def test():
cmgr = WorkCounterManager(); cmgr.start()
c = WorkCounter(10)
c.add_subwork(10, weights=(1.1,2.2,3,4,5,6,7,8,9,10))
for i in xrange(10):
print c
c[i].count()
c.count()
sleep(1)
print c
def _main(self):
import time
import DegenPrimer.TD_Functions as tdf
from DegenPrimer.Primer import Primer
from DegenPrimer.SeqUtils import load_sequence
from DegenPrimer.WorkCounter import WorkCounterManager
from BioUtils.Tools import WaitingThread
from DegenPrimer.iPCR import iPCR
from threading import Lock
import cProfile
tdf.PCR_P.PCR_T = 53
tdf.PCR_P.Mg = 3e-3
tdf.PCR_P.dNTP = 300e-6
tdf.PCR_P.DNA = 1e-10
fwd_primer = Primer(load_sequence('ATATTCTACRACGGCTATCC', 'fwd_test', 'fwd_test'), 0.43e-6, True)
rev_primer = Primer(load_sequence('GAASGCRAAKATYGGGAAC', 'rev_test', 'rev_test'), 0.43e-6, True)
ipcr = iPCR(self.abort_event,
max_mismatches=6,
job_id='test-job',
primers=[fwd_primer,
rev_primer],
min_amplicon=50,
max_amplicon=2000,
polymerase=40000,
with_exonuclease=False,
num_cycles=30,
side_reactions=None,
side_concentrations=None,
include_side_annealings=True)
cmgr = WorkCounterManager()
cmgr.start()
counter = cmgr.WorkCounter()
plock = Lock()
job = WaitingThread(plock, 1, target=ipcr.simulate_PCR,
name='simulate_PCR',
args=(counter,
(
'../data/ThGa.fa', #single sequence
# '../data/Ch5_gnm.fa', '../data/ThDS1.fa', '../data/ThES1.fa', #long sequences
'../data/ThDS1-FC.fa', '../data/ThDS1-850b-product.fa', #short sequences
),))
job.start(); print ''
while job.is_alive():
if counter.changed_percent():
with plock: print counter
time.sleep(1)
job.join()
with plock: print counter
ipcr.write_report()
cProfile.runctx('for i in xrange(100): ipcr.write_reports()', globals(), locals(), 'iPCR.write_reports.profile')
def test():
cmgr = WorkCounterManager()
cmgr.start()
c = WorkCounter(10)
c.add_subwork(10, weights=(1.1, 2.2, 3, 4, 5, 6, 7, 8, 9, 10))
for i in xrange(10):
print c
c[i].count()
c.count()
sleep(1)
print c
def _main(self):
import time
import DegenPrimer.TD_Functions as tdf
from DegenPrimer.Primer import Primer
from DegenPrimer.SeqUtils import load_sequence
from DegenPrimer.WorkCounter import WorkCounterManager
from BioUtils.Tools import WaitingThread
from DegenPrimer.iPCR import iPCR
from threading import Lock
import cProfile
tdf.PCR_P.PCR_T = 53
tdf.PCR_P.Mg = 3e-3
tdf.PCR_P.dNTP = 300e-6
tdf.PCR_P.DNA = 1e-10
fwd_primer = Primer(
load_sequence('ATATTCTACRACGGCTATCC', 'fwd_test', 'fwd_test'),
0.43e-6, True)
rev_primer = Primer(
load_sequence('GAASGCRAAKATYGGGAAC', 'rev_test', 'rev_test'),
0.43e-6, True)
ipcr = iPCR(self.abort_event,
max_mismatches=6,
job_id='test-job',
primers=[fwd_primer, rev_primer],
min_amplicon=50,
max_amplicon=2000,
polymerase=40000,
with_exonuclease=False,
num_cycles=30,
side_reactions=None,
side_concentrations=None,
include_side_annealings=True)
cmgr = WorkCounterManager()
cmgr.start()
counter = cmgr.WorkCounter()
plock = Lock()
job = WaitingThread(
plock,
1,
target=ipcr.simulate_PCR,
name='simulate_PCR',
args=(
counter,
(
'../data/ThGa.fa', #single sequence
# '../data/Ch5_gnm.fa', '../data/ThDS1.fa', '../data/ThES1.fa', #long sequences
'../data/ThDS1-FC.fa',
'../data/ThDS1-850b-product.fa', #short sequences
),
))
job.start()
print ''
while job.is_alive():
if counter.changed_percent():
with plock:
print counter
time.sleep(1)
job.join()
with plock:
print counter
ipcr.write_report()
cProfile.runctx('for i in xrange(100): ipcr.write_reports()',
globals(), locals(), 'iPCR.write_reports.profile')
'R-TGAM_0055-624-d4'), 0.43e-6, True)
blastp = BlastPrimers(abort_event,
job_id='F-TGAM_0057-268_d1-R-TGAM_0055-624-d4',
primers=[fwd_primer, rev_primer],
min_amplicon=50,
max_amplicon=2000,
polymerase=40000,
with_exonuclease=False,
num_cycles=30,
side_reactions=None,
side_concentrations=None,
include_side_annealings=False)
if not blastp.have_saved_results(): sys.exit()
cmgr = WorkCounterManager()
cmgr.start()
plock = Lock()
counter = cmgr.WorkCounter()
job = WaitingThread(plock,
1,
target=blastp.load_and_analyze,
name='load_and_analyze',
kwargs=dict(counter=counter))
job.start()
print ''
while job.is_alive():
if counter.changed_percent():
with plock:
blastp = BlastPrimers(abort_event,
job_id='F-TGAM_0057-268_d1-R-TGAM_0055-624-d4',
primers=[fwd_primer,
rev_primer],
min_amplicon=50,
max_amplicon=2000,
polymerase=40000,
with_exonuclease=False,
num_cycles=30,
side_reactions=None,
side_concentrations=None,
include_side_annealings=False)
if not blastp.have_saved_results(): sys.exit()
cmgr = WorkCounterManager()
cmgr.start()
plock = Lock()
counter = cmgr.WorkCounter()
job = WaitingThread(plock, 1, target=blastp.load_and_analyze,
name='load_and_analyze', kwargs=dict(counter=counter))
job.start(); print ''
while job.is_alive():
if counter.changed_percent():
with plock: print counter #.rstr()
sleep(0.1)
job.join()
with plock: print counter #.rstr()
