def setUp(self):
self._database = DictDatabase()
self._database.set_reaction('rxn_1', parse_reaction('|A| <=>'))
self._database.set_reaction('rxn_2', parse_reaction('|A| <=> |B|'))
self._database.set_reaction('rxn_3', parse_reaction('|C| <=> |B|'))
self._database.set_reaction('rxn_4', parse_reaction('|C| <=>'))
self._mm = MetabolicModel.load_model(self._database,
self._database.reactions)
self._strategy = randomsparse.ReactionDeletionStrategy(self._mm)
def test_random_sparse_reaction_strategy(self):
expected = [({'rxn_1', 'rxn_6', 'ex_A', 'rxn_2',
'rxn_4'}, {'rxn_3', 'rxn_5'}),
({'rxn_1', 'rxn_6', 'ex_A', 'rxn_3',
'rxn_5'}, {'rxn_2', 'rxn_4'})]
strategy = randomsparse.ReactionDeletionStrategy(self._mm)
essential, deleted = randomsparse.random_sparse(strategy,
self._prob,
self._obj_reaction,
flux_threshold=100)
self.assertTrue((essential, deleted) in expected)