def filter(args):
    """
    %prog filter <deltafile|coordsfile>

    Produce a new delta/coords file and filter based on id% or cov%.
    Use `delta-filter` for .delta file.
    """
    p = OptionParser(filter.__doc__)
    p.set_align(pctid=0, hitlen=0)
    p.add_option("--overlap", default=False, action="store_true",
            help="Print overlap status (e.g. terminal, contained)")

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

    pctid = opts.pctid
    hitlen = opts.hitlen

    filename, = args
    if pctid == 0 and hitlen == 0:
        return filename

    pf, suffix = filename.rsplit(".", 1)
    outfile = "".join((pf, ".P{0}L{1}.".format(int(pctid), int(hitlen)), suffix))
    if not need_update(filename, outfile):
        return outfile

    if suffix == "delta":
        cmd = "delta-filter -i {0} -l {1} {2}".format(pctid, hitlen, filename)
        sh(cmd, outfile=outfile)
        return outfile

    fp = open(filename)
    fw = must_open(outfile, "w")
    for row in fp:
        try:
            c = CoordsLine(row)
        except __HOLE__:
            continue

        if c.identity < pctid:
            continue
        if c.len2 < hitlen:
            continue
        if opts.overlap and not c.overlap:
            continue

        outrow = row.rstrip()
        if opts.overlap:
            ov = Overlap_types[c.overlap]
            outrow += "\t" + ov
        print >> fw, outrow

    return outfile
dataset/ETHPy150Open tanghaibao/jcvi/formats/coords.py/filter