############################################################################ # Copyright (c) 2015-2022 Saint Petersburg State University # Copyright (c) 2011-2015 Saint Petersburg Academic University # All Rights Reserved # See file LICENSE for details. ############################################################################ import os from quast_libs import plotter, reporting, qconfig, qutils from quast_libs.ca_utils.misc import print_file from quast_libs.log import get_logger logger = get_logger(qconfig.LOGGER_META_NAME) def get_results_for_metric(full_ref_names, metric, contigs_num, labels, output_dirpath, report_fname): all_rows = [] ref_names = full_ref_names row = {'metricName': 'References', 'values': ref_names} all_rows.append(row) results = [] for i in range(contigs_num): row = {'metricName': labels[i], 'values': []} all_rows.append(row) for i, ref_name in enumerate(full_ref_names): results.append([]) cur_results = [None] * len(labels) results_fpath = os.path.join(output_dirpath, ref_name, report_fname) if ref_name == qconfig.not_aligned_name: results_fpath = os.path.join(os.path.dirname(output_dirpath), ref_name, report_fname) if os.path.exists(results_fpath): results_file = open(results_fpath, 'r') columns = [s.strip() for s in results_file.readline().split('\t')] if metric in columns: next_values = [s.strip() for s in results_file.readline().split('\t')] cur_results = [None] * len(labels) for j in range(contigs_num): values = next_values if values[0]: metr_res = values[columns.index(metric)].split()[0] next_values = [s.strip() for s in results_file.readline().split('\t')] index_contig = labels.index(values[0]) cur_results[index_contig] = metr_res elif ref_name == qconfig.not_aligned_name: ref_names.pop(i) continue for j in range(contigs_num): all_rows[j + 1]['values'].append(cur_results[j]) results[-1].append(cur_results[j]) return results, all_rows, ref_names def get_labels(combined_output_dirpath, report_fname): results_fpath = os.path.join(combined_output_dirpath, report_fname) results_file = open(results_fpath, 'r') values = [s.strip() for s in results_file.readline().split('\t')] return values[1:] def do(html_fpath, output_dirpath, combined_output_dirpath, output_dirpath_per_ref, metrics, misassembly_metrics, ref_names): labels = get_labels(combined_output_dirpath, qconfig.report_prefix + '.tsv') contigs_num = len(labels) plots_dirname = qconfig.plot_extension.upper() for ext in ['TXT', plots_dirname, 'TEX', 'TSV']: if not os.path.isdir(os.path.join(output_dirpath, ext)): os.mkdir(os.path.join(output_dirpath, ext)) for metric in metrics: if not isinstance(metric, tuple): metric_fname = metric.replace(' (%)', '').replace('#', 'num').replace('>=', 'ge').replace(' ', '_').replace("'", "") summary_txt_fpath = os.path.join(output_dirpath, 'TXT', metric_fname + '.txt') summary_tex_fpath = os.path.join(output_dirpath, 'TEX', metric_fname + '.tex') summary_tsv_fpath = os.path.join(output_dirpath, 'TSV', metric_fname + '.tsv') summary_plot_fname = os.path.join(output_dirpath, plots_dirname, metric_fname) results, all_rows, cur_ref_names = \ get_results_for_metric(ref_names, metric, contigs_num, labels, output_dirpath_per_ref, qconfig.transposed_report_prefix + '.tsv') if not results or all(not value for result in results for value in result): continue if cur_ref_names: transposed_table = [{'metricName': 'Assemblies', 'values': [all_rows[i]['metricName'] for i in range(1, len(all_rows))],}] for i in range(len(all_rows[0]['values'])): values = [] for j in range(1, len(all_rows)): values.append(all_rows[j]['values'][i]) transposed_table.append({'metricName': all_rows[0]['values'][i], # name of reference 'values': values}) print_file(transposed_table, summary_txt_fpath) reporting.save_tsv(summary_tsv_fpath, transposed_table) reporting.save_tex(summary_tex_fpath, transposed_table) reverse = False if reporting.get_quality(metric) == reporting.Fields.Quality.MORE_IS_BETTER: reverse = True y_label = None if metric in [reporting.Fields.TOTALLEN, reporting.Fields.TOTALLENS__FOR_1000_THRESHOLD, reporting.Fields.TOTALLENS__FOR_10000_THRESHOLD, reporting.Fields.TOTALLENS__FOR_50000_THRESHOLD]: y_label = 'Total length' elif metric == reporting.Fields.TOTAL_ALIGNED_LEN: y_label = 'Aligned length' elif metric in [reporting.Fields.LARGCONTIG, reporting.Fields.N50, reporting.Fields.NGA50, reporting.Fields.MIS_EXTENSIVE_BASES]: y_label = 'Contig length' elif metric == reporting.Fields.LARGALIGN: y_label = 'Alignment length' plotter.draw_meta_summary_plot(html_fpath, output_dirpath, labels, cur_ref_names, results, summary_plot_fname, title=metric, reverse=reverse, yaxis_title=y_label, print_all_refs=True, logger=logger) if metric == reporting.Fields.MISASSEMBL: mis_results = [] report_fname = os.path.join(qconfig.detailed_contigs_reports_dirname, qconfig.transposed_report_prefix + '_misassemblies' + '.tsv') if ref_names[-1] == qconfig.not_aligned_name: cur_ref_names = ref_names[:-1] for misassembly_metric in misassembly_metrics: results, all_rows, cur_ref_names = \ get_results_for_metric(cur_ref_names, misassembly_metric[len(reporting.Fields.TAB):], contigs_num, labels, output_dirpath_per_ref, report_fname) if results: mis_results.append(results) if mis_results: json_points = [] for contig_num in range(contigs_num): plot_fpath = os.path.join(output_dirpath, plots_dirname, qutils.slugify(labels[contig_num]) + '_misassemblies') json_points.append(plotter.draw_meta_summary_misassemblies_plot(mis_results, cur_ref_names, contig_num, plot_fpath, title=labels[contig_num])) if qconfig.html_report: from quast_libs.html_saver import html_saver if ref_names[-1] == qconfig.not_aligned_name: cur_ref_names = ref_names[:-1] if json_points: html_saver.save_meta_misassemblies(html_fpath, output_dirpath, json_points, labels, cur_ref_names) logger.main_info('') logger.main_info(' Text versions of reports and plots for each metric (for all references and assemblies) are saved to ' + output_dirpath + '/')