def test_get_reaction_set_with_directionality(self):
reaction = Reaction("React1")
metabolite1 = Metabolite("Met1")
metabolite2 = Metabolite("Met2")
stoichiometry = {metabolite1: -1,
metabolite2: 1}
reaction.add_metabolites(stoichiometry)
assert get_reaction_set(reaction, remove_directionality=False) == \
frozenset([frozenset([(metabolite1, -1)]), frozenset([(metabolite2, 1)])])
def test_merging_metabolites(self):
met1 = Metabolite("m1")
met2 = Metabolite("m2")
met3 = Metabolite("m3")
reaction = Reaction()
original_metabolites = {met1: -1, met2: 1}
reaction.add_metabolites(original_metabolites)
merged = merge_metabolites([met1, met3], met3)
# Check that met1 has been substituted with met3
assert merged == [met1]
assert reaction.metabolites == {met3: -1, met2: 1}
def test_passes_custom_filter(self):
""" Should raise not implemented error a number outside of options
is chosen"""
self.proxyModel.custom_filter = len(self.proxyModel.options)
with pytest.raises(NotImplementedError):
self.proxyModel.passes_custom_filter(Reaction())
def test_assigned_gene(self):
custom_proxy = GeneProxyFilter()
gene = Gene()
reaction = Reaction()
reaction.add_child(gene)
# Test all genes
custom_proxy.custom_filter = 0
assert custom_proxy.passes_custom_filter(gene) is True
# Test unassigned
custom_proxy.custom_filter = 1
assert custom_proxy.passes_custom_filter(gene) is False
# Test all filters checked
custom_proxy.custom_filter = 2
with pytest.raises(NotImplementedError):
assert custom_proxy.passes_custom_filter(gene)
def test_add_coefficients_in_overlapping_reactions1(self):
""" If merged metabolites are involved in the same
reaction make sure the coefficients are added when
merging. """
met1 = Metabolite("met1")
met2 = Metabolite("met2")
met3 = Metabolite("met3")
react = Reaction("r1")
react.add_metabolites({met1: -1,
met2: -1,
met3: 1})
merged = merge_metabolites([met1, met2], met1)
assert merged == [met2]
assert react.metabolites[met1] == -2
assert react.metabolites[met3] == 1
def test_group_duplicate_reactions(self):
reaction1 = Reaction("React1")
reaction2 = Reaction("React2")
metabolite1 = Metabolite("Met1")
metabolite2 = Metabolite("Met2")
reaction1.add_metabolites({metabolite1: -1,
metabolite2: 1})
reaction2.add_metabolites({metabolite1: 1,
metabolite2: -1})
result = group_duplicate_reactions([reaction1, reaction2])
assert len(result) == 1
assert reaction1 in list(result.values())[0]
assert reaction2 in list(result.values())[0]
def test_match_for_different_directionality(self):
r1 = Reaction("r1")
r2 = Reaction("r2")
m1 = Metabolite("m1")
m2 = Metabolite("m2")
r1.add_metabolites({m1: -1, m2: 1})
r2.add_metabolites({m1: 1, m2: -1})
assert get_reaction_set(r1, remove_directionality=True) == \
get_reaction_set(r2, remove_directionality=True)
assert get_reaction_set(r1, remove_directionality=False) != \
get_reaction_set(r2, remove_directionality=False)
def test_group_duplicates_reactions_different_reactions(self):
reaction1 = Reaction("React1")
reaction2 = Reaction("React2")
metabolite1 = Metabolite("Met1")
metabolite2 = Metabolite("Met2")
reaction1.add_metabolites({metabolite1: -1,
metabolite2: 1})
reaction2.add_metabolites({metabolite1: 1,
metabolite2: -2})
result = group_duplicate_reactions([reaction1, reaction2])
assert len(result) == 2
assert all(len(x) == 1 for x in itertools.chain(result.values()))
assert reaction1 in itertools.chain(*result.values())
assert reaction2 in itertools.chain(*result.values())
def test_get_gene_statistics(self):
model = Model()
reaction = Reaction("r1")
annotation = Annotation("chebi", "CHEBI:1233")
gene1 = Gene("g1")
gene1.annotation.add(annotation)
gene2 = Gene("g2")
gene2.annotation.add(annotation)
reaction.add_child(gene2)
gene3 = Gene("g3")
reaction.add_child(gene3)
for x in [gene1, gene2, gene3]:
model.add_gene(x)
# Action
gene_stats = gene_statistics(model)
# Return value
# ("Total", num_genes),
# ("Unassigned", num_unassigned),
# ("Verified location", num_exp_verified_localization),
# ("Predicted location", num_predicted_localization),
# ("Known function", num_known_function)
# Check Total
assert gene_stats["Total"] == 3
# Check Unassigned
assert gene_stats["Unassigned"] == 1
# Check Verified location
# Todo: Implement test
assert True
# Check Predicted location
# Todo: Implement test
assert True
# Check Known function
# Todo: Implement test
assert True
def test_merging_reaction(self):
model = Model("m1")
react1 = Reaction("r1")
anno1 = Annotation(collection="ec-code", identifier="2.1.7.0")
react1.add_annotation(anno1)
evidence1 = Evidence(entity=react1)
gene1 = Gene("g1")
react1.add_child(gene1)
model.add_evidence(evidence1)
react2 = Reaction("r2")
anno2 = Annotation(collection="ec-code", identifier="2.1.7.1")
react2.add_annotation(anno2)
evidence2 = Evidence(entity=react2)
gene2 = Gene("g2")
react2.add_child(gene2)
model.add_evidence(evidence2)
react3 = Reaction("r3")
anno3 = Annotation(collection="ec-code", identifier="2.1.7.1")
react3.add_annotation(anno3)
evidence3 = Evidence(entity=react3)
gene3 = Gene("g3")
react3.add_child(gene3)
model.add_evidence(evidence3)
model.add_genes((gene1, gene2, gene3))
model.add_reactions((react1, react2, react3))
model.setup_reaction_table()
# Action
merge_reactions([react1, react2, react3], react1)
# Check annotation added
assert anno1 in react1.annotation
assert anno2 in react1.annotation
assert anno3 in react3.annotation
# Check evidences transferred during merge
assert evidence2 not in react2.evidences
assert evidence2 in react1.evidences
assert react1 is evidence2.entity
assert evidence3 not in react3.evidences
assert evidence3 in react1.evidences
assert react1 is evidence3.entity
# Check merged reactions removed
assert react2 not in model.reactions
assert react3 not in model.reactions
# Check genes transferred during merge
assert react2 not in gene2.reactions
assert react1 in gene2.reactions
assert react3 not in gene3.reactions
assert react1 in gene3.reactions
# Check new genegroup is formed
group = list(react1._children)[0]
assert gene1 in group._children
assert gene2 in group._children
assert gene3 in group._children
assert group.type == "or"
def transport_reaction(self):
reaction = Reaction("r1")
metabolite = Metabolite("m1", compartment="c")
metabolite2 = Metabolite("m2", compartment="e")
reaction.add_metabolites({metabolite: -1, metabolite2: 1})
return reaction
def normal_reaction(self):
reaction = Reaction("r1")
metabolite = Metabolite("m1")
metabolite2 = Metabolite("m2")
reaction.add_metabolites({metabolite: -1, metabolite2: 1})
return reaction
def boundary_reaction(self):
reaction = Reaction("r1")
metabolite = Metabolite("m1")
reaction.add_metabolites({metabolite: -1})
return reaction
def test_get_reaction_statistics(self, progress):
model = Model("model1")
metabolite1 = Metabolite("m1")
metabolite2 = Metabolite("m2")
metabolite7 = Metabolite("m7")
# Add inverted reactions
reaction1 = Reaction("r1")
reaction1.add_metabolites({metabolite1: -1, metabolite2: 1})
reaction2 = Reaction("r2")
reaction2.add_metabolites({metabolite1: 1, metabolite2: -1})
# Add boundary reaction
reaction3 = Reaction("r3")
reaction3.add_metabolites({metabolite1: -1})
# Add transport reaction
metabolite3 = Metabolite("m3", compartment="c")
metabolite4 = Metabolite("m4", compartment="e")
reaction4 = Reaction("r4")
reaction4.add_metabolites({metabolite3: -1, metabolite4: 1})
# Add unbalanced reaction
metabolite5 = Metabolite("m5", formula="H")
metabolite6 = Metabolite("m6", formula="C")
reaction5 = Reaction("r5")
reaction5.add_metabolites({metabolite5: -1, metabolite6: 1})
# Add reaction with gene
reaction6 = Reaction("r6")
reaction6.add_metabolites({metabolite1: -1, metabolite7: 1})
gene = Gene()
reaction6.add_child(gene)
# Add reaction with annotation
reaction7 = Reaction("r7")
reaction7.add_metabolites({metabolite2: -1, metabolite7: 1})
reaction7.add_annotation(Annotation("chebi", "CHEBI:1235"))
model.add_reactions([
reaction1, reaction2, reaction3, reaction4, reaction5, reaction6,
reaction7
])
# Action
output_statistics = reaction_statistics(model)
# Return value of reaction_statistics:
#
# ("Total", num_reactions),
# ("Transport", num_transport),
# ("Boundary", num_boundary),
# ("Unbalanced", num_unbalanced),
# ("Annotated", num_annotated),
# ("No genes", num_no_genes),
# ("Evidence for presence", num_has_presence_evidence),
# ("Known gene", num_known_gene)
# Check total state
assert output_statistics["Total"] == 7
# Check transport reactions
assert output_statistics["Transport"] == 1
# Check boundary reactions
assert output_statistics["Boundary"] == 1
# Check boundary reactions
assert output_statistics["Unbalanced"] == 1
# Check annotated
assert output_statistics["Annotated"] == 1
# Check no genes
# Note: Boundary reactions are excluded from the counting
assert output_statistics["No genes"] == 5
# Check evidence for presence
# Todo: Implement test
assert True
# Check known gene
# Todo: Implement test
assert True
# Check that tests exist for all gathered statistics
assert len(output_statistics) == 8 # Change to number of tests