def simulate_loops_sbml(self,ijo1366_sbml,data_fva):
'''Simulate FVA after closing exchange reactions and setting ATPM to 0
reactions with flux will be involved in loops'''
# Read in the sbml file and define the model conditions
cobra_model = create_cobra_model_from_sbml_file(ijo1366_sbml, print_time=True)
# Change all uptake reactions to 0
for rxn in cobra_model.reactions:
if 'EX_' in rxn.id and '_LPAREN_e_RPAREN_' in rxn.id:
rxn.lower_bound = 0.0;
# Set ATPM to 0
cobra_model.reactions.get_by_id('ATPM').lower_bound = 0.0
# calculate the reaction bounds using FVA
reaction_bounds = flux_variability_analysis(cobra_model, fraction_of_optimum=0.9,
objective_sense='maximize', the_reactions=None,
allow_loops=True, solver='gurobi',
the_problem='return', tolerance_optimality=1e-6,
tolerance_feasibility=1e-6, tolerance_barrier=1e-8,
lp_method=1, lp_parallel=0, new_objective=None,
relax_b=None, error_reporting=None,
number_of_processes=1, copy_model=False);
# Update the data file
with open(data_fva, 'wb') as outfile:
json.dump(reaction_bounds, outfile, indent=4);
def categorize_reactions(model, db, category):
fva_result_dict = {}
# Wide range of ATP Synthase flux values can be positive or negative
category_1_dict = {}
# ATP Synthase flux can only be negative
category_2_dict = {}
# ATP Synthase flux can only be positive
category_3_dict = {}
model = create_cobra_model_from_sbml_file(model)
rxn_list = pickle.load(open(db, 'rb'))
for run in rxn_list.keys():
model_test = model.copy()
fva_list = [model_test.reactions.ATPS]
for rxn in rxn_list[run]:
addID = re.search('(rxn\d{5}_reverse)|(rxn\d{5})', rxn).group(0)
formula = re.search('(cpd\d{5}.*$)|(\d+.\d+\scpd\d{5}.*$)', rxn).group(0)
rxn = Reaction(addID)
model_test.add_reaction(rxn)
rxn.reaction = formula
fva_list.append(rxn)
fva_result = flux_analysis.flux_variability_analysis(model_test, fva_list)
fva_result_dict[run] = fva_result
for run in fva_result_dict:
if fva_result_dict[run]['ATPS']['maximum'] > 0 and fva_result_dict[run]['ATPS']['minimum'] < 0:
category_1_dict[run] = fva_result_dict[run]
elif fva_result_dict[run]['ATPS']['maximum'] > 0:
category_2_dict[run] = fva_result_dict[run]
else:
category_3_dict[run] = fva_result_dict[run]
if category == 1:
return category_1_dict.keys()
elif category == 2:
return category_2_dict.keys()
else:
return category_3_dict.keys()
def _gapsplit(model, depth, cpus):
fva = flux_variability_analysis(model, model.reactions, fraction_of_optimum=0.001, processes=cpus)
# only split reactions with feasible range >= min_range
idxs = (fva.maximum - fva.minimum >= 1e-5).to_numpy().nonzero()[0]
weights = (1.0 / (fva.maximum - fva.minimum) ** 2).to_numpy()
samples = numpy.zeros((depth, len(model.reactions)))
k = 0
for try_ in range(1000):
relative, target, width = _maxgap(samples[0:k,idxs], fva.iloc[idxs,:])
primary_var = numpy.argmax(relative)
primary_target = target[primary_var]
primary_lb = primary_target - 0.001*width[primary_var]
primary_ub = primary_target + 0.001*width[primary_var]
new_sample = _generate_sample(model, idxs[primary_var], primary_lb, primary_ub)
if new_sample is not None:
new_sample[new_sample > fva.maximum] = fva.maximum[new_sample > fva.maximum]
new_sample[new_sample < fva.minimum] = fva.minimum[new_sample < fva.minimum]
samples[k,:] = new_sample
k += 1
if k >= depth: break
if k < depth:
# max_tries reached; return fewer samples
samples = samples[:k,:]
return pandas.DataFrame(data=samples, columns=fva.maximum.index)
def cobra_fva(pk, model_sbml, reaction_list, loopless, fraction_of_optimum,
pfba_factor, deleted_genes):
cobra_model = load_sbml(model_sbml)
if len(deleted_genes) > 0:
cobra.manipulation.delete_model_genes(cobra_model,
deleted_genes,
cumulative_deletions=True)
try:
result_frame = json.loads(
flux_variability_analysis(cobra_model, reaction_list, loopless,
fraction_of_optimum,
pfba_factor).to_json())
result = {
'components': [{
'name': name,
'minimum': result_frame['minimum'][name],
'maximum': result_frame['maximum'][name],
} for name in result_frame['minimum'].keys()],
}
except Exception as error:
error_result = report_cobra_computation_error(error)
app.send_task(
**get_result_kwargs('fba', pk, error_result, is_error=True))
return
app.send_task(**get_result_kwargs('fva', pk, result))
def limiting_reactions(cobra_model, reactions=None):
"""
Determine limiting reactions
"""
if reactions == None:
reactions = cobra_model.reactions
sol = cobra_model.optimize()
fva_rxns = []
for rxn in reactions:
limited_below = isclose(sol.fluxes[rxn.id],
rxn.lower_bound,
rel_tol=1e-2)
limited_above = isclose(sol.fluxes[rxn.id],
rxn.upper_bound,
rel_tol=1e-2)
if limited_below or limited_above:
if rxn.lower_bound < rxn.upper_bound and not isclose(
rxn.lower_bound, rxn.upper_bound, rel_tol=1e-2):
fva_rxns.append(rxn)
fva = flux_variability_analysis(cobra_model, reaction_list=fva_rxns)
for rxn, fmin, fmax in zip(fva.index, fva['minimum'].values,
fva['maximum'].values):
if fmin < sol.fluxes[rxn] and not isclose(
sol.fluxes[rxn], fmin, rel_tol=1e-2):
yield rxn
elif fmax > sol.fluxes[rxn] and not isclose(
sol.fluxes[rxn], fmax, rel_tol=1e-2):
yield rxn
def simulate_loops(self,cobra_model_I=None,data_fva='loops_fva.json'):
'''Simulate FVA after closing exchange reactions and setting ATPM to 0
reactions with flux will be involved in loops'''
if cobra_model_I: cobra_model = cobra_model_I.copy();
else: cobra_model = self.model.copy();
# Change all uptake reactions to 0
system_boundaries = [x.id for x in cobra_model.reactions if x.boundary == 'system_boundary'];
for rxn in cobra_model.reactions:
if rxn.id in system_boundaries:
cobra_model.reactions.get_by_id(rxn.id).lower_bound = 0.0;
cobra_model.reactions.get_by_id(rxn.id).upper_bound = 0.0;
# Set ATPM to 0
cobra_model.reactions.get_by_id('ATPM').lower_bound = 0.0;
# set the objective function to a default value
cobra_model.change_objective('Ec_biomass_iJO1366_WT_53p95M')
cobra_model.reactions.get_by_id('Ec_biomass_iJO1366_WT_53p95M').lower_bound=0.0
cobra_model.reactions.get_by_id('Ec_biomass_iJO1366_WT_53p95M').upper_bound=1e6
# calculate the reaction bounds using FVA
reaction_bounds = flux_variability_analysis(cobra_model, fraction_of_optimum=1.0,
the_reactions=None, solver='gurobi');
# Update the data file
with open(data_fva, 'wb') as outfile:
json.dump(reaction_bounds, outfile, indent=4);
def simulate_loops(self, cobra_model_I=None, data_fva='loops_fva.json'):
'''Simulate FVA after closing exchange reactions and setting ATPM to 0
reactions with flux will be involved in loops'''
if cobra_model_I: cobra_model = cobra_model_I.copy()
else: cobra_model = self.model.copy()
# Change all uptake reactions to 0
system_boundaries = [
x.id for x in cobra_model.reactions
if x.boundary == 'system_boundary'
]
for rxn in cobra_model.reactions:
if rxn.id in system_boundaries:
cobra_model.reactions.get_by_id(rxn.id).lower_bound = 0.0
cobra_model.reactions.get_by_id(rxn.id).upper_bound = 0.0
# Set ATPM to 0
cobra_model.reactions.get_by_id('ATPM').lower_bound = 0.0
# set the objective function to a default value
cobra_model.change_objective('Ec_biomass_iJO1366_WT_53p95M')
cobra_model.reactions.get_by_id(
'Ec_biomass_iJO1366_WT_53p95M').lower_bound = 0.0
cobra_model.reactions.get_by_id(
'Ec_biomass_iJO1366_WT_53p95M').upper_bound = 1e6
# calculate the reaction bounds using FVA
reaction_bounds = flux_variability_analysis(cobra_model,
fraction_of_optimum=1.0,
the_reactions=None,
solver='gurobi')
# Update the data file
with open(data_fva, 'wb') as outfile:
json.dump(reaction_bounds, outfile, indent=4)
def _create_visualisation(model_filename, svg_filename, output_filename, analysis_type='FBA',
analysis_results=None, intermediate_filename=None):
# Check arguments
supported_analysis_types = {"FBA", "FVA"}
if analysis_type not in supported_analysis_types:
message = "Analysis type is wrong. It has to be one of the values: {}"
raise ValueError(message.format(supported_analysis_types))
try:
model = cio.load_json_model(model_filename)
except Exception as exc:
raise CobraModelFileError("Failed to load model from given JSON : {}".format(exc.args))
# Set default arguments if none provided
if analysis_results is None:
fba_results = model.optimize()
if analysis_type == 'FBA':
fba_results.fluxes = fba_results.fluxes.round(5)
analysis_results = fba_results
elif analysis_type == 'FVA':
fva_results = flux_variability_analysis(model, fraction_of_optimum=0.5)
fva_results = fva_results.round(3)
analysis_results = fva_results
vizan_kwargs = {
'model': model,
'file_source_path': svg_filename,
'analysis_results': analysis_results,
'analysis_type': analysis_type,
'output_filename': output_filename,
}
if intermediate_filename is None:
with NamedTemporaryFile(mode="w") as intermediate_file:
vizan_kwargs['intermediate_filename'] = intermediate_file.name
produce_output_file(**vizan_kwargs)
else:
vizan_kwargs['intermediate_filename'] = intermediate_filename
produce_output_file(**vizan_kwargs)
def test_metabolite_summary_interface(model, opt_solver):
"""Test that a summary can be created successfully."""
model.solver = opt_solver
metabolite = model.metabolites.get_by_id("q8_c")
MetaboliteSummary(
metabolite=metabolite,
model=model,
)
MetaboliteSummary(
metabolite=metabolite,
model=model,
solution=pfba(model),
)
MetaboliteSummary(
metabolite=metabolite,
model=model,
fva=0.95,
)
MetaboliteSummary(
metabolite=metabolite,
model=model,
fva=flux_variability_analysis(
model, reaction_list=["CYTBD", "NADH16", "SUCDi"]
),
)
def simulate_loops(ijo1366_sbml,data_fva):
'''Simulate FVA after closing exchange reactions and setting ATPM to 0
reactions with flux will be involved in loops'''
# Read in the sbml file and define the model conditions
cobra_model = create_cobra_model_from_sbml_file(ijo1366_sbml, print_time=True)
# Change all uptake reactions to 0
for rxn in cobra_model.reactions:
if 'EX_' in rxn.id and '_LPAREN_e_RPAREN_' in rxn.id:
rxn.lower_bound = 0.0;
# Set ATPM to 0
cobra_model.reactions.get_by_id('ATPM').lower_bound = 0.0
# calculate the reaction bounds using FVA
reaction_bounds = flux_variability_analysis(cobra_model, fraction_of_optimum=0.9,
objective_sense='maximize', the_reactions=None,
allow_loops=True, solver='gurobi',
the_problem='return', tolerance_optimality=1e-6,
tolerance_feasibility=1e-6, tolerance_barrier=1e-8,
lp_method=1, lp_parallel=0, new_objective=None,
relax_b=None, error_reporting=None,
number_of_processes=1, copy_model=False);
# Update the data file
with open(data_fva, 'wb') as outfile:
json.dump(reaction_bounds, outfile, indent=4);
def fva(self) -> pd.DataFrame:
"""Create DataFrame file with minimum and maximum value of FVA.
Runs flux variability analysis.
see https://cobrapy.readthedocs.io/en/latest/simulating.html#Running-FVA
"""
model = self.read_model()
solution = model.optimize()
fluxes = solution.fluxes
try:
df = flux_variability_analysis(model,
model.reactions,
fraction_of_optimum=1.0)
df_out = pd.DataFrame({
"model": self.model_path.name,
"objective": self.objective_id,
"reaction": df.index,
"flux": fluxes,
"status": CuratorConstants.STATUS_OPTIMAL,
"minimum": df.minimum,
"maximum": df.maximum,
})
except OptimizationError as e:
logger.error(f"{e}")
df_out = pd.DataFrame({
"model": self.model_path.name,
"objective": self.objective_id,
"reaction": [r.id for r in model.reactions],
"flux": fluxes,
"status": CuratorConstants.STATUS_INFEASIBLE,
"minimum": CuratorConstants.VALUE_INFEASIBLE,
"maximum": CuratorConstants.VALUE_INFEASIBLE,
})
return df_out
def find_stoichiometrically_balanced_cycles(model):
u"""
Find metabolic reactions in stoichiometrically balanced cycles (SBCs).
Identify forward and reverse cycles by closing all exchanges and using FVA.
Parameters
----------
model : cobra.Model
The metabolic model under investigation.
Notes
-----
"SBCs are artifacts of metabolic reconstructions due to insufficient
constraints (e.g., thermodynamic constraints and regulatory
constraints) [1]_." They are defined by internal reactions that carry
flux in spite of closed exchange reactions.
References
----------
.. [1] Thiele, I., & Palsson, B. Ø. (2010, January). A protocol for
generating a high-quality genome-scale metabolic reconstruction.
Nature protocols. Nature Publishing Group.
http://doi.org/10.1038/nprot.2009.203
"""
helpers.close_boundaries_sensibly(model)
fva_result = flux_variability_analysis(model, loopless=False)
return fva_result.index[(fva_result["minimum"] == -1) |
(fva_result["maximum"] == 1)].tolist()
def calculate_common_substrate_flux(model):
boundary_reactions = model.exchanges
# generate model exchange reactions
fva_results = flux_variability_analysis(
model, reaction_list=boundary_reactions,
fraction_of_optimum=1)
# Generate FVA results
fva_results = fva_results.sort_values(by='minimum', ascending=True)
# sort FVA results ascending order
substrates = fva_results['minimum'] < 0
fva_results_substrates = fva_results[substrates].sort_values(by='minimum', ascending=True)
# Generate dataframe where only consuming reactions are taken into account
reaction_consist_carbon = []
for reaction in fva_results_substrates.index:
reaction_cobrapy = model.reactions.get_by_id(reaction)
for metabolite in reaction_cobrapy.reactants:
if 'C' in metabolite.elements.keys():
reaction_consist_carbon.append(str(reaction))
# Filter from FVA substrate list reactions which HAVE NOT included
flux_sum = 0
for reaction in reaction_consist_carbon:
flux_sum = flux_sum + fva_results.loc[reaction, 'minimum']
return flux_sum
def get_r_id2fva_bounds(model, threshold=None, rs=None):
r_id2min_max = flux_variability_analysis(model, reaction_list=rs)
r_id2bounds = {}
for r_id, values in r_id2min_max.items():
min_v, max_v = round_value(values['minimum']), round_value(values['maximum'])
if threshold is None or abs(min_v) > threshold or abs(max_v) > threshold:
r_id2bounds[r_id] = min_v, max_v
return r_id2bounds
def find_reactions_with_unbounded_flux_default_condition(model):
"""
Return list of reactions whose flux is unbounded in the default condition.
Parameters
----------
model : cobra.Model
The metabolic model under investigation.
Returns
-------
tuple
list
A list of reactions that in default modeling conditions are able to
carry flux as high/low as the systems maximal and minimal bounds.
float
The fraction of the amount of unbounded reactions to the amount of
non-blocked reactions.
list
A list of reactions that in default modeling conditions are not able
to carry flux at all.
"""
try:
fva_result = flux_variability_analysis(model, fraction_of_optimum=1.0)
except Infeasible as err:
LOGGER.error("Failed to find reactions with unbounded flux "
"because '{}'. This may be a bug.".format(err))
raise Infeasible("It was not possible to run flux variability "
"analysis on the model. Make sure that the model "
"can be solved! Check if the constraints are not "
"too strict.")
# Per reaction (row) the flux is below threshold (close to zero).
conditionally_blocked = fva_result.loc[fva_result.abs().max(
axis=1) < TOLERANCE_THRESHOLD].index.tolist()
small, large = helpers.find_bounds(model)
# Find those reactions whose flux is close to or outside of the median
# upper or lower bound, i.e., appears unconstrained.
unlimited_flux = fva_result.loc[
np.isclose(fva_result["maximum"], large, atol=TOLERANCE_THRESHOLD) |
(fva_result["maximum"] > large)
| np.isclose(fva_result["minimum"], small, atol=TOLERANCE_THRESHOLD) |
(fva_result["minimum"] < small)].index.tolist()
try:
fraction = len(unlimited_flux) / \
(len(model.reactions) - len(conditionally_blocked))
except ZeroDivisionError:
LOGGER.error("Division by Zero! Failed to calculate the "
"fraction of unbounded reactions. Does this model "
"have any reactions at all?")
raise ZeroDivisionError("It was not possible to calculate the "
"fraction of unbounded reactions to "
"un-blocked reactions. This may be because"
"the model doesn't have any reactions at "
"all or that none of the reactions can "
"carry a flux larger than zero!")
return unlimited_flux, fraction, conditionally_blocked
def simulate(model, biomass_reaction, method, objective_id,
objective_direction):
if method not in METHODS:
raise ValueError(f"Unsupported simulation method '{method}'")
if objective_id:
model.objective = model.reactions.get_by_id(objective_id)
if objective_direction:
model.objective_direction = objective_direction
try:
logger.info(f"Simulating model {model.id} with {method}")
if method == "fba":
solution = model.optimize(raise_error=True)
elif method == "pfba":
solution = pfba(model)
elif method == "fva":
# FIXME: accept list of relevant fva reactions to calculate
solution = flux_variability_analysis(model)
elif method == "pfba-fva":
# FIXME: accept list of relevant fva reactions to calculate
solution = flux_variability_analysis(model,
fraction_of_optimum=1,
pfba_factor=1.05)
except OptimizationError as error:
logger.info(f"Optimization Error: {error}")
raise
else:
if method in ("fba", "pfba"):
flux_distribution = solution.fluxes.to_dict()
growth_rate = flux_distribution[biomass_reaction]
elif method in ("fva", "pfba-fva"):
df = solution.rename(index=str,
columns={
"maximum": "upper_bound",
"minimum": "lower_bound"
})
for key in ["lower_bound", "upper_bound"]:
df[key] = df[key].astype("float")
flux_distribution = df.T.to_dict()
growth_rate = flux_distribution[biomass_reaction]["upper_bound"]
logger.info(
f"Simulation was successful with growth rate {growth_rate}")
return flux_distribution, growth_rate
def test_fastcc_against_fva_nonblocked_rxns(model: Model,
all_solvers: List[str]) -> None:
"""Test non-blocked reactions obtained by FASTCC against FVA."""
model.solver = all_solvers
fastcc_consistent_model = fastcc(model)
fva = flux_variability_analysis(model, fraction_of_optimum=0.0)
nonblocked_rxns_fva = fva.index[(fva.minimum.abs() > model.tolerance) |
(fva.maximum.abs() > model.tolerance)]
assert all(fastcc_consistent_model.reactions) == all(
nonblocked_rxns_fva.tolist())
def _perform_fva(model):
'''Perform FVA.'''
flux_var = flux_variability_analysis(model, model.reactions)
blocked = flux_var.loc[(abs(flux_var['minimum']) < 1e-6) &
(abs(flux_var['maximum']) < 1e-6)]
print 'Blocked: %d/%d\n' % (len(blocked), len(flux_var))
flux_var.to_csv('flux_var.csv')
blocked.to_csv('blocked.csv')
def find_stoichiometrically_balanced_cycles(model):
u"""
Find metabolic rxns in stoichiometrically balanced cycles (SBCs).
The flux distribution of nominal FVA is compared with loopless FVA
(loopless=True) to determine reactions that participate in loops, as
participation in loops would increase the flux through a given reactions
to the maximal bounds. This function then returns reactions where the
flux differs between the two FVA calculations.
Parameters
----------
model : cobra.Model
The metabolic model under investigation.
Notes
-----
"SBCs are artifacts of metabolic reconstructions due to insufficient
constraints (e.g., thermodynamic constraints and regulatory
constraints) [1]_." They are defined by internal reactions that carry
flux in spite of closed exchange reactions.
References
----------
.. [1] Thiele, I., & Palsson, B. Ø. (2010, January). A protocol for
generating a high-quality genome-scale metabolic reconstruction.
Nature protocols. Nature Publishing Group.
http://doi.org/10.1038/nprot.2009.203
"""
try:
fva_result = flux_variability_analysis(model, loopless=False)
fva_result_loopless = flux_variability_analysis(model, loopless=True)
except Infeasible as err:
LOGGER.error("Failed to find stoichiometrically balanced cycles "
"because '{}'. This may be a bug.".format(err))
return []
row_ids_max = fva_result[
fva_result.maximum != fva_result_loopless.maximum].index
row_ids_min = fva_result[
fva_result.minimum != fva_result_loopless.minimum].index
differential_fluxes = set(row_ids_min).union(set(row_ids_max))
return [model.reactions.get_by_id(id) for id in differential_fluxes]
def perform_analysis(model, analysis_type):
fba_results = model.optimize()
if analysis_type == 'FBA':
fba_results.fluxes = fba_results.fluxes.round(5)
analysis_results = fba_results
elif analysis_type == 'FVA':
fva_results = flux_variability_analysis(model, fraction_of_optimum=0.5)
fva_results = fva_results.round(3)
analysis_results = fva_results
return model, analysis_results
def variability_analysis(self, measured_metabolites):
if type(self.drug) == list:
self.combined_drug_knockout()
elif self.drug != '':
self.drug_knock_out()
elif self.target != '':
self.model.genes.get_by_id(self.target).knock_out()
self.set_objective(measured_metabolites)
return flux_variability_analysis(self.model)
def _constrain_and_analyze_model(model, coefficient_dict, fraction, sampling_depth, objective, tasks, minimum_threshold, cpus):
constrained_model = copy.deepcopy(model)
# Set previous objective as a constraint, allow deviation
if objective == True:
prev_obj_val = constrained_model.slim_optimize()
prev_obj_constraint = constrained_model.problem.Constraint(constrained_model.objective.expression, lb=prev_obj_val*fraction, ub=prev_obj_val)
constrained_model.add_cons_vars([prev_obj_constraint])
constrained_model.solver.update()
# Apply weigths to new expression
pfba_expr = symengine.RealDouble(0)
for rxn in constrained_model.reactions:
try:
pfba_expr += coefficient_dict[rxn.id] * rxn.forward_variable
pfba_expr += coefficient_dict[rxn.id] * rxn.reverse_variable
except KeyError:
continue
if sampling_depth == 0:
# Include metabolic task constraints
if len(tasks) >= 1:
constrained_model = _integrate_tasks(constrained_model, tasks)
# Determine reactions that do not carry any flux in highly constrained solution space
constrained_model.objective = constrained_model.problem.Objective(pfba_expr, direction='min', sloppy=True)
constrained_model.solver.update()
solution = constrained_model.optimize()
inactive_rxns = set([rxn.id for rxn in constrained_model.reactions if abs(solution.fluxes[rxn.id]) <= minimum_threshold])
return inactive_rxns
else:
# Explore solution space of constrained model with flux sampling, allow deviation
constrained_model.objective = constrained_model.problem.Objective(pfba_expr, direction='max', sloppy=True)
constrained_model.solver.update()
flux_sum_obj_val = constrained_model.slim_optimize()
flux_sum_constraint = constrained_model.problem.Constraint(pfba_expr, lb=flux_sum_obj_val*fraction, ub=flux_sum_obj_val)
constrained_model.add_cons_vars([flux_sum_constraint])
constrained_model.solver.update()
# Analyze flux ranges and calculate concordance
if sampling_depth != 1:
warnings.filterwarnings('ignore') # Handle possible infeasible warnings
flux_samples = _gapsplit(constrained_model, depth=sampling_depth, cpus=cpus)
warnings.filterwarnings('default')
concordance = _calc_concordance(flux_samples, coefficient_dict)
else:
flux_samples = 'Not performed'
concordance = 'Not performed'
fva = flux_variability_analysis(constrained_model, fraction_of_optimum=fraction, processes=cpus)
return flux_samples, fva, concordance
def set_fva_bounds(cobra_model):
"""
Sets reaction bounds using FVA.
"""
fva = flux_variability_analysis(cobra_model, fraction_of_optimum=0)
for rxn in cobra_model.reactions:
assert rxn.lower_bound <= rxn.upper_bound
rxn.lower_bound = fva['minimum'][rxn.id]
rxn.upper_bound = max(fva['maximum'][rxn.id], fva['minimum'][rxn.id])
def generate_fva_data(self, cobra_model, fraction_of_optimum=0.9,
objective_sense='maximize', reaction_list=None,
allow_loops=True, solver='glpk'):
print('FVA...')
#add in loop law constrain
if not allow_loops: cobra_model=construct_loopless_model(cobra_model);
# calculate the reaction bounds using FVA
self.fva_data = flux_variability_analysis(cobra_model, fraction_of_optimum=0.9,
objective_sense='maximize', solver=solver,
reaction_list=reaction_list,
);
def variability_analysis(self, measured_metabolites):
if type(self.drug) == list:
self.combined_drug_knockout()
elif self.drug != '':
self.drug_knock_out()
elif self.target != '':
self.model.genes.get_by_id(self.target).knock_out()
# TODO This is the point where I will add reactions most likely
# print(measured_metabolites)
self.set_objective(measured_metabolites)
return flux_variability_analysis(self.model)
def results_genes_flux(model, rxn_name, flux_gene_off_on):
'''
results_genes_flux utility:
essential genes of model outputted nicely AND flux through the reactions being changed outputted
Input:
(1) model: model structure
(2) rxn_name: string reaction name in list e.g. ['rxn00123','rxn00456',....]
(3) flux_gene_off_on is list containing two binary values to turn off the reaction functionalities either
[1,0] [0,0] or [0,1] first element is flux second is gene deletions is on
Output:
essential genes in pandas data arrary
'''
#two models taken from the original
try:
if flux_gene_off_on[0] == 0:
del_results = []
print('no gene del results returned')
else:
#Essential Genes Before - Biomass Results Before - Gene Knockouts
print('Single Gene Deletion of Model Entered')
model_genes = copy.deepcopy(model)
del_results = single_gene_deletion(model_genes)
if flux_gene_off_on[1] == 0:
fluxes = []
print('No fluxes returned')
else:
model_flux = copy.deepcopy(model)
#flux through reaction
fluxes = []
loop_reactions = []
print('Rxn flux loop entered')
for i in range(0, len(rxn_name)):
loop_reactions.append(
model_flux.reactions.get_by_id(rxn_name[i]))
if i % 10 == 0:
print('Flux reaction number', i)
fluxes = (flux_variability_analysis(model_flux,
reaction_list=loop_reactions,
loopless=True)
) #range of fluxes through the reaction
except:
print('You must enter a cobra model structure')
raise
return [del_results, fluxes]
def generate_fva_data(self, cobra_model, fraction_of_optimum=0.9,
objective_sense='maximize', reaction_list=None,
allow_loops=True, solver='glpk', verbose_I=True):
if verbose_I:
print('FVA...')
#add in loop law constrain
if not allow_loops: cobra_model=construct_loopless_model(cobra_model)
# calculate the reaction bounds using FVA
cobra_model.solver = solver
fva_data = flux_variability_analysis(cobra_model, fraction_of_optimum=0.9,
objective_sense='maximize',
reaction_list=reaction_list,
)
self.fva_data = dict(zip(list(fva_data.index),fva_data.to_dict('records')))
def test_model_summary_interface(model, opt_solver):
"""Test that a summary can be created successfully."""
model.solver = opt_solver
ModelSummary(model=model, )
ModelSummary(
model=model,
solution=pfba(model),
)
ModelSummary(
model=model,
fva=0.95,
)
ModelSummary(
model=model,
fva=flux_variability_analysis(
model, reaction_list=["CYTBD", "NADH16", "SUCDi"]),
)
def _generate(
self,
model: "Model",
solution: Optional["Solution"],
fva: Optional[Union[float, pd.DataFrame]],
) -> None:
"""
Prepare the data for the summary instance.
Parameters
----------
model : cobra.Model
The metabolic model for which to generate a metabolite summary.
solution : cobra.Solution, optional
A previous model solution to use for generating the summary. If
``None``, the summary method will generate a parsimonious flux
distribution.
fva : pandas.DataFrame or float, optional
Whether or not to include flux variability analysis in the output.
If given, `fva` should either be a previous FVA solution matching the
model or a float between 0 and 1 representing the fraction of the
optimum objective to be searched.
"""
super()._generate(model=model, solution=solution, fva=fva)
if solution is None:
logger.info("Generating new parsimonious flux distribution.")
solution = pfba(model)
if isinstance(fva, float):
logger.info("Performing flux variability analysis.")
fva = flux_variability_analysis(
model,
reaction_list=[self._reaction],
fraction_of_optimum=fva,
)
# Create the basic flux table.
self._flux = pd.DataFrame(
data={"flux": [solution[self._reaction.id]]},
index=[self._reaction.id],
)
if fva is not None:
self._flux = self._flux.join(fva)
def fva(self,
reaction_list=None,
loopless=False,
fraction_of_optimum=1.0,
pfba_factor=None,
processes=None):
try:
return flux_variability_analysis(model=self.model,
reaction_list=reaction_list,
loopless=loopless,
fraction_of_optimum=fraction_of_optimum,
pfba_factor=pfba_factor,
processes=processes)
except Infeasible:
return DataFrame()
def simulatingFVA(model):
# FBA will not give always give unique solution, because multiple flux
# states can achieve the same optimum. FVA (or flux variability analysis)
# finds the ranges of each metabolic flux at the optimum.
from cobra.flux_analysis import flux_variability_analysis
print(flux_variability_analysis(model, model.reactions[:10]))
# Setting parameter fraction_of_optimium=0.90 would give the flux ranges for reactions at 90% optimality.
print(
cobra.flux_analysis.flux_variability_analysis(model,
model.reactions[:10],
fraction_of_optimum=0.9,
loopless=True))
model.optimize()
model.summary(
fva=0.95
) # Flux variability analysis can also be embedded in calls to summary methods.
model.metabolites.pyr_c.summary(fva=0.95)
def main():
print('================ SUBTASK 1: Building the Model ================')
model = build_model()
print("Reactions")
print("---------")
for x in model.reactions:
print(f"{x.id}:{x.reaction}")
print("")
print("Metabolites")
print("-----------")
for x in model.metabolites:
print(x.id)
print(
'\n================ SUBTASK 2: Computing the maximum flow through the growth reaction ================\n'
)
solution = model.optimize()
print(model.summary())
print('\n================ SUBTASK 3: FVA ================\n')
fva = flux_variability_analysis(model)
print(fva)
print(
'\n================ SUBTASK 4: Find essential reactions ================\n'
)
#Knock out each reaction. If the objective value is 0, the reaction is essential.
for reaction in model.reactions:
with model as model:
reaction.knock_out()
model.optimize()
if round(model.objective.value, 6) == 0:
print(
f"{reaction.id} blocked, new growth rate {round(model.objective.value,6)} -------> ESSENTIAL"
)
else:
print(
f"{reaction.id} blocked, new growth rate {round(model.objective.value,6)}"
)
def find_universally_blocked_reactions(model):
"""
Find metabolic reactions that are blocked.
Parameters
----------
model : cobra.Model
The metabolic model under investigation.
Notes
-----
Blocked reactions are those reactions that when optimized for cannot carry
any flux while all exchanges are open.
"""
with model:
helpers.open_boundaries(model)
fva_result = flux_variability_analysis(model)
blocked = fva_result.loc[(fva_result["maximum"] == 0.0)
& (fva_result["minimum"] == 0.0)]
return [model.reactions.get_by_id(name) for name in blocked.index]
def test_reaction_summary_interface(model, opt_solver):
"""Test that a summary can be created successfully."""
model.solver = opt_solver
reaction = model.reactions.get_by_id("FUM")
ReactionSummary(
reaction=reaction,
model=model,
)
ReactionSummary(
reaction=reaction,
model=model,
solution=pfba(model),
)
ReactionSummary(
reaction=reaction,
model=model,
fva=0.95,
)
ReactionSummary(
reaction=reaction,
model=model,
fva=flux_variability_analysis(model, reaction_list=["FUM"]),
)
fva_result_dict = {}
atps_dict = {}
for run in rxn_list.keys():
model_test = model.copy()
rxns_added = []
fva_list = [model_test.reactions.ATPS, model_test.reactions.Eha_FSLASH_Ehb]
for rxn in rxn_list[run]:
addID = re.search('(rxn\d{5}_reverse)|(rxn\d{5})', rxn).group(0)
formula = re.search('(cpd\d{5}.*$)|(\d+.\d+\scpd\d{5}.*$)', rxn).group(0)
rxn = Reaction(addID)
model_test.add_reaction(rxn)
rxn.reaction = formula
fva_list.append(rxn)
rxns_added.append(rxn)
fva_result = flux_analysis.flux_variability_analysis(model_test, fva_list)
fva_result_dict[run] = fva_result, rxns_added
rxns_added = []
for run in fva_result_dict.keys():
if fva_result_dict[run][0]['ATPS']['minimum'] > 0 and fva_result_dict[run][0]['ATPS']['maximum'] == 1000 \
and fva_result_dict[run][0]['Eha_FSLASH_Ehb']['maximum'] < 0:
atps_dict[run] = fva_result_dict[run]
for run in atps_dict.keys():
print run
model_testing = model.copy()
for i in range(len(atps_dict[run][1])):
model_testing.add_reaction(atps_dict[run][1][i])
print atps_dict[run][1][i].build_reaction_string(True)
print atps_dict[run][1][i].reaction