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
def test_find_disconnected(model, num):
"""Expect the appropriate amount of disconnected to be found."""
disconnected = consistency.find_disconnected(model)
assert len(disconnected) == num