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):
summary_txt_fpath = os.path.join(output_dirpath, 'TXT',
metric.replace(' ', '_') + '.txt')
summary_tex_fpath = os.path.join(output_dirpath, 'TEX',
metric.replace(' ', '_') + '.tex')
summary_tsv_fpath = os.path.join(output_dirpath, 'TSV',
metric.replace(' ', '_') + '.tsv')
summary_plot_fpath = os.path.join(output_dirpath, plots_dirname,
metric.replace(' ', '_'))
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 not results[0]:
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_fpath,
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(
'contigs_reports', 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 + '/')
def do(html_fpath, output_dirpath, combined_output_dirpath, output_dirpath_per_ref, metrics, misassembl_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):
summary_txt_fpath = os.path.join(output_dirpath, 'TXT', metric.replace(' ', '_') + '.txt')
summary_tex_fpath = os.path.join(output_dirpath, 'TEX', metric.replace(' ', '_') + '.tex')
summary_tsv_fpath = os.path.join(output_dirpath, 'TSV', metric.replace(' ', '_') + '.tsv')
summary_png_fpath = os.path.join(output_dirpath, plots_dirname, metric.replace(' ', '_') + '.' + qconfig.plot_extension)
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 not results[0]:
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 == reporting.Fields.TOTALLEN:
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, all_rows, results,
summary_png_fpath, title=metric, reverse=reverse, yaxis_title=y_label)
if metric == reporting.Fields.MISASSEMBL:
mis_results = []
report_fname = os.path.join('contigs_reports', qconfig.transposed_report_prefix + '_misassemblies' + '.tsv')
if ref_names[-1] == qconfig.not_aligned_name:
cur_ref_names = ref_names[:-1]
for misassembl_metric in misassembl_metrics:
results, all_rows, cur_ref_names = get_results_for_metric(cur_ref_names, misassembl_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_misassembl_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 + '/')
def get_blast_output_fpath(blast_output_fpath, label):
return blast_output_fpath + '_' + slugify(label)
def get_blast_output_fpath(blast_output_fpath, label):
return blast_output_fpath + '_' + slugify(label)