code: def fastq(args):
      
      from jcvi.formats.fastq import guessoffset
  
      p = OptionParser(fastq.__doc__)
      p.add_option("--outtie", dest="outtie", default=False, action="store_true",
              help="Are these outie reads? [default: %default]")
      p.set_phred()
      p.set_size()
  
      opts, args = p.parse_args(args)
  
      if len(args) < 1:
          sys.exit(p.print_help())
  
      fastqfiles = [get_abs_path(x) for x in args]
      size = opts.size
      outtie = opts.outtie
      if size > 1000 and (not outtie):
          logging.debug("[warn] long insert size {0} but not outtie".format(size))
  
      mated = (size != 0)
      libname = op.basename(args[0]).split(".")[0]
      libname = libname.replace("_1_sequence", "")
  
      frgfile = libname + ".frg"
      mean, sv = get_mean_sv(opts.size)
  
      cmd = "fastqToCA"
      cmd += " -libraryname {0} ".format(libname)
      fastqs = " ".join("-reads {0}".format(x) for x in fastqfiles)
      if mated:
          assert len(args) in (1, 2), "you need one or two fastq files for mated library"
          fastqs = "-mates {0}".format(",".join(fastqfiles))
          cmd += "-insertsize {0} {1} ".format(mean, sv)
      cmd += fastqs
  
      offset = int(opts.phred) if opts.phred else guessoffset([fastqfiles[0]])
      illumina = (offset == 64)
      if illumina:
          cmd += " -type illumina"
      if outtie:
          cmd += " -outtie"
  
      sh(cmd, outfile=frgfile)
docs: %prog fastq fastqfile
  
      Convert reads formatted as FASTQ file, and convert to CA frg file.