def test_gapFind_exp(self):
solver = GlpkSolverLazy()
model = '../../../examples/models/toy_model'
self.model = read_model_from_file(model, kind=CONSTRAINT_BASED)
fix_bigg_model(self.model)
print self.model
framed_result = GapFind(self.model, solver, root_gaps_only=True)
print framed_result
def testRun(self):
model = load_sbml_model(SMALL_TEST_MODEL, kind=CONSTRAINT_BASED)
fix_bigg_model(model)
write_model_to_file(model, PLAIN_TEXT_COPY)
model_copy = read_model_from_file(PLAIN_TEXT_COPY, kind=CONSTRAINT_BASED)
solution = FBA(model_copy)
self.assertEqual(solution.status, Status.OPTIMAL)
self.assertAlmostEqual(solution.fobj, GROWTH_RATE, places=2)
def test_gapFind_gurobi_simpleToyModel(self):
solver = GlpkSolverLazy()
model = '../../../examples/models/gapFill/toy_model_simple_holes'
reactionsDB = '../../../examples/models/gapFill/toy_model_simple_DB'
self.model = read_model_from_file(model, kind=CONSTRAINT_BASED)
fix_bigg_model(self.model)
framed_result = GapFill(self.model, reactionsDB, solver, 'R_EX_Biomass', 0.05, 'txt')
self.assertEquals(framed_result[1], ['R_EX_gluc1', 'R_gluc1_A', 'R_A_B'])
def testRun(self):
model = load_sbml_model(SMALL_TEST_MODEL, kind=CONSTRAINT_BASED)
write_model_to_file(model, PLAIN_TEXT_COPY)
model_copy = read_model_from_file(PLAIN_TEXT_COPY, kind=CONSTRAINT_BASED)
self.assertListEqual(sorted(model.metabolites.keys()),
sorted(model_copy.metabolites.keys()))
self.assertListEqual(model.reactions.keys(), model_copy.reactions.keys())
self.assertDictEqual(dict(model.stoichiometry),
dict(model_copy.stoichiometry))
self.assertDictEqual(model.bounds, model_copy.bounds)
