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