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_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 __call__(self, strategy, *args, **kwargs):
(host, model, pathway) = (strategy[0], strategy[1], strategy[2])
with TimeMachine() as tm:
pathway.plug_model(model, tm)
objective = biomass_product_coupled_yield(model.biomass,
pathway.product,
model.carbon_source)
opt = GeneKnockoutOptimization(model=model, objective_function=objective, progress=True, plot=False)
return opt.run(product=pathway.product.id, max_evaluations=10000)
def test_biomass_product_coupled_yield(self):
solution = self._MockupSolution()
solution.set_primal('biomass', 0.6)
solution.set_primal('product', 2)
solution.set_primal('substrate', -10)
of = biomass_product_coupled_yield("biomass", "product", "substrate")
fitness = of(None, solution, None)
self.assertAlmostEqual((0.6 * 2) / 10, fitness)
solution.set_primal('substrate', 0)
fitness = of(None, solution, None)
self.assertEquals(0, fitness)
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
from cobra.io import read_sbml_model
from optlang import glpk_interface
import inspyred
from cameo.strain_design.heuristic.multiprocess import MultiprocessReactionKnockoutOptimization
from cameo.strain_design.heuristic.objective_functions import biomass_product_coupled_yield
from cameo.flux_analysis.simulation import fba
from cameo.core.solver_based_model import to_solver_based_model
model = read_sbml_model("../tests/data/iJO1366.xml")
model = to_solver_based_model(model, solver_interface=glpk_interface)
of = biomass_product_coupled_yield("Ec_biomass_iJO1366_core_53p95M", "EX_ac_LPAREN_e_RPAREN_",
"EX_glc_LPAREN_e_RPAREN_")
mp = MultiprocessReactionKnockoutOptimization(model=model, heuristic_method=inspyred.ec.GA,
objective_function=of, simulation_method=fba)
mp.run(max_evaluations=300, n=2)
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
from cobra.io import read_sbml_model
from optlang import glpk_interface
import inspyred
from cameo.strain_design.heuristic.multiprocess import MultiprocessReactionKnockoutOptimization
from cameo.strain_design.heuristic.objective_functions import biomass_product_coupled_yield
from cameo.flux_analysis.simulation import fba
from cameo.core.solver_based_model import to_solver_based_model
model = read_sbml_model("../tests/data/iJO1366.xml")
model = to_solver_based_model(model, solver_interface=glpk_interface)
of = biomass_product_coupled_yield("Ec_biomass_iJO1366_core_53p95M",
"EX_ac_LPAREN_e_RPAREN_",
"EX_glc_LPAREN_e_RPAREN_")
mp = MultiprocessReactionKnockoutOptimization(model=model,
heuristic_method=inspyred.ec.GA,
objective_function=of,
simulation_method=fba)
mp.run(max_evaluations=300, n=2)
