def _process_reads_worker(fast5_q, snp_calls_q, caller_conn, model_info,
device, do_false_ref):
model_info.prep_model_worker(device)
map_thr_buf = mappy.ThreadBuffer()
while True:
try:
fast5_fn, read_id = fast5_q.get(block=False)
except queue.Empty:
sleep(0.001)
continue
if fast5_fn is None:
if caller_conn is not None:
caller_conn.send(True)
break
try:
raw_sig = fast5_io.get_signal(fast5_fn, read_id)
read_snp_calls = process_read(raw_sig, read_id, model_info,
caller_conn, map_thr_buf,
do_false_ref)
snp_calls_q.put((True, read_snp_calls))
except Exception as e:
snp_calls_q.put((False, str(e)))
pass
return
def _map_read_worker(aligner, map_conn, allow_supps):
LOGGER.debug('MappingWorkerStarting')
# get mappy aligner thread buffer
map_thr_buf = mappy.ThreadBuffer()
LOGGER.debug('MappingWorkerInitComplete')
while True:
try:
q_seq, read_id = map_conn.recv()
except EOFError:
LOGGER.debug('MappingWorkerClosing')
break
map_conn.send(
align_read(q_seq, aligner, map_thr_buf, read_id, allow_supps))
def mpile(seqs):
if seqs is None: return([])
thrbuf = mp.ThreadBuffer()
hits = []
chrom=None
for hit in a.map(seqs[1], buf=thrbuf):
if (hit.NM<=min_mis_match) and ('S' not in hit.cigar_str) and ('H' not in hit.cigar_str):
if chrom is None:
chrom=mapping[hit.ctg]
hits.append((hit.ctg, hit.r_st-1, hit.r_en))
elif mapping[hit.ctg] == chrom:
hits.append((hit.ctg, hit.r_st-1, hit.r_en))
else:
break
return(hits)
def _map_read_worker(aligner, map_conn, mo_q):
# get mappy aligner thread buffer
map_thr_buf = mappy.ThreadBuffer()
while True:
try:
q_seq, read_id = map_conn.recv()
except Exception:
# exit gracefully
return
if q_seq is None:
break
map_res, full_res = align_read(q_seq, aligner, map_thr_buf, read_id)
map_conn.send(map_res)
if mo_q is not None and full_res is not None:
mo_q.put((map_res[0], full_res))
def _map_read_worker(aligner, map_conn):
LOGGER.debug('MappingWorkerStarting')
# get mappy aligner thread buffer
map_thr_buf = mappy.ThreadBuffer()
LOGGER.debug('MappingWorkerInitComplete')
while True:
try:
q_seq, read_id = map_conn.recv()
except EOFError:
LOGGER.debug('MappingWorkerClosing')
break
map_res = align_read(q_seq, aligner, map_thr_buf, read_id)
if map_res is not None:
# only convert to tuple if result is valid
map_res = tuple(map_res)
map_conn.send(map_res)
def _process_reads_worker(bc_q, var_calls_q, caller_conn, do_false_ref):
LOGGER.debug("InitWorker")
map_thr_buf = mappy.ThreadBuffer()
while True:
try:
bc_res = bc_q.get(block=True, timeout=0.1)
except queue.Empty:
continue
if bc_res is None:
LOGGER.debug("Closing")
if caller_conn is not None:
caller_conn.close()
break
try:
read_var_calls = process_read(bc_res, caller_conn, map_thr_buf,
do_false_ref)
var_calls_q.put((True, read_var_calls))
except Exception as e:
var_calls_q.put((False, str(e)))
