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

    Sum the total lengths of the intervals.
    """
    p = OptionParser(summary.__doc__)
    p.add_option("--sizes", default=False, action="store_true",
                 help="Write .sizes file")
    p.add_option("--all", default=False, action="store_true",
                 help="Write summary stats per seqid")
    opts, args = p.parse_args(args)

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

    bedfile, = args
    bed = Bed(bedfile)
    bs = BedSummary(bed)
    if opts.sizes:
        sizesfile = bedfile + ".sizes"
        fw = open(sizesfile, "w")
        for span, accn in bs.mspans:
            print >> fw, span
        fw.close()
        logging.debug("Spans written to `{0}`.".format(sizesfile))
        return bs

    if not opts.all:
        bs.report()
        return bs

    for seqid, subbeds in bed.sub_beds():
        bs = BedSummary(subbeds)
        print "\t".join((seqid, str(bs)))
dataset/ETHPy150Open tanghaibao/jcvi/formats/bed.py/summary/original