def bed(args):
    p = OptionParser(bed.__doc__)
    p.add_option("--query", default=False, action="store_true",
            help="print out query intervals rather than ref [default: %default]")
    p.add_option("--pctid", default=False, action="store_true",
            help="use pctid in score [default: %default]")
    p.add_option("--cutoff", dest="cutoff", default=0, type="float",
            help="get all the alignments with quality above threshold " +\
                 "[default: %default]")

    opts, args = p.parse_args(args)
    if len(args) != 1:
        sys.exit(p.print_help())

    coordsfile, = args
    query = opts.query
    pctid = opts.pctid
    quality_cutoff = opts.cutoff

    coords = Coords(coordsfile)

    for c in coords:
        if c.quality < quality_cutoff:
            continue
        line = c.qbedline(pctid=pctid) if query else c.bedline(pctid=pctid)
        print line
%prog bed coordsfile
dataset/ETHPy150Open tanghaibao/jcvi/formats/coords.py/bed