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 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