def test_get_gene_statistics(self):
model = Model()
metabolite1 = Metabolite("m1")
annotation = Annotation("chebi", "CHEBI:1233")
metabolite1.annotation.add(annotation)
metabolite2 = Metabolite("m2")
model.add_metabolites([metabolite1, metabolite2])
# Action
metabolite_stats = metabolite_statistics(model)
# Return value:
# ("Total", len(model.metabolites)),
# ("Annotated", num_anotated),
# ("DeadEnd", num_dead_ends)
# 1) Check Total
assert metabolite_stats["Total"] == 2
# 2) Check Annotated
assert metabolite_stats["Annotated"] == 1
# 3) Check DeadEnd
assert metabolite_stats["DeadEnd"] == 2
# Check that there is a test for all options
assert len(metabolite_stats) == 3
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_get_yield_not_working_if_input_formula_missing(self):
model = Model("test")
met1 = Metabolite(id="S7P")
met2 = Metabolite(id="T3P1", formula="C3H7O6P")
met3 = Metabolite(id="E4P", formula="C4H9O7P")
met4 = Metabolite(id="F6P", formula="C6H13O9P")
model.add_metabolites((met1, met2, met3, met4))
react1 = Reaction(id="r1", name="Transaldolase")
react1.add_metabolites({met1: -1, met2: -1, met3: 1, met4: 1})
react2 = Reaction(id="r2")
react2.add_metabolites({met1: -1})
react3 = Reaction(id="r3")
react3.add_metabolites({met2: -1})
react4 = Reaction(id="r4")
react4.add_metabolites({met3: -1})
react5 = Reaction(id="r5")
react5.add_metabolites({met4: -1})
model.add_reactions((react1, react2, react3, react4, react5))
fluxes = {
react1.id: 1,
react2.id: -1,
react3.id: -1,
react4.id: 1,
react5.id: 1
}
status, _ = get_yields(fluxes, model)
assert status is False
def test_setting_item(self):
parent = QWidget()
widget = ReferenceDisplayWidget(parent)
test = ModelTest()
model = Model()
widget.dataTable.populate_table = Mock()
widget.set_item(test, model)
widget.dataTable.populate_table.assert_called_once_with(
test.references)
assert widget.model is model
assert widget.item is test
def test_addition_emits_changed(self):
parent = QWidget()
widget = ReferenceDisplayWidget(parent)
test = ModelTest()
reference = Reference()
test.add_reference(reference)
model = Model()
widget.set_item(test, model)
detector = Mock()
widget.changed.connect(detector.test)
widget.dataTable.update_row_from_item(Reference())
assert detector.test.called is True
assert widget.content_changed is True
def test_get_yield(self):
model = Model("test")
met1 = Metabolite(id="S7P", formula="C7H15O10P")
met2 = Metabolite(id="T3P1", formula="C3H7O6P")
met3 = Metabolite(id="E4P", formula="C4H9O7P")
met4 = Metabolite(id="F6P", formula="C6H13O9P")
model.add_metabolites((met1, met2, met3, met4))
react1 = Reaction(id="r1", name="Transaldolase")
react1.add_metabolites({met1: -1, met2: -1, met3: 1, met4: 1})
react2 = Reaction(id="r2")
react2.add_metabolites({met1: -1})
react3 = Reaction(id="r3")
react3.add_metabolites({met2: -1})
react4 = Reaction(id="r4")
react4.add_metabolites({met3: -1})
react5 = Reaction(id="r5")
react5.add_metabolites({met4: -1})
model.add_reactions((react1, react2, react3, react4, react5))
fluxes = {
react1.id: 1,
react2.id: -1,
react3.id: -1,
react4.id: 1,
react5.id: 1
}
status, yields = get_yields(fluxes, model)
assert status is True
assert yields == {
"C": {
met3: 0.4,
met4: 0.6
},
"H": {
met3: 9 / 22,
met4: 13 / 22
},
"O": {
met3: 7 / 16,
met4: 9 / 16
},
"P": {
met3: 0.5,
met4: 0.5
}
}
def test_reference_statistics(self):
model = Model("m1")
ref1 = Reference()
modeltest = ModelTest()
modeltest.add_reference(ref1)
ref2 = Reference()
evidence = Evidence()
evidence.add_reference(ref2)
ref3 = Reference()
model.add_reference(ref1)
model.add_reference(ref2)
model.add_reference(ref3)
model.setup_tables()
result = reference_statistics(model)
assert result["Total"] == 3
assert result["Unassigned"] == 1
def test_deletion_emits_changed(self):
parent = QWidget()
widget = ReferenceDisplayWidget(parent)
test = ModelTest()
reference = Reference()
test.add_reference(reference)
model = Model()
widget.set_item(test, model)
detector = Mock()
widget.changed.connect(detector.test)
widget.tableView.selectRow(0)
QtTest.QTest.mouseClick(widget.button_del_item, QtCore.Qt.LeftButton)
assert widget.dataTable.rowCount() == 0
assert detector.test.called is True
assert widget.content_changed is True
def test_saving_items(self):
parent = QWidget()
widget = ReferenceDisplayWidget(parent)
test = ModelTest()
reference = Reference()
test.add_reference(reference)
model = Model()
widget.set_item(test, model)
new_test = ModelTest()
widget.item = new_test
assert len(new_test.references) == 0
widget.save_state()
assert len(new_test.references) == 1
new_reference = list(new_test.references)[0]
assert new_reference is reference
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 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