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 = "******"
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 if data_to_display: try: report_components = generate_reports(OUTPUT_DIR, coverage, dr, counts) except ValueError:
template_vars["start_site_complexity"] = results[1]["start_site_complexity"] template_vars["contig_cv"] = results[1]["contig_cv"] results_divs += result_div % template_vars plot_coverage(contig[1], starts[1], path=image_name) results_divs += "</div>" report_components["results_divs"] = results_divs report_components["updates"] = proc_update return report_components if __name__ == "__main__": coverage = SamCoverage(GENOME) if len(sys.argv) == 2: coverage.parse_sam(sys.argv[1]) else: coverage.parse_sam(TEST_SAM) threshold = 1 counts = {} for ercc, count in coverage.count_iter(): if count >= threshold: counts[ercc] = count ercc_conc = load_ercc_conc(filter=counts.keys()) dr = dose_response(coverage, ercc_conc) generate_reports(coverage, dr)
template_vars['start_site_coverage_pct'] = results[1]['start_site_coverage_pct'] template_vars['unique_start_sites'] = results[1]['unique_start_sites'] template_vars['start_site_complexity'] = results[1]['start_site_complexity'] template_vars['contig_cv'] = results[1]['contig_cv'] results_divs += (result_div % template_vars) plot_coverage(contig[1], starts[1], path = image_name) results_divs += '</div>' report_components['results_divs'] = results_divs report_components['updates'] = proc_update return report_components if __name__=='__main__': coverage = SamCoverage(GENOME) if len(sys.argv) == 2: coverage.parse_sam(sys.argv[1]) else: coverage.parse_sam(TEST_SAM) threshold = 1 counts = {} for ercc, count in coverage.count_iter(): if count >= threshold: counts[ercc] = count ercc_conc = load_ercc_conc(filter = counts.keys()) dr = dose_response(coverage, ercc_conc) generate_reports(coverage, dr)
template_vars['start_site_coverage_pct'] = results[1]['start_site_coverage_pct'] template_vars['unique_start_sites'] = results[1]['unique_start_sites'] template_vars['start_site_complexity'] = results[1]['start_site_complexity'] template_vars['contig_cv'] = results[1]['contig_cv'] results_divs += (result_div % template_vars) plot_coverage(contig[1], starts[1], path = outdir+image_name) results_divs += '</div>' report_components['results_divs'] = results_divs report_components['updates'] = proc_update return report_components if __name__=='__main__': coverage = SamCoverage(GENOME) if len(sys.argv) == 2: coverage.parse_sam(sys.argv[1]) else: coverage.parse_sam(TEST_SAM) threshold = 1 counts = {} for ercc, count in coverage.count_iter(): if count >= threshold: counts[ercc] = count ercc_conc = load_ercc_conc(filter = counts.keys()) dr = dose_response(coverage, ercc_conc) generate_reports(coverage, dr)