def annotate(args):
    """
    %prog annotate coordsfile

    Annotate coordsfile to append an additional column, with the following
    overlaps: {0}.
    """
    p = OptionParser(annotate.__doc__.format(", ".join(Overlap_types)))
    p.add_option("--maxhang", default=100, type="int",
                 help="Max hang to call dovetail overlap [default: %default]")
    p.add_option("--all", default=False, action="store_true",
                 help="Output all lines [default: terminal/containment]")

    opts, args = p.parse_args(args)

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

    coordsfile, = args
    fp = open(coordsfile)

    for row in fp:
        try:
            c = CoordsLine(row)
        except __HOLE__:
            continue

        ov = c.overlap(opts.maxhang)
        if not opts.all and ov == 0:
            continue

        print "{0}\t{1}".format(row.strip(), Overlap_types[ov])
dataset/ETHPy150Open tanghaibao/jcvi/formats/coords.py/annotate