Python write_output_counts_file 예제들

예제 #1

파일: run_ERCC_analysis.py 프로젝트: skner/TS

data_to_display = True
msg_to_user = ""

if FASTQ_FILE_CREATED != 'N':
    coverage = SamCoverage(GENOME)

    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."

예제 #2

파일: ERCC_Analysis.py 프로젝트: bdiegel/TS

  MINIMUM_COUNTS = 1
try:
  ERCC_POOL_NBR = int(sys.argv[8])
except:
  ERCC_POOL_NBR = 1

coverage = SamCoverage(GENOME)

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])
counts, all_ercc_counts, total_counts, mean_mapqs = write_output_counts_file(RAW_SAM_FILE,FILTERED_SAM_FILE,COUNTS_FILE,transcript_names) # side-effect is to write counts file, filtered sam file
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)

data_to_display = True
msg_to_user = ""

예제 #3

파일: run_ERCC_analysis.py 프로젝트: basmaNasser/TS

  
data_to_display = True
msg_to_user = ""  
  
if FASTQ_FILE_CREATED != 'N':
  coverage = SamCoverage(GENOME)

  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

예제 #4

  
data_to_display = True
msg_to_user = ""  
  
if FASTQ_FILE_CREATED != 'N':
  coverage = SamCoverage(GENOME)

  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])
  counts, all_ercc_counts, total_counts, mean_mapqs = write_output_counts_file(RAW_SAM_FILE,FILTERED_SAM_FILE,COUNTS_FILE,transcript_names) # side-effect is to write counts file, filtered sam file
  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