def test_find_reactions_unbounded_flux_default_condition(model):
"""
Expect the fraction of unbounded reactions to be low.
A large fraction of model reactions able to carry unlimited flux under
default conditions indicates problems with reaction directionality,
missing cofactors, incorrectly defined transport reactions and more.
Implementation:
Without changing the default constraints run flux variability analysis.
From the FVA results identify those reactions that carry flux equal to the
model's maximal or minimal flux.
"""
ann = test_find_reactions_unbounded_flux_default_condition.annotation
unbounded_rxn_ids, fraction, _ = \
consistency.find_reactions_with_unbounded_flux_default_condition(model)
ann["data"] = unbounded_rxn_ids
ann["metric"] = fraction
ann["message"] = wrapper.fill(
""" A fraction of {:.2%} of the non-blocked reactions (in total {}
reactions) can carry unbounded flux in the default model
condition. Unbounded reactions may be involved in
thermodynamically infeasible cycles: {}""".format(
ann["metric"], len(ann["data"]), truncate(ann["data"])
)
)
# TODO: Arbitrary threshold right now! Update after meta study!
assert ann["metric"] <= 0.1, ann["message"]
def test_find_reactions_unbounded_flux_default_condition(read_only_model):
"""
Expect the fraction of unbounded reactions to be low.
A large fraction of model reactions able to carry unlimited flux under
default conditions indicates problems with reaction directionality,
missing cofactors, incorrectly defined transport reactions and more.
"""
# TODO: Arbitrary threshold right now! Update after meta study!
ann = test_find_reactions_unbounded_flux_default_condition.annotation
unbounded_rxns, fraction, _ = \
consistency.find_reactions_with_unbounded_flux_default_condition(
read_only_model
)
ann["data"] = get_ids(unbounded_rxns)
ann["metric"] = fraction
ann["message"] = wrapper.fill(
""" A fraction of {:.2%} of the non-blocked reactions (in total {}
reactions) can carry unbounded flux in the default model
condition. Unbounded reactions may be involved in
thermodynamically infeasible cycles: {}""".format(
len(ann["data"]), ann["metric"], truncate(ann["data"])
)
)
assert ann["metric"] <= 0.1, ann["message"]
def test_find_reactions_unbounded_flux_default_condition(model):
"""
Expect the fraction of unbounded reactions to be low.
A large fraction of model reactions able to carry unlimited flux under
default conditions indicates problems with reaction directionality,
missing cofactors, incorrectly defined transport reactions and more.
Implementation:
Without changing the default constraints run flux variability analysis.
From the FVA results identify those reactions that carry flux equal to the
model's maximal or minimal flux.
"""
ann = test_find_reactions_unbounded_flux_default_condition.annotation
unbounded_rxn_ids, fraction, _ = \
consistency.find_reactions_with_unbounded_flux_default_condition(model)
ann["data"] = unbounded_rxn_ids
ann["metric"] = fraction
ann["message"] = wrapper.fill(
""" A fraction of {:.2%} of the non-blocked reactions (in total {}
reactions) can carry unbounded flux in the default model
condition. Unbounded reactions may be involved in
thermodynamically infeasible cycles: {}""".format(
ann["metric"], len(ann["data"]), truncate(ann["data"])))
# TODO: Arbitrary threshold right now! Update after meta study!
assert ann["metric"] <= 0.1, ann["message"]
def test_find_reactions_with_unbounded_flux_default_condition_errors(model):
"""Expect the number of unbounded and blocked metabolites to be correct."""
consistency.find_reactions_with_unbounded_flux_default_condition(model)
def test_find_reactions_with_unbounded_flux_default_condition(model, fraction):
"""Expect the number of unbounded and blocked metabolites to be correct."""
_, unb_fraction, _ = \
consistency.find_reactions_with_unbounded_flux_default_condition(model)
assert unb_fraction == fraction
def test_find_reactions_with_unbounded_flux_default_condition_errors(model):
"""Expect the number of unbounded and blocked metabolites to be correct."""
consistency.find_reactions_with_unbounded_flux_default_condition(model)
def test_find_reactions_with_unbounded_flux_default_condition(model, fraction):
"""Expect the number of unbounded and blocked metabolites to be correct."""
_, unb_fraction, _ = \
consistency.find_reactions_with_unbounded_flux_default_condition(model)
assert unb_fraction == fraction