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_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_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
}
}