def do(ref_fpath, aligned_contigs_fpaths, output_dirpath, features_dict, operons_fpaths,
detailed_contigs_reports_dirpath, genome_stats_dirpath):
coords_dirpath = os.path.join(detailed_contigs_reports_dirpath, qconfig.minimap_output_dirname)
from quast_libs import search_references_meta
if search_references_meta.is_quast_first_run:
coords_dirpath = os.path.join(coords_dirpath, 'raw')
logger.print_timestamp()
logger.main_info('Running Genome analyzer...')
if not os.path.isdir(genome_stats_dirpath):
os.mkdir(genome_stats_dirpath)
genome_size, reference_chromosomes, ns_by_chromosomes = fastaparser.get_genome_stats(ref_fpath)
# reading genome size
# genome_size = fastaparser.get_lengths_from_fastafile(reference)[0]
# reading reference name
# >gi|48994873|gb|U00096.2| Escherichia coli str. K-12 substr. MG1655, complete genome
# ref_file = open(reference, 'r')
# reference_name = ref_file.readline().split()[0][1:]
# ref_file.close()
# RESULTS file
result_fpath = os.path.join(genome_stats_dirpath, 'genome_info.txt')
res_file = open(result_fpath, 'w')
containers = []
for feature, feature_fpath in features_dict.items():
containers.append(FeatureContainer([feature_fpath], feature))
if not features_dict:
logger.notice('No file with genomic features were provided. '
'Use the --features option if you want to specify it.\n', indent=' ')
if operons_fpaths:
containers.append(FeatureContainer(operons_fpaths, 'operon'))
else:
logger.notice('No file with operons were provided. '
'Use the -O option if you want to specify it.', indent=' ')
for container in containers:
if not container.fpaths:
continue
for fpath in container.fpaths:
container.region_list += genes_parser.get_genes_from_file(fpath, container.kind)
if len(container.region_list) == 0:
logger.warning('No genomic features of type "' + container.kind + '" were loaded.', indent=' ')
res_file.write('Genomic features of type "' + container.kind + '" loaded: ' + 'None' + '\n')
else:
logger.info(' Loaded ' + str(len(container.region_list)) + ' genomic features of type "' + container.kind + '"')
res_file.write('Genomic features of type "' + container.kind + '" loaded: ' + str(len(container.region_list)) + '\n')
container.chr_names_dict = chromosomes_names_dict(container.kind, container.region_list, list(reference_chromosomes.keys()))
ref_genes_num, ref_operons_num = None, None
for contigs_fpath in aligned_contigs_fpaths:
report = reporting.get(contigs_fpath)
genomic_features = 0
for container in containers:
if container.kind == 'operon':
ref_operons_num = len(container.region_list)
report.add_field(reporting.Fields.REF_OPERONS, len(container.region_list))
else:
genomic_features += len(container.region_list)
if genomic_features:
ref_genes_num = genomic_features
report.add_field(reporting.Fields.REF_GENES, genomic_features)
# for cumulative plots:
files_features_in_contigs = {} # "filename" : [ genes in sorted contigs (see below) ]
files_unsorted_features_in_contigs = {} # "filename" : [ genes in sorted contigs (see below) ]
files_operons_in_contigs = {}
files_unsorted_operons_in_contigs = {}
# for histograms
genome_mapped = []
full_found_genes = []
full_found_operons = []
# process all contig files
num_nf_errors = logger._num_nf_errors
n_jobs = min(len(aligned_contigs_fpaths), qconfig.max_threads)
parallel_run_args = [(contigs_fpath, index, coords_dirpath, genome_stats_dirpath,
reference_chromosomes, ns_by_chromosomes, containers)
for index, contigs_fpath in enumerate(aligned_contigs_fpaths)]
ref_lengths, results_genes_operons_tuples = run_parallel(process_single_file, parallel_run_args, n_jobs, filter_results=True)
num_nf_errors += len(aligned_contigs_fpaths) - len(ref_lengths)
logger._num_nf_errors = num_nf_errors
if not ref_lengths:
logger.main_info('Genome analyzer failed for all the assemblies.')
res_file.close()
return
for ref in reference_chromosomes:
ref_lengths_by_contigs[ref] = [ref_lengths[i][ref] for i in range(len(ref_lengths))]
res_file.write('reference chromosomes:\n')
for chr_name, chr_len in reference_chromosomes.items():
aligned_len = max(ref_lengths_by_contigs[chr_name])
res_file.write('\t' + chr_name + ' (total length: ' + str(chr_len) + ' bp, ' +
'total length without N\'s: ' + str(chr_len - len(ns_by_chromosomes[chr_name])) +
' bp, maximal covered length: ' + str(aligned_len) + ' bp)\n')
res_file.write('\n')
res_file.write('total genome size: ' + str(genome_size) + '\n\n')
res_file.write('gap min size: ' + str(qconfig.min_gap_size) + '\n')
res_file.write('partial gene/operon min size: ' + str(qconfig.min_gene_overlap) + '\n\n')
# header
# header
res_file.write('\n\n')
res_file.write('%-25s| %-10s| %-12s| %-10s| %-10s| %-10s| %-10s| %-10s|\n'
% ('assembly', 'genome', 'duplication', 'gaps', 'genes', 'partial', 'operons', 'partial'))
res_file.write('%-25s| %-10s| %-12s| %-10s| %-10s| %-10s| %-10s| %-10s|\n'
% ('', 'fraction', 'ratio', 'number', '', 'genes', '', 'operons'))
res_file.write('=' * 120 + '\n')
for contigs_fpath, (results, unsorted_features_in_contigs, features_in_contigs, unsorted_operons_in_contigs, operons_in_contigs)\
in zip(aligned_contigs_fpaths, results_genes_operons_tuples):
assembly_name = qutils.name_from_fpath(contigs_fpath)
files_features_in_contigs[contigs_fpath] = features_in_contigs
files_unsorted_features_in_contigs[contigs_fpath] = unsorted_features_in_contigs
files_operons_in_contigs[contigs_fpath] = operons_in_contigs
files_unsorted_operons_in_contigs[contigs_fpath] = unsorted_operons_in_contigs
full_found_genes.append(sum(features_in_contigs))
full_found_operons.append(sum(operons_in_contigs))
gaps_count = results["gaps_count"]
genes_full = results[reporting.Fields.GENES + "_full"]
genes_part = results[reporting.Fields.GENES + "_partial"]
operons_full = results[reporting.Fields.OPERONS + "_full"]
operons_part = results[reporting.Fields.OPERONS + "_partial"]
report = reporting.get(contigs_fpath)
res_file.write('%-25s| %-10s| %-12s| %-10s|'
% (assembly_name[:24], report.get_field(reporting.Fields.MAPPEDGENOME), report.get_field(reporting.Fields.DUPLICATION_RATIO), gaps_count))
genome_mapped.append(float(report.get_field(reporting.Fields.MAPPEDGENOME)))
for (field, full, part) in [(reporting.Fields.GENES, genes_full, genes_part),
(reporting.Fields.OPERONS, operons_full, operons_part)]:
if full is None and part is None:
res_file.write(' %-10s| %-10s|' % ('-', '-'))
else:
res_file.write(' %-10s| %-10s|' % (full, part))
report.add_field(field, '%s + %s part' % (full, part))
res_file.write('\n')
res_file.close()
if qconfig.html_report:
from quast_libs.html_saver import html_saver
if ref_genes_num:
html_saver.save_features_in_contigs(output_dirpath, aligned_contigs_fpaths, 'features', files_features_in_contigs, ref_genes_num)
if ref_operons_num:
html_saver.save_features_in_contigs(output_dirpath, aligned_contigs_fpaths, 'operons', files_operons_in_contigs, ref_operons_num)
if qconfig.draw_plots:
# cumulative plots:
from . import plotter
from quast_libs.ca_utils.misc import contigs_aligned_lengths
if ref_genes_num:
plotter.genes_operons_plot(ref_genes_num, aligned_contigs_fpaths, files_features_in_contigs,
genome_stats_dirpath + '/features_cumulative_plot', 'genomic features')
plotter.frc_plot(output_dirpath, ref_fpath, aligned_contigs_fpaths, contigs_aligned_lengths, files_unsorted_features_in_contigs,
genome_stats_dirpath + '/features_frcurve_plot', 'genomic features')
plotter.histogram(aligned_contigs_fpaths, full_found_genes, genome_stats_dirpath + '/complete_features_histogram',
'# complete genomic features')
if ref_operons_num:
plotter.genes_operons_plot(ref_operons_num, aligned_contigs_fpaths, files_operons_in_contigs,
genome_stats_dirpath + '/operons_cumulative_plot', 'operons')
plotter.frc_plot(output_dirpath, ref_fpath, aligned_contigs_fpaths, contigs_aligned_lengths, files_unsorted_operons_in_contigs,
genome_stats_dirpath + '/operons_frcurve_plot', 'operons')
plotter.histogram(aligned_contigs_fpaths, full_found_operons, genome_stats_dirpath + '/complete_operons_histogram',
'# complete operons')
plotter.histogram(aligned_contigs_fpaths, genome_mapped, genome_stats_dirpath + '/genome_fraction_histogram',
'Genome fraction, %', top_value=100)
logger.main_info('Done.')
return containers
def do(ref_fpath, aligned_contigs_fpaths, output_dirpath, features_dict,
operons_fpaths, detailed_contigs_reports_dirpath, genome_stats_dirpath):
coords_dirpath = os.path.join(detailed_contigs_reports_dirpath,
qconfig.minimap_output_dirname)
from quast_libs import search_references_meta
if search_references_meta.is_quast_first_run:
coords_dirpath = os.path.join(coords_dirpath, 'raw')
logger.print_timestamp()
logger.main_info('Running Genome analyzer...')
if not os.path.isdir(genome_stats_dirpath):
os.mkdir(genome_stats_dirpath)
genome_size, reference_chromosomes, ns_by_chromosomes = fastaparser.get_genome_stats(
ref_fpath)
# reading genome size
# genome_size = fastaparser.get_lengths_from_fastafile(reference)[0]
# reading reference name
# >gi|48994873|gb|U00096.2| Escherichia coli str. K-12 substr. MG1655, complete genome
# ref_file = open(reference, 'r')
# reference_name = ref_file.readline().split()[0][1:]
# ref_file.close()
# RESULTS file
result_fpath = os.path.join(genome_stats_dirpath, 'genome_info.txt')
res_file = open(result_fpath, 'w')
containers = []
for feature, feature_fpath in features_dict.items():
containers.append(FeatureContainer([feature_fpath], feature))
if not features_dict:
logger.notice(
'No file with genomic features were provided. '
'Use the --features option if you want to specify it.\n',
indent=' ')
if operons_fpaths:
containers.append(FeatureContainer(operons_fpaths, 'operon'))
else:
logger.notice(
'No file with operons were provided. '
'Use the -O option if you want to specify it.',
indent=' ')
for container in containers:
if not container.fpaths:
continue
for fpath in container.fpaths:
container.region_list += genes_parser.get_genes_from_file(
fpath, container.kind)
if len(container.region_list) == 0:
logger.warning('No genomic features of type "' + container.kind +
'" were loaded.',
indent=' ')
res_file.write('Genomic features of type "' + container.kind +
'" loaded: ' + 'None' + '\n')
else:
logger.info(' Loaded ' + str(len(container.region_list)) +
' genomic features of type "' + container.kind + '"')
res_file.write('Genomic features of type "' + container.kind +
'" loaded: ' + str(len(container.region_list)) +
'\n')
container.chr_names_dict = chromosomes_names_dict(
container.kind, container.region_list,
list(reference_chromosomes.keys()))
ref_genes_num, ref_operons_num = None, None
for contigs_fpath in aligned_contigs_fpaths:
report = reporting.get(contigs_fpath)
genomic_features = 0
for container in containers:
if container.kind == 'operon':
ref_operons_num = len(container.region_list)
report.add_field(reporting.Fields.REF_OPERONS,
len(container.region_list))
else:
genomic_features += len(container.region_list)
if genomic_features:
ref_genes_num = genomic_features
report.add_field(reporting.Fields.REF_GENES, genomic_features)
# for cumulative plots:
files_features_in_contigs = {
} # "filename" : [ genes in sorted contigs (see below) ]
files_unsorted_features_in_contigs = {
} # "filename" : [ genes in sorted contigs (see below) ]
files_operons_in_contigs = {}
files_unsorted_operons_in_contigs = {}
# for histograms
genome_mapped = []
full_found_genes = []
full_found_operons = []
# process all contig files
num_nf_errors = logger._num_nf_errors
n_jobs = min(len(aligned_contigs_fpaths), qconfig.max_threads)
if is_python2():
from joblib2 import Parallel, delayed
else:
from joblib3 import Parallel, delayed
if not qconfig.memory_efficient:
process_results = Parallel(n_jobs=n_jobs)(
delayed(process_single_file)(
contigs_fpath, index, coords_dirpath, genome_stats_dirpath,
reference_chromosomes, ns_by_chromosomes, containers)
for index, contigs_fpath in enumerate(aligned_contigs_fpaths))
else:
process_results = [
process_single_file(contigs_fpath, index, coords_dirpath,
genome_stats_dirpath, reference_chromosomes,
ns_by_chromosomes, containers)
for index, contigs_fpath in enumerate(aligned_contigs_fpaths)
]
num_nf_errors += len([res for res in process_results if res is None])
logger._num_nf_errors = num_nf_errors
process_results = [res for res in process_results if res]
if not process_results:
logger.main_info('Genome analyzer failed for all the assemblies.')
res_file.close()
return
ref_lengths = [process_results[i][0] for i in range(len(process_results))]
results_genes_operons_tuples = [
process_results[i][1] for i in range(len(process_results))
]
for ref in reference_chromosomes:
ref_lengths_by_contigs[ref] = [
ref_lengths[i][ref] for i in range(len(ref_lengths))
]
res_file.write('reference chromosomes:\n')
for chr_name, chr_len in reference_chromosomes.items():
aligned_len = max(ref_lengths_by_contigs[chr_name])
res_file.write('\t' + chr_name + ' (total length: ' + str(chr_len) +
' bp, ' + 'total length without N\'s: ' +
str(chr_len - len(ns_by_chromosomes[chr_name])) +
' bp, maximal covered length: ' + str(aligned_len) +
' bp)\n')
res_file.write('\n')
res_file.write('total genome size: ' + str(genome_size) + '\n\n')
res_file.write('gap min size: ' + str(qconfig.min_gap_size) + '\n')
res_file.write('partial gene/operon min size: ' +
str(qconfig.min_gene_overlap) + '\n\n')
# header
# header
res_file.write('\n\n')
res_file.write(
'%-25s| %-10s| %-12s| %-10s| %-10s| %-10s| %-10s| %-10s|\n' %
('assembly', 'genome', 'duplication', 'gaps', 'genes', 'partial',
'operons', 'partial'))
res_file.write(
'%-25s| %-10s| %-12s| %-10s| %-10s| %-10s| %-10s| %-10s|\n' %
('', 'fraction', 'ratio', 'number', '', 'genes', '', 'operons'))
res_file.write('=' * 120 + '\n')
for contigs_fpath, (results, unsorted_features_in_contigs, features_in_contigs, unsorted_operons_in_contigs, operons_in_contigs)\
in zip(aligned_contigs_fpaths, results_genes_operons_tuples):
assembly_name = qutils.name_from_fpath(contigs_fpath)
files_features_in_contigs[contigs_fpath] = features_in_contigs
files_unsorted_features_in_contigs[
contigs_fpath] = unsorted_features_in_contigs
files_operons_in_contigs[contigs_fpath] = operons_in_contigs
files_unsorted_operons_in_contigs[
contigs_fpath] = unsorted_operons_in_contigs
full_found_genes.append(sum(features_in_contigs))
full_found_operons.append(sum(operons_in_contigs))
gaps_count = results["gaps_count"]
genes_full = results[reporting.Fields.GENES + "_full"]
genes_part = results[reporting.Fields.GENES + "_partial"]
operons_full = results[reporting.Fields.OPERONS + "_full"]
operons_part = results[reporting.Fields.OPERONS + "_partial"]
report = reporting.get(contigs_fpath)
res_file.write(
'%-25s| %-10s| %-12s| %-10s|' %
(assembly_name[:24], report.get_field(
reporting.Fields.MAPPEDGENOME),
report.get_field(reporting.Fields.DUPLICATION_RATIO), gaps_count))
genome_mapped.append(
float(report.get_field(reporting.Fields.MAPPEDGENOME)))
for (field, full,
part) in [(reporting.Fields.GENES, genes_full, genes_part),
(reporting.Fields.OPERONS, operons_full, operons_part)]:
if full is None and part is None:
res_file.write(' %-10s| %-10s|' % ('-', '-'))
else:
res_file.write(' %-10s| %-10s|' % (full, part))
report.add_field(field, '%s + %s part' % (full, part))
res_file.write('\n')
res_file.close()
if qconfig.html_report:
from quast_libs.html_saver import html_saver
if ref_genes_num:
html_saver.save_features_in_contigs(output_dirpath,
aligned_contigs_fpaths,
'features',
files_features_in_contigs,
ref_genes_num)
if ref_operons_num:
html_saver.save_features_in_contigs(output_dirpath,
aligned_contigs_fpaths,
'operons',
files_operons_in_contigs,
ref_operons_num)
if qconfig.draw_plots:
# cumulative plots:
from . import plotter
from quast_libs.ca_utils.misc import contigs_aligned_lengths
if ref_genes_num:
plotter.genes_operons_plot(
ref_genes_num, aligned_contigs_fpaths,
files_features_in_contigs,
genome_stats_dirpath + '/features_cumulative_plot',
'genomic features')
plotter.frc_plot(output_dirpath, ref_fpath, aligned_contigs_fpaths,
contigs_aligned_lengths,
files_unsorted_features_in_contigs,
genome_stats_dirpath + '/features_frcurve_plot',
'genomic features')
plotter.histogram(
aligned_contigs_fpaths, full_found_genes,
genome_stats_dirpath + '/complete_features_histogram',
'# complete genomic features')
if ref_operons_num:
plotter.genes_operons_plot(
ref_operons_num, aligned_contigs_fpaths,
files_operons_in_contigs,
genome_stats_dirpath + '/operons_cumulative_plot', 'operons')
plotter.frc_plot(output_dirpath, ref_fpath, aligned_contigs_fpaths,
contigs_aligned_lengths,
files_unsorted_operons_in_contigs,
genome_stats_dirpath + '/operons_frcurve_plot',
'operons')
plotter.histogram(
aligned_contigs_fpaths, full_found_operons,
genome_stats_dirpath + '/complete_operons_histogram',
'# complete operons')
plotter.histogram(aligned_contigs_fpaths,
genome_mapped,
genome_stats_dirpath + '/genome_fraction_histogram',
'Genome fraction, %',
top_value=100)
logger.main_info('Done.')
return containers
def do(reference,
contigs_fpaths,
is_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...')
success_compilation = compile_aligner(logger)
if not success_compilation:
logger.main_info(
'Failed aligning the contigs for all the assemblies. Only basic stats are going to be evaluated.'
)
return dict(
zip(contigs_fpaths,
[AlignerStatus.FAILED] * len(contigs_fpaths))), None
num_nf_errors = logger._num_nf_errors
create_minimap_output_dir(output_dir)
n_jobs = min(len(contigs_fpaths), qconfig.max_threads)
threads = max(1, qconfig.max_threads // n_jobs)
if is_python2():
from joblib2 import Parallel, delayed
else:
from joblib3 import Parallel, delayed
genome_size, reference_chromosomes, ns_by_chromosomes = get_genome_stats(
reference, skip_ns=True)
threads = qconfig.max_threads if qconfig.memory_efficient else threads
args = [(is_cyclic, i, contigs_fpath, output_dir, reference,
reference_chromosomes, ns_by_chromosomes, old_contigs_fpath,
bed_fpath, threads)
for i, (contigs_fpath, old_contigs_fpath
) in enumerate(zip(contigs_fpaths, old_contigs_fpaths))]
statuses, results, aligned_lengths, misassemblies_in_contigs, aligned_lengths_by_contigs = run_parallel(
align_and_analyze, args, n_jobs)
reports = []
aligner_statuses = dict(zip(contigs_fpaths, statuses))
aligned_lengths_per_fpath = dict(zip(contigs_fpaths, aligned_lengths))
misc.contigs_aligned_lengths = dict(
zip(contigs_fpaths, aligned_lengths_by_contigs))
if AlignerStatus.OK in aligner_statuses.values():
if qconfig.is_combined_ref:
save_combined_ref_stats(results, contigs_fpaths,
ref_labels_by_chromosomes, output_dir,
logger)
for index, fname in enumerate(contigs_fpaths):
report = reporting.get(fname)
if statuses[index] == AlignerStatus.OK:
reports.append(
save_result(results[index], report, fname, reference,
genome_size))
elif statuses[index] == AlignerStatus.NOT_ALIGNED:
save_result_for_unaligned(results[index], report)
if AlignerStatus.OK in aligner_statuses.values():
reporting.save_misassemblies(output_dir)
reporting.save_unaligned(output_dir)
from . import plotter
if qconfig.draw_plots:
plotter.draw_misassemblies_plot(
reports, join(output_dir, 'misassemblies_plot'),
'Misassemblies')
if qconfig.draw_plots or qconfig.html_report:
misassemblies_in_contigs = dict(
(contigs_fpaths[i], misassemblies_in_contigs[i])
for i in range(len(contigs_fpaths)))
plotter.frc_plot(dirname(output_dir), reference, contigs_fpaths,
misc.contigs_aligned_lengths,
misassemblies_in_contigs,
join(output_dir, 'misassemblies_frcurve_plot'),
'misassemblies')
oks = list(aligner_statuses.values()).count(AlignerStatus.OK)
not_aligned = list(aligner_statuses.values()).count(
AlignerStatus.NOT_ALIGNED)
failed = list(aligner_statuses.values()).count(AlignerStatus.FAILED)
errors = list(aligner_statuses.values()).count(AlignerStatus.ERROR)
problems = not_aligned + failed + errors
all = len(aligner_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 aligner_statuses, aligned_lengths_per_fpath
def do(reference, contigs_fpaths, is_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...')
success_compilation = compile_aligner(logger)
if not success_compilation:
logger.main_info('Failed aligning the contigs for all the assemblies. Only basic stats are going to be evaluated.')
return dict(zip(contigs_fpaths, [AlignerStatus.FAILED] * len(contigs_fpaths))), None
num_nf_errors = logger._num_nf_errors
create_minimap_output_dir(output_dir)
n_jobs = min(len(contigs_fpaths), qconfig.max_threads)
threads = max(1, qconfig.max_threads // n_jobs)
genome_size, reference_chromosomes, ns_by_chromosomes = get_genome_stats(reference, skip_ns=True)
threads = qconfig.max_threads if qconfig.memory_efficient else threads
args = [(is_cyclic, i, contigs_fpath, output_dir, reference, reference_chromosomes, ns_by_chromosomes,
old_contigs_fpath, bed_fpath, threads)
for i, (contigs_fpath, old_contigs_fpath) in enumerate(zip(contigs_fpaths, old_contigs_fpaths))]
statuses, results, aligned_lengths, misassemblies_in_contigs, aligned_lengths_by_contigs = run_parallel(align_and_analyze, args, n_jobs)
reports = []
aligner_statuses = dict(zip(contigs_fpaths, statuses))
aligned_lengths_per_fpath = dict(zip(contigs_fpaths, aligned_lengths))
misc.contigs_aligned_lengths = dict(zip(contigs_fpaths, aligned_lengths_by_contigs))
if AlignerStatus.OK in aligner_statuses.values():
if qconfig.is_combined_ref:
save_combined_ref_stats(results, contigs_fpaths, ref_labels_by_chromosomes, output_dir, logger)
for index, fname in enumerate(contigs_fpaths):
report = reporting.get(fname)
if statuses[index] == AlignerStatus.OK:
reports.append(save_result(results[index], report, fname, reference, genome_size))
elif statuses[index] == AlignerStatus.NOT_ALIGNED:
save_result_for_unaligned(results[index], report)
if AlignerStatus.OK in aligner_statuses.values():
reporting.save_misassemblies(output_dir)
reporting.save_unaligned(output_dir)
from . import plotter
if qconfig.draw_plots:
plotter.draw_misassemblies_plot(reports, join(output_dir, 'misassemblies_plot'), 'Misassemblies')
if qconfig.draw_plots or qconfig.html_report:
misassemblies_in_contigs = dict((contigs_fpaths[i], misassemblies_in_contigs[i]) for i in range(len(contigs_fpaths)))
plotter.frc_plot(dirname(output_dir), reference, contigs_fpaths, misc.contigs_aligned_lengths, misassemblies_in_contigs,
join(output_dir, 'misassemblies_frcurve_plot'), 'misassemblies')
oks = list(aligner_statuses.values()).count(AlignerStatus.OK)
not_aligned = list(aligner_statuses.values()).count(AlignerStatus.NOT_ALIGNED)
failed = list(aligner_statuses.values()).count(AlignerStatus.FAILED)
errors = list(aligner_statuses.values()).count(AlignerStatus.ERROR)
problems = not_aligned + failed + errors
all = len(aligner_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 aligner_statuses, aligned_lengths_per_fpath