def run(self, fastani_verification, genomes):
"""Using the instance defined number of CPUs, run FastANI."""
manager = multiprocessing.Manager()
out_q = manager.dict()
procs = []
nprocs = self.cpus
for item in splitchunks(fastani_verification, nprocs):
p = multiprocessing.Process(target=self._fastaniWorker,
args=(item, genomes, out_q))
procs.append(p)
p.start()
# Wait for all worker processes to finish
for p in procs:
p.join()
if p.exitcode == 1:
raise FastANIException(
"A process returned a non-zero exit code.")
all_fastani_dict = dict(out_q)
return all_fastani_dict
def align_marker_set(self, db_genome_ids, marker_set_id):
manager = multiprocessing.Manager()
out_q = manager.Queue()
procs = []
nprocs = self.threads
for item in splitchunks(db_genome_ids, nprocs):
p = multiprocessing.Process(target=self._worker,
args=(item, out_q, marker_set_id))
procs.append(p)
p.start()
# Collect all results into a single result dict. We know how many dicts
# with results to expect.
while out_q.empty():
time.sleep(1)
# Wait for all worker processes to finish
results = {}
for i in range(len(db_genome_ids)):
gid, sequence = out_q.get()
results[gid] = sequence
return results
def test_splitchunks(self):
test_dict = {'k1': 'v1', 'k2': 'v2',
'k3': 'v3', 'k4': 'v4'}
my_gen = tools.splitchunks(test_dict, 2)
self.assertEqual(len(next(my_gen)), 2)