def sff(args):
    """
    %prog sff sffiles

    Convert reads formatted as 454 SFF file, and convert to CA frg file.
    Turn --nodedup on if another deduplication mechanism is used (e.g.
    CD-HIT-454). See assembly.sff.deduplicate().
    """
    p = OptionParser(sff.__doc__)
    p.add_option("--prefix", dest="prefix", default=None,
            help="Output frg filename prefix")
    p.add_option("--nodedup", default=False, action="store_true",
            help="Do not remove duplicates [default: %default]")
    p.set_size()
    opts, args = p.parse_args(args)

    if len(args) < 1:
        sys.exit(p.print_help())

    sffiles = args
    plates = [x.split(".")[0].split("_")[-1] for x in sffiles]

    mated = (opts.size != 0)
    mean, sv = get_mean_sv(opts.size)

    if len(plates) > 1:
        plate = plates[0][:-1] + 'X'
    else:
        plate = "_".join(plates)

    if mated:
        libname = "Titan{0}Kb-".format(opts.size / 1000) + plate
    else:
        libname = "TitanFrags-" + plate

    if opts.prefix:
        libname = opts.prefix

    cmd = "sffToCA"
    cmd += " -libraryname {0} -output {0} ".format(libname)
    cmd += " -clear 454 -trim chop "
    if mated:
        cmd += " -linker titanium -insertsize {0} {1} ".format(mean, sv)
    if opts.nodedup:
        cmd += " -nodedup "

    cmd += " ".join(sffiles)

    sh(cmd)
%prog sff sffiles

    Convert reads formatted as 454 SFF file, and convert to CA frg file.
    Turn --nodedup on if another deduplication mechanism is used (e.g.
    CD-HIT-454). See assembly.sff.deduplicate().