def create_mismatches_plot(assembly, window_size, ref_len, root_dir,
output_dir):
assembly_label = qutils.label_from_fpath_for_fname(assembly.fpath)
aligner_dirpath = join(root_dir, '..',
qconfig.detailed_contigs_reports_dirname)
coords_basename = join(create_minimap_output_dir(aligner_dirpath),
assembly_label)
_, coords_filtered_fpath, _, _ = get_aux_out_fpaths(coords_basename)
if not exists(coords_filtered_fpath) or not qconfig.show_snps:
return None
mismatches_fpath = join(output_dir, assembly_label + '.mismatches.txt')
mismatch_density_by_chrom = defaultdict(lambda: [0] *
(ref_len // window_size + 1))
with open(coords_filtered_fpath) as coords_file:
for line in coords_file:
s1 = int(line.split('|')[0].split()[0])
chrom = line.split()[11].strip()
cigar = line.split()[-1].strip()
ref_pos = s1
for op in parse_cs_tag(cigar):
n_bases = len(op) - 1
if op.startswith('*'):
mismatch_density_by_chrom[chrom][int(ref_pos) //
window_size] += 1
ref_pos += 1
elif not op.startswith('+'):
ref_pos += n_bases
with open(mismatches_fpath, 'w') as out_f:
for chrom, density_list in mismatch_density_by_chrom.items():
start, end = 0, 0
for i, density in enumerate(density_list):
if density == 0:
end = (i + 1) * window_size
else:
if end:
out_f.write(
'\t'.join([chrom, str(start),
str(end), '0']) + '\n')
out_f.write('\t'.join([
chrom,
str(i * window_size),
str(((i + 1) * window_size)),
str(density)
]) + '\n')
start = (i + 1) * window_size
end = None
if end:
out_f.write('\t'.join([chrom, str(start),
str(end), '0']) + '\n')
return mismatches_fpath
def create_mismatches_plot(assembly, window_size, ref_len, root_dir, output_dir):
assembly_label = qutils.label_from_fpath_for_fname(assembly.fpath)
aligner_dirpath = join(root_dir, '..', 'contigs_reports')
coords_basename = join(create_minimap_output_dir(aligner_dirpath), assembly_label)
_, coords_filtered_fpath, _, _ = get_aux_out_fpaths(coords_basename)
if not exists(coords_filtered_fpath) or not qconfig.show_snps:
return None
mismatches_fpath = join(output_dir, assembly_label + '.mismatches.txt')
mismatch_density_by_chrom = defaultdict(lambda : [0] * (ref_len // window_size + 1))
with open(coords_filtered_fpath) as coords_file:
for line in coords_file:
s1 = int(line.split('|')[0].split()[0])
chrom = line.split()[11].strip()
cigar = line.split()[-1].strip()
ref_pos = s1
for op in parse_cs_tag(cigar):
n_bases = len(op) - 1
if op.startswith('*'):
mismatch_density_by_chrom[chrom][int(ref_pos) // window_size] += 1
ref_pos += 1
elif not op.startswith('+'):
ref_pos += n_bases
with open(mismatches_fpath, 'w') as out_f:
for chrom, density_list in mismatch_density_by_chrom.items():
start, end = 0, 0
for i, density in enumerate(density_list):
if density == 0:
end = (i + 1) * window_size
else:
if end:
out_f.write('\t'.join([chrom, str(start), str(end), '0']) + '\n')
out_f.write('\t'.join([chrom, str(i * window_size), str(((i + 1) * window_size)), str(density)]) + '\n')
start = (i + 1) * window_size
end = None
if end:
out_f.write('\t'.join([chrom, str(start), str(end), '0']) + '\n')
return mismatches_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)
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 align_and_analyze(is_cyclic,
index,
contigs_fpath,
output_dirpath,
ref_fpath,
reference_chromosomes,
ns_by_chromosomes,
old_contigs_fpath,
bed_fpath,
threads=1):
tmp_output_dirpath = create_minimap_output_dir(output_dirpath)
assembly_label = qutils.label_from_fpath(contigs_fpath)
corr_assembly_label = qutils.label_from_fpath_for_fname(contigs_fpath)
out_basename = join(tmp_output_dirpath, corr_assembly_label)
logger.info(' ' + qutils.index_to_str(index) + assembly_label)
if not qconfig.space_efficient:
log_out_fpath = join(
output_dirpath,
qconfig.contig_report_fname_pattern % corr_assembly_label +
'.stdout')
log_err_fpath = join(
output_dirpath,
qconfig.contig_report_fname_pattern % corr_assembly_label +
'.stderr')
icarus_out_fpath = join(
output_dirpath,
qconfig.icarus_report_fname_pattern % corr_assembly_label)
misassembly_fpath = join(
output_dirpath,
qconfig.contig_report_fname_pattern % corr_assembly_label +
'.mis_contigs.info')
unaligned_info_fpath = join(
output_dirpath,
qconfig.contig_report_fname_pattern % corr_assembly_label +
'.unaligned.info')
else:
log_out_fpath = '/dev/null'
log_err_fpath = '/dev/null'
icarus_out_fpath = '/dev/null'
misassembly_fpath = '/dev/null'
unaligned_info_fpath = '/dev/null'
icarus_out_f = open(icarus_out_fpath, 'w')
icarus_header_cols = [
'S1', 'E1', 'S2', 'E2', 'Reference', 'Contig', 'IDY', 'Ambiguous',
'Best_group'
]
icarus_out_f.write('\t'.join(icarus_header_cols) + '\n')
misassembly_f = open(misassembly_fpath, 'w')
if not qconfig.space_efficient:
logger.info(' ' + qutils.index_to_str(index) + 'Logging to files ' +
log_out_fpath + ' and ' + os.path.basename(log_err_fpath) +
'...')
else:
logger.info(' ' + qutils.index_to_str(index) + 'Logging is disabled.')
coords_fpath, coords_filtered_fpath, unaligned_fpath, used_snps_fpath = get_aux_out_fpaths(
out_basename)
status = align_contigs(coords_fpath, out_basename, ref_fpath,
contigs_fpath, old_contigs_fpath, index, threads,
log_out_fpath, log_err_fpath)
if status != AlignerStatus.OK:
with open(log_err_fpath, 'a') as log_err_f:
if status == AlignerStatus.ERROR:
logger.error(
' ' + qutils.index_to_str(index) +
'Failed aligning contigs ' +
qutils.label_from_fpath(contigs_fpath) +
' to the reference (non-zero exit code). ' +
('Run with the --debug flag to see additional information.'
if not qconfig.debug else ''))
elif status == AlignerStatus.FAILED:
log_err_f.write(
qutils.index_to_str(index) + 'Alignment failed for ' +
contigs_fpath + ':' + coords_fpath + 'doesn\'t exist.\n')
logger.info(' ' + qutils.index_to_str(index) +
'Alignment failed for ' + '\'' + assembly_label +
'\'.')
elif status == AlignerStatus.NOT_ALIGNED:
log_err_f.write(
qutils.index_to_str(index) + 'Nothing aligned for ' +
contigs_fpath + '\n')
logger.info(' ' + qutils.index_to_str(index) +
'Nothing aligned for ' + '\'' + assembly_label +
'\'.')
return status, {}, [], [], []
log_out_f = open(log_out_fpath, 'a')
# Loading the alignment files
log_out_f.write('Parsing coords...\n')
aligns = {}
with open(coords_fpath) as coords_file:
for line in coords_file:
mapping = Mapping.from_line(line)
aligns.setdefault(mapping.contig, []).append(mapping)
# Loading the reference sequences
log_out_f.write('Loading reference...\n') # TODO: move up
ref_features = {}
# Loading the regions (if any)
regions = {}
total_reg_len = 0
total_regions = 0
# # TODO: gff
# log_out_f.write('Loading regions...\n')
# log_out_f.write('\tNo regions given, using whole reference.\n')
for name, seq_len in reference_chromosomes.items():
log_out_f.write('\tLoaded [%s]\n' % name)
regions.setdefault(name, []).append([1, seq_len])
total_regions += 1
total_reg_len += seq_len
log_out_f.write('\tTotal Regions: %d\n' % total_regions)
log_out_f.write('\tTotal Region Length: %d\n' % total_reg_len)
ca_output = CAOutput(stdout_f=log_out_f,
misassembly_f=misassembly_f,
coords_filtered_f=open(coords_filtered_fpath, 'w'),
icarus_out_f=icarus_out_f)
log_out_f.write('Analyzing contigs...\n')
result, ref_aligns, total_indels_info, aligned_lengths, misassembled_contigs, misassemblies_in_contigs, aligned_lengths_by_contigs =\
analyze_contigs(ca_output, contigs_fpath, unaligned_fpath, unaligned_info_fpath, aligns, ref_features, reference_chromosomes, is_cyclic)
log_out_f.write('Analyzing coverage...\n')
if qconfig.show_snps:
log_out_f.write('Writing SNPs into ' + used_snps_fpath + '\n')
total_aligned_bases, indels_info = analyze_coverage(
ref_aligns, reference_chromosomes, ns_by_chromosomes, used_snps_fpath)
total_indels_info += indels_info
cov_stats = {
'SNPs': total_indels_info.mismatches,
'indels_list': total_indels_info.indels_list,
'total_aligned_bases': total_aligned_bases
}
result.update(cov_stats)
result = print_results(contigs_fpath, log_out_f, used_snps_fpath,
total_indels_info, result)
if not qconfig.space_efficient:
## outputting misassembled contigs to separate file
fasta = [(name, seq)
for name, seq in fastaparser.read_fasta(contigs_fpath)
if name in misassembled_contigs.keys()]
fastaparser.write_fasta(
join(output_dirpath,
qutils.name_from_fpath(contigs_fpath) + '.mis_contigs.fa'),
fasta)
if qconfig.is_combined_ref:
alignment_tsv_fpath = join(
output_dirpath, "alignments_" + corr_assembly_label + '.tsv')
unique_contigs_fpath = join(
output_dirpath,
qconfig.unique_contigs_fname_pattern % corr_assembly_label)
logger.debug(' ' + qutils.index_to_str(index) + 'Alignments: ' +
qutils.relpath(alignment_tsv_fpath))
used_contigs = set()
with open(unique_contigs_fpath, 'w') as unique_contigs_f:
with open(alignment_tsv_fpath, 'w') as alignment_tsv_f:
for chr_name, aligns in ref_aligns.items():
alignment_tsv_f.write(chr_name)
contigs = set([align.contig for align in aligns])
for contig in contigs:
alignment_tsv_f.write('\t' + contig)
if qconfig.is_combined_ref:
ref_name = ref_labels_by_chromosomes[chr_name]
align_by_contigs = defaultdict(int)
for align in aligns:
align_by_contigs[align.contig] += align.len2
for contig, aligned_len in align_by_contigs.items():
if contig in used_contigs:
continue
used_contigs.add(contig)
len_cov_pattern = re.compile(
r'_length_([\d\.]+)_cov_([\d\.]+)')
if len_cov_pattern.findall(contig):
contig_len = len_cov_pattern.findall(
contig)[0][0]
contig_cov = len_cov_pattern.findall(
contig)[0][1]
if aligned_len / float(contig_len) > 0.9:
unique_contigs_f.write(ref_name + '\t' +
str(aligned_len) +
'\t' + contig_cov +
'\n')
alignment_tsv_f.write('\n')
close_handlers(ca_output)
logger.info(' ' + qutils.index_to_str(index) + 'Analysis is finished.')
logger.debug('')
if not ref_aligns:
return AlignerStatus.NOT_ALIGNED, result, aligned_lengths, misassemblies_in_contigs, aligned_lengths_by_contigs
else:
return AlignerStatus.OK, result, aligned_lengths, misassemblies_in_contigs, aligned_lengths_by_contigs
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
def align_and_analyze(is_cyclic, index, contigs_fpath, output_dirpath, ref_fpath,
reference_chromosomes, ns_by_chromosomes, old_contigs_fpath, bed_fpath, threads=1):
tmp_output_dirpath = create_minimap_output_dir(output_dirpath)
assembly_label = qutils.label_from_fpath(contigs_fpath)
corr_assembly_label = qutils.label_from_fpath_for_fname(contigs_fpath)
out_basename = join(tmp_output_dirpath, corr_assembly_label)
logger.info(' ' + qutils.index_to_str(index) + assembly_label)
if not qconfig.space_efficient:
log_out_fpath = join(output_dirpath, qconfig.contig_report_fname_pattern % corr_assembly_label + '.stdout')
log_err_fpath = join(output_dirpath, qconfig.contig_report_fname_pattern % corr_assembly_label + '.stderr')
icarus_out_fpath = join(output_dirpath, qconfig.icarus_report_fname_pattern % corr_assembly_label)
misassembly_fpath = join(output_dirpath, qconfig.contig_report_fname_pattern % corr_assembly_label + '.mis_contigs.info')
unaligned_info_fpath = join(output_dirpath, qconfig.contig_report_fname_pattern % corr_assembly_label + '.unaligned.info')
else:
log_out_fpath = '/dev/null'
log_err_fpath = '/dev/null'
icarus_out_fpath = '/dev/null'
misassembly_fpath = '/dev/null'
unaligned_info_fpath = '/dev/null'
icarus_out_f = open(icarus_out_fpath, 'w')
icarus_header_cols = ['S1', 'E1', 'S2', 'E2', 'Reference', 'Contig', 'IDY', 'Ambiguous', 'Best_group']
icarus_out_f.write('\t'.join(icarus_header_cols) + '\n')
misassembly_f = open(misassembly_fpath, 'w')
if not qconfig.space_efficient:
logger.info(' ' + qutils.index_to_str(index) + 'Logging to files ' + log_out_fpath +
' and ' + os.path.basename(log_err_fpath) + '...')
else:
logger.info(' ' + qutils.index_to_str(index) + 'Logging is disabled.')
coords_fpath, coords_filtered_fpath, unaligned_fpath, used_snps_fpath = get_aux_out_fpaths(out_basename)
status = align_contigs(coords_fpath, out_basename, ref_fpath, contigs_fpath, old_contigs_fpath, index, threads,
log_out_fpath, log_err_fpath)
if status != AlignerStatus.OK:
with open(log_err_fpath, 'a') as log_err_f:
if status == AlignerStatus.ERROR:
logger.error(' ' + qutils.index_to_str(index) +
'Failed aligning contigs ' + qutils.label_from_fpath(contigs_fpath) +
' to the reference (non-zero exit code). ' +
('Run with the --debug flag to see additional information.' if not qconfig.debug else ''))
elif status == AlignerStatus.FAILED:
log_err_f.write(qutils.index_to_str(index) + 'Alignment failed for ' + contigs_fpath + ':' + coords_fpath + 'doesn\'t exist.\n')
logger.info(' ' + qutils.index_to_str(index) + 'Alignment failed for ' + '\'' + assembly_label + '\'.')
elif status == AlignerStatus.NOT_ALIGNED:
log_err_f.write(qutils.index_to_str(index) + 'Nothing aligned for ' + contigs_fpath + '\n')
logger.info(' ' + qutils.index_to_str(index) + 'Nothing aligned for ' + '\'' + assembly_label + '\'.')
return status, {}, [], [], []
log_out_f = open(log_out_fpath, 'a')
# Loading the alignment files
log_out_f.write('Parsing coords...\n')
aligns = {}
with open(coords_fpath) as coords_file:
for line in coords_file:
mapping = Mapping.from_line(line)
aligns.setdefault(mapping.contig, []).append(mapping)
# Loading the reference sequences
log_out_f.write('Loading reference...\n') # TODO: move up
ref_features = {}
# Loading the regions (if any)
regions = {}
total_reg_len = 0
total_regions = 0
# # TODO: gff
# log_out_f.write('Loading regions...\n')
# log_out_f.write('\tNo regions given, using whole reference.\n')
for name, seq_len in reference_chromosomes.items():
log_out_f.write('\tLoaded [%s]\n' % name)
regions.setdefault(name, []).append([1, seq_len])
total_regions += 1
total_reg_len += seq_len
log_out_f.write('\tTotal Regions: %d\n' % total_regions)
log_out_f.write('\tTotal Region Length: %d\n' % total_reg_len)
ca_output = CAOutput(stdout_f=log_out_f, misassembly_f=misassembly_f, coords_filtered_f=open(coords_filtered_fpath, 'w'),
icarus_out_f=icarus_out_f)
log_out_f.write('Analyzing contigs...\n')
result, ref_aligns, total_indels_info, aligned_lengths, misassembled_contigs, misassemblies_in_contigs, aligned_lengths_by_contigs =\
analyze_contigs(ca_output, contigs_fpath, unaligned_fpath, unaligned_info_fpath, aligns, ref_features, reference_chromosomes, is_cyclic)
log_out_f.write('Analyzing coverage...\n')
if qconfig.show_snps:
log_out_f.write('Writing SNPs into ' + used_snps_fpath + '\n')
total_aligned_bases, indels_info = analyze_coverage(ref_aligns, reference_chromosomes, ns_by_chromosomes, used_snps_fpath)
total_indels_info += indels_info
cov_stats = {'SNPs': total_indels_info.mismatches, 'indels_list': total_indels_info.indels_list, 'total_aligned_bases': total_aligned_bases}
result.update(cov_stats)
result = print_results(contigs_fpath, log_out_f, used_snps_fpath, total_indels_info, result)
if not qconfig.space_efficient:
## outputting misassembled contigs to separate file
fasta = [(name, seq) for name, seq in fastaparser.read_fasta(contigs_fpath)
if name in misassembled_contigs.keys()]
fastaparser.write_fasta(join(output_dirpath, qutils.name_from_fpath(contigs_fpath) + '.mis_contigs.fa'), fasta)
if qconfig.is_combined_ref:
alignment_tsv_fpath = join(output_dirpath, "alignments_" + corr_assembly_label + '.tsv')
unique_contigs_fpath = join(output_dirpath, qconfig.unique_contigs_fname_pattern % corr_assembly_label)
logger.debug(' ' + qutils.index_to_str(index) + 'Alignments: ' + qutils.relpath(alignment_tsv_fpath))
used_contigs = set()
with open(unique_contigs_fpath, 'w') as unique_contigs_f:
with open(alignment_tsv_fpath, 'w') as alignment_tsv_f:
for chr_name, aligns in ref_aligns.items():
alignment_tsv_f.write(chr_name)
contigs = set([align.contig for align in aligns])
for contig in contigs:
alignment_tsv_f.write('\t' + contig)
if qconfig.is_combined_ref:
ref_name = ref_labels_by_chromosomes[chr_name]
align_by_contigs = defaultdict(int)
for align in aligns:
align_by_contigs[align.contig] += align.len2
for contig, aligned_len in align_by_contigs.items():
if contig in used_contigs:
continue
used_contigs.add(contig)
len_cov_pattern = re.compile(r'_length_([\d\.]+)_cov_([\d\.]+)')
if len_cov_pattern.findall(contig):
contig_len = len_cov_pattern.findall(contig)[0][0]
contig_cov = len_cov_pattern.findall(contig)[0][1]
if aligned_len / float(contig_len) > 0.9:
unique_contigs_f.write(ref_name + '\t' + str(aligned_len) + '\t' + contig_cov + '\n')
alignment_tsv_f.write('\n')
close_handlers(ca_output)
logger.info(' ' + qutils.index_to_str(index) + 'Analysis is finished.')
logger.debug('')
if not ref_aligns:
return AlignerStatus.NOT_ALIGNED, result, aligned_lengths, misassemblies_in_contigs, aligned_lengths_by_contigs
else:
return AlignerStatus.OK, result, aligned_lengths, misassemblies_in_contigs, aligned_lengths_by_contigs
