def fill(args):
    """
    %prog fill gaps.bed bad.fasta

    Perform gap filling of one assembly (bad) using sequences from another.
    """
    p = OptionParser(fill.__doc__)
    p.add_option("--extend", default=2000, type="int",
                 help="Extend seq flanking the gaps [default: %default]")
    opts, args = p.parse_args(args)

    if len(args) != 2:
        sys.exit(not p.print_help())

    gapsbed, badfasta = args
    Ext = opts.extend

    gapdist = 2 * Ext + 1  # This is to prevent to replacement ranges intersect
    gapsbed = mergeBed(gapsbed, d=gapdist, nms=True)

    bed = Bed(gapsbed)
    sizes = Sizes(badfasta).mapping
    pf = gapsbed.rsplit(".", 1)[0]
    extbed = pf + ".ext.bed"
    fw = open(extbed, "w")
    for b in bed:
        gapname = b.accn
        start, end = max(0, b.start - Ext - 1), b.start - 1
        print("\t".join(str(x) for x in \
                             (b.seqid, start, end, gapname + "L")), file=fw)
        start, end = b.end, min(sizes[b.seqid], b.end + Ext)
        print("\t".join(str(x) for x in \
                             (b.seqid, start, end, gapname + "R")), file=fw)
    fw.close()

    fastaFromBed(extbed, badfasta, name=True)
%prog fill gaps.bed bad.fasta

    Perform gap filling of one assembly (bad) using sequences from another.