def checkproducebilty(self):
self.set_busy(True)
self.textBox.append('\nChecking draftnet for unproducible targets ...')
model = query.get_unproducible(self.draftnet, self.targets, self.seeds)
self.textBox.append('done.')
self.textBox.append(' '+str(len(model))+' unproducible targets:')
self.print_met(model.to_list())
unproducible_targets = TermSet()
for a in model :
target= str(a)[13:]
t = String2TermSet(target)
unproducible_targets = unproducible_targets.union(t)
if(self.repairnet != 0):
all_reactions = self.draftnet
all_reactions = all_reactions.union(self.repairnet)
self.textBox.append('\nChecking draftnet + repairnet for unproducible targets ...')
model = query.get_unproducible(all_reactions, self.seeds, self.targets)
self.textBox.append('done.')
self.textBox.append(' still '+str(len(model))+' unproducible targets:')
self.print_met(model.to_list())
never_producible = TermSet()
for a in model :
target= str(a)[13:]
#print target
t = String2TermSet(target)
never_producible = never_producible.union(t)
reconstructable_targets = TermSet()
for t in unproducible_targets:
if not (t in never_producible) : reconstructable_targets.add(t)
self.textBox.append('\n '+str(len(reconstructable_targets))+' targets to reconstruct:')
self.print_met(reconstructable_targets)
utils.clean_up()
self.set_busy(False)
self.checkState()
return
print('Reading seeds from ',seeds_sbml,'...',end=' ')
sys.stdout.flush()
seeds = sbml.readSBMLseeds(seeds_sbml)
print('done.')
#seeds.to_file("seeds.lp")
print('Reading targets from ',targets_sbml,'...',end=' ')
sys.stdout.flush()
targets = sbml.readSBMLtargets(targets_sbml)
print('done.')
#targets.to_file("targets.lp")
print('\nChecking draftnet for unproducible targets ...',end=' ')
sys.stdout.flush()
model = query.get_unproducible(draftnet, targets, seeds)
print('done.')
print(' ',len(model),'unproducible targets:')
utils.print_met(model.to_list())
unproducible_targets = TermSet()
for a in model :
target= str(a)[13:]
t = String2TermSet(target)
unproducible_targets = TermSet(unproducible_targets.union(t))
print('\nReading repair network from ',repair_sbml,'...',end=' ')
sys.stdout.flush()
repairnet = sbml.readSBMLnetwork(repair_sbml, 'repairnet')
print('done.')
#repairnet.to_file("repairnet.lp")
def run(self):
self.emit(SIGNAL("asignal"),'\nChecking draftnet for unproducible targets ...')
model = query.get_unproducible(self.wid.draftnet, self.wid.targets, self.wid.seeds)
self.emit(SIGNAL("asignal"),'done.')
self.emit(SIGNAL("asignal"),' '+str(len(model))+' unproducible targets:')
self.print_met(model.to_list())
unproducible_targets = TermSet()
for a in model :
target = str(a)[13:]
t = String2TermSet(target)
unproducible_targets = unproducible_targets.union(t)
if(self.wid.repairnet != 0):
all_reactions = self.wid.draftnet
all_reactions = all_reactions.union(self.wid.repairnet)
self.emit(SIGNAL("asignal"),'\nChecking draftnet + repairnet for unproducible targets ...')
model = query.get_unproducible(all_reactions, self.wid.seeds, self.wid.targets)
self.emit(SIGNAL("asignal"),'done.')
self.emit(SIGNAL("asignal"),' still '+str(len(model))+' unproducible targets:')
self.print_met(model.to_list())
never_producible = TermSet()
for a in model :
target = str(a)[13:]
t = String2TermSet(target)
never_producible = never_producible.union(t)
reconstructable_targets = TermSet()
for t in unproducible_targets:
if not (t in never_producible) : reconstructable_targets.add(t)
self.emit(SIGNAL("asignal"),'\n '+str(len(reconstructable_targets))+' targets to reconstruct:')
self.print_met(reconstructable_targets)
if len(reconstructable_targets)== 0 :
utils.clean_up()
self.emit(SIGNAL("finishedsignal"),False)
return
essential_reactions = TermSet()
for t in reconstructable_targets:
single_target = TermSet()
single_target.add(t)
self.emit(SIGNAL("asignal"),'\nComputing essential reactions for '+str(t)+' ...')
essentials = query.get_intersection_of_completions(self.wid.draftnet, self.wid.repairnet, self.wid.seeds, single_target)
self.emit(SIGNAL("asignal"),'done.')
self.emit(SIGNAL("asignal"),' '+str(len(essentials))+' essential reactions found:')
self.print_met(essentials.to_list())
essential_reactions = essential_reactions.union(essentials)
self.emit(SIGNAL("asignal"),'\n Overall '+str(len(essential_reactions))+' essential reactions found.')
self.print_met(essential_reactions)
self.emit(SIGNAL("asignal"),'\n Add essential reactions to network.')
ndraftnet = essential_reactions.union(self.wid.draftnet)
utils.clean_up()
self.emit(SIGNAL("asignal"),'\nComputing one minimal completion to produce all targets ...')
optimum, models = query.get_minimal_completion_size(ndraftnet, self.wid.repairnet, self.wid.seeds, reconstructable_targets)
self.emit(SIGNAL("asignal"),'done.')
self.emit(SIGNAL("asignal"),' minimal size = '+str(optimum[0]))
self.print_met(models[0].to_list())
self.emit(SIGNAL("asignal"),'\nComputing common reactions in all completion with size '+str(optimum[0])+' ...')
model = query.get_intersection_of_optimal_completions(ndraftnet, self.wid.repairnet, self.wid.seeds, reconstructable_targets, optimum[0])
self.emit(SIGNAL("asignal"),'done.')
self.print_met(model.to_list())
self.emit(SIGNAL("asignal"),'\nComputing union of reactions from all completion with size '+str(optimum[0])+' ...')
model = query.get_union_of_optimal_completions(ndraftnet, self.wid.repairnet, self.wid.seeds, reconstructable_targets, optimum[0])
self.emit(SIGNAL("asignal"),'done.')
self.print_met(model.to_list())
#do_repair= raw_input('\nDo you want to compute all completions with size '+str(optimum[0])+' Y/n:')
#if wid.do_repair:
#self.emit(SIGNAL("asignal"),'\nComputing all completions with size '+str(optimum[0])+' ...')
#models = query.get_optimal_completions(ndraftnet, self.wid.repairnet, self.wid.seeds, reconstructable_targets, optimum[0])
#self.emit(SIGNAL("asignal"),'done.')
#count = 1
#for model in models:
#self.emit(SIGNAL("asignal"),'Completion '+str(count)+':')
#count+=1
#self.print_met(model.to_list())
utils.clean_up()
self.emit(SIGNAL("finishedsignal"),False)
