def test_parallel_find_metabolites_not_consumed_with_open_bounds(model, num):
"""Expect the appropriate amount of nonconsumed metabolites to be found."""
badmets = consistency.find_metabolites_not_consumed_with_open_bounds(
model, 1)
multi_badmets = consistency.find_metabolites_not_consumed_with_open_bounds(
model, 2)
assert badmets == multi_badmets
def test_find_metabolites_not_consumed_with_open_bounds(model):
"""
Expect metabolites to be consumable in complete medium.
In complete medium, a model should be able to divert flux from every
metabolite. This test opens all the boundary reactions i.e. simulates a
complete medium and checks if any metabolite cannot be consumed
individually using flux balance analysis. Metabolites that cannot be
consumed this way are likely dead-end metabolites or upstream of reactions
with fixed constraints. To pass this test all metabolites should be
consumable.
Implementation:
Open all model boundary reactions, then for each metabolite in the model
add a boundary reaction and minimize it with FBA.
"""
ann = test_find_metabolites_not_consumed_with_open_bounds.annotation
ann["data"] = get_ids(
consistency.find_metabolites_not_consumed_with_open_bounds(model)
)
ann["metric"] = len(ann["data"]) / len(model.metabolites)
ann["message"] = wrapper.fill(
"""A total of {} ({:.2%}) metabolites cannot be consumed in complete
medium: {}""".format(
len(ann["data"]), ann["metric"], truncate(ann["data"])))
assert len(ann["data"]) == 0, ann["message"]
def test_find_metabolites_not_consumed_with_open_bounds(read_only_model):
"""
Expect metabolites to be consumable in complete medium.
In complete medium, a model should be able to divert flux from every
metabolite. This test opens all the boundary reactions i.e. simulates a
complete medium and checks if any metabolite cannot be consumed
individually using flux balance analysis. Metabolites that cannot be
consumed this way are likely dead-end metabolites or upstream of reactions
with fixed constraints. To pass this test all metabolites should be
consumable.
"""
ann = test_find_metabolites_not_consumed_with_open_bounds.annotation
ann["data"] = get_ids(
consistency.find_metabolites_not_consumed_with_open_bounds(
read_only_model
)
)
ann["metric"] = len(ann["data"]) / len(read_only_model.metabolites)
ann["message"] = wrapper.fill(
"""A total of {} ({:.2%}) metabolites cannot be consumed in complete
medium: {}""".format(
len(ann["data"]), ann["metric"], truncate(ann["data"])))
assert len(ann["data"]) == 0, ann["message"]
def test_find_metabolites_not_consumed_with_open_bounds(model, num):
"""Expect the appropriate amount of nonconsumed metabolites to be found."""
badmets = consistency.find_metabolites_not_consumed_with_open_bounds(model)
assert len(badmets) == num
def test_find_metabolites_not_consumed_with_open_bounds(model, num):
"""Expect the appropriate amount of nonconsumed metabolites to be found."""
badmets = consistency.find_metabolites_not_consumed_with_open_bounds(model)
assert len(badmets) == num
