def __init__(self, abort_event):
PrimerTaskBase.__init__(self, abort_event)
self._print_lock = Lock()
self._out_queue = OutQueueWithID()
self._counter_mgr = WorkCounterManager()
self._counter_mgr.start()
self._subroutines = []
self._time0 = time()
self._newline_last = False
def __init__(self, abort_event):
PrimerTaskBase.__init__(self, abort_event)
self._print_lock = Lock()
self._out_queue = OutQueueWithID()
self._counter_mgr = WorkCounterManager()
self._counter_mgr.start()
self._subroutines = []
self._time0 = time()
self._newline_last = False
class AnalysisTask(PrimerTaskBase):
'''This class gathers all calculations in a single pipeline with
parallelized subroutines for CPU-intensive computations.'''
#file format for saving primers
_fmt = 'fasta'
_counter_threshold = 60
def __init__(self, abort_event):
PrimerTaskBase.__init__(self, abort_event)
self._print_lock = Lock()
self._out_queue = OutQueueWithID()
self._counter_mgr = WorkCounterManager()
self._counter_mgr.start()
self._subroutines = []
self._time0 = time()
self._newline_last = False
#end def
def __del__(self):
self._counter_mgr.shutdown()
self._clean_subroutines()
#end def
def _clean_subroutines(self):
for p_entry in self._subroutines:
try:
p_entry['manager'].shutdown()
except:
pass
self._subroutines = []
#end def
def _generate_subroutine_entry(self):
_id = (len(self._subroutines) + 1)
with self._out_queue.set_id(_id):
manager = SubroutineManager()
manager.start()
p_entry = {
'id': _id,
'manager': manager,
'process': None,
'counter': self._counter_mgr.WorkCounter()
}
self._subroutines.append(p_entry)
return p_entry
#end def
def _run_subroutine(self, func, args, p_entry, p_name=None):
'''Run a func in a thread with args'''
routine_name = p_name if p_name else func.__name__
routine_id = p_entry['id']
args = [p_entry['counter']] + (list(args) if args else [])
subroutine = WaitingThread(self._print_lock,
routine_id,
target=func,
name=routine_name,
args=args)
p_entry['process'] = subroutine
with self._print_lock:
self._print(
('\nStarting CPU-intensive task #%d:\n '
' %s\nThis may take awhile...') % (routine_id, routine_name))
subroutine.start()
#end def
def _run_analysis(self, args):
analysis_routines = []
#--------generate components calculate Tms and save the primers--------#
if not self._prepare_primers(args): return None
if not self._save_primers(): return None
#----------------------------------------------------------------------#
#following computations are CPU intensive, so they need parallelization#
#check primers for hairpins, dimers and cross-dimers #
self._print(
'\nSearching for stable secondary structures of the primers...')
p_entry = self._generate_subroutine_entry()
all_sec_structures = p_entry['manager'].AllSecStructures(
self._abort_event, args.job_id, self._primers)
all_sec_structures.find_structures()
if self.aborted(): return None
analysis_routines.append(all_sec_structures)
side_reactions = all_sec_structures.reactions()
side_concentrations = all_sec_structures.concentrations()
with self._print_lock:
self._print('Done.')
self._run_subroutine(
all_sec_structures.calculate_equilibrium, None, p_entry,
'Calculate relative concentrations of secondary structures at Tm.')
#----------------------------------------------------------------------#
#in-silico PCR simulation. This is only available if sequence database #
#is provided in some form #
if args.template_files:
p_entry = self._generate_subroutine_entry()
ipcr = p_entry['manager'].iPCR(self._abort_event,
args.max_mismatches, args.job_id,
self._primers, args.min_amplicon,
args.max_amplicon, args.polymerase,
args.with_exonuclease, args.cycles,
side_reactions, side_concentrations,
args.analyse_all_annealings)
analysis_routines.append(ipcr)
#connect to sequence database
self._run_subroutine(
ipcr.simulate_PCR, (args.template_files, args.use_sequences),
p_entry,
'Simulate PCR using provided sequences as DNA templates.')
#-----------------test for primers specificity by BLAST----------------#
p_entry = self._generate_subroutine_entry()
blast_primers = p_entry['manager'].BlastPrimers(
self._abort_event,
args.job_id,
self._primers,
args.min_amplicon,
args.max_amplicon,
args.polymerase,
args.with_exonuclease,
args.cycles,
side_reactions,
side_concentrations,
include_side_annealings=args.analyse_all_annealings)
analysis_routines.append(blast_primers)
#if --do-blast flag was provided, make an actual query
if args.do_blast:
#construct Entrez query
entrez_query = ''
if args.organisms:
for organism in args.organisms:
if entrez_query: entrez_query += ' OR '
entrez_query += organism + '[organism]'
#do the blast and analyze the results
self._run_subroutine(
blast_primers.blast_and_analyze, (entrez_query, ), p_entry,
'Make BLAST query, then simulate PCR using returned alignments.'
)
#else, try to load previously saved results and analyze them with current parameters
elif blast_primers.have_saved_results():
self._run_subroutine(
blast_primers.load_and_analyze, None, p_entry,
'Simulate PCR using alignments in BLAST results.')
#----------------------------------------------------------------------#
return analysis_routines
#end def
def _save_primers(self):
for primer in self._primers:
if self.aborted(): return False
if not primer: continue
filename = primer.id + '.' + self._fmt
try:
SeqIO.write(primer.all_seq_records, filename, self._fmt)
except Exception, e:
self._print(
'\nFailed to write %s primer and it\'s unambiguous components to:\n %s'
% (primer.id, filename))
print e
return False
self._print(
'\n%s primer and it\'s unambiguous components were written to:\n %s'
% (primer.id, filename))
return True
class AnalysisTask(PrimerTaskBase):
'''This class gathers all calculations in a single pipeline with
parallelized subroutines for CPU-intensive computations.'''
#file format for saving primers
_fmt = 'fasta'
_counter_threshold = 60
def __init__(self, abort_event):
PrimerTaskBase.__init__(self, abort_event)
self._print_lock = Lock()
self._out_queue = OutQueueWithID()
self._counter_mgr = WorkCounterManager()
self._counter_mgr.start()
self._subroutines = []
self._time0 = time()
self._newline_last = False
#end def
def __del__(self):
self._counter_mgr.shutdown()
self._clean_subroutines()
#end def
def _clean_subroutines(self):
for p_entry in self._subroutines:
try: p_entry['manager'].shutdown()
except: pass
self._subroutines = []
#end def
def _generate_subroutine_entry(self):
_id = (len(self._subroutines)+1)
with self._out_queue.set_id(_id):
manager = SubroutineManager()
manager.start()
p_entry = {'id' : _id,
'manager' : manager,
'process' : None,
'counter' : self._counter_mgr.WorkCounter()}
self._subroutines.append(p_entry)
return p_entry
#end def
def _run_subroutine(self, func, args, p_entry, p_name=None):
'''Run a func in a thread with args'''
routine_name = p_name if p_name else func.__name__
routine_id = p_entry['id']
args = [p_entry['counter']]+(list(args) if args else [])
subroutine = WaitingThread(self._print_lock, routine_id, target=func,
name=routine_name, args=args)
p_entry['process'] = subroutine
with self._print_lock:
self._print(('\nStarting CPU-intensive task #%d:\n '
' %s\nThis may take awhile...') %
(routine_id, routine_name))
subroutine.start()
#end def
def _run_analysis(self, args):
analysis_routines = []
#--------generate components calculate Tms and save the primers--------#
if not self._prepare_primers(args): return None
if not self._save_primers(): return None
#----------------------------------------------------------------------#
#following computations are CPU intensive, so they need parallelization#
#check primers for hairpins, dimers and cross-dimers #
self._print('\nSearching for stable secondary structures of the primers...')
p_entry = self._generate_subroutine_entry()
all_sec_structures = p_entry['manager'].AllSecStructures(self._abort_event, args.job_id, self._primers)
all_sec_structures.find_structures()
if self.aborted(): return None
analysis_routines.append(all_sec_structures)
side_reactions = all_sec_structures.reactions()
side_concentrations = all_sec_structures.concentrations()
with self._print_lock: self._print('Done.')
self._run_subroutine(all_sec_structures.calculate_equilibrium, None, p_entry,
'Calculate relative concentrations of secondary structures at Tm.')
#----------------------------------------------------------------------#
#in-silico PCR simulation. This is only available if sequence database #
#is provided in some form #
if args.template_files:
p_entry = self._generate_subroutine_entry()
ipcr = p_entry['manager'].iPCR(self._abort_event,
args.max_mismatches,
args.job_id,
self._primers,
args.min_amplicon,
args.max_amplicon,
args.polymerase,
args.with_exonuclease,
args.cycles,
side_reactions,
side_concentrations,
args.analyse_all_annealings)
analysis_routines.append(ipcr)
#connect to sequence database
self._run_subroutine(ipcr.simulate_PCR,
(args.template_files,
args.use_sequences), p_entry,
'Simulate PCR using provided sequences as DNA templates.')
#-----------------test for primers specificity by BLAST----------------#
p_entry = self._generate_subroutine_entry()
blast_primers = p_entry['manager'].BlastPrimers(self._abort_event,
args.job_id,
self._primers,
args.min_amplicon,
args.max_amplicon,
args.polymerase,
args.with_exonuclease,
args.cycles,
side_reactions,
side_concentrations,
include_side_annealings=args.analyse_all_annealings)
analysis_routines.append(blast_primers)
#if --do-blast flag was provided, make an actual query
if args.do_blast:
#construct Entrez query
entrez_query = ''
if args.organisms:
for organism in args.organisms:
if entrez_query: entrez_query += ' OR '
entrez_query += organism+'[organism]'
#do the blast and analyze the results
self._run_subroutine(blast_primers.blast_and_analyze,
(entrez_query,),
p_entry,
'Make BLAST query, then simulate PCR using returned alignments.')
#else, try to load previously saved results and analyze them with current parameters
elif blast_primers.have_saved_results():
self._run_subroutine(blast_primers.load_and_analyze,
None,
p_entry,
'Simulate PCR using alignments in BLAST results.')
#----------------------------------------------------------------------#
return analysis_routines
#end def
def _save_primers(self):
for primer in self._primers:
if self.aborted(): return False
if not primer: continue
filename = primer.id+'.'+self._fmt
try:
SeqIO.write(primer.all_seq_records, filename, self._fmt)
except Exception, e:
self._print('\nFailed to write %s primer and it\'s unambiguous components to:\n %s' % (primer.id, filename))
print e
return False
self._print('\n%s primer and it\'s unambiguous components were written to:\n %s' % (primer.id, filename))
return True