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);