docs: def cufflinks_conversion():
      """
      convert Cufflinks output GTF files into tables of score and FPKM.
      """
      for size, md5, fn in cufflinks_tables:
          fn = os.path.join(args.data_dir, fn)
          table = fn.replace('.gtf.gz', '.table')
          if not _up_to_date(md5, table):
              logger.info("Converting Cufflinks GTF %s to table" % fn)
              fout = open(table, 'w')
              fout.write('id\tscore\tfpkm\n')
              x = pybedtools.BedTool(fn)
              seen = set()
              for i in x:
                  accession = i['transcript_id'].split('.')[0]
                  if accession not in seen:
                      seen.update([accession])
                      fout.write(
                          '\t'.join([accession, i.score, i['FPKM']]) + '\n')
              fout.close()