfile

    Convert to bedpe format. Use --span to write another bed file that contain
    the span of the read pairs.
    """
    from jcvi.assembly.coverage import bed_to_bedpe

    p = OptionParser(bedpe.__doc__)
    p.add_option("--span", default=False, action="store_true",
                 help="Write span bed file [default: %default]")
    p.add_option("--mates", help="Check the library stats from .mates file")
    opts, args = p.parse_args(args)

    if len(args) != 1:
        sys.exit(not p.print_help())

    bedfile, = args
    pf = bedfile.rsplit(".", 1)[0]
    bedpefile = pf + ".bedpe"
    bedspanfile = pf + ".spans.bed" if opts.span else None
    bed_to_bedpe(bedfile, bedpefile, \
                 pairsbedfile=bedspanfile, matesfile=opts.mates)
    return bedpefile, bedspanfile
dataset/ETHPy150Open tanghaibao/jcvi/formats/bed.py/bedpe/original