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 _main(self):
from threading import Lock
from BioUtils.Tools import WaitingThread
from DegenPrimer.Primer import Primer
from DegenPrimer.SeqUtils import load_sequence
from DegenPrimer.PCR_Optimizer import PCR_Optimizer
from DegenPrimer import TD_Functions as tdf
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)
optimizer = PCR_Optimizer(self.abort_event,
100, 5,
max_mismatches=5,
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=False)
plock = Lock()
job = WaitingThread(plock, 1, target=optimizer.optimize_PCR_parameters,
name='optimize PCR',
args=('../data/ThGa.fa',
({'start':47920, 'end':49321},),
(
{'name':'PCR_T',
'min':50, 'ini':60, 'max':72},
# {'name':'dNTP',
# 'min':100e-6, 'ini':200e-6, 'max':900e-6},
),
))
job.start(); print ''
job.join()
optimizer.write_report()
def _main(self):
from threading import Lock
from BioUtils.Tools import WaitingThread
from DegenPrimer.Primer import Primer
from DegenPrimer.SeqUtils import load_sequence
from DegenPrimer.PCR_Optimizer import PCR_Optimizer
from DegenPrimer import TD_Functions as tdf
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)
optimizer = PCR_Optimizer(self.abort_event,
100,
5,
max_mismatches=5,
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=False)
plock = Lock()
job = WaitingThread(
plock,
1,
target=optimizer.optimize_PCR_parameters,
name='optimize PCR',
args=(
'../data/ThGa.fa',
({
'start': 47920,
'end': 49321
}, ),
({
'name': 'PCR_T',
'min': 50,
'ini': 60,
'max': 72
},
# {'name':'dNTP',
# 'min':100e-6, 'ini':200e-6, 'max':900e-6},
),
))
job.start()
print ''
job.join()
optimizer.write_report()
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')
from DegenPrimer.TD_Functions import PCR_P
from DegenPrimer.BlastPrimers import BlastPrimers
from threading import Lock
os.chdir('../')
mgr = Manager()
abort_event = mgr.Event()
PCR_P.PCR_T = 53
PCR_P.Mg = 3e-3
PCR_P.dNTP = 300e-6
PCR_P.DNA = 1e-10
fwd_primer = Primer(
load_sequence('ATATTCTACRACGGCTATCC', 'F-TGAM_0057-268_d1',
'F-TGAM_0057-268_d1'), 0.43e-6, True)
rev_primer = Primer(
load_sequence('GAASGCRAAKATYGGGAAC', 'R-TGAM_0055-624-d4',
'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)
from DegenPrimer.WaitingThread import WaitingThread
from DegenPrimer.TD_Functions import PCR_P
from DegenPrimer.BlastPrimers import BlastPrimers
from threading import Lock
os.chdir('../')
mgr = Manager()
abort_event = mgr.Event()
PCR_P.PCR_T = 53
PCR_P.Mg = 3e-3
PCR_P.dNTP = 300e-6
PCR_P.DNA = 1e-10
fwd_primer = Primer(load_sequence('ATATTCTACRACGGCTATCC', 'F-TGAM_0057-268_d1', 'F-TGAM_0057-268_d1'), 0.43e-6, True)
rev_primer = Primer(load_sequence('GAASGCRAAKATYGGGAAC', 'R-TGAM_0055-624-d4', '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()