def test_ensemble_initial_conditions(self):
root_path = join(dirname(__file__), "ensemble2")
models_files = {
filename: join(root_path, filename)
for filename in listdir(root_path)
if filename.endswith(".bnet")
}
istates_files = {
splitext(filename)[0]+".bnet": join(root_path, filename)
for filename in listdir(root_path)
if filename.endswith(".json")
}
individual_istates = {}
for name, filename in istates_files.items():
with open(filename, 'r') as f:
json_data = loads(f.read())
istate = {node.replace("-", "_"): value for node, value in json_data['states']['AD15'].items()}
individual_istates.update({name: istate})
ensemble_model = Ensemble(
root_path,
outputs=['ADIPOQ', 'CEBPA', 'FABP4', 'LPL'],
mutations={'JUN': 'ON', 'TTF1': 'ON', 'ESR1': 'OFF', 'NFKB1': 'OFF'},
individual_istates=individual_istates,
individual_results=True
)
self.assertEqual(len(ensemble_model.get_mini_bns()), 11)
results = ensemble_model.run()
results.plotSteadyStatesDistribution()
results.plotSteadyStatesNodesDistribution()
def test_ensemble_zip(self):
ensemble_model = Ensemble(join(dirname(__file__), "ensemble.zip"),
join(dirname(__file__), "simple_config.cfg"))
results = ensemble_model.run()
results.get_fptable()
results.get_states_probtraj()
def test_ensemble_individual(self):
ensemble_model = Ensemble(join(dirname(__file__), "ensemble"),
join(dirname(__file__), "simple_config.cfg"),
outputs=['AHR', 'BCL6', 'CEBPB'],
individual_results=True)
self.assertEqual(len(ensemble_model.get_mini_bns()), 5)
results = ensemble_model.run()
results.plotSteadyStatesDistribution()
results.plotSteadyStatesNodesDistribution()
def test_maboss_ensemble(self):
root_path = join(dirname(__file__), "ensemble_bnd")
ensemble_model = Ensemble(root_path, individual_results=True)
ensemble_res = ensemble_model.run()
self.assertEqual(
list(ensemble_res.get_fptable()['State'].sort_values().values), [
'ATP -- cIAP',
'BCL2 -- ROS -- ATP -- XIAP -- NFkB -- DISC_FAS -- DISC_TNF -- cFLIP -- IKK -- FADD -- TNFR -- TNF -- RIP1 -- cIAP -- RIP1ub -- RIP1K -- Survival'
])
self.assertEqual(
list(ensemble_res.get_fptable()['Proba'].sort_values().values),
[0.5, 0.5])