def test_gimme_model(self):
f = ['gene\texpression', 'gene_1\t15', 'gene_2\t20',
'gene_3\t15', 'gene_4\t25', 'gene_5\t10', 'gene_6\t25']
threshold_dict = gimme.parse_transcriptome_file(f, 20)
mm_irreversible, reversible_gene_assoc, split_rxns = \
gimme.make_irreversible(self._mm, self._assoc,
exclude_list=['ex_A', 'rxn_6'])
p = fluxanalysis.FluxBalanceProblem(mm_irreversible, generic.Solver())
final_model, used_exchange, below_threshold_ids, incon_score = \
gimme.solve_gimme_problem(p, mm_irreversible, 'rxn_6',
reversible_gene_assoc, split_rxns, threshold_dict, MaybeRelative(20))
self.assertEqual(incon_score, 100)
self.assertEqual(final_model, set(['rxn_1', 'rxn_2', 'rxn_4']))
self.assertEqual(below_threshold_ids, set(['rxn_1', 'rxn_3', 'rxn_5']))
def test_invalid(self):
with self.assertRaises(ValueError):
arg = MaybeRelative('abc')
def test_resolve_relative(self):
arg = MaybeRelative('40%')
arg.reference = 200.0
self.assertAlmostEqual(float(arg), 80.0)
def test_init_from_percentage(self):
arg = MaybeRelative('110%')
self.assertTrue(arg.relative)
self.assertIsNone(arg.reference)
with self.assertRaises(ValueError):
float(arg)
def test_init_from_float_string(self):
arg = MaybeRelative('-10')
self.assertFalse(arg.relative)
self.assertIsNone(arg.reference)
self.assertAlmostEqual(float(arg), -10.0)
def test_init_from_float(self):
arg = MaybeRelative(24.5)
self.assertFalse(arg.relative)
self.assertIsNone(arg.reference)
self.assertAlmostEqual(float(arg), 24.5)
def test_resolve_relative(self):
arg = MaybeRelative('40%')
arg.reference = 200.0
self.assertAlmostEqual(float(arg), 80.0)