if not (t in never_producible) : reconstructable_targets.add(t)
print('\n ',len(reconstructable_targets),'targets to reconstruct:')
utils.print_met(reconstructable_targets)
if len(reconstructable_targets)== 0 :
utils.clean_up()
quit()
essential_reactions = TermSet()
for t in reconstructable_targets:
single_target = TermSet()
single_target.add(t)
print('\nComputing essential reactions for',t,'...',end=' ')
sys.stdout.flush()
essentials = query.get_intersection_of_completions(draftnet, repairnet, seeds, single_target)
print('done.')
print(' ',len(essentials), 'essential reactions found:')
utils.print_met(essentials.to_list())
essential_reactions = TermSet(essential_reactions.union(essentials))
print('\nOverall',len(essential_reactions), 'essential reactions found.')
utils.print_met(essential_reactions)
print('\nAdding essential reactions to network.')
draftnet = TermSet(draftnet.union(essential_reactions))
utils.clean_up()
#draftnet.to_file("draft.lp")
#repairnet.to_file("repairnet.lp")
#unproducible_targets.to_file("targets.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)