def test_random_sparse_gene_strategy(self):
expected = [({'gene_1', 'gene_2'}, {'gene_3', 'gene_4'}),
({'gene_1', 'gene_3'}, {'gene_2', 'gene_4'})]
strategy = randomsparse.GeneDeletionStrategy(self._mm, self._assoc)
essential, deleted = randomsparse.random_sparse(strategy,
self._prob,
self._obj_reaction,
flux_threshold=100)
self.assertTrue((essential, deleted) in expected)
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._assoc = {'rxn_2': boolean.Expression('gene_1 or gene_2')}
self._strategy = randomsparse.GeneDeletionStrategy(
self._mm, self._assoc)