def _ParallelPCR(counter, abort_event, pcr, mixture_paths):
parallelize = at_manager(Parallelizer, 'parallelize_work_to_shelf')
return parallelize(abort_event,
False,
0.1,
run_pcr_from_file(pcr),
mixture_paths,
counter=counter)
@author: Allis Tauri <*****@*****.**>
'''
from BioUtils.Tools.Output import simple_timeit
from BioUtils.Tools.UMP import FuncManager, at_manager
from BioUtils.Tools.Multiprocessing import raise_tb_on_error
from BioUtils.Tools.Text import wrap_text, hr
from .PCR_ProductsFinder import PPFManager
from .SearchEngine import mp_better
from .iPCR_Base import iPCR_Base
#manager to isolate forking point in a low-memory process
SearchManager = FuncManager(
'SearchManager',
(at_manager(PPFManager, 'find'), at_manager(PPFManager, 'batch_find')))
class iPCR(iPCR_Base):
'''
Using PCR_Simulation and SeqDB classes runs PCR simulation with given
primers and report results in human readable form in a text file.
'''
def __init__(self, *args, **kwargs):
iPCR_Base.__init__(self, *args, **kwargs)
self._PCR_Simulation = self._new_PCR_Simulation()
self._ProductsFinder = self._new_PCR_ProductsFinder()
self._searcher = SearchManager()
self._searcher.start()
#end def
def _parallel_OV(abort_event, OVCs, mixture_paths):
parallelize = at_manager(Parallelizer, 'parallelize_both')
return parallelize(abort_event, False, 0.1, OVCs, mixture_paths)
#end def
def __call__(self, mixture_path):
pcr_results = self._pcr(ShelvedMixture(mixture_path))
if pcr_results is None: return 1
return self._compute_prod_C(pcr_results)
#end class
def _parallel_OV(abort_event, OVCs, mixture_paths):
parallelize = at_manager(Parallelizer, 'parallelize_both')
return parallelize(abort_event, False, 0.1, OVCs, mixture_paths)
#end def
OVC_Manager = FuncManager('OVC_Manager', (_parallel_OV,))
SearchManager = FuncManager('SearchManager',
(at_manager(PPFManager, 'matches_to_mixture'),
at_manager(PPFManager, 'find_matches')))
class PCR_Optimizer(iPCR_Base):
'''
Repeatedly perform PCR simulation varying parameters
to find optimal conditions
'''
_PCR_report_suffix = 'PCR-optimization'
_epsilon = 1e-8 #dx for finite-difference approximation of the gradient
def __init__(self,
abort_event, max_steps, purity,
*args, **kwargs):
def _ParallelPCR(counter, abort_event, pcr, mixture_paths):
parallelize = at_manager(Parallelizer, 'parallelize_work_to_shelf')
return parallelize(abort_event, False, 0.1, run_pcr_from_file(pcr),
mixture_paths, counter=counter)
def _parallel_OV(abort_event, OVCs, mixture_paths):
parallelize = at_manager(Parallelizer, 'parallelize_both')
return parallelize(abort_event, False, 0.1, OVCs, mixture_paths)
if pcr_results is None: return 1
return self._compute_prod_C(pcr_results)
#end class
def _parallel_OV(abort_event, OVCs, mixture_paths):
parallelize = at_manager(Parallelizer, 'parallelize_both')
return parallelize(abort_event, False, 0.1, OVCs, mixture_paths)
#end def
OVC_Manager = FuncManager('OVC_Manager', (_parallel_OV, ))
SearchManager = FuncManager('SearchManager', (at_manager(
PPFManager, 'matches_to_mixture'), at_manager(PPFManager, 'find_matches')))
class PCR_Optimizer(iPCR_Base):
'''
Repeatedly perform PCR simulation varying parameters
to find optimal conditions
'''
_PCR_report_suffix = 'PCR-optimization'
_epsilon = 1e-8 #dx for finite-difference approximation of the gradient
def __init__(self, abort_event, max_steps, purity, *args, **kwargs):
iPCR_Base.__init__(self, abort_event, *args, **kwargs)
#PCR simulations
self._PCR_ProductsFinder = self._new_PCR_ProductsFinder()
@author: Allis Tauri <*****@*****.**>
'''
from BioUtils.Tools.Output import simple_timeit
from BioUtils.Tools.UMP import FuncManager, at_manager
from BioUtils.Tools.Multiprocessing import raise_tb_on_error
from BioUtils.Tools.Text import wrap_text, hr
from .PCR_ProductsFinder import PPFManager
from .SearchEngine import mp_better
from .iPCR_Base import iPCR_Base
#manager to isolate forking point in a low-memory process
SearchManager = FuncManager('SearchManager',
(at_manager(PPFManager, 'find'),
at_manager(PPFManager, 'batch_find')))
class iPCR(iPCR_Base):
'''
Using PCR_Simulation and SeqDB classes runs PCR simulation with given
primers and report results in human readable form in a text file.
'''
def __init__(self, *args, **kwargs):
iPCR_Base.__init__(self, *args, **kwargs)
self._PCR_Simulation = self._new_PCR_Simulation()
self._ProductsFinder = self._new_PCR_ProductsFinder()
self._searcher = SearchManager()
self._searcher.start()
#end def