def filter(args):
    p = OptionParser(filter.__doc__)
    p.add_option("--minsize", default=0, type="int",
                 help="Minimum feature length")
    p.add_option("--maxsize", default=1000000000, type="int",
                 help="Minimum feature length")
    p.add_option("--minaccn", type="int",
                 help="Minimum value of accn, useful to filter based on coverage")
    p.add_option("--minscore", type="int", help="Minimum score")
    p.set_outfile()

    opts, args = p.parse_args(args)

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

    bedfile, = args
    fp = must_open(bedfile)
    fw = must_open(opts.outfile, "w")
    minsize, maxsize = opts.minsize, opts.maxsize
    minaccn = opts.minaccn
    minscore = opts.minscore
    total = []
    keep = []
    for row in fp:
        try:
            b = BedLine(row)
        except IndexError:
            print >> fw, row.strip()
            continue
        span = b.span
        total.append(span)
        if not minsize <= span <= maxsize:
            continue
        if minaccn and int(b.accn) < minaccn:
            continue
        if minscore and int(b.score) < minscore:
            continue
        print >> fw, b
        keep.append(span)

    logging.debug("Stats: {0} features kept.".\
                    format(percentage(len(keep), len(total))))
    logging.debug("Stats: {0} bases kept.".\
                    format(percentage(sum(keep), sum(total))))
%prog filter bedfile
dataset/ETHPy150Open tanghaibao/jcvi/formats/bed.py/filter