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def poll_data(port):
align_client = yield from bwa.align_client(align_port)
replay_client = yield from replayfast5.replay_client(replay_port)
yield from asyncio.sleep(5)
start_time = now()
target_count = 0
while True:
time_saved = yield from replay_client.call.time_saved()
total_pore_time = (now() - start_time) * len(channels)
total_strand_time = yield from replay_client.call.cumulative_good_read_time()
try:
pore_time_saved = time_saved/total_pore_time
except:
pore_time_saved = 0
try:
strand_time_saved = time_saved/total_strand_time
except:
strand_time_saved = 0
logger.info("Total pore time saved: {:.2f}% [{:.2f}/{:.2f}]".format(
aligning to these references will be ejected. If `whitelist` is `True`
any read alinging to a reference other than those contained in this
list will be ejected. Unidentified reads are never ejected.
:param whitelist: see `target`.
"""
logger = logging.getLogger('ReadUntil App')
good_class = 'strand'
time_warp=2
event_loop = asyncio.get_event_loop()
set_wakeup()
port = start_port
# Setup replay service
replay_port = port
replay_server = event_loop.create_task(replayfast5.replay_server(
fast5, channels, replay_port, good_class, time_warp=time_warp
))
port += 1
# Setup alignment service
align_port = port
align_server = event_loop.create_task(bwa.align_server(
bwa_index, align_port
))
identified_reads = {}
unidentified_reads = defaultdict(list)
unblocks = Counter()
###
# The read until app