def find_inactive_rxns(model, method=1):
""" ** Runnable only in jupyter notebook **
Find all inactive (blocked) reactions in a cobra model using either fastFVA or FASTCC methods
Input:
- model: cobra.io.core.model.Model
- method: fastFVA(1, default) or FASTCC (2)
Output:
- inactive_rxns: list of inactive reactions """
# inactive_rxns = []
if method == 1: # fastFVA (by default, if no method number is given)
print("Checking all reactions (fastFVA)...")
# set all objective coefficients to 0
for react in range(len(model.reactions)):
model.reactions[react].objective_coefficient = 0
inactive_rxns = find_blocked_reactions(model)
#####################################################################################
# ** ALTERNATIVELY: **
# following code delivers the same inactive reactions as find_blocked_reactions
#####################################################################################
# conduct FVA analysis
#fva = flux_variability_analysis(model) # add number of allowed tasks (threads) to run at the same time
#print("FVA is done...")
# store all maximum and all minimum flux-values after FVA
#opt_max = []
#opt_min = []
#for i in range(len(fva)):
# opt_max.append(fva.iloc[i][1])
# opt_min.append(fva.iloc[i][0])
#print("storing done...")
# set constraints to consider a reaction "inactive"
#abs_max = [i for i in range(len(opt_max)) if abs(opt_max[i]) < 1e-6]
#abs_min = [i for i in range(len(opt_min)) if abs(opt_min[i]) < 1e-6]
#print("Constraints done..")
#is_inactive = [rxn_id for rxn_id in abs_max if rxn_id in abs_min]
# get all (inactive) blocked reactions' id
#inactive_rxns = []
#for rxn_id in is_inactive:
# inactive_rxns.append(model.reactions[rxn_id].id)
#########################################################################
else: # otherwise use FASTCC
print("Checking all reactions (FASTCC)...")
# get non-blocked reactions, * in MATLAB the fastcc function gives less is_active reactions *
is_active = fastcc(model, zero_cutoff=1e-4).reactions
# get all active reactions' id
active_rxns = [rxn.id for rxn in is_active]
# get all model's reactions
all_model_rxns = [rxns.id for rxns in model.reactions]
# get difference, which are then the inactive reactions
inactive_rxns = list(set(all_model_rxns) - set(active_rxns))
print('Model consists of %s blocked (inactive) reactions' %
len(inactive_rxns))
return inactive_rxns
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 test_opposing(opposing_model: Model, all_solvers: List[str]) -> None:
"""Test FASTCC."""
opposing_model.solver = all_solvers
consistent_model = fastcc(opposing_model)
expected_reactions = {"v1", "v2", "v3", "v4"}
assert expected_reactions == {rxn.id for rxn in consistent_model.reactions}
def test_figure1(figure1_model: Model, all_solvers: List[str]) -> None:
"""Test FASTCC."""
figure1_model.solver = all_solvers
consistent_model = fastcc(figure1_model)
expected_reactions = {"v1", "v3", "v4", "v5", "v6"}
assert expected_reactions == {rxn.id for rxn in consistent_model.reactions}
def test_opposing(opposing_model, all_solvers):
"""Test fastcc."""
opposing_model.solver = all_solvers
consistent_model = fastcc(opposing_model)
expected_reactions = {'v1', 'v2', 'v3', 'v4'}
assert expected_reactions == {rxn.id for rxn in consistent_model.reactions}
def test_figure1(figure1_model, all_solvers):
"""Test fastcc."""
figure1_model.solver = all_solvers
consistent_model = fastcc(figure1_model)
expected_reactions = {'v1', 'v3', 'v4', 'v5', 'v6'}
assert expected_reactions == {rxn.id for rxn in consistent_model.reactions}
def test_opposing(opposing_model, all_solvers):
"""Test fastcc."""
opposing_model.solver = all_solvers
consistent_model = fastcc(opposing_model)
expected_reactions = {'v1', 'v2', 'v3', 'v4'}
assert expected_reactions == {rxn.id for rxn in consistent_model.reactions}
def test_figure1(figure1_model, all_solvers):
"""Test fastcc."""
figure1_model.solver = all_solvers
consistent_model = fastcc(figure1_model)
expected_reactions = {'v1', 'v3', 'v4', 'v5', 'v6'}
assert expected_reactions == {rxn.id for rxn in consistent_model.reactions}
def test_opposing(opposing_model, all_solvers):
"""Test fastcc."""
opposing_model.solver = all_solvers
consistent_model = fastcc(opposing_model)
expected_reactions = {"v1", "v2", "v3", "v4"}
assert expected_reactions == {rxn.id for rxn in consistent_model.reactions}
def test_figure1(figure1_model, all_solvers):
"""Test fastcc."""
figure1_model.solver = all_solvers
consistent_model = fastcc(figure1_model)
expected_reactions = {"v1", "v3", "v4", "v5", "v6"}
assert expected_reactions == {rxn.id for rxn in consistent_model.reactions}