def singleSimulation(self,
carbon_source='r_1714',
cs_lb=-1.5,
geneko=None,
o2_lb=None,
type='fba'):
with self.model as m:
m.set_carbon_source(carbon_source, lb=cs_lb)
if o2_lb is not None:
m.reactions.get_by_id('r_1992').lower_bound = float(o2_lb)
if geneko is not None:
if type == 'lmoma':
r = pfba(m)
m.set_environmental_conditions(gene_knockout=geneko)
res = lmoma(m, r)
else:
m.set_environmental_conditions(gene_knockout=geneko)
if type == 'fba':
res = fba(m)
elif type == 'pfba':
res = pfba(m)
elif type == 'fva':
res = fva(m, reaction_list=m.reactions, fix_biomass=True)
return res
def testO2EthanolProd (self, g_knockout = None, react_id = 'r_2115', cs = 'glucose', range_o2 = list(np.arange(-20, 0, 2))):
res = {}
for i in range_o2:
with self.model as m:
m.set_carbon_source(self.cs_reaction[cs], lb = self.cs_lb[cs])
m.reactions.get_by_id('r_1992').lower_bound = float(i)
if g_knockout is not None:
m.set_environmental_conditions(gene_knockout = g_knockout)
r = pfba(m)
if hasattr(r, 'x_dict'): #if legacy solution
fluxes = pd.DataFrame(list(r.x_dict.items())).set_index(0)
else:
fluxes = r.fluxes
res[str(i)] = fluxes.loc[react_id]
for key, val in sorted(res.items()): print(key, '\t', val)
return res
#Reaction Bounds
for r in model.reactions:
print(r.id, '\t', r.lower_bound, '\t', r.upper_bound)
#SIMULATIONS
#FBA
res_fba = fba(model)
res_fba.objective_value # The (optimal) value for the objective function.
res_fba.status # The solver status related to the solution.
res_fba.fluxes # Contains the reaction fluxes (primal values of variables).
res_fba.reduced_costs # Contains reaction reduced costs (dual values of variables).
res_fba.shadow_prices # Contains metabolite shadow prices (dual values of constraints).
#PFBA
res_pfba = pfba(model)
res_pfba.objective_value
res_pfba.status
res_pfba.fluxes
res_pfba.reduced_costs
res_pfba.shadow_prices
#FVA
res_fva = fva(model, reaction_list=model.reactions) #pandas dataframe
res_fva.to_csv('fva_res.csv', sep='\t')
#RANDOM TESTS
model.get_model_id()
model.get_biomass_id()
model.get_biomass()
model.get_exchanges_ids()