code: def sff(args):
      
      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)
docs: %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().