def assert_dataframes_equal(df, expected):
try:
assert_frame_equal(df, expected, check_names=False)
return True
except AssertionError:
return False
TESTDIR = os.path.dirname(__file__)
REFERENCE_FVA_SOLUTION_ECOLI_CORE = pandas.read_csv(os.path.join(TESTDIR, 'data/REFERENCE_flux_ranges_EcoliCore.csv'),
index_col=0)
REFERENCE_PPP_o2_EcoliCore = pandas.read_csv(os.path.join(TESTDIR, 'data/REFERENCE_PPP_o2_EcoliCore.csv'))
REFERENCE_PPP_o2_glc_EcoliCore = pandas.read_csv(os.path.join(TESTDIR, 'data/REFERENCE_PPP_o2_glc_EcoliCore.csv'))
CORE_MODEL = load_model(os.path.join(TESTDIR, 'data/EcoliCore.xml'), sanitize=False)
iJO_MODEL = load_model(os.path.join(TESTDIR, 'data/iJO1366.xml'), sanitize=False)
iJO_MODEL_COBRAPY = load_model(os.path.join(TESTDIR, 'data/iJO1366.xml'), solver_interface=None, sanitize=False)
TOY_MODEL_PAPIN_2004 = load_model(os.path.join(TESTDIR, "data/toy_model_Papin_2003.xml"))
class Wrapper:
class AbstractTestFindBlockedReactions(unittest.TestCase):
def test_find_blocked_reactions(self):
self.model.reactions.PGK.knock_out() # there are no blocked reactions in EcoliCore
blocked_reactions = find_blocked_reactions(self.model)
self.assertEqual(blocked_reactions, [self.model.reactions.GAPD, self.model.reactions.PGK])
class AbstractTestFluxVariabilityAnalysis(unittest.TestCase):
# try:
# minho_models = index_models_minho()
# except requests.ConnectionError as e:
# minho.no_models_available = "Cameo couldn't reach http://darwin.di.uminho.pt/models at initialization time." \
# "Are you connected to the internet?"
# logger.debug(e)
# except Exception as e:
# minho.no_models_available = "Cameo could reach http://darwin.di.uminho.pt/models at initialization time" \
# "but something went wrong while decoding the server response."
# logger.debug(e)
# else:
# model_indices = minho_models.id
# model_ids = minho_models.name
# for index, id in zip(model_indices, model_ids):
# setattr(minho, str_to_valid_variable_name(id), lazy_object_proxy.Proxy(partial(get_model_from_uminho, index)))
#
# validated_models = minho_models[minho_models.validated]
# minho.validated = ModelDB()
# model_indices = validated_models.id
# model_ids = validated_models.name
# for index, id in zip(model_indices, model_ids):
# setattr(minho.validated, str_to_valid_variable_name(id),
# lazy_object_proxy.Proxy(partial(get_model_from_uminho, index)))
if __name__ == "__main__":
print(index_models_minho())
from cameo.io import load_model
model = load_model(get_sbml_file(2))
print(model.objective)
assert_frame_equal(df, expected, check_names=False)
return True
except AssertionError:
return False
TESTDIR = os.path.dirname(__file__)
REFERENCE_FVA_SOLUTION_ECOLI_CORE = pandas.read_csv(os.path.join(
TESTDIR, 'data/REFERENCE_flux_ranges_EcoliCore.csv'),
index_col=0)
REFERENCE_PPP_o2_EcoliCore = pandas.read_csv(
os.path.join(TESTDIR, 'data/REFERENCE_PPP_o2_EcoliCore.csv'))
REFERENCE_PPP_o2_glc_EcoliCore = pandas.read_csv(
os.path.join(TESTDIR, 'data/REFERENCE_PPP_o2_glc_EcoliCore.csv'))
CORE_MODEL = load_model(os.path.join(TESTDIR, 'data/EcoliCore.xml'),
sanitize=False)
iJO_MODEL = load_model(os.path.join(TESTDIR, 'data/iJO1366.xml'),
sanitize=False)
iJO_MODEL_COBRAPY = load_model(os.path.join(TESTDIR, 'data/iJO1366.xml'),
solver_interface=None,
sanitize=False)
TOY_MODEL_PAPIN_2004 = load_model(
os.path.join(TESTDIR, "data/toy_model_Papin_2003.xml"))
class Wrapper:
class AbstractTestFindBlockedReactions(unittest.TestCase):
def test_find_blocked_reactions(self):
self.model.reactions.PGK.knock_out(
import time
from copy import copy
from cameo.io import load_model
from cameo.basics import flux_variability_analysis, production_envelope
from cameo.methods import DifferentialFVA
from cameo.config import ViewFacade
from multiprocessing import Pool
model = load_model('../tests/data/iJO1366.pickle')
reference_model = copy(model)
reference_model.reactions.get_by_id('Ec_biomass_iJO1366_core_53p95M').lower_bound = 0.9823718127270133
# t1 = time.time()
# fva_solution = flux_variability_analysis(model)
# t2 = time.time()
# print "Execution time: %s" % (t2-t1)
# t1 = time.time()
# fva_solution = flux_variability_analysis(model, view=ViewFacade())
# t2 = time.time()
# print "Execution time: %s" % (t2-t1)
# t1 = time.time()
# fva_solution = flux_variability_analysis(model, )
# t2 = time.time()
# print "Execution time: %s" % (t2-t1)
dFVA = DifferentialFVA(design_space_model=model,
reference_model=reference_model,
# minho_models = index_models_minho()
# except requests.ConnectionError as e:
# minho.no_models_available = "Cameo couldn't reach http://darwin.di.uminho.pt/models at initialization time." \
# "Are you connected to the internet?"
# logger.debug(e)
# except Exception as e:
# minho.no_models_available = "Cameo could reach http://darwin.di.uminho.pt/models at initialization time" \
# "but something went wrong while decoding the server response."
# logger.debug(e)
# else:
# model_indices = minho_models.id
# model_ids = minho_models.name
# for index, id in zip(model_indices, model_ids):
# setattr(minho, str_to_valid_variable_name(id), lazy_object_proxy.Proxy(partial(get_model_from_uminho, index)))
#
# validated_models = minho_models[minho_models.validated]
# minho.validated = ModelDB()
# model_indices = validated_models.id
# model_ids = validated_models.name
# for index, id in zip(model_indices, model_ids):
# setattr(minho.validated, str_to_valid_variable_name(id),
# lazy_object_proxy.Proxy(partial(get_model_from_uminho, index)))
if __name__ == "__main__":
print(index_models_minho())
from cameo.io import load_model
model = load_model(get_sbml_file(2))
print(model.objective)
