def try_run_ovlp_filter(n_core, ovl, fofn, max_diff, max_cov, min_cov, min_len,
bestn, db_fn):
io.LOG('starting ovlp_filter')
file_list = io.validated_fns(ovl) if ovl != None else io.validated_fns(
fofn)
io.LOG('fofn %r: %r' % (ovl if ovl != None else fofn, file_list))
n_core = min(n_core, len(file_list))
exe_pool = Pool(n_core)
try:
run_ovlp_filter(exe_pool, ovl, file_list, max_diff, max_cov, min_cov,
min_len, bestn, db_fn)
io.LOG('finished ovlp_filter')
except:
io.LOG('terminating ovlp_filter workers...')
exe_pool.terminate()
raise
def try_run_ovlp_stats(n_core, fofn, min_len):
io.LOG('starting ovlp_stats')
file_list = io.validated_fns(fofn)
io.LOG('fofn %r: %r' %(fofn, file_list))
n_core = min(n_core, len(file_list))
exe_pool = Pool(n_core)
try:
run_ovlp_stats(exe_pool, file_list, min_len)
io.LOG('finished ovlp_stats')
except KeyboardInterrupt:
io.LOG('terminating ovlp_stats workers...')
exe_pool.terminate()
def try_run_ovlp_stats(n_core, fofn, min_len):
io.LOG('starting ovlp_stats')
file_list = io.validated_fns(fofn)
io.LOG('fofn %r: %r' % (fofn, file_list))
n_core = min(n_core, len(file_list))
exe_pool = Pool(n_core)
try:
run_ovlp_stats(exe_pool, file_list, min_len)
io.LOG('finished ovlp_stats')
except KeyboardInterrupt:
io.LOG('terminating ovlp_stats workers...')
exe_pool.terminate()
def try_run_ovlp_filter(n_core, fofn, max_diff, max_cov, min_cov, min_len, bestn, db_fn):
io.LOG("starting ovlp_filter")
file_list = io.validated_fns(fofn)
io.LOG("fofn %r: %r" % (fofn, file_list))
n_core = min(n_core, len(file_list))
exe_pool = Pool(n_core)
try:
run_ovlp_filter(exe_pool, file_list, max_diff, max_cov, min_cov, min_len, bestn, db_fn)
io.LOG("finished ovlp_filter")
except KeyboardInterrupt:
io.LOG("terminating ovlp_filter workers...")
exe_pool.terminate()
def try_run_ovlp_filter(n_core, fofn, max_diff, max_cov, min_cov, min_len, bestn, db_fn):
io.LOG('starting ovlp_filter')
file_list = io.validated_fns(fofn)
io.LOG('fofn %r: %r' %(fofn, file_list))
n_core = min(n_core, len(file_list))
exe_pool = Pool(n_core)
try:
run_ovlp_filter(exe_pool, file_list, max_diff, max_cov, min_cov, min_len, bestn, db_fn)
io.LOG('finished ovlp_filter')
except:
io.LOG('terminating ovlp_filter workers...')
exe_pool.terminate()
raise
def try_run_ovlp_stats(n_core, db_fn, fofn, min_len):
io.LOG('starting ovlp_stats')
file_list = io.validated_fns(fofn)
io.LOG('fofn {!r}: {}'.format(fofn, file_list))
io.LOG('db {!r}; n_core={}'.format(db_fn, n_core))
n_core = min(n_core, len(file_list))
exe_pool = Pool(n_core)
try:
run_ovlp_stats(exe_pool, db_fn, file_list, min_len)
io.LOG('finished ovlp_stats')
except KeyboardInterrupt:
io.LOG('terminating ovlp_stats workers...')
exe_pool.terminate()
def try_run_ovlp_stats(n_core, db_fn, fofn, min_len):
io.LOG('starting ovlp_stats')
file_list = io.validated_fns(fofn)
io.LOG('fofn {!r}: {}'.format(fofn, file_list))
io.LOG('db {!r}; n_core={}'.format(db_fn, n_core))
n_core = min(n_core, len(file_list))
exe_pool = Pool(n_core)
try:
run_ovlp_stats(exe_pool, db_fn, file_list, min_len)
io.LOG('finished ovlp_stats')
except KeyboardInterrupt:
io.LOG('terminating ovlp_stats workers...')
exe_pool.terminate()
def try_run_ovlp_filter(out_fn, n_core, fofn, max_diff, max_cov, min_cov, min_len, min_idt, ignore_indels, bestn, db_fn):
io.LOG('starting ovlp_filter')
file_list = io.validated_fns(fofn)
io.LOG('fofn %r: %r' % (fofn, file_list))
n_core = min(n_core, len(file_list))
exe_pool = Pool(n_core)
tmp_out_fn = out_fn + '.tmp'
try:
with open(tmp_out_fn, 'w') as outs:
run_ovlp_filter(outs, exe_pool, file_list, max_diff, max_cov,
min_cov, min_len, min_idt, ignore_indels, bestn, db_fn)
os.rename(tmp_out_fn, out_fn)
io.LOG('finished ovlp_filter')
except:
io.LOG('terminating ovlp_filter workers...')
exe_pool.terminate()
raise
def try_run_ovlp_filter(out_fn, n_core, fofn, max_diff, max_cov, min_cov, min_len, bestn, db_fn):
io.LOG('starting ovlp_filter')
file_list = io.validated_fns(fofn)
io.LOG('fofn %r: %r' % (fofn, file_list))
n_core = min(n_core, len(file_list))
exe_pool = Pool(n_core)
tmp_out_fn = out_fn + '.tmp'
try:
with open(tmp_out_fn, 'w') as outs:
run_ovlp_filter(outs, exe_pool, file_list, max_diff, max_cov,
min_cov, min_len, bestn, db_fn)
outs.write('---\n')
os.rename(tmp_out_fn, out_fn)
io.LOG('finished ovlp_filter')
except:
io.LOG('terminating ovlp_filter workers...')
exe_pool.terminate()
raise
