Python load_ercc_conc Examples

Example #1

File: run_ERCC_analysis.py Project: skner/TS

        for line in ercc_genome:
            parsed_line = line.split()
            transcript_names.append(parsed_line[0])
            transcript_sizes.append(parsed_line[1])
    # write counts file and filtered sam file, return stats tuple
    counts, all_ercc_counts, total_counts, mean_mapqs = write_output_counts_file(
        RAW_SAM_FILE, FILTERED_SAM_FILE, COUNTS_FILE, transcript_names,
        ONLY_FWD_READS)
    if (total_counts > 0):
        percent_total_counts_ercc = '%.2f' % (100 *
                                              (all_ercc_counts / total_counts))
        percent_total_counts_non_ercc = 100 - float(percent_total_counts_ercc)

    coverage.parse_sam(FILTERED_SAM_FILE)

    ercc_conc = load_ercc_conc(filter=counts.keys(), pool=ERCC_POOL_NBR)
    ercc_conc.sort()

    dr = dose_response(coverage, ercc_conc, counts, MINIMUM_COUNTS)
    trendline_points = generate_trendline_points(dr)
else:
    msg_to_user = "******" + BARCODE_ENTERED + ", is not found.  This is most likely to result when the barcode is typed incorrectly, or the run was originally processed with a Torrent Suite version less than 3.4."
    data_to_display = False

if data_to_display:
    try:
        report_components = generate_reports(OUTPUT_DIR, coverage, dr, counts)
    except ValueError:
        msg_to_user = "******"
        data_to_display = False

Example #2

File: run_ERCC_analysis.py Project: basmaNasser/TS

  transcript_names = []
  transcript_sizes = []
  with open(GENOME) as ercc_genome:
      for line in ercc_genome:
          parsed_line = line.split()
          transcript_names.append(parsed_line[0])
          transcript_sizes.append(parsed_line[1])
  # write counts file and filtered sam file, return stats tuple
  counts, all_ercc_counts, total_counts, mean_mapqs = write_output_counts_file(RAW_SAM_FILE,FILTERED_SAM_FILE,COUNTS_FILE,transcript_names,ONLY_FWD_READS)
  if (total_counts > 0):
    percent_total_counts_ercc = '%.2f' % (100 * (all_ercc_counts / total_counts))
    percent_total_counts_non_ercc = 100 - float(percent_total_counts_ercc)
  
  coverage.parse_sam(FILTERED_SAM_FILE)
  
  ercc_conc = load_ercc_conc(filter = counts.keys(), pool = ERCC_POOL_NBR)
  ercc_conc.sort()
  
  
  dr = dose_response(coverage,ercc_conc,counts,MINIMUM_COUNTS)
  trendline_points = generate_trendline_points(dr)
else:
  msg_to_user = "******"+BARCODE_ENTERED+", is not found.  This is most likely to result when the barcode is typed incorrectly, or the run was originally processed with a Torrent Suite version less than 3.4."
  data_to_display = False

if data_to_display:
  try:
    report_components = generate_reports(OUTPUT_DIR, coverage, dr, counts)
  except ValueError:
    msg_to_user = "******"
    data_to_display = False