def execute_makeExchangeFluxes(self, simulation_id_I,simulation_dateAndTimes_I=[],normalize_rxn_id_I=None,convert_netRxn2IndividualRxns_I=False, calculate_fluxStdevFromLBAndUB_I=True,calculate_fluxAverageFromLBAndUB_I=True,substitute_zeroFluxForNone_I=True, lower_bound_I=None,upper_bound_I=None): '''Determine the exchange flux of reversible reactions INPUT: normalize_rxn_id_I = rxn_id to normalize all fluxes to conver_netRxn2IndividualRxns_I = break apart lumped reactions into individual reactions calculate_fluxStdevFromLBAndUB_I = substitute the calculated standard deviation with the lb/ub as follows: (flux_ub_I - flux_lb_I)/4 calculate_fluxAverageFromLBAndUB_I = calculate the flux average from the mean of the lb/ub substitute_zeroFluxForNone_I = substitute 0.0 for None lower_bound_I = lower bound for the reaction flux upper_bound_I = upper bound for the reaction flux''' mfamethods = MFA_methods(); isotopomernetRxns = isotopomer_netRxns(); data_O = []; # simulation_dateAndTime if simulation_dateAndTimes_I: simulation_dateAndTimes = [self.convert_string2datetime(x) for x in simulation_dateAndTimes_I]; else: simulation_dateAndTimes = []; simulation_dateAndTimes = self.get_simulationDateAndTimes_simulationID_dataStage02IsotopomerfittedFluxes(simulation_id_I); for simulation_dateAndTime in simulation_dateAndTimes: # get all reactions included in the simulation (in alphabetical order) rxns = []; rxns = self.get_rxnIDs_simulationIDAndSimulationDateAndTime_dataStage02IsotopomerfittedFluxes(simulation_id_I,simulation_dateAndTime) # group into forward and reverse reactions rxns_pairs = {}; rxn_pair = []; for rxn_cnt,rxn in enumerate(rxns): #if rxn == 'ValSYN': # print('check'); if not rxn_pair: rxn_pair.append(rxn); else: if '_reverse' in rxn and rxn_pair[0] in rxn: rxn_pair.append(rxn); rxns_pairs[rxn_pair[0]]=rxn_pair; rxn_pair = []; elif '_reverse' in rxn_pair[0]: rxn_pair.insert(0,None); rxn_name = rxn_pair[1].replace('_reverse',''); rxns_pairs[rxn_name]=rxn_pair; rxn_pair = []; rxn_pair.append(rxn); if rxn_cnt == len(rxns)-1: #final rxn rxn_pair.insert(0,None); rxn_name = rxn_pair[1].replace('_reverse',''); rxns_pairs[rxn_name]=rxn_pair; rxn_pair = []; else: rxn_pair.append(None); rxns_pairs[rxn_pair[0]]=rxn_pair; rxn_pair = []; rxn_pair.append(rxn); if rxn_cnt == len(rxns)-1: #final rxn rxn_pair.append(None); rxns_pairs[rxn_pair[0]]=rxn_pair; rxn_pair = []; # query the maximum and minimum flux: if not lower_bound_I is None or not upper_bound_I is None: min_flux,max_flux=lower_bound_I,upper_bound_I; else: min_flux,max_flux=None,None min_flux,max_flux = self.get_fluxMinAndMax_simulationIDAndSimulationDateAndTime_dataStage02IsotopomerfittedFluxes(simulation_id_I,simulation_dateAndTime); # query the normalized rxn flux if normalize_rxn_id_I: flux_average_norm,flux_stdev_norm,flux_lb_norm,flux_ub_norm,flux_units_norm = None,None,None,None,None; flux_average_norm,flux_stdev_norm,flux_lb_norm,flux_ub_norm,flux_units_norm = self.get_flux_simulationIDAndSimulationDateAndTimeAndRxnID_dataStage02IsotopomerfittedFluxes(simulation_id_I,simulation_dateAndTime,normalize_rxn_id_I); min_flux = min_flux/flux_average_norm max_flux = max_flux/flux_average_norm # check if the sign switched if max_flux < min_flux: min_flux_tmp = min_flux; max_flux_tmp = min_flux; max_flux = min_flux_tmp min_flux = max_flux_tmp # calculate the net reaction flux average, stdev, lb and ub unique_rxn_ids = []; #add only unique rxn_ids for k,v in rxns_pairs.items(): flux_average_1 = 0.0 flux_average_2 = 0.0 flux_average_net = 0.0 flux_stdev_1 = 0.0 flux_stdev_2 = 0.0 flux_stdev_net = 0.0 flux_lb_1 = 0.0 flux_lb_2 = 0.0 flux_lb_net = 0.0 flux_ub_1 = 0.0 flux_ub_2 = 0.0 flux_ub_net = 0.0 flux_units_1 = '' flux_units_2 = '' flux_units_net = '' # get the flux data if v[0]: flux_average_1,flux_stdev_1,flux_lb_1,flux_ub_1,flux_units_1 = self.get_flux_simulationIDAndSimulationDateAndTimeAndRxnID_dataStage02IsotopomerfittedFluxes(simulation_id_I,simulation_dateAndTime,v[0]); if v[1]: flux_average_2,flux_stdev_2,flux_lb_2,flux_ub_2,flux_units_2 = self.get_flux_simulationIDAndSimulationDateAndTimeAndRxnID_dataStage02IsotopomerfittedFluxes(simulation_id_I,simulation_dateAndTime,v[1]); # determine if the fluxes are observable observable_1 = mfamethods.check_observableFlux(flux_average_1,flux_lb_1,flux_ub_1) observable_2 = mfamethods.check_observableFlux(flux_average_2,flux_lb_2,flux_ub_2) # normalize the flux to normalize_rxn_id_I if there was a flux if normalize_rxn_id_I: if flux_units_1!='': flux_average_1,flux_stdev_1,flux_lb_1,flux_ub_1,flux_units_1=mfamethods.normalize_flux(normalize_rxn_id_I,flux_average_norm,flux_stdev_norm,flux_lb_norm,flux_ub_norm,flux_average_1,flux_stdev_1,flux_lb_1,flux_ub_1); if flux_units_2!='': flux_average_2,flux_stdev_2,flux_lb_2,flux_ub_2,flux_units_2=mfamethods.normalize_flux(normalize_rxn_id_I,flux_average_norm,flux_stdev_norm,flux_lb_norm,flux_ub_norm,flux_average_2,flux_stdev_2,flux_lb_2,flux_ub_2); # get the net flux if flux_units_1!='': flux_average_net,flux_stdev_net,flux_lb_net,flux_ub_net,flux_units_net = self.get_flux_simulationIDAndSimulationDateAndTimeAndFluxUnitsAndRxnID_dataStage02IsotopomerfittedNetFluxes( simulation_id_I,simulation_dateAndTime,flux_units_1,k); elif flux_units_2!='': flux_average_net,flux_stdev_net,flux_lb_net,flux_ub_net,flux_units_net = self.get_flux_simulationIDAndSimulationDateAndTimeAndFluxUnitsAndRxnID_dataStage02IsotopomerfittedNetFluxes( simulation_id_I,simulation_dateAndTime,flux_units_2,k); ## calculate the net flux #if k=='PGM': # print('check'); flux_average,flux_stdev,flux_lb,flux_ub,flux_units,\ flux_normalized_average,flux_normalized_stdev,flux_normalized_lb,flux_normalized_ub,flux_normalized_units = mfamethods.calculate_exchangeFlux( flux_average_1,flux_stdev_1,flux_lb_1,flux_ub_1,flux_units_1, flux_average_2,flux_stdev_2,flux_lb_2,flux_ub_2,flux_units_2, flux_average_net,flux_stdev_net,flux_lb_net,flux_ub_net,flux_units_net, min_flux,max_flux) # correct the flux stdev if calculate_fluxStdevFromLBAndUB_I: flux_stdev = mfamethods.calculate_fluxStdevFromLBAndUB(flux_lb,flux_ub); #default = true for flux_normalized if calculate_fluxAverageFromLBAndUB_I: flux_average = mfamethods.calculate_fluxAverageFromLBAndUB(flux_average,flux_lb,flux_ub); #default = true for flux_normalized if substitute_zeroFluxForNone_I: flux_average = mfamethods.substitute_zeroFluxForNone(flux_average); flux_normalized_average = mfamethods.substitute_zeroFluxForNone(flux_normalized_average); # record net reaction flux if convert_netRxn2IndividualRxns_I: rxns_O,fluxes_O,fluxes_stdev_O,fluxes_lb_O,fluxes_ub_O,fluxes_units_O = isotopomernetRxns.convert_netRxn2IndividualRxns(k,flux_average,flux_stdev,flux_lb,flux_ub,flux_units); rxns_normalized_O,fluxes_normalized_O,fluxes_normalized_stdev_O,fluxes_normalized_lb_O,fluxes_normalized_ub_O,fluxes_normalized_units_O = isotopomernetRxns.convert_netRxn2IndividualRxns(k,flux_normalized_average,flux_normalized_stdev,flux_normalized_lb,flux_normalized_ub,flux_normalized_units); if fluxes_O: for i,flux in enumerate(fluxes_O): if not rxns_O[i] in unique_rxn_ids: unique_rxn_ids.append(rxns_O[i]); data_O.append({'simulation_id':simulation_id_I, 'simulation_dateAndTime':simulation_dateAndTime, 'rxn_id':rxns_O[i], 'flux_exchange':fluxes_O[i], 'flux_exchange_stdev':fluxes_stdev_O[i], 'flux_exchange_lb':fluxes_lb_O[i], 'flux_exchange_ub':fluxes_ub_O[i], 'flux_exchange_units':fluxes_units_O[i], 'flux_exchange_normalized':fluxes_normalized_O[i], 'flux_exchange_normalized_stdev':fluxes_normalized_stdev_O[i], 'flux_exchange_normalized_lb':fluxes_normalized_lb_O[i], 'flux_exchange_normalized_ub':fluxes_normalized_ub_O[i], 'flux_exchange_normalized_units':fluxes_normalized_units_O[i], 'used_':True, 'comment_':None}) else: if not k in unique_rxn_ids: unique_rxn_ids.append(k); data_O.append({'simulation_id':simulation_id_I, 'simulation_dateAndTime':simulation_dateAndTime, 'rxn_id':k, 'flux_exchange':flux_average, 'flux_exchange_stdev':flux_stdev, 'flux_exchange_lb':flux_lb, 'flux_exchange_ub':flux_ub, 'flux_exchange_units':flux_units, 'flux_exchange_normalized':flux_normalized_average, 'flux_exchange_normalized_stdev':flux_normalized_stdev, 'flux_exchange_normalized_lb':flux_normalized_lb, 'flux_exchange_normalized_ub':flux_normalized_ub, 'flux_exchange_normalized_units':flux_normalized_units, 'used_':True, 'comment_':None}) else: data_O.append({'simulation_id':simulation_id_I, 'simulation_dateAndTime':simulation_dateAndTime, 'rxn_id':k, 'flux_exchange':flux_average, 'flux_exchange_stdev':flux_stdev, 'flux_exchange_lb':flux_lb, 'flux_exchange_ub':flux_ub, 'flux_exchange_units':flux_units, 'flux_exchange_normalized':flux_normalized_average, 'flux_exchange_normalized_stdev':flux_normalized_stdev, 'flux_exchange_normalized_lb':flux_normalized_lb, 'flux_exchange_normalized_ub':flux_normalized_ub, 'flux_exchange_normalized_units':flux_normalized_units, 'used_':True, 'comment_':None}) # add data to the database: self.add_data_stage02_isotopomer_fittedExchangeFluxes(data_O);
def execute_calculateFluxSplits(self,simulation_id_I,simulation_dateAndTimes_I=[],flux_splits_I=None, calculate_fluxStdevFromLBAndUB_I=True, calculate_fluxAverageFromLBAndUB_I=False, criteria_I = 'flux_lb/flux_ub'): '''calculate the flux splits INPUT: calculate_fluxStdevFromLBAndUB_I = substitute the calculated standard deviation with the lb/ub as follows: (flux_ub_I - flux_lb_I)/4 calculate_fluxAverageFromLBAndUB_I = calculate the flux average from the mean of the lb/ub criteria_I = string, flux_lb/flux_ub: use flux_lb and flux_ub to determine the confidence intervals (default) flux_mean/flux_stdev: use the flux_mean and flux_stdev to determine the confidence intervals ''' #Input: # simulation_id_I = string, simulation id # flux_splits_I = dict, {split_id:[rxn_id_1,rxn_id_2]} mfamethods = MFA_methods(); if not flux_splits_I: flux_splits = isotopomer_fluxSplits(); flux_splits_I=flux_splits.isotopomer_splits; data_O = []; print('calculating flux splits...') # simulation_dateAndTime if simulation_dateAndTimes_I: simulation_dateAndTimes = [self.convert_string2datetime(x) for x in simulation_dateAndTimes_I]; else: simulation_dateAndTimes = []; simulation_dateAndTimes = self.get_simulationDateAndTimes_simulationID_dataStage02IsotopomerfittedNetFluxes(simulation_id_I); for simulation_dateAndTime in simulation_dateAndTimes: print('calculating flux splits for simulation_dateAndTime ' + str(simulation_dateAndTime)) # get all flux_units flux_units = []; flux_units = self.get_fluxUnits_simulationIDAndSimulationDateAndTime_dataStage02IsotopomerfittedNetFluxes(simulation_id_I,simulation_dateAndTime) for flux_unit_cnt,flux_unit in enumerate(flux_units): # check for more than 1 flux_unit if flux_unit_cnt>0: break; #splits do not depend on the flux_unit print('calculating flux splits for flux_unit ' + str(flux_unit)) for k,v in flux_splits_I.items(): print('flux_split ' + str(k)) # get the fluxes flux_average_1,flux_stdev_1,flux_lb_1,flux_ub_1,flux_units_1=[],[],[],[],[] for rxn_id in v: flux_average_2,flux_stdev_2,flux_lb_2,flux_ub_2,flux_units_2 = self.get_flux_simulationIDAndSimulationDateAndTimeAndFluxUnitsAndRxnID_dataStage02IsotopomerfittedNetFluxes(simulation_id_I,simulation_dateAndTime,flux_unit,rxn_id); flux_average_1.append(flux_average_2); flux_stdev_1.append(flux_stdev_2); flux_lb_1.append(flux_lb_2); flux_ub_1.append(flux_ub_2); flux_units_1.append(flux_units_2); # calculate the split split,split_stdev,split_lb,split_ub,split_units=mfamethods.calculate_fluxSplit(flux_average_1,flux_stdev_1,flux_lb_1,flux_ub_1,flux_units_1,criteria_I) # correct the flux stdev if calculate_fluxStdevFromLBAndUB_I: split_stdev = mfamethods.calculate_fluxStdevFromLBAndUB(split_lb,split_ub); if calculate_fluxAverageFromLBAndUB_I: split = mfamethods.calculate_fluxAverageFromLBAndUB(split,split_lb,split_ub); # record the data for rxn_id_cnt,rxn_id in enumerate(v): data_O.append({'simulation_id':simulation_id_I, 'simulation_dateAndTime':simulation_dateAndTime, 'split_id':k, 'split_rxn_ids':rxn_id, 'split':split[rxn_id_cnt], 'split_stdev':split_stdev[rxn_id_cnt], 'split_lb':split_lb[rxn_id_cnt], 'split_ub':split_ub[rxn_id_cnt], 'split_units':split_units[rxn_id_cnt], 'used_':True, 'comment_':None}) # add the data to the database: for d in data_O: row=None; row=data_stage02_isotopomer_fittedFluxSplits(d['simulation_id'], d['simulation_dateAndTime'], d['split_id'], d['split_rxn_ids'], d['split'], d['split_stdev'], d['split_lb'], d['split_ub'], d['split_units'], d['used_'], d['comment_']); self.session.add(row); self.session.commit();