def test_find_disconnected(read_only_model, store): """Expect no disconnected metabolites to be present.""" store["disconnected_metabolites"] = [ met.id for met in consistency.find_disconnected(read_only_model) ] assert len(store["disconnected_metabolites"]) == 0,\ "The following metabolites are not associated with any " \ "reaction of the model: {}".format( ", ".join(store["disconnected_metabolites"]))
def test_find_disconnected(read_only_model): """ Expect no disconnected metabolites to be present. Disconnected metabolites are not part of any reaction in the model. They are most likely left-over from the reconstruction process, but may also point to network gaps. """ ann = test_find_disconnected.annotation ann["data"] = get_ids(consistency.find_disconnected(read_only_model)) ann["metric"] = len(ann["data"]) / len(read_only_model.metabolites) ann["message"] = wrapper.fill( """A total of {} ({:.2%}) metabolites are not associated with any reaction of the model: {}""".format( len(ann["data"]), ann["metric"], truncate(ann["data"]))) assert len(ann["data"]) == 0, ann["message"]
def test_find_disconnected(model): """ Expect no disconnected metabolites to be present. Disconnected metabolites are not part of any reaction in the model. They are most likely left-over from the reconstruction process, but may also point to network and knowledge gaps. Implementation: Check for any metabolites of the cobra.Model object with emtpy reaction attribute. """ ann = test_find_disconnected.annotation ann["data"] = get_ids(consistency.find_disconnected(model)) ann["metric"] = len(ann["data"]) / len(model.metabolites) ann["message"] = wrapper.fill( """A total of {} ({:.2%}) metabolites are not associated with any reaction of the model: {}""".format( len(ann["data"]), ann["metric"], truncate(ann["data"]))) assert len(ann["data"]) == 0, ann["message"]
def test_find_disconnected(model, num): """Expect the appropriate amount of disconnected to be found.""" disconnected = consistency.find_disconnected(model) assert len(disconnected) == num