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."
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 = ""
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
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