# -*- 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.
"""Perform basic tests on an instance of ``cobra.Model``."""
from __future__ import absolute_import, division
import memote.support.basic as basic
import memote.support.helpers as helpers
from memote.utils import annotate, get_ids, truncate, wrapper
[docs]@annotate(title="Model Identifier", type="string")
def test_model_id_presence(read_only_model):
"""
Expect that the model has an identifier.
The MIRIAM guidelines require a model to be named. While it is not
required, the ID will be displayed on the memote reports, which helps to
distinguish the output clearly.
"""
ann = test_model_id_presence.annotation
assert hasattr(read_only_model, "id")
ann["data"] = read_only_model.id
assert bool(read_only_model.id)
[docs]@annotate(title="Total Number of Genes", type="length")
def test_genes_presence(read_only_model):
"""
Expect that more than one gene is defined in the model.
A metabolic model can still be a useful tool without any
genes, however there are certain methods which rely on the presence of
genes and, more importantly, the corresponding gene-protein-reaction
rules. This test requires that there is at least one gene defined.
"""
ann = test_genes_presence.annotation
assert hasattr(read_only_model, "genes")
ann["data"] = get_ids(read_only_model.genes)
ann["message"] = "{:d} genes are defined in the model.".format(
len(ann["data"]))
assert len(ann["data"]) >= 1, ann["message"]
[docs]@annotate(title="Total Number of Reactions", type="length")
def test_reactions_presence(read_only_model):
"""
Expect that more than one reaction is defined in the model.
To be useful a metabolic model should consist at least of a few reactions.
This test simply checks if there are more than one.
"""
ann = test_reactions_presence.annotation
assert hasattr(read_only_model, "reactions")
ann["data"] = get_ids(read_only_model.reactions)
ann["message"] = "{:d} reactions are defined in the model.".format(
len(ann["data"]))
assert len(ann["data"]) >= 1, ann["message"]
[docs]@annotate(title="Total Number of Transport Reactions", type="length")
def test_transport_reaction_presence(read_only_model):
"""
Expect more than one transport reaction to be defined in the model.
Cellular metabolism in any organism usually involves the transport of
metabolites across a lipid bi-layer. Hence, this test checks that there is
at least one reaction, which transports metabolites from one compartment
to another.
A transport reaction is defined as follows:
1. It contains metabolites from at least two compartments and
2. at least one metabolite undergoes no chemical conversion, i.e.,
the formula stays the same on both sides of the equation.
This test will not be able to identify transport via the PTS System.
"""
ann = test_transport_reaction_presence.annotation
ann["data"] = get_ids(helpers.find_transport_reactions(read_only_model))
ann["message"] = wrapper.fill(
"""A total of {:d} ({:.2%}) transport reactions are defined in the
model, this excludes purely metabolic reactions, exchanges, or
pseudo-reactions: {}""".format(
len(ann["data"]), ann["metric"], truncate(ann["data"])))
assert len(ann["data"]) >= 1, ann["message"]
[docs]@annotate(title="Reactions without GPR", type="length")
def test_gene_protein_reaction_rule_presence(read_only_model):
"""
Expect all non-exchange reactions to have a GPR rule.
Gene-Protein-Reaction rules express which gene has what function.
The presence of this annotation is important to justify the existence
of reactions in the model, and is required to conduct in silico gene
deletion studies. However, reactions without GPR may also be valid:
Spontaneous reactions, or known reactions with yet undiscovered genes
likely lack GPR.
"""
ann = test_gene_protein_reaction_rule_presence.annotation
missing_gpr_metabolic_rxns = set(
basic.check_gene_protein_reaction_rule_presence(read_only_model)
).difference(set(read_only_model.exchanges))
ann["data"] = get_ids(missing_gpr_metabolic_rxns)
ann["metric"] = len(ann["data"]) / len(read_only_model.reactions)
ann["message"] = wrapper.fill(
"""There are a total of {} reactions ({:.2%}) without GPR:
{}""".format(len(ann["data"]), ann["metric"], truncate(ann["data"])))
assert len(ann["data"]) == 0, ann["message"]
[docs]@annotate(title="Non-Growth Associated Maintenance Reaction", type="length")
def test_ngam_presence(read_only_model):
"""
Expect a single non growth-associated maintenance reaction.
The Non-Growth Associated Maintenance reaction (NGAM) is an
ATP-hydrolysis reaction added to metabolic models to represent energy
expenses that the cell invests in continuous processes independent of
the growth rate.
"""
ann = test_ngam_presence.annotation
ann["data"] = get_ids(basic.find_ngam(read_only_model))
ann["message"] = wrapper.fill(
"""A total of {} NGAM reactions could be identified:
{}""".format(len(ann["data"]), truncate(ann["data"])))
assert len(ann["data"]) == 1, ann["message"]
[docs]@annotate(title="Total Number of Compartments", type="length")
def test_compartments_presence(read_only_model):
"""
Expect that more than two compartments are defined in the model.
While simplified metabolic models may be perfectly viable, generally
across the tree of life organisms contain at least one distinct
compartment: the cytosol or cytoplasm. In the case of prokaryotes there is
usually a periplasm, and eurkaryotes are more complex. In addition to the
internal compartment, a metabolic model also reflects the extracellular
environment i.e. the medium/ metabolic context in which the modelled cells
grow. Hence, in total, at least two compartments can be expected from a
metabolic model.
"""
# TODO: Fix the test in a later PR! Should expect 2 compartments instead!
ann = test_compartments_presence.annotation
assert hasattr(read_only_model, "compartments")
ann["data"] = list(read_only_model.get_metabolite_compartments())
ann["message"] = wrapper.fill(
"""A total of {:d} compartments are defined in the model: {}""".format(
len(ann["data"]), truncate(ann["data"])))
assert len(ann["data"]) >= 3, ann["message"]
[docs]@annotate(title="Number of Enzyme Complexes", type="length")
def test_protein_complex_presence(read_only_model):
"""
Expect that more than one enzyme complex is present in the model.
Based on the gene-protein-reaction (GPR) rules, it is possible to infer
whether a reaction is catalyzed by a single gene product, isozymes or by a
heteromeric protein complex. This test checks that at least one
such protein complex is defined in the GPR of the model. For S. cerevisiae
it could be shown that "essential proteins tend to [cluster] together in
essential complexes" (https://doi.org/10.1074%2Fmcp.M800490-MCP200).
This might also be a relevant metric for other organisms.
"""
ann = test_protein_complex_presence.annotation
ann["data"] = list(basic.find_protein_complexes(read_only_model))
ann["message"] = wrapper.fill(
"""A total of {:d} protein complexes are defined through GPR rules in
the model.""".format(len(ann["data"])))
assert len(ann["data"]) >= 1, ann["message"]
[docs]@annotate(title="Number of Transport Reactions", type="length")
def test_find_transport_reactions(read_only_model):
"""Expect >= 1 transport reactions are present in the read_only_model."""
ann = test_find_transport_reactions.annotation
ann["data"] = get_ids(helpers.find_transport_reactions(read_only_model))
ann["metric"] = len(ann["data"]) / len(read_only_model.reactions)
ann["message"] = wrapper.fill(
"""A total of {:d} ({:.2%}) transport reactions are defined in the
model, this excludes purely metabolic reactions, exchanges, or
pseudo-reactions: {}""".format(
len(ann["data"]), ann["metric"], truncate(ann["data"])))
assert len(ann["data"]) >= 1, ann["message"]
[docs]@annotate(title="Fraction of Transport Reactions without GPR", type="length")
def test_transport_reaction_gpr_presence(read_only_model):
"""
Expect a small fraction of transport reactions not to have a GPR rule.
As it is hard to identify the exact transport processes within a cell,
transport reactions are often added purely for modeling purposes.
Highlighting where assumptions have been made vs where
there is proof may help direct the efforts to improve transport and
transport energetics of the tested metabolic model.
However, transport reactions without GPR may also be valid:
Diffusion, or known reactions with yet undiscovered genes likely lack GPR.
"""
# TODO: Update threshold with improved insight from meta study.
ann = test_transport_reaction_gpr_presence.annotation
ann["data"] = get_ids(
basic.check_transport_reaction_gpr_presence(read_only_model)
)
ann["metric"] = len(ann["data"]) / len(
helpers.find_transport_reactions(read_only_model)
)
ann["message"] = wrapper.fill(
"""There are a total of {} transport reactions ({:.2%} of all
transport reactions) without GPR:
{}""".format(len(ann["data"]), ann["metric"], truncate(ann["data"])))
assert len(ann["metric"]) < 0.2, ann["message"]
