def run(self):
while True:
data = self.receiver.recv_json()
ref = "this is %s" % data['ref']
struct_file = data['structure_file']
alignment_pair = data['alignment_pair']
print(alignment_pair)
structures = run_distance.read_structure_file(struct_file)
print(structures)
run_distance.run_distance_pexpect(ref, structures)
print('done')
def run_with_poll(self):
self.start_poll()
while True:
socks = dict(self.poller.poll(1000))
if socks:
if socks.get(self.receiver) == zmq.POLLIN:
print ("got message ")
data = self.receiver.recv_json(zmq.NOBLOCK)
ref = "this is %s" % data['ref']
struct_file = data['structure_file']
alignment_pair = data['alignment_pair']
print(alignment_pair)
structures = run_distance.read_structure_file(struct_file)
print(structures)
run_distance.run_distance_pexpect(ref, structures)
print('done')
else:
print('still watiing')
def testPexpect(self):
results = run_distance.run_distance_pexpect(self.reference, self.structures)
self.assertTrue(len(results), 5)
print(results)
sinker = context.socket(zmq.PUSH)
sinker.connect(sinker_ip)
while True:
data = receiver.recv_json()
ref = data['ref']
struct_file = data['structure_file']
alignment_pair = data['alignment_pair']
sys.stdout.write('working on %s\n' %alignment_pair)
sys.stdout.flush()
structures = run_distance.read_structure_file(struct_file)
structures = set(structures)
results = run_distance.run_distance_pexpect(ref, structures)
out_file = "data/rnadistance_results/%s.rnadist.results.txt" % alignment_pair
with open(out_file, 'w+') as f:
for score in results:
f.write("%s\n" % score)
sinker.send_json({
'sender' : 'worker',
'body' : "%s\tcompleted" % alignment_pair
})