Source code for test_consistency
# -*- coding: utf-8 -*-
# Copyright 2017 Novo Nordisk Foundation Center for Biosustainability,
# Technical University of Denmark.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
"""Stoichiometric consistency tests for an instance of ``cobra.Model``."""
from __future__ import absolute_import
import pytest
import memote.support.consistency as consistency
[docs]def test_stoichiometric_consistency(read_only_model, store):
"""Expect that the stoichiometry is mass-balanced."""
is_consistent = consistency.check_stoichiometric_consistency(
read_only_model)
store["is_consistent"] = is_consistent
unconserved = [] if is_consistent else [
met.id for met in consistency.find_unconserved_metabolites(
read_only_model)]
store["unconserved_metabolites"] = unconserved
assert is_consistent,\
"The following metabolites are involved in inconsistent reactions:"\
" {}".format(", ".join(unconserved))
@pytest.mark.parametrize(
"read_only_model, store, met",
[("read_only_model", "store", x) for x in consistency.ENERGY_COUPLES],
indirect=["read_only_model", "store"])
[docs]def test_detect_energy_generating_cycles(read_only_model, store, met):
"""Expect that no energy metabolite can be produced out of nothing."""
try:
result = \
consistency.detect_energy_generating_cycles(read_only_model, met)
except KeyError:
result = "not found"
store["magic_{}_production".format(met)] = result
if result == "not found":
assert False,\
"The metabolite '{}' was not found in the model.".format(met)
elif result == "infeasible":
assert False,\
"Solving the model is infeasible. Often this is due to missing " \
"or disconnected metabolites, or too strict constraints."
else:
assert len(result) == 0,\
"The model can produce '{}' without requiring resources. This is " \
"likely caused by improperly constrained reactions leading to " \
"erroneous energy-generating cycles.".format(met)
[docs]def test_reaction_charge_balance(read_only_model, store):
"""Expect all reactions to be charge balanced."""
store["charge_imbalanced_reactions"] = [
rxn.id for rxn in consistency.find_charge_imbalanced_reactions(
read_only_model)]
assert len(store["charge_imbalanced_reactions"]) == 0,\
"The following reactions are charge imbalanced or at least one " \
"metabolite participating in a reaction doesn't have a charge" \
": {}".format(", ".join(store["charge_imbalanced_reactions"]))
[docs]def test_reaction_mass_balance(read_only_model, store):
"""Expect all reactions to be mass balanced."""
store["mass_imbalanced_reactions"] = [
rxn.id for rxn in consistency.find_mass_imbalanced_reactions(
read_only_model)]
assert len(store["mass_imbalanced_reactions"]) == 0,\
"The following reactions are mass imbalanced or at least one " \
"metabolite participating in a reaction doesn't have a formula" \
": {}".format(", ".join(store["mass_imbalanced_reactions"]))
[docs]def test_blocked_reactions(read_only_model, store):
"""Expect all reactions to be able to carry flux."""
store["blocked_reactions"] = [
rxn.id for rxn in consistency.find_blocked_reactions(read_only_model)]
assert len(store["blocked_reactions"]) == 0,\
"The following reactions are blocked: {}".format(
", ".join(store["blocked_reactions"]))
@pytest.mark.skip(reason="Loopless FVA currently runs too slow for large "
"models.")
[docs]def test_find_stoichiometrically_balanced_cycles(read_only_model, store):
"""Expect no stoichiometrically balanced loops to be present."""
store["looped_reactions"] = [
rxn.id for rxn in consistency.find_stoichiometrically_balanced_cycles(
read_only_model
)]
assert len(store["looped_reactions"]) == 0,\
"The following reactions participate in stoichiometrically balanced" \
" cycles: {}".format(
", ".join(store["looped_reactions"]))
[docs]def test_find_orphans(read_only_model, store):
"""Expect no orphans to be present."""
store["orphan_metabolites"] = [
met.id for met in consistency.find_orphans(read_only_model)]
assert len(store["orphan_metabolites"]) == 0,\
"The following metabolites are not produced by any " \
"reaction of the model: {}".format(
", ".join(store["orphan_metabolites"]))
[docs]def test_find_deadends(read_only_model, store):
"""Expect no deadends to be present."""
store["deadend_metabolites"] = [
met.id for met in consistency.find_deadends(read_only_model)]
assert len(store["deadend_metabolites"]) == 0,\
"The following metabolites are not consumed by any " \
"reaction of the model: {}".format(
", ".join(store["deadend_metabolites"]))
[docs]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"]))