def test_run_single_objective(self):
result_file = os.path.join(CURRENT_PATH, "data", "reaction_knockout_single_objective.pkl")
objective = biomass_product_coupled_yield(
"Biomass_Ecoli_core_N_LPAREN_w_FSLASH_GAM_RPAREN__Nmet2",
"EX_ac_LPAREN_e_RPAREN_",
"EX_glc_LPAREN_e_RPAREN_")
rko = ReactionKnockoutOptimization(model=self.model,
simulation_method=fba,
objective_function=objective,
seed=SEED)
# self.assertEqual(rko.random.random(), 0.1915194503788923)
results = rko.run(max_evaluations=3000, pop_size=10, view=SequentialView())
# self.assertEqual(rko.random.random(), 0.9268454219291495)
with open(result_file, 'rb') as in_file:
if six.PY3:
expected_results = pickle.load(in_file, encoding="latin1")
else:
expected_results = pickle.load(in_file)
assert_frame_equal(results.solutions, expected_results.solutions)
def test_run_multiobjective(self):
result_file = os.path.join(CURRENT_PATH, "data", "reaction_knockout_multi_objective.pkl")
objective1 = biomass_product_coupled_yield(
"Biomass_Ecoli_core_N_LPAREN_w_FSLASH_GAM_RPAREN__Nmet2",
"EX_ac_LPAREN_e_RPAREN_",
"EX_glc_LPAREN_e_RPAREN_")
objective2 = number_of_knockouts()
objective = [objective1, objective2]
rko = ReactionKnockoutOptimization(model=self.model,
simulation_method=fba,
objective_function=objective,
heuristic_method=inspyred.ec.emo.NSGA2,
seed=SEED)
# self.assertEqual(rko.random.random(), 0.1915194503788923)
results = rko.run(max_evaluations=3000, pop_size=10, view=SequentialView())
# print(rko.random.random(), 0.545818634701)
with open(result_file, 'rb') as in_file:
if six.PY3:
expected_results = pickle.load(in_file, encoding="latin1")
else:
expected_results = pickle.load(in_file)
assert_frame_equal(results.solutions, expected_results.solutions)
def test_initialize(self):
rko = ReactionKnockoutOptimization(model=self.model,
simulation_method=fba,
seed=SEED)
self.assertTrue(sorted(self.essential_reactions) == sorted(rko.essential_reactions))
self.assertEqual(rko._ko_type, "reaction")
self.assertTrue(isinstance(rko._decoder, ReactionKnockoutDecoder))
