code: def soapX(args):
      
      p = OptionParser(soapX.__doc__)
      opts, args = p.parse_args(args)
  
      if len(args) < 2:
          sys.exit(not p.print_help())
  
      folder, tag = args[:2]
      extra = args[2:]
      extra = [get_abs_path(x) for x in extra]
      tag = tag.split(",")
      for p, pf in iter_project(folder, n=3):
          soap_trios(p, pf, tag, extra)
docs: %prog soapX folder tag [*.fastq]
  
      Run SOAP on a folder of paired reads and apply tag before assembly.
      Optional *.fastq in the argument list will be symlinked in each folder and
      co-assembled.