def patcher(args):
    """
    %prog patcher backbone.bed other.bed

    Given optical map alignment, prepare the patchers. Use --backbone to suggest
    which assembly is the major one, and the patchers will be extracted from
    another assembly.
    """
    from jcvi.formats.bed import uniq

    p = OptionParser(patcher.__doc__)
    p.add_option("--backbone", default="OM",
                 help="Prefix of the backbone assembly [default: %default]")
    p.add_option("--object", default="object",
                 help="New object name [default: %default]")
    opts, args = p.parse_args(args)

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

    backbonebed, otherbed = args
    backbonebed = uniq([backbonebed])
    otherbed = uniq([otherbed])

    pf = backbonebed.split(".")[0]
    key = lambda x: (x.seqid, x.start, x.end)

    # Make a uniq bed keeping backbone at redundant intervals
    cmd = "intersectBed -v -wa"
    cmd += " -a {0} -b {1}".format(otherbed, backbonebed)
    outfile = otherbed.rsplit(".", 1)[0] + ".not." + backbonebed
    sh(cmd, outfile=outfile)

    uniqbed = Bed()
    uniqbedfile = pf + ".merged.bed"
    uniqbed.extend(Bed(backbonebed))
    uniqbed.extend(Bed(outfile))
    uniqbed.print_to_file(uniqbedfile, sorted=True)

    # Condense adjacent intervals, allow some chaining
    bed = uniqbed
    key = lambda x: range_parse(x.accn).seqid

    bed_fn = pf + ".patchers.bed"
    bed_fw = open(bed_fn, "w")

    for k, sb in groupby(bed, key=key):
        sb = list(sb)
        chr, start, end, strand = merge_ranges(sb)

        print("\t".join(str(x) for x in \
                (chr, start, end, opts.object, 1000, strand)), file=bed_fw)

    bed_fw.close()
%prog patcher backbone.bed other.bed

    Given optical map alignment, prepare the patchers. Use --backbone to suggest
    which assembly is the major one, and the patchers will be extracted from
    another assembly.