def _get_mod_stats_queue(
mod_stats_q,
mod_conn,
out_dir,
mod_names,
ref_names_and_lens,
out_suffix,
write_mod_lp,
mod_output_fmts,
):
def get_mod_site():
# function for profiling purposes
return mod_stats_q.get(block=True, timeout=0.01)
agg_mod_bn = mh.get_megalodon_fn(out_dir, mh.MOD_NAME)
if out_suffix is not None:
agg_mod_bn += "." + out_suffix
agg_mod_fps = []
if mh.MOD_BEDMETHYL_NAME in mod_output_fmts:
agg_mod_fps.append(mods.ModBedMethylWriter(agg_mod_bn, mod_names, "w"))
if mh.MOD_VCF_NAME in mod_output_fmts:
agg_mod_fps.append(
mods.ModVcfWriter(
agg_mod_bn,
mod_names,
"w",
ref_names_and_lens=ref_names_and_lens,
write_mod_lp=write_mod_lp,
))
if mh.MOD_WIG_NAME in mod_output_fmts:
agg_mod_fps.append(mods.ModWigWriter(agg_mod_bn, mod_names, "w"))
while True:
try:
mod_sites_batch = get_mod_site()
for mod_site in mod_sites_batch:
for agg_mod_fp in agg_mod_fps:
agg_mod_fp.write_mod_site(mod_site)
except queue.Empty:
if mod_conn.poll():
break
continue
while not mod_stats_q.empty():
mod_sites_batch = mod_stats_q.get(block=False)
for mod_site in mod_sites_batch:
for agg_mod_fp in agg_mod_fps:
agg_mod_fp.write_mod_site(mod_site)
for agg_mod_fp in agg_mod_fps:
agg_mod_fp.close()
def _get_mod_stats_queue(mod_stats_q, mod_conn, out_dir, mod_names,
ref_names_and_lens, out_suffix, write_mod_lp,
mod_output_fmts):
def get_mod_site():
# function for profiling purposes
return mod_stats_q.get(block=False)
def do_sleep():
# function for profiling purposes
sleep(0.001)
return
agg_mod_bn = mh.get_megalodon_fn(out_dir, mh.MOD_NAME)
if out_suffix is not None:
agg_mod_bn += '.' + out_suffix
agg_mod_fps = []
if mh.MOD_BEDMETHYL_NAME in mod_output_fmts:
agg_mod_fps.append(mods.ModBedMethylWriter(agg_mod_bn, mod_names, 'w'))
if mh.MOD_VCF_NAME in mod_output_fmts:
agg_mod_fps.append(
mods.ModVcfWriter(agg_mod_bn,
mod_names,
'w',
ref_names_and_lens=ref_names_and_lens,
write_mod_lp=write_mod_lp))
if mh.MOD_WIG_NAME in mod_output_fmts:
agg_mod_fps.append(mods.ModWigWriter(agg_mod_bn, mod_names, 'w'))
while True:
try:
mod_site = get_mod_site()
for agg_mod_fp in agg_mod_fps:
agg_mod_fp.write_mod_site(mod_site)
except queue.Empty:
if mod_conn.poll():
break
do_sleep()
continue
while not mod_stats_q.empty():
mod_site = mod_stats_q.get(block=False)
for agg_mod_fp in agg_mod_fps:
agg_mod_fp.write_mod_site(mod_site)
for agg_mod_fp in agg_mod_fps:
agg_mod_fp.close()
return