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sample_concentrations.py
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Fri, Oct 18, 09:52

sample_concentrations.py
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import numpy as np
from cobra import Model, Reaction, Metabolite
#from optlang import Variable, Constraint, Objective, Model
from cobra.sampling import sample
from scipy.sparse import diags
EPSILON = 1e-7
def sample_initial_concentrations(kmodel,
reference_concentrations,
lower_bound=0.8,
upper_bound=1.2,
n_samples=10,
absolute_bounds = False):
concentrations = np.array([reference_concentrations[k] for k in kmodel.variables])
if kmodel.conservation_relation is None:
N = len(kmodel.variables)
rand = np.random.uniform(low=lower_bound,
high=upper_bound,
size=(N,n_samples))
#
else:
# Todo Also allow
lower_bound = {k: v * lower_bound for k,v in reference_concentrations.items()}
upper_bound = {k: v * upper_bound for k, v in reference_concentrations.items()}
# Account for volume differences in compartments
if kmodel.volume_ratio_func is None:
effective_conservation_relations = kmodel.conservation_relation.todense()
else:
param_values = {p.symbol: p.value for p in kmodel.parameters.values()}
volume_ratios = kmodel.volume_ratio_func(param_values)
inv_volume_ratio_matrix = diags(1./np.array(volume_ratios)).todense()
effective_conservation_relations = kmodel.conservation_relation.todense()\
.dot(inv_volume_ratio_matrix)
# Create a linear problem and sample it
rhs = effective_conservation_relations.dot(concentrations)
linmodel = create_linear_model(effective_conservation_relations,
rhs,
kmodel.reactants,
lower_bound=lower_bound,
upper_bound=upper_bound)
return sample(linmodel, n_samples, )
def create_linear_model(A, rhs, variables, lower_bound=None, upper_bound=None):
# This is a bit retarded but this way we can use the sampling functions from cobra
model = Model('lin_model')
# TODO have cases for lower and upper bound None
rxns = np.array([ Reaction(v, lower_bound=lower_bound[v],
upper_bound=upper_bound[v]) for v in variables])
model.add_reactions(rxns)
lin_variables = np.array([r.forward_variable for r in rxns])
NR, NC = A.shape
constraints = [model.problem.Constraint( (A[i,:].dot(lin_variables))[0,0] ,
lb=np.float(rhs[:,i]),
ub=np.float(rhs[:,i])) for i in range(NR)]
model.add_cons_vars(constraints)
return model

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