def search_sv_with_manta(main_ref_fpath, meta_ref_fpaths, output_dirpath, err_path):
logger.info(' Searching structural variations with Manta...')
final_bed_fpath = os.path.join(output_dirpath, qconfig.manta_sv_fname)
if os.path.exists(final_bed_fpath):
logger.info(' Using existing file: ' + final_bed_fpath)
return final_bed_fpath
if meta_ref_fpaths:
from joblib import Parallel, delayed
n_jobs = min(len(meta_ref_fpaths), qconfig.max_threads)
bed_fpaths = Parallel(n_jobs=n_jobs)(delayed(process_one_ref)(cur_ref_fpath, output_dirpath, err_path) for cur_ref_fpath in meta_ref_fpaths)
bed_fpaths = [f for f in bed_fpaths if f is not None]
if bed_fpaths:
qutils.cat_files(bed_fpaths, final_bed_fpath)
else:
process_one_ref(main_ref_fpath, output_dirpath, err_path, bed_fpath=final_bed_fpath)
logger.info(' Saving to: ' + final_bed_fpath)
return final_bed_fpath
def search_sv_with_manta(main_ref_fpath, meta_ref_fpaths, output_dirpath,
err_path):
logger.info(' Searching structural variations with Manta...')
final_bed_fpath = os.path.join(output_dirpath, qconfig.manta_sv_fname)
if os.path.exists(final_bed_fpath):
logger.info(' Using existing file: ' + final_bed_fpath)
return final_bed_fpath
if meta_ref_fpaths:
from joblib import Parallel, delayed
n_jobs = min(len(meta_ref_fpaths), qconfig.max_threads)
bed_fpaths = Parallel(n_jobs=n_jobs)(
delayed(process_one_ref)(cur_ref_fpath, output_dirpath, err_path)
for cur_ref_fpath in meta_ref_fpaths)
bed_fpaths = [f for f in bed_fpaths if f is not None]
if bed_fpaths:
qutils.cat_files(bed_fpaths, final_bed_fpath)
else:
process_one_ref(main_ref_fpath,
output_dirpath,
err_path,
bed_fpath=final_bed_fpath)
logger.info(' Saving to: ' + final_bed_fpath)
return final_bed_fpath
def run_processing_reads(main_ref_fpath, meta_ref_fpaths, ref_labels,
reads_fpaths, output_dirpath, res_path, log_path,
err_path):
ref_name = qutils.name_from_fpath(main_ref_fpath)
sam_fpath = os.path.join(output_dirpath, ref_name + '.sam')
bam_fpath = os.path.join(output_dirpath, ref_name + '.bam')
bam_sorted_fpath = os.path.join(output_dirpath, ref_name + '.sorted')
sam_sorted_fpath = os.path.join(output_dirpath, ref_name + '.sorted.sam')
bed_fpath = os.path.join(res_path, ref_name + '.bed')
if is_non_empty_file(bed_fpath):
logger.info(' Using existing BED-file: ' + bed_fpath)
return bed_fpath
logger.info(' ' + 'Pre-processing for searching structural variations...')
logger.info(' ' + 'Logging to %s...' % err_path)
if is_non_empty_file(sam_fpath):
logger.info(' Using existing SAM-file: ' + sam_fpath)
else:
logger.info(' Running Bowtie2...')
abs_reads_fpaths = [
] # use absolute paths because we will change workdir
for reads_fpath in reads_fpaths:
abs_reads_fpaths.append(os.path.abspath(reads_fpath))
prev_dir = os.getcwd()
os.chdir(output_dirpath)
cmd = [bin_fpath('bowtie2-build'), main_ref_fpath, ref_name]
qutils.call_subprocess(cmd,
stdout=open(log_path, 'a'),
stderr=open(err_path, 'a'),
logger=logger)
cmd = bin_fpath('bowtie2') + ' -x ' + ref_name + ' -1 ' + abs_reads_fpaths[0] + ' -2 ' + abs_reads_fpaths[1] + ' -S ' + \
sam_fpath + ' --no-unal -a -p %s' % str(qconfig.max_threads)
qutils.call_subprocess(shlex.split(cmd),
stdout=open(log_path, 'a'),
stderr=open(err_path, 'a'),
logger=logger)
logger.info(' Done.')
os.chdir(prev_dir)
if not os.path.exists(sam_fpath) or os.path.getsize(sam_fpath) == 0:
logger.error(' Failed running Bowtie2 for the reference. See ' +
log_path + ' for information.')
logger.info(' Failed searching structural variations.')
return None
logger.info(' Sorting SAM-file...')
if is_non_empty_file(sam_sorted_fpath):
logger.info(' Using existing sorted SAM-file: ' + sam_sorted_fpath)
else:
qutils.call_subprocess([
samtools_fpath('samtools'), 'view', '-@',
str(qconfig.max_threads), '-bS', sam_fpath
],
stdout=open(bam_fpath, 'w'),
stderr=open(err_path, 'a'),
logger=logger)
qutils.call_subprocess([
samtools_fpath('samtools'), 'sort', '-@',
str(qconfig.max_threads), bam_fpath, bam_sorted_fpath
],
stderr=open(err_path, 'a'),
logger=logger)
qutils.call_subprocess([
samtools_fpath('samtools'), 'view', '-@',
str(qconfig.max_threads), bam_sorted_fpath + '.bam'
],
stdout=open(sam_sorted_fpath, 'w'),
stderr=open(err_path, 'a'),
logger=logger)
if meta_ref_fpaths:
logger.info(' Splitting SAM-file by references...')
headers = []
seq_name_length = {}
with open(sam_fpath) as sam_file:
for line in sam_file:
if not line.startswith('@'):
break
if line.startswith('@SQ') and 'SN:' in line and 'LN:' in line:
seq_name = line.split('\tSN:')[1].split('\t')[0]
seq_length = int(line.split('\tLN:')[1].split('\t')[0])
seq_name_length[seq_name] = seq_length
headers.append(line.strip())
need_ref_splitting = False
if meta_ref_fpaths:
ref_files = {}
for cur_ref_fpath in meta_ref_fpaths:
ref = qutils.name_from_fpath(cur_ref_fpath)
new_ref_sam_fpath = os.path.join(output_dirpath, ref + '.sam')
if is_non_empty_file(new_ref_sam_fpath):
logger.info(' Using existing split SAM-file for %s: %s' %
(ref, new_ref_sam_fpath))
ref_files[ref] = None
else:
new_ref_sam_file = open(new_ref_sam_fpath, 'w')
new_ref_sam_file.write(headers[0] + '\n')
chrs = []
for h in (h for h in headers
if h.startswith('@SQ') and 'SN:' in h):
seq_name = h.split('\tSN:')[1].split('\t')[0]
if seq_name in ref_labels and ref_labels[seq_name] == ref:
new_ref_sam_file.write(h + '\n')
chrs.append(seq_name)
new_ref_sam_file.write(headers[-1] + '\n')
ref_files[ref] = new_ref_sam_file
need_ref_splitting = True
deletions = []
trivial_deletions_fpath = os.path.join(output_dirpath,
qconfig.trivial_deletions_fname)
logger.info(
' Looking for trivial deletions (long zero-covered fragments)...')
need_trivial_deletions = True
if os.path.exists(trivial_deletions_fpath):
need_trivial_deletions = False
logger.info(' Using existing file: ' + trivial_deletions_fpath)
if need_trivial_deletions or need_ref_splitting:
with open(sam_sorted_fpath) as sam_file:
cur_deletion = None
for line in sam_file:
mapping = Mapping.parse(line)
if mapping:
# common case: continue current deletion (potential) on the same reference
if cur_deletion and cur_deletion.ref == mapping.ref:
if cur_deletion.next_bad is None: # previous mapping was in region BEFORE 0-covered fragment
# just passed 0-covered fragment
if mapping.start - cur_deletion.prev_bad > QuastDeletion.MIN_GAP:
cur_deletion.set_next_bad(mapping)
if mapping.mapq >= Mapping.MIN_MAP_QUALITY:
cur_deletion.set_next_good(mapping)
if cur_deletion.is_valid():
deletions.append(cur_deletion)
cur_deletion = QuastDeletion(
mapping.ref).set_prev_good(mapping)
# continue region BEFORE 0-covered fragment
elif mapping.mapq >= Mapping.MIN_MAP_QUALITY:
cur_deletion.set_prev_good(mapping)
else:
cur_deletion.set_prev_bad(mapping)
else: # previous mapping was in region AFTER 0-covered fragment
# just passed another 0-cov fragment between end of cur_deletion BAD region and this mapping
if mapping.start - cur_deletion.next_bad_end > QuastDeletion.MIN_GAP:
if cur_deletion.is_valid(
): # add previous fragment's deletion if needed
deletions.append(cur_deletion)
cur_deletion = QuastDeletion(
mapping.ref).set_prev_bad(
position=cur_deletion.next_bad_end)
# continue region AFTER 0-covered fragment (old one or new/another one -- see "if" above)
if mapping.mapq >= Mapping.MIN_MAP_QUALITY:
cur_deletion.set_next_good(mapping)
if cur_deletion.is_valid():
deletions.append(cur_deletion)
cur_deletion = QuastDeletion(
mapping.ref).set_prev_good(mapping)
else:
cur_deletion.set_next_bad_end(mapping)
# special case: just started or just switched to the next reference
else:
if cur_deletion and cur_deletion.ref in seq_name_length: # switched to the next ref
cur_deletion.set_next_good(
position=seq_name_length[cur_deletion.ref])
if cur_deletion.is_valid():
deletions.append(cur_deletion)
cur_deletion = QuastDeletion(
mapping.ref).set_prev_good(mapping)
if need_ref_splitting:
cur_ref = ref_labels[mapping.ref]
if mapping.ref_next.strip(
) == '=' or cur_ref == ref_labels[mapping.ref_next]:
if ref_files[cur_ref] is not None:
ref_files[cur_ref].write(line)
if cur_deletion and cur_deletion.ref in seq_name_length: # switched to the next ref
cur_deletion.set_next_good(
position=seq_name_length[cur_deletion.ref])
if cur_deletion.is_valid():
deletions.append(cur_deletion)
if need_ref_splitting:
for ref_handler in ref_files.values():
if ref_handler is not None:
ref_handler.close()
if need_trivial_deletions:
logger.info(' Trivial deletions: %d found' % len(deletions))
logger.info(' Saving to: ' + trivial_deletions_fpath)
with open(trivial_deletions_fpath, 'w') as f:
for deletion in deletions:
f.write(str(deletion) + '\n')
if os.path.exists(config_manta_fpath):
manta_sv_fpath = search_sv_with_manta(main_ref_fpath, meta_ref_fpaths,
output_dirpath, err_path)
qutils.cat_files([manta_sv_fpath, trivial_deletions_fpath], bed_fpath)
elif os.path.exists(trivial_deletions_fpath):
shutil.copy(trivial_deletions_fpath, bed_fpath)
if os.path.exists(bed_fpath):
logger.main_info(' Structural variations saved to ' + bed_fpath)
return bed_fpath
else:
logger.main_info(' Failed searching structural variations.')
return None
def run_processing_reads(main_ref_fpath, meta_ref_fpaths, ref_labels, reads_fpaths, output_dirpath, res_path, log_path, err_path):
ref_name = qutils.name_from_fpath(main_ref_fpath)
sam_fpath = os.path.join(output_dirpath, ref_name + '.sam')
bam_fpath = os.path.join(output_dirpath, ref_name + '.bam')
bam_sorted_fpath = os.path.join(output_dirpath, ref_name + '.sorted')
sam_sorted_fpath = os.path.join(output_dirpath, ref_name + '.sorted.sam')
bed_fpath = os.path.join(res_path, ref_name + '.bed')
if is_non_empty_file(bed_fpath):
logger.info(' Using existing BED-file: ' + bed_fpath)
return bed_fpath
logger.info(' ' + 'Pre-processing for searching structural variations...')
logger.info(' ' + 'Logging to %s...' % err_path)
if is_non_empty_file(sam_fpath):
logger.info(' Using existing SAM-file: ' + sam_fpath)
else:
logger.info(' Running Bowtie2...')
abs_reads_fpaths = [] # use absolute paths because we will change workdir
for reads_fpath in reads_fpaths:
abs_reads_fpaths.append(os.path.abspath(reads_fpath))
prev_dir = os.getcwd()
os.chdir(output_dirpath)
cmd = [bin_fpath('bowtie2-build'), main_ref_fpath, ref_name]
qutils.call_subprocess(cmd, stdout=open(log_path, 'a'), stderr=open(err_path, 'a'), logger=logger)
cmd = bin_fpath('bowtie2') + ' -x ' + ref_name + ' -1 ' + abs_reads_fpaths[0] + ' -2 ' + abs_reads_fpaths[1] + ' -S ' + \
sam_fpath + ' --no-unal -a -p %s' % str(qconfig.max_threads)
qutils.call_subprocess(shlex.split(cmd), stdout=open(log_path, 'a'), stderr=open(err_path, 'a'), logger=logger)
logger.info(' Done.')
os.chdir(prev_dir)
if not os.path.exists(sam_fpath) or os.path.getsize(sam_fpath) == 0:
logger.error(' Failed running Bowtie2 for the reference. See ' + log_path + ' for information.')
logger.info(' Failed searching structural variations.')
return None
logger.info(' Sorting SAM-file...')
if is_non_empty_file(sam_sorted_fpath):
logger.info(' Using existing sorted SAM-file: ' + sam_sorted_fpath)
else:
qutils.call_subprocess([samtools_fpath('samtools'), 'view', '-@', str(qconfig.max_threads), '-bS', sam_fpath], stdout=open(bam_fpath, 'w'),
stderr=open(err_path, 'a'), logger=logger)
qutils.call_subprocess([samtools_fpath('samtools'), 'sort', '-@', str(qconfig.max_threads), bam_fpath, bam_sorted_fpath],
stderr=open(err_path, 'a'), logger=logger)
qutils.call_subprocess([samtools_fpath('samtools'), 'view', '-@', str(qconfig.max_threads), bam_sorted_fpath + '.bam'], stdout=open(sam_sorted_fpath, 'w'),
stderr=open(err_path, 'a'), logger=logger)
if meta_ref_fpaths:
logger.info(' Splitting SAM-file by references...')
headers = []
seq_name_length = {}
with open(sam_fpath) as sam_file:
for line in sam_file:
if not line.startswith('@'):
break
if line.startswith('@SQ') and 'SN:' in line and 'LN:' in line:
seq_name = line.split('\tSN:')[1].split('\t')[0]
seq_length = int(line.split('\tLN:')[1].split('\t')[0])
seq_name_length[seq_name] = seq_length
headers.append(line.strip())
need_ref_splitting = False
if meta_ref_fpaths:
ref_files = {}
for cur_ref_fpath in meta_ref_fpaths:
ref = qutils.name_from_fpath(cur_ref_fpath)
new_ref_sam_fpath = os.path.join(output_dirpath, ref + '.sam')
if is_non_empty_file(new_ref_sam_fpath):
logger.info(' Using existing split SAM-file for %s: %s' % (ref, new_ref_sam_fpath))
ref_files[ref] = None
else:
new_ref_sam_file = open(new_ref_sam_fpath, 'w')
new_ref_sam_file.write(headers[0] + '\n')
chrs = []
for h in (h for h in headers if h.startswith('@SQ') and 'SN:' in h):
seq_name = h.split('\tSN:')[1].split('\t')[0]
if seq_name in ref_labels and ref_labels[seq_name] == ref:
new_ref_sam_file.write(h + '\n')
chrs.append(seq_name)
new_ref_sam_file.write(headers[-1] + '\n')
ref_files[ref] = new_ref_sam_file
need_ref_splitting = True
deletions = []
trivial_deletions_fpath = os.path.join(output_dirpath, qconfig.trivial_deletions_fname)
logger.info(' Looking for trivial deletions (long zero-covered fragments)...')
need_trivial_deletions = True
if os.path.exists(trivial_deletions_fpath):
need_trivial_deletions = False
logger.info(' Using existing file: ' + trivial_deletions_fpath)
if need_trivial_deletions or need_ref_splitting:
with open(sam_sorted_fpath) as sam_file:
cur_deletion = None
for line in sam_file:
mapping = Mapping.parse(line)
if mapping:
# common case: continue current deletion (potential) on the same reference
if cur_deletion and cur_deletion.ref == mapping.ref:
if cur_deletion.next_bad is None: # previous mapping was in region BEFORE 0-covered fragment
# just passed 0-covered fragment
if mapping.start - cur_deletion.prev_bad > QuastDeletion.MIN_GAP:
cur_deletion.set_next_bad(mapping)
if mapping.mapq >= Mapping.MIN_MAP_QUALITY:
cur_deletion.set_next_good(mapping)
if cur_deletion.is_valid():
deletions.append(cur_deletion)
cur_deletion = QuastDeletion(mapping.ref).set_prev_good(mapping)
# continue region BEFORE 0-covered fragment
elif mapping.mapq >= Mapping.MIN_MAP_QUALITY:
cur_deletion.set_prev_good(mapping)
else:
cur_deletion.set_prev_bad(mapping)
else: # previous mapping was in region AFTER 0-covered fragment
# just passed another 0-cov fragment between end of cur_deletion BAD region and this mapping
if mapping.start - cur_deletion.next_bad_end > QuastDeletion.MIN_GAP:
if cur_deletion.is_valid(): # add previous fragment's deletion if needed
deletions.append(cur_deletion)
cur_deletion = QuastDeletion(mapping.ref).set_prev_bad(position=cur_deletion.next_bad_end)
# continue region AFTER 0-covered fragment (old one or new/another one -- see "if" above)
if mapping.mapq >= Mapping.MIN_MAP_QUALITY:
cur_deletion.set_next_good(mapping)
if cur_deletion.is_valid():
deletions.append(cur_deletion)
cur_deletion = QuastDeletion(mapping.ref).set_prev_good(mapping)
else:
cur_deletion.set_next_bad_end(mapping)
# special case: just started or just switched to the next reference
else:
if cur_deletion and cur_deletion.ref in seq_name_length: # switched to the next ref
cur_deletion.set_next_good(position=seq_name_length[cur_deletion.ref])
if cur_deletion.is_valid():
deletions.append(cur_deletion)
cur_deletion = QuastDeletion(mapping.ref).set_prev_good(mapping)
if need_ref_splitting:
cur_ref = ref_labels[mapping.ref]
if mapping.ref_next.strip() == '=' or cur_ref == ref_labels[mapping.ref_next]:
if ref_files[cur_ref] is not None:
ref_files[cur_ref].write(line)
if cur_deletion and cur_deletion.ref in seq_name_length: # switched to the next ref
cur_deletion.set_next_good(position=seq_name_length[cur_deletion.ref])
if cur_deletion.is_valid():
deletions.append(cur_deletion)
if need_ref_splitting:
for ref_handler in ref_files.values():
if ref_handler is not None:
ref_handler.close()
if need_trivial_deletions:
logger.info(' Trivial deletions: %d found' % len(deletions))
logger.info(' Saving to: ' + trivial_deletions_fpath)
with open(trivial_deletions_fpath, 'w') as f:
for deletion in deletions:
f.write(str(deletion) + '\n')
if os.path.exists(config_manta_fpath):
manta_sv_fpath = search_sv_with_manta(main_ref_fpath, meta_ref_fpaths, output_dirpath, err_path)
qutils.cat_files([manta_sv_fpath, trivial_deletions_fpath], bed_fpath)
elif os.path.exists(trivial_deletions_fpath):
shutil.copy(trivial_deletions_fpath, bed_fpath)
if os.path.exists(bed_fpath):
logger.main_info(' Structural variations saved to ' + bed_fpath)
return bed_fpath
else:
logger.main_info(' Failed searching structural variations.')
return None
