def get_downloaded_refs_with_alignments(genome_info_fpath, ref_fpaths,
chromosomes_by_refs):
refs_len = {}
with open(genome_info_fpath, 'r') as report_file:
report_file.readline()
for line in report_file:
if line == '\n' or not line:
break
lengths = re.findall(r'length: (\d+)', line)
if lengths and len(lengths) == 2:
line = line.split()
refs_len[line[0]] = (lengths[0], lengths[1])
corr_refs = []
for ref_fpath in ref_fpaths:
ref_fname = os.path.basename(ref_fpath)
ref, ref_fasta_ext = qutils.splitext_for_fasta_file(ref_fname)
aligned_len = 0
all_len = 0
for chromosome in chromosomes_by_refs[ref]:
if chromosome[0] in refs_len:
aligned_len += int(refs_len[chromosome[0]][1])
all_len += int(refs_len[chromosome[0]][0])
if not aligned_len:
continue
if aligned_len > all_len * qconfig.downloaded_ref_min_aligned_rate:
corr_refs.append(ref_fpath)
return corr_refs
def get_downloaded_refs_with_alignments(genome_info_fpath, ref_fpaths, chromosomes_by_refs):
refs_len = {}
with open(genome_info_fpath, 'r') as report_file:
report_file.readline()
for line in report_file:
if line == '\n' or not line:
break
line = line.split()
refs_len[line[0]] = (line[3], line[8])
corr_refs = []
for ref_fpath in ref_fpaths:
ref_fname = os.path.basename(ref_fpath)
ref, ref_fasta_ext = qutils.splitext_for_fasta_file(ref_fname)
aligned_len = 0
all_len = 0
for chromosome in chromosomes_by_refs[ref]:
if chromosome[0] in refs_len:
aligned_len += int(refs_len[chromosome[0]][1])
all_len += int(refs_len[chromosome[0]][0])
if not aligned_len:
continue
if aligned_len > all_len * qconfig.downloaded_ref_min_aligned_rate:
corr_refs.append(ref_fpath)
return corr_refs
def correct_meta_references(ref_fpaths, corrected_dirpath, downloaded_refs=False):
corrected_ref_fpaths = []
combined_ref_fpath = os.path.join(corrected_dirpath, qconfig.combined_ref_name)
chromosomes_by_refs = {}
def _proceed_seq(seq_name, seq, ref_name, ref_fasta_ext, total_references, ref_fpath):
seq_fname = ref_name
seq_fname += ref_fasta_ext
if total_references > 1:
corr_seq_fpath = corrected_ref_fpaths[-1]
else:
corr_seq_fpath = qutils.unique_corrected_fpath(os.path.join(corrected_dirpath, seq_fname))
corrected_ref_fpaths.append(corr_seq_fpath)
corr_seq_name = qutils.name_from_fpath(corr_seq_fpath) + '_' + seq_name
if not qconfig.no_check:
corr_seq = correct_seq(seq, ref_fpath)
if not corr_seq:
return None, None
fastaparser.write_fasta(corr_seq_fpath, [(corr_seq_name, seq)], 'a')
contigs_analyzer.ref_labels_by_chromosomes[corr_seq_name] = qutils.name_from_fpath(corr_seq_fpath)
chromosomes_by_refs[ref_name].append((corr_seq_name, len(seq)))
return corr_seq_name, corr_seq_fpath
ref_fnames = [os.path.basename(ref_fpath) for ref_fpath in ref_fpaths]
ref_names = []
for ref_fname in ref_fnames:
ref_name, ref_fasta_ext = qutils.splitext_for_fasta_file(ref_fname)
ref_names.append(ref_name)
excluded_ref_fpaths = []
ref_names = qutils.process_labels(ref_fpaths)
for ref_fpath, ref_name in zip(ref_fpaths, ref_names):
total_references = 0
ref_fname = os.path.basename(ref_fpath)
_, ref_fasta_ext = qutils.splitext_for_fasta_file(ref_fname)
chromosomes_by_refs[ref_name] = []
used_seq_names = defaultdict(int)
corr_seq_fpath = None
for i, (seq_name, seq) in enumerate(fastaparser.read_fasta(ref_fpath)):
total_references += 1
seq_name = correct_name(seq_name, qutils.MAX_CONTIG_NAME - len(ref_name) - 1)
uniq_seq_name = get_uniq_name(seq_name, used_seq_names)
used_seq_names[seq_name] += 1
corr_seq_name, corr_seq_fpath = _proceed_seq(uniq_seq_name, seq, ref_name, ref_fasta_ext, total_references, ref_fpath)
if not corr_seq_name:
break
if corr_seq_fpath:
logger.main_info(' ' + ref_fpath + ' ==> ' + qutils.name_from_fpath(corr_seq_fpath) + '')
fastaparser.write_fasta(combined_ref_fpath, fastaparser.read_fasta(corr_seq_fpath), 'a')
elif downloaded_refs:
logger.warning('Skipping ' + ref_fpath + ' because it'
' is empty or contains incorrect sequences (header-only or with non-ACGTN characters)!')
# cleaning
for corr_seq_name, _ in chromosomes_by_refs[ref_name]:
del contigs_analyzer.ref_labels_by_chromosomes[corr_seq_name]
del chromosomes_by_refs[ref_name]
corrected_ref_fpaths.pop()
excluded_ref_fpaths.append(ref_fpath)
else:
logger.error('Reference file ' + ref_fpath +
' is empty or contains incorrect sequences (header-only or with non-ACGTN characters)!',
exit_with_code=1)
for excluded in excluded_ref_fpaths:
ref_fpaths.remove(excluded)
if len(chromosomes_by_refs) > 0:
logger.main_info(' All references were combined in ' + qconfig.combined_ref_name)
else:
logger.warning('All references were skipped!')
return corrected_ref_fpaths, combined_ref_fpath, chromosomes_by_refs, ref_fpaths
def do(ref_fpath, original_ref_fpath, output_dirpath):
logger.print_timestamp()
logger.main_info("Generating Upper Bound Assembly...")
if not reads_analyzer.compile_reads_analyzer_tools(logger):
logger.warning(
' Sorry, can\'t create Upper Bound Assembly '
'(failed to compile necessary third-party read processing tools [bwa, bedtools, minimap2]), skipping...'
)
return None
if qconfig.platform_name == 'linux_32':
logger.warning(
' Sorry, can\'t create Upper Bound Assembly on this platform '
'(only linux64 and macOS are supported), skipping...')
return None
red_dirpath = get_dir_for_download('red', 'Red', ['Red'], logger)
binary_fpath = download_external_tool('Red',
red_dirpath,
'red',
platform_specific=True,
is_executable=True)
if not binary_fpath or not os.path.isfile(binary_fpath):
logger.warning(
' Sorry, can\'t create Upper Bound Assembly '
'(failed to install/download third-party repeat finding tool [Red]), skipping...'
)
return None
insert_size = qconfig.optimal_assembly_insert_size
if insert_size == 'auto' or not insert_size:
insert_size = qconfig.optimal_assembly_default_IS
ref_basename, fasta_ext = splitext_for_fasta_file(
os.path.basename(ref_fpath))
result_basename = '%s.%s.is%d.fasta' % (
ref_basename, qconfig.optimal_assembly_basename, insert_size)
long_reads = qconfig.pacbio_reads or qconfig.nanopore_reads
if long_reads:
result_basename = add_suffix(result_basename,
long_reads_polished_suffix)
elif qconfig.mate_pairs:
result_basename = add_suffix(result_basename, mp_polished_suffix)
result_fpath = os.path.join(output_dirpath, result_basename)
original_ref_basename, fasta_ext = splitext_for_fasta_file(
os.path.basename(original_ref_fpath))
prepared_optimal_assembly_basename = '%s.%s.is%d.fasta' % (
original_ref_basename, qconfig.optimal_assembly_basename, insert_size)
if long_reads:
prepared_optimal_assembly_basename = add_suffix(
prepared_optimal_assembly_basename, long_reads_polished_suffix)
elif qconfig.mate_pairs:
prepared_optimal_assembly_basename = add_suffix(
prepared_optimal_assembly_basename, mp_polished_suffix)
ref_prepared_optimal_assembly = os.path.join(
os.path.dirname(original_ref_fpath),
prepared_optimal_assembly_basename)
already_done_fpath = check_prepared_optimal_assembly(
insert_size, result_fpath, ref_prepared_optimal_assembly)
if already_done_fpath:
return already_done_fpath
uncovered_fpath = None
reads_analyzer_dir = join(dirname(output_dirpath),
qconfig.reads_stats_dirname)
if qconfig.reads_fpaths or qconfig.reference_sam or qconfig.reference_bam:
sam_fpath, bam_fpath, uncovered_fpath = reads_analyzer.align_reference(
ref_fpath,
reads_analyzer_dir,
using_reads='all',
calculate_coverage=True)
if qconfig.optimal_assembly_insert_size != 'auto' and qconfig.optimal_assembly_insert_size != insert_size:
calculated_insert_size = qconfig.optimal_assembly_insert_size
result_fpath = result_fpath.replace('is' + str(insert_size),
'is' + str(calculated_insert_size))
prepared_optimal_assembly_basename = prepared_optimal_assembly_basename.replace(
'is' + str(insert_size), 'is' + str(calculated_insert_size))
insert_size = calculated_insert_size
ref_prepared_optimal_assembly = os.path.join(
os.path.dirname(original_ref_fpath),
prepared_optimal_assembly_basename)
already_done_fpath = check_prepared_optimal_assembly(
insert_size, result_fpath, ref_prepared_optimal_assembly)
if already_done_fpath:
return already_done_fpath
log_fpath = os.path.join(output_dirpath, 'upper_bound_assembly.log')
tmp_dir = os.path.join(output_dirpath, 'tmp')
if os.path.isdir(tmp_dir):
shutil.rmtree(tmp_dir)
os.makedirs(tmp_dir)
unique_covered_regions, repeats_regions = get_unique_covered_regions(
ref_fpath,
tmp_dir,
log_fpath,
binary_fpath,
insert_size,
uncovered_fpath,
use_long_reads=long_reads)
if unique_covered_regions is None:
logger.error(
' Failed to create Upper Bound Assembly, see log for details: ' +
log_fpath)
return None
reference = list(fastaparser.read_fasta(ref_fpath))
result_fasta = []
if long_reads or qconfig.mate_pairs:
if long_reads:
join_reads = 'pacbio' if qconfig.pacbio_reads else 'nanopore'
else:
join_reads = 'mp'
sam_fpath, bam_fpath, _ = reads_analyzer.align_reference(
ref_fpath, reads_analyzer_dir, using_reads=join_reads)
joiners = get_joiners(qutils.name_from_fpath(ref_fpath), sam_fpath,
bam_fpath, tmp_dir, log_fpath, join_reads)
uncovered_regions = parse_bed(
uncovered_fpath) if join_reads == 'mp' else defaultdict(list)
mp_len = calculate_read_len(sam_fpath) if join_reads == 'mp' else None
for chrom, seq in reference:
region_pairing = get_regions_pairing(unique_covered_regions[chrom],
joiners[chrom], mp_len)
ref_coords_to_output = scaffolding(unique_covered_regions[chrom],
region_pairing)
get_fasta_entries_from_coords(result_fasta, (chrom, seq),
ref_coords_to_output,
repeats_regions[chrom],
uncovered_regions[chrom])
else:
for chrom, seq in reference:
for idx, region in enumerate(unique_covered_regions[chrom]):
if region[1] - region[0] >= MIN_CONTIG_LEN:
result_fasta.append(
(chrom + '_' + str(idx), seq[region[0]:region[1]]))
fastaparser.write_fasta(result_fpath, result_fasta)
logger.info(' ' + 'Theoretical Upper Bound Assembly is saved to ' +
result_fpath)
logger.notice(
'(on reusing *this* Upper Bound Assembly in the *future* evaluations on *the same* dataset)\n'
'\tThe next time, you can simply provide this file as an additional assembly (you could also rename it to UpperBound.fasta for the clarity). '
'In this case, you do not need to specify --upper-bound-assembly and provide files with reads (--pe1/pe2, etc).\n'
'\t\tOR\n'
'\tYou can copy ' + result_fpath + ' to ' +
ref_prepared_optimal_assembly + '. '
'The next time you evaluate assemblies with --upper-bound-assembly option and against the same reference ('
+ original_ref_fpath + ') and '
'the same reads (or if you specify the insert size of the paired-end reads explicitly with --est-insert-size '
+ str(insert_size) + '), '
'QUAST will reuse this Upper Bound Assembly.\n')
if not qconfig.debug:
shutil.rmtree(tmp_dir)
logger.main_info('Done.')
return result_fpath
def correct_meta_references(ref_fpaths,
corrected_dirpath,
downloaded_refs=False):
corrected_ref_fpaths = []
combined_ref_fpath = os.path.join(corrected_dirpath,
qconfig.combined_ref_name)
chromosomes_by_refs = {}
def _proceed_seq(seq_name, seq, ref_name, ref_fasta_ext, total_references,
ref_fpath):
seq_fname = ref_name
seq_fname += ref_fasta_ext
if total_references > 1:
corr_seq_fpath = corrected_ref_fpaths[-1]
else:
corr_seq_fpath = qutils.unique_corrected_fpath(
os.path.join(corrected_dirpath, seq_fname))
corrected_ref_fpaths.append(corr_seq_fpath)
corr_seq_name = qutils.name_from_fpath(corr_seq_fpath) + '_' + seq_name
if not qconfig.no_check:
corr_seq = correct_seq(seq, ref_fpath)
if not corr_seq:
return None, None
fastaparser.write_fasta(corr_seq_fpath, [(corr_seq_name, seq)], 'a')
contigs_analyzer.ref_labels_by_chromosomes[
corr_seq_name] = qutils.name_from_fpath(corr_seq_fpath)
chromosomes_by_refs[ref_name].append((corr_seq_name, len(seq)))
return corr_seq_name, corr_seq_fpath
ref_fnames = [os.path.basename(ref_fpath) for ref_fpath in ref_fpaths]
ref_names = []
for ref_fname in ref_fnames:
ref_name, ref_fasta_ext = qutils.splitext_for_fasta_file(ref_fname)
ref_names.append(ref_name)
excluded_ref_fpaths = []
ref_names = qutils.process_labels(ref_fpaths)
for ref_fpath, ref_name in zip(ref_fpaths, ref_names):
total_references = 0
ref_fname = os.path.basename(ref_fpath)
_, ref_fasta_ext = qutils.splitext_for_fasta_file(ref_fname)
chromosomes_by_refs[ref_name] = []
used_seq_names = defaultdict(int)
corr_seq_fpath = None
for i, (seq_name, seq) in enumerate(fastaparser.read_fasta(ref_fpath)):
total_references += 1
seq_name = correct_name(seq_name,
qutils.MAX_CONTIG_NAME - len(ref_name) - 1)
uniq_seq_name = get_uniq_name(seq_name, used_seq_names)
used_seq_names[seq_name] += 1
corr_seq_name, corr_seq_fpath = _proceed_seq(
uniq_seq_name, seq, ref_name, ref_fasta_ext, total_references,
ref_fpath)
if not corr_seq_name:
break
if corr_seq_fpath:
logger.main_info(' ' + ref_fpath + ' ==> ' +
qutils.name_from_fpath(corr_seq_fpath) + '')
fastaparser.write_fasta(combined_ref_fpath,
fastaparser.read_fasta(corr_seq_fpath),
'a')
elif downloaded_refs:
logger.warning(
'Skipping ' + ref_fpath + ' because it'
' is empty or contains incorrect sequences (header-only or with non-ACGTN characters)!'
)
# cleaning
for corr_seq_name, _ in chromosomes_by_refs[ref_name]:
del contigs_analyzer.ref_labels_by_chromosomes[corr_seq_name]
del chromosomes_by_refs[ref_name]
corrected_ref_fpaths.pop()
excluded_ref_fpaths.append(ref_fpath)
else:
logger.error(
'Reference file ' + ref_fpath +
' is empty or contains incorrect sequences (header-only or with non-ACGTN characters)!',
exit_with_code=1)
for excluded in excluded_ref_fpaths:
ref_fpaths.remove(excluded)
if len(chromosomes_by_refs) > 0:
logger.main_info(' All references were combined in ' +
qconfig.combined_ref_name)
else:
logger.warning('All references were skipped!')
return corrected_ref_fpaths, combined_ref_fpath, chromosomes_by_refs, ref_fpaths
def split_seq_ext(cls, fname):
return qutils.splitext_for_fasta_file(fname)
def do(ref_fpath, original_ref_fpath, output_dirpath):
logger.print_timestamp()
logger.main_info("Simulating Optimal Assembly...")
uncovered_fpath = None
reads_analyzer_dir = join(dirname(output_dirpath),
qconfig.reads_stats_dirname)
if qconfig.reads_fpaths or qconfig.reference_sam or qconfig.reference_bam:
sam_fpath, bam_fpath, uncovered_fpath = reads_analyzer.align_reference(
ref_fpath,
reads_analyzer_dir,
using_reads='all',
calculate_coverage=True)
insert_size = qconfig.optimal_assembly_insert_size
if insert_size == 'auto' or not insert_size:
insert_size = qconfig.optimal_assembly_default_IS
ref_basename, fasta_ext = splitext_for_fasta_file(
os.path.basename(ref_fpath))
result_basename = '%s.%s.is%d.fasta' % (
ref_basename, qconfig.optimal_assembly_basename, insert_size)
long_reads = qconfig.pacbio_reads or qconfig.nanopore_reads
if long_reads:
result_basename = add_suffix(result_basename,
long_reads_polished_suffix)
elif qconfig.mate_pairs:
result_basename = add_suffix(result_basename, mp_polished_suffix)
result_fpath = os.path.join(output_dirpath, result_basename)
original_ref_basename, fasta_ext = splitext_for_fasta_file(
os.path.basename(original_ref_fpath))
prepared_optimal_assembly_basename = '%s.%s.is%d.fasta' % (
original_ref_basename, qconfig.optimal_assembly_basename, insert_size)
ref_prepared_optimal_assembly = os.path.join(
os.path.dirname(original_ref_fpath),
prepared_optimal_assembly_basename)
if os.path.isfile(result_fpath) or os.path.isfile(
ref_prepared_optimal_assembly):
already_done_fpath = result_fpath if os.path.isfile(
result_fpath) else ref_prepared_optimal_assembly
logger.notice(
' Will reuse already generated Optimal Assembly with insert size %d (%s)'
% (insert_size, already_done_fpath))
return already_done_fpath
if qconfig.platform_name == 'linux_32':
logger.warning(
' Sorry, can\'t create Optimal Assembly on this platform, skipping...'
)
return None
red_dirpath = get_dir_for_download('red', 'Red', ['Red'], logger)
binary_fpath = download_external_tool('Red',
red_dirpath,
'red',
platform_specific=True,
is_executable=True)
if not binary_fpath or not os.path.isfile(binary_fpath):
logger.warning(' Sorry, can\'t create Optimal Assembly, skipping...')
return None
log_fpath = os.path.join(output_dirpath, 'optimal_assembly.log')
tmp_dir = os.path.join(output_dirpath, 'tmp')
if os.path.isdir(tmp_dir):
shutil.rmtree(tmp_dir)
os.makedirs(tmp_dir)
unique_covered_regions, repeats_regions = get_unique_covered_regions(
ref_fpath, tmp_dir, log_fpath, binary_fpath, insert_size,
uncovered_fpath)
if unique_covered_regions is None:
logger.error(
' Failed to create Optimal Assembly, see log for details: ' +
log_fpath)
return None
reference = list(fastaparser.read_fasta(ref_fpath))
result_fasta = []
if long_reads or qconfig.mate_pairs:
if long_reads:
join_reads = 'pacbio' if qconfig.pacbio_reads else 'nanopore'
else:
join_reads = 'mp'
sam_fpath, bam_fpath, _ = reads_analyzer.align_reference(
ref_fpath, reads_analyzer_dir, using_reads=join_reads)
joiners = get_joiners(qutils.name_from_fpath(ref_fpath), sam_fpath,
bam_fpath, tmp_dir, log_fpath, join_reads)
uncovered_regions = parse_uncovered_fpath(
uncovered_fpath, ref_fpath, return_covered_regions=False
) if join_reads == 'mp' else defaultdict(list)
mp_len = calculate_read_len(sam_fpath) if join_reads == 'mp' else None
for chrom, seq in reference:
region_pairing = get_regions_pairing(unique_covered_regions[chrom],
joiners[chrom], mp_len)
ref_coords_to_output = scaffolding(unique_covered_regions[chrom],
region_pairing)
get_fasta_entries_from_coords(result_fasta, (chrom, seq),
ref_coords_to_output,
repeats_regions[chrom],
uncovered_regions[chrom])
else:
for chrom, seq in reference:
for idx, region in enumerate(unique_covered_regions[chrom]):
if region[1] - region[0] >= MIN_CONTIG_LEN:
result_fasta.append(
(chrom + '_' + str(idx), seq[region[0]:region[1]]))
fastaparser.write_fasta(result_fpath, result_fasta)
logger.info(' ' + 'Theoretically optimal Assembly saved to ' +
result_fpath)
logger.notice(
'You can copy it to ' + ref_prepared_optimal_assembly +
' and QUAST will reuse it in further runs against the same reference ('
+ original_ref_fpath + ')')
if not qconfig.debug:
shutil.rmtree(tmp_dir)
logger.main_info('Done.')
return result_fpath
def do(ref_fpath, original_ref_fpath, output_dirpath):
logger.print_timestamp()
logger.main_info("Simulating Ideal Assembly...")
uncovered_fpath = None
if qconfig.paired_reads or qconfig.reference_sam or qconfig.reference_sam:
sam_fpath, uncovered_fpath = reads_analyzer.align_reference(ref_fpath, join(dirname(output_dirpath),
qconfig.reads_stats_dirname), using_reads='paired_end')
insert_size = qconfig.ideal_assembly_insert_size
if insert_size == 'auto' or not insert_size:
insert_size = qconfig.ideal_assembly_default_IS
if insert_size % 2 == 0:
insert_size += 1
logger.notice(' Current implementation cannot work with even insert sizes, '
'will use the closest odd value (%d)' % insert_size)
ref_basename, fasta_ext = splitext_for_fasta_file(os.path.basename(ref_fpath))
result_basename = '%s.%s.is%d.fasta' % (ref_basename, qconfig.ideal_assembly_basename, insert_size)
if qconfig.paired_reads and qconfig.unpaired_reads:
result_basename = add_suffix(result_basename, single_polished_suffix)
if qconfig.paired_reads and qconfig.mate_pairs:
result_basename = add_suffix(result_basename, mp_polished_suffix)
result_fpath = os.path.join(output_dirpath, result_basename)
original_ref_basename, fasta_ext = splitext_for_fasta_file(os.path.basename(original_ref_fpath))
prepared_ideal_assembly_basename = '%s.%s.is%d.fasta' % (original_ref_basename, qconfig.ideal_assembly_basename, insert_size)
ref_prepared_ideal_assembly = os.path.join(os.path.dirname(original_ref_fpath), prepared_ideal_assembly_basename)
if os.path.isfile(result_fpath) or os.path.isfile(ref_prepared_ideal_assembly):
already_done_fpath = result_fpath if os.path.isfile(result_fpath) else ref_prepared_ideal_assembly
logger.notice(' Will reuse already generated Ideal Assembly with insert size %d (%s)' %
(insert_size, already_done_fpath))
return already_done_fpath
if qconfig.platform_name == 'linux_32':
logger.warning(' Sorry, can\'t create Ideal Assembly on this platform, skipping...')
return None
base_aux_dir = os.path.join(qconfig.LIBS_LOCATION, 'ideal_assembly')
configs_dir = os.path.join(base_aux_dir, 'configs')
binary_fpath = download_external_tool('spades', os.path.join(base_aux_dir, 'bin'), 'spades', platform_specific=True)
if not os.path.isfile(binary_fpath):
logger.warning(' Sorry, can\'t create Ideal Assembly, skipping...')
return None
log_fpath = os.path.join(output_dirpath, 'spades.log')
tmp_dir = os.path.join(output_dirpath, 'tmp')
if os.path.isdir(tmp_dir):
shutil.rmtree(tmp_dir)
os.makedirs(tmp_dir)
processed_ref_fpath = preprocess_reference(ref_fpath, tmp_dir, uncovered_fpath)
dst_configs = os.path.join(tmp_dir, 'configs')
main_config = os.path.join(dst_configs, 'config.info')
dir_util._path_created = {} # see http://stackoverflow.com/questions/9160227/dir-util-copy-tree-fails-after-shutil-rmtree
dir_util.copy_tree(configs_dir, dst_configs, preserve_times=False)
prepare_config_spades(main_config, insert_size, processed_ref_fpath, tmp_dir)
log_file = open(log_fpath, 'w')
spades_output_fpath = os.path.join(tmp_dir, 'K%d' % insert_size, 'ideal_assembly.fasta')
logger.info(' ' + 'Running SPAdes with K=' + str(insert_size) + '...')
return_code = qutils.call_subprocess(
[binary_fpath, main_config], stdout=log_file, stderr=log_file, indent=' ')
if return_code != 0 or not os.path.isfile(spades_output_fpath):
logger.error(' Failed to create Ideal Assembly, see log for details: ' + log_fpath)
return None
if qconfig.mate_pairs or qconfig.unpaired_reads:
spades_output_fpath = polish_assembly(ref_fpath, spades_output_fpath, output_dirpath, tmp_dir)
shutil.move(spades_output_fpath, result_fpath)
logger.info(' ' + 'Ideal Assembly saved to ' + result_fpath)
logger.notice('You can copy it to ' + ref_prepared_ideal_assembly +
' and QUAST will reuse it in further runs against the same reference (' + original_ref_fpath + ')')
if not qconfig.debug:
shutil.rmtree(tmp_dir)
logger.main_info('Done.')
return result_fpath
def correct_meta_references(ref_fpaths, corrected_dirpath):
corrected_ref_fpaths = []
combined_ref_fpath = os.path.join(corrected_dirpath, qconfig.combined_ref_name)
chromosomes_by_refs = {}
def _proceed_seq(seq_name, seq, ref_name, ref_fasta_ext, total_references, ref_fpath):
seq_fname = ref_name
seq_fname += ref_fasta_ext
if total_references > 1:
corr_seq_fpath = corrected_ref_fpaths[-1]
else:
corr_seq_fpath = qutils.unique_corrected_fpath(os.path.join(corrected_dirpath, seq_fname))
corrected_ref_fpaths.append(corr_seq_fpath)
corr_seq_name = qutils.name_from_fpath(corr_seq_fpath) + '_' + seq_name
if not qconfig.no_check:
corr_seq = correct_seq(seq, ref_fpath)
if not corr_seq:
return None, None
fastaparser.write_fasta(corr_seq_fpath, [(corr_seq_name, seq)], 'a')
fastaparser.write_fasta(combined_ref_fpath, [(corr_seq_name, seq)], 'a')
contigs_analyzer.ref_labels_by_chromosomes[corr_seq_name] = qutils.name_from_fpath(corr_seq_fpath)
chromosomes_by_refs[ref_name].append((corr_seq_name, len(seq)))
return corr_seq_name, corr_seq_fpath
ref_fnames = [os.path.basename(ref_fpath) for ref_fpath in ref_fpaths]
ref_names = []
for ref_fname in ref_fnames:
ref_name, ref_fasta_ext = qutils.splitext_for_fasta_file(ref_fname)
ref_names.append(ref_name)
dupl_ref_names = [ref_name for ref_name in ref_names if ref_names.count(ref_name) > 1]
for ref_fpath in ref_fpaths:
total_references = 0
ref_fname = os.path.basename(ref_fpath)
ref_name, ref_fasta_ext = qutils.splitext_for_fasta_file(ref_fname)
if ref_name in dupl_ref_names:
ref_name = qutils.get_label_from_par_dir_and_fname(ref_fpath)
chromosomes_by_refs[ref_name] = []
used_seq_names = defaultdict(int)
corr_seq_fpath = None
for i, (seq_name, seq) in enumerate(fastaparser.read_fasta(ref_fpath)):
total_references += 1
seq_name = correct_name(seq_name, qutils.MAX_CONTIG_NAME - len(ref_name) - 1)
uniq_seq_name = get_uniq_name(seq_name, used_seq_names)
used_seq_names[seq_name] += 1
corr_seq_name, corr_seq_fpath = _proceed_seq(uniq_seq_name, seq, ref_name, ref_fasta_ext, total_references, ref_fpath)
if not corr_seq_name:
break
if corr_seq_fpath:
logger.main_info(' ' + ref_fpath + ' ==> ' + qutils.name_from_fpath(corr_seq_fpath) + '')
logger.main_info(' All references combined in ' + qconfig.combined_ref_name)
return corrected_ref_fpaths, combined_ref_fpath, chromosomes_by_refs, ref_fpaths
