code: def fromsra(args):
      
      p = OptionParser(fromsra.__doc__)
      p.add_option("--paired", default=False, action="store_true",
              help="Specify if library layout is paired-end " + \
                   "[default: %default]")
      p.add_option("--compress", default=None, choices=["gzip", "bzip2"],
              help="Compress output fastq files [default: %default]")
      p.set_outdir()
      p.set_grid()
      opts, args = p.parse_args(args)
  
      if len(args) != 1:
          sys.exit(not p.print_help())
  
      srafile, = args
      paired = opts.paired
      compress = opts.compress
      outdir = opts.outdir
  
      script_path = which("fastq-dump")
      if not script_path:
          logging.error("Cannot find `fastq-dump` in the PATH")
          sys.exit()
  
      cmd = [script_path]
      if compress:
          cmd.append("--{0}".format(compress))
      if paired:
          cmd.append("--split-files")
      if outdir:
          cmd.append("--outdir {0}".format(outdir))
      cmd.append(srafile)
  
      outcmd = " ".join(cmd)
      sh(outcmd, grid=opts.grid)
docs: %prog fromsra srafile
  
      Convert sra file to fastq using the sratoolkit `fastq-dump`