def convert_cobra_to_tfa(cobra_model):
"""
Make tfa analysis of the model
"""
path_to_data = join(this_directory, '..', 'data/thermo_data.thermodb')
thermo_data = load_thermoDB(path_to_data)
tmodel = pytfa.ThermoModel(thermo_data, cobra_model)
# for comp in tmodel.compartments.values():
# comp['c_min'] = 1e-8
tmodel.prepare()
tmodel.convert(add_displacement=True)
# Set the solver
tmodel.solver = GLPK
# Set solver options
# GLPK option optimality and integrality deprecated
#tmodel.solver.configuration.tolerances.optimality = 1e-9
#tmodel.solver.configuration.tolerances.integrality = 1e-9
tmodel.solver.configuration.tolerances.feasibility = 1e-9
# Find a solution
solution = tmodel.optimize()
return tmodel
def convert2thermo(model, name):
# Initialize the model
tmodel = pytfa.ThermoModel(thermo_data, model)
tmodel.name = name
# Annotate the model
annotate_from_lexicon(tmodel, lexicon)
apply_compartment_data(tmodel, compartment_data)
## TFA conversion
tmodel.prepare()
tmodel.convert()
tmodel.solver = solver
return tmodel
#sol.to_csv('sol.csv',encoding='utf-8')
return pd.DataFrame.from_dict(data=res,
orient='index',
columns=['minimum', 'maximum'])
# In[32]:
cobra_model = import_matlab_model(
'C:/Users/farza/Documents/Master_3/Systemes biology/small_ecoli.mat')
fba_solution = cobra_model.optimize()
thermo_data = load_thermoDB(
'C:/Users/farza/Documents/Master_3/Systemes biology/thermo_data.thermodb')
tfa_model = pytfa.ThermoModel(thermo_data, cobra_model)
tfa_model.solver = 'optlang-glpk'
tfa_model.prepare()
tfa_model.convert()
## Info on the model
tfa_model.print_info()
## Optimality
tfa_solution = tfa_model.optimize()
# integrating metabolomics data (comment out this part if not integrating)
df = pd.read_csv('metabolomics_data.csv', sep=';')
df['model ID'] = df['model ID'].astype(str)
from skimpy.utils.general import sanitize_cobra_vars
from skimpy.utils.tabdict import TabDict
from skimpy.analysis.oracle import *
"""
Import and curate a model
"""
this_cobra_model = import_matlab_model('../../models/toy_model.mat', 'model')
"""
Make tfa model
"""
# Convert to a thermodynamics model
thermo_data = load_thermoDB('../../data/thermo_data.thermodb')
this_pytfa_model = pytfa.ThermoModel(thermo_data, this_cobra_model)
GLPK = 'optlang-glpk'
this_pytfa_model.solver = GLPK
## TFA conversion
this_pytfa_model.prepare()
this_pytfa_model.convert(add_displacement=True)
"""
Generate a draft Kinetic Model
"""
# Generate the KineticModel
# Define the molecules that should be considered small-molecules
# These molecules will not be accounted explicitly in the kinetic mechanism as
