def _thread_worker(aln_reader, chunk_feeder, platform, results_queue,
error_queue):
try:
while True:
ctg_region = chunk_feeder.get_chunk()
if ctg_region is None:
break
ctg_aln = aln_reader.get_alignments(ctg_region.ctg_id,
ctg_region.start,
ctg_region.end)
ctg_id = ctg_region.ctg_id
if len(ctg_aln) == 0:
continue
ctg_aln = aln_reader.trim_and_transpose(ctg_aln, ctg_region.start,
ctg_region.end)
ctg_aln, _mean_cov = get_uniform_alignments(ctg_aln)
profile, aln_errors = _contig_profile(ctg_aln, platform)
sequence = _flatten_profile(profile)
results_queue.put((ctg_id, ctg_region.start, sequence, aln_errors))
except Exception as e:
logger.error("Thread exception")
logger.error(traceback.format_exc())
error_queue.put(e)
def _thread_worker(aln_reader, chunk_feeder, contigs_info, err_mode,
results_queue, error_queue, bubbles_file,
bubbles_file_lock):
"""
Will run in parallel
"""
try:
while True:
ctg_region = chunk_feeder.get_chunk()
if ctg_region is None:
break
ctg_aln = aln_reader.get_alignments(ctg_region.ctg_id,
ctg_region.start,
ctg_region.end)
ctg_id = ctg_region.ctg_id
if len(ctg_aln) == 0:
continue
ref_seq = aln_reader.get_region_sequence(ctg_region.ctg_id,
ctg_region.start,
ctg_region.end)
#since we are working with contig chunks, tranform alignment coorinates
ctg_aln = aln_reader.trim_and_transpose(ctg_aln, ctg_region.start,
ctg_region.end)
ctg_aln, mean_cov = get_uniform_alignments(ctg_aln)
profile, aln_errors = _compute_profile(ctg_aln, ref_seq)
partition, num_long_bubbles = _get_partition(profile, err_mode)
ctg_bubbles = _get_bubble_seqs(ctg_aln, profile, partition, ctg_id)
##
coverage_cap = 0.9 * cfg.vals["max_read_coverage"]
if mean_cov > coverage_cap:
mean_cov = aln_reader.get_median_depth(ctg_region.ctg_id,
ctg_region.start,
ctg_region.end)
##
ctg_bubbles, num_empty = _postprocess_bubbles(ctg_bubbles)
ctg_bubbles, num_long_branch = _split_long_bubbles(ctg_bubbles)
#transform coordinates back
for b in ctg_bubbles:
b.position += ctg_region.start
with bubbles_file_lock:
_output_bubbles(ctg_bubbles, open(bubbles_file, "a"))
results_queue.put(
(ctg_id, len(ctg_bubbles), num_long_bubbles, num_empty,
num_long_branch, aln_errors, mean_cov))
del profile
del ctg_bubbles
except Exception as e:
logger.error("Thread exception")
logger.error(traceback.format_exc())
error_queue.put(e)
def _contig_profile(alignment, platform, genome_len):
"""
Computes alignment profile
"""
#leave the best uniform alignments
alignment = get_uniform_alignments(alignment, genome_len)
aln_errors = []
profile = [Profile() for _ in range(genome_len)]
#max_aln_err = cfg.vals["err_modes"][platform]["max_aln_error"]
for aln in alignment:
#if aln.err_rate > max_aln_err: continue
aln_errors.append(aln.err_rate)
#after gap shifting it is possible that
#two gaps are aligned against each other
qry_seq = shift_gaps(aln.trg_seq, aln.qry_seq)
trg_seq = shift_gaps(qry_seq, aln.trg_seq)
trg_pos = aln.trg_start
for trg_nuc, qry_nuc in zip(trg_seq, qry_seq):
if trg_nuc == "-":
trg_pos -= 1
if trg_pos >= genome_len:
trg_pos -= genome_len
#total += 1
prof_elem = profile[trg_pos]
if trg_nuc == "-" and qry_nuc != "-":
prof_elem.insertions[aln.qry_id] += qry_nuc
else:
prof_elem.nucl = trg_nuc
prof_elem.matches[qry_nuc] += 1
trg_pos += 1
#print "len", genome_len, "median coverage", cov_threshold
#print "total bases: ", total, "discarded bases: ", discarded
#print "filtered", float(discarded) / total
#print ""
return profile, aln_errors
def _thread_worker(aln_reader, contigs_info, err_mode, results_queue,
error_queue, bubbles_file_handle, bubbles_file_lock):
"""
Will run in parallel
"""
try:
aln_reader.init_reading()
while not aln_reader.is_eof():
ctg_id, ctg_aln = aln_reader.get_chunk()
if ctg_id is None:
break
#logger.debug("Processing {0}".format(ctg_id))
#get top unifom alignments
ctg_aln = get_uniform_alignments(ctg_aln,
contigs_info[ctg_id].length)
profile, aln_errors = _compute_profile(ctg_aln, err_mode,
contigs_info[ctg_id].length)
partition, num_long_bubbles = _get_partition(profile, err_mode)
ctg_bubbles = _get_bubble_seqs(ctg_aln, err_mode, profile,
partition, contigs_info[ctg_id])
mean_cov = sum([len(b.branches)
for b in ctg_bubbles]) // (len(ctg_bubbles) + 1)
ctg_bubbles, num_empty, num_long_branch = \
_postprocess_bubbles(ctg_bubbles)
results_queue.put(
(ctg_id, len(ctg_bubbles), num_long_bubbles, num_empty,
num_long_branch, aln_errors, mean_cov))
with bubbles_file_lock:
_output_bubbles(ctg_bubbles, bubbles_file_handle)
del profile
del ctg_bubbles
aln_reader.stop_reading()
except Exception as e:
error_queue.put(e)
