def save_combined_ref_stats(results, contigs_fpaths, ref_labels_by_chromosomes, output_dir, logger):
ref_misassemblies = [result['istranslocations_by_refs'] if result else [] for result in results]
potential_misassemblies_by_refs = [result['potential_misassemblies_by_refs'] if result else [] for result in results]
all_refs = sorted(list(set([ref for ref in ref_labels_by_chromosomes.values()])))
misassemblies_by_refs_rows = []
row = {'metricName': 'References', 'values': all_refs}
misassemblies_by_refs_rows.append(row)
if ref_misassemblies:
for i, fpath in enumerate(contigs_fpaths):
row = {'metricName': qutils.label_from_fpath(fpath), 'values': []}
misassemblies_by_refs_rows.append(row)
if ref_misassemblies[i]:
assembly_name = qutils.name_from_fpath(fpath)
all_rows = []
row = {'metricName': 'References', 'values': [ref_num + 1 for ref_num in range(len(all_refs))]}
all_rows.append(row)
for k in all_refs:
row = {'metricName': k, 'values': []}
for ref in all_refs:
if ref == k or ref not in ref_misassemblies[i]:
row['values'].append(None)
else:
row['values'].append(ref_misassemblies[i][ref][k])
misassemblies_by_refs_rows[-1]['values'].append(max(0, sum([r for r in row['values'] if r]) +
potential_misassemblies_by_refs[i][k]))
all_rows.append(row)
misassembly_by_ref_fpath = os.path.join(output_dir, 'interspecies_translocations_by_refs_%s.info' % assembly_name)
with open(misassembly_by_ref_fpath, 'w') as misassembly_by_ref_file:
misassembly_by_ref_file.write('Number of interspecies translocations by references: \n')
print_file(all_rows, misassembly_by_ref_fpath, append_to_existing_file=True)
with open(misassembly_by_ref_fpath, 'a') as misassembly_by_ref_file:
misassembly_by_ref_file.write('References:\n')
for ref_num, ref in enumerate(all_refs):
misassembly_by_ref_file.write(str(ref_num + 1) + ' - ' + ref + '\n')
logger.info(' Information about interspecies translocations by references for %s is saved to %s' %
(assembly_name, misassembly_by_ref_fpath))
misassemblies = []
if qconfig.draw_plots:
from quast_libs import plotter
aligned_contigs_labels = []
for row in misassemblies_by_refs_rows[1:]:
if row['values']:
aligned_contigs_labels.append(row['metricName'])
else:
misassemblies_by_refs_rows.remove(row)
for i in range(len(all_refs)):
cur_results = []
for row in misassemblies_by_refs_rows[1:]:
if row['values']:
cur_results.append(row['values'][i])
misassemblies.append(cur_results)
is_translocations_plot_fpath = os.path.join(output_dir, 'intergenomic_misassemblies.' + qconfig.plot_extension)
plotter.draw_meta_summary_plot('', output_dir, aligned_contigs_labels, all_refs, misassemblies_by_refs_rows,
misassemblies, is_translocations_plot_fpath,
title='Intergenomic misassemblies (found and supposed)', reverse=False,
yaxis_title=None, print_all_refs=True)
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 save_combined_ref_stats(results, contigs_fpaths, ref_labels_by_chromosomes, output_dir, logger):
istranslocations_by_asm = [result['istranslocations_by_refs'] if result else None for result in results]
misassemblies_by_asm = [result['misassemblies_by_ref'] if result else None for result in results]
all_refs = []
for ref in ref_labels_by_chromosomes.values():
if ref not in all_refs:
all_refs.append(ref)
if not qconfig.use_input_ref_order:
all_refs.sort()
misassemblies_by_refs_rows = []
row = {'metricName': 'References', 'values': all_refs}
misassemblies_by_refs_rows.append(row)
if not istranslocations_by_asm:
return
for i, fpath in enumerate(contigs_fpaths):
label = qutils.label_from_fpath(fpath)
row = {'metricName': label, 'values': []}
misassemblies_by_refs_rows.append(row)
istranslocations_by_ref = istranslocations_by_asm[i]
intergenomic_misassemblies_by_asm[label] = defaultdict(list)
for ref in all_refs:
intergenomic_misassemblies_by_asm[label][ref] = misassemblies_by_asm[i][ref] if misassemblies_by_asm[i] else []
if istranslocations_by_ref:
assembly_name = qutils.name_from_fpath(fpath)
all_rows = []
row = {'metricName': 'References', 'values': [ref_num + 1 for ref_num in range(len(all_refs))]}
all_rows.append(row)
for ref in all_refs:
row = {'metricName': ref, 'values': []}
for second_ref in all_refs:
if ref == second_ref or second_ref not in istranslocations_by_ref:
row['values'].append(None)
else:
row['values'].append(istranslocations_by_ref[ref][second_ref])
possible_misassemblies = 0
misassemblies_by_ref = misassemblies_by_asm[i]
if misassemblies_by_ref:
possible_misassemblies = misassemblies_by_ref[ref].count(Misassembly.POSSIBLE_MISASSEMBLIES)
istranslocations = max(0, sum([r for r in row['values'] if r]))
misassemblies_by_refs_rows[-1]['values'].append(istranslocations + possible_misassemblies)
all_rows.append(row)
misassembly_by_ref_fpath = os.path.join(output_dir, 'interspecies_translocations_by_refs_%s.info' % assembly_name)
with open(misassembly_by_ref_fpath, 'w') as misassembly_by_ref_file:
misassembly_by_ref_file.write('Number of interspecies translocations by references: \n')
print_file(all_rows, misassembly_by_ref_fpath, append_to_existing_file=True)
with open(misassembly_by_ref_fpath, 'a') as misassembly_by_ref_file:
misassembly_by_ref_file.write('References:\n')
for ref_num, ref in enumerate(all_refs):
misassembly_by_ref_file.write(str(ref_num + 1) + ' - ' + ref + '\n')
logger.info(' Information about interspecies translocations by references for %s is saved to %s' %
(assembly_name, misassembly_by_ref_fpath))
misassemblies = []
if qconfig.draw_plots:
from quast_libs import plotter
aligned_contigs_labels = []
for row in misassemblies_by_refs_rows[1:]:
if row['values']:
aligned_contigs_labels.append(row['metricName'])
else:
misassemblies_by_refs_rows.remove(row)
for i in range(len(all_refs)):
cur_results = []
for row in misassemblies_by_refs_rows[1:]:
if row['values']:
cur_results.append(row['values'][i])
misassemblies.append(cur_results)
is_translocations_plot_fpath = os.path.join(output_dir, 'intergenomic_misassemblies')
plotter.draw_meta_summary_plot('', output_dir, aligned_contigs_labels, all_refs,
misassemblies, is_translocations_plot_fpath,
title='Intergenomic misassemblies (found and supposed)', reverse=False,
yaxis_title=None, print_all_refs=True, logger=logger)
def save_combined_ref_stats(results, contigs_fpaths, ref_labels_by_chromosomes,
output_dir, logger):
istranslocations_by_asm = [
result['istranslocations_by_refs'] if result else None
for result in results
]
misassemblies_by_asm = [
result['misassemblies_by_ref'] if result else None
for result in results
]
all_refs = []
for ref in ref_labels_by_chromosomes.values():
if ref not in all_refs:
all_refs.append(ref)
if not qconfig.use_input_ref_order:
all_refs.sort()
misassemblies_by_refs_rows = []
row = {'metricName': 'References', 'values': all_refs}
misassemblies_by_refs_rows.append(row)
if not istranslocations_by_asm:
return
for i, fpath in enumerate(contigs_fpaths):
label = qutils.label_from_fpath(fpath)
row = {'metricName': label, 'values': []}
misassemblies_by_refs_rows.append(row)
istranslocations_by_ref = istranslocations_by_asm[i]
intergenomic_misassemblies_by_asm[label] = defaultdict(list)
for ref in all_refs:
intergenomic_misassemblies_by_asm[label][
ref] = misassemblies_by_asm[i][ref] if misassemblies_by_asm[
i] else []
if istranslocations_by_ref:
assembly_name = qutils.name_from_fpath(fpath)
all_rows = []
row = {
'metricName': 'References',
'values': [ref_num + 1 for ref_num in range(len(all_refs))]
}
all_rows.append(row)
for ref in all_refs:
row = {'metricName': ref, 'values': []}
for second_ref in all_refs:
if ref == second_ref or second_ref not in istranslocations_by_ref:
row['values'].append(None)
else:
row['values'].append(
istranslocations_by_ref[ref][second_ref])
possible_misassemblies = 0
misassemblies_by_ref = misassemblies_by_asm[i]
if misassemblies_by_ref:
possible_misassemblies = misassemblies_by_ref[ref].count(
Misassembly.POSSIBLE_MISASSEMBLIES)
istranslocations = max(0, sum([r for r in row['values'] if r]))
misassemblies_by_refs_rows[-1]['values'].append(
istranslocations + possible_misassemblies)
all_rows.append(row)
misassembly_by_ref_fpath = os.path.join(
output_dir,
'interspecies_translocations_by_refs_%s.info' % assembly_name)
with open(misassembly_by_ref_fpath,
'w') as misassembly_by_ref_file:
misassembly_by_ref_file.write(
'Number of interspecies translocations by references: \n')
print_file(all_rows,
misassembly_by_ref_fpath,
append_to_existing_file=True)
with open(misassembly_by_ref_fpath,
'a') as misassembly_by_ref_file:
misassembly_by_ref_file.write('References:\n')
for ref_num, ref in enumerate(all_refs):
misassembly_by_ref_file.write(
str(ref_num + 1) + ' - ' + ref + '\n')
logger.info(
' Information about interspecies translocations by references for %s is saved to %s'
% (assembly_name, misassembly_by_ref_fpath))
misassemblies = []
if qconfig.draw_plots:
from quast_libs import plotter
aligned_contigs_labels = []
for row in misassemblies_by_refs_rows[1:]:
if row['values']:
aligned_contigs_labels.append(row['metricName'])
else:
misassemblies_by_refs_rows.remove(row)
for i in range(len(all_refs)):
cur_results = []
for row in misassemblies_by_refs_rows[1:]:
if row['values']:
cur_results.append(row['values'][i])
misassemblies.append(cur_results)
is_translocations_plot_fpath = os.path.join(
output_dir, 'intergenomic_misassemblies')
plotter.draw_meta_summary_plot(
'',
output_dir,
aligned_contigs_labels,
all_refs,
misassemblies,
is_translocations_plot_fpath,
title='Intergenomic misassemblies (found and supposed)',
reverse=False,
yaxis_title=None,
print_all_refs=True,
logger=logger)
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 do(reference,
contigs_fpaths,
cyclic,
output_dir,
old_contigs_fpaths,
bed_fpath=None):
if not os.path.isdir(output_dir):
os.mkdir(output_dir)
logger.print_timestamp()
logger.main_info('Running Contig analyzer...')
num_nf_errors = logger._num_nf_errors
if not compile_aligner(logger):
logger.main_info(
'Failed aligning the contigs for all the assemblies. Only basic stats are going to be evaluated.'
)
return dict(
zip(contigs_fpaths,
[NucmerStatus.FAILED] * len(contigs_fpaths))), None
create_nucmer_output_dir(output_dir)
n_jobs = min(len(contigs_fpaths), qconfig.max_threads)
if qconfig.memory_efficient:
threads = 1
else:
threads = max(int(qconfig.max_threads / n_jobs), 1)
from joblib import Parallel, delayed
if not qconfig.splitted_ref:
statuses_results_lengths_tuples = Parallel(n_jobs=n_jobs)(
delayed(align_and_analyze)(cyclic,
i,
contigs_fpath,
output_dir,
reference,
old_contigs_fpath,
bed_fpath,
threads=threads)
for i, (contigs_fpath, old_contigs_fpath
) in enumerate(zip(contigs_fpaths, old_contigs_fpaths)))
else:
if len(contigs_fpaths) >= len(
qconfig.splitted_ref) and not qconfig.memory_efficient:
statuses_results_lengths_tuples = Parallel(n_jobs=n_jobs)(
delayed(align_and_analyze)(cyclic,
i,
contigs_fpath,
output_dir,
reference,
old_contigs_fpath,
bed_fpath,
threads=threads)
for i, (contigs_fpath, old_contigs_fpath) in enumerate(
zip(contigs_fpaths, old_contigs_fpaths)))
else:
statuses_results_lengths_tuples = []
for i, (contigs_fpath, old_contigs_fpath) in enumerate(
zip(contigs_fpaths, old_contigs_fpaths)):
statuses_results_lengths_tuples.append(
align_and_analyze(cyclic,
i,
contigs_fpath,
output_dir,
reference,
old_contigs_fpath,
bed_fpath,
parallel_by_chr=True,
threads=qconfig.max_threads))
# unzipping
statuses, results, aligned_lengths = [x[0] for x in statuses_results_lengths_tuples], \
[x[1] for x in statuses_results_lengths_tuples], \
[x[2] for x in statuses_results_lengths_tuples]
reports = []
if qconfig.is_combined_ref:
ref_misassemblies = [
result['istranslocations_by_refs'] if result else []
for result in results
]
if ref_misassemblies:
for i, fpath in enumerate(contigs_fpaths):
if ref_misassemblies[i]:
assembly_name = qutils.name_from_fpath(fpath)
all_rows = []
all_refs = sorted(
list(
set([
ref
for ref in ref_labels_by_chromosomes.values()
])))
row = {
'metricName': 'References',
'values':
[ref_num + 1 for ref_num in range(len(all_refs))]
}
all_rows.append(row)
for k in all_refs:
row = {'metricName': k, 'values': []}
for ref in all_refs:
if ref == k or ref not in ref_misassemblies[i]:
row['values'].append(None)
else:
row['values'].append(
ref_misassemblies[i][ref][k])
all_rows.append(row)
misassembly_by_ref_fpath = join(
output_dir,
'interspecies_translocations_by_refs_%s.info' %
assembly_name)
print >> open(
misassembly_by_ref_fpath, 'w'
), 'Number of interspecies translocations by references: \n'
print_file(all_rows,
misassembly_by_ref_fpath,
append_to_existing_file=True)
print >> open(misassembly_by_ref_fpath,
'a'), '\nReferences: '
for ref_num, ref in enumerate(all_refs):
print >> open(misassembly_by_ref_fpath,
'a'), str(ref_num + 1) + ' - ' + ref
logger.info(
' Information about interspecies translocations by references for %s is saved to %s'
% (assembly_name, misassembly_by_ref_fpath))
for index, fname in enumerate(contigs_fpaths):
report = reporting.get(fname)
if statuses[index] == NucmerStatus.OK:
reports.append(save_result(results[index], report, fname))
elif statuses[index] == NucmerStatus.NOT_ALIGNED:
save_result_for_unaligned(results[index], report)
nucmer_statuses = dict(zip(contigs_fpaths, statuses))
aligned_lengths_per_fpath = dict(zip(contigs_fpaths, aligned_lengths))
if NucmerStatus.OK in nucmer_statuses.values():
reporting.save_misassemblies(output_dir)
reporting.save_unaligned(output_dir)
if qconfig.draw_plots:
import plotter
plotter.draw_misassembl_plot(reports,
join(output_dir, 'misassemblies_plot'),
'Misassemblies')
oks = nucmer_statuses.values().count(NucmerStatus.OK)
not_aligned = nucmer_statuses.values().count(NucmerStatus.NOT_ALIGNED)
failed = nucmer_statuses.values().count(NucmerStatus.FAILED)
errors = nucmer_statuses.values().count(NucmerStatus.ERROR)
problems = not_aligned + failed + errors
all = len(nucmer_statuses)
logger._num_nf_errors = num_nf_errors + errors
if oks == all:
logger.main_info('Done.')
if oks < all and problems < all:
logger.main_info(
'Done for ' + str(all - problems) + ' out of ' + str(all) +
'. For the rest, only basic stats are going to be evaluated.')
if problems == all:
logger.main_info(
'Failed aligning the contigs for all the assemblies. Only basic stats are going to be evaluated.'
)
return nucmer_statuses, aligned_lengths_per_fpath
