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()