def test_nh_ext2(self, callMock):
self.func_args['prediction_method'] = 'rnafold'
a, b, c = repredict_structures_for_homol_seqs(**self.func_args)
self.assertIsNone(a)
self.assertIsNone(b)
self.assertTrue(
c[0].startswith('Query sequence contains ambiguous characters'))
def test_TurboFold(self, callMock):
self.func_args['prediction_method'] = 'Turbo-fast'
self.func_args['threads'] = 1
a, b, c = repredict_structures_for_homol_seqs(**self.func_args)
# check that sequences are returned does not have Turbofold structure and have error message that turbo failed
for s in a:
self.assertNotIn('ss0', s.letter_annotations)
self.assertEqual(['expected_error_TurboFold'],
s.annotations['msgs'])
def test_wrong_pm(self):
self.func_args['prediction_method'] = 'blabla'
with self.assertRaises(AssertionError):
a, b, c = repredict_structures_for_homol_seqs(**self.func_args)
def test_hybrid_ss_min(self, callMock):
self.func_args['prediction_method'] = 'fq-sub'
a, b, c = repredict_structures_for_homol_seqs(**self.func_args)
self.assertIsNone(a)
self.assertIsNone(b)
self.assertEqual(c, ["expected_error_hybrid_ss_min"])
def test_clustalo_profile(self, callMock):
self.func_args['prediction_method'] = 'C-A-r-Rc'
a, b, c = repredict_structures_for_homol_seqs(**self.func_args)
self.assertIsNone(a)
self.assertIsNone(b)
self.assertEqual(c, ["expected_error_clustalo"])
def test_nh_ext(self, callMock):
self.func_args['prediction_method'] = 'rnafold'
a, b, c = repredict_structures_for_homol_seqs(**self.func_args)
self.assertIsNone(a)
self.assertIsNone(b)
self.assertTrue(c[0].startswith('No sequence was inferred homologous'))
def test_muscle(self, callMock):
self.func_args['prediction_method'] = 'M-A-U-r-Rc'
a, b, c = repredict_structures_for_homol_seqs(**self.func_args)
self.assertIsNone(a)
self.assertIsNone(b)
self.assertEqual(c, ["expected_error_muscle"])
def test_centroid_homfold(self, callMock):
self.func_args['prediction_method'] = 'centroid-fast'
a, b, c = repredict_structures_for_homol_seqs(**self.func_args)
self.assertIsNone(a)
self.assertIsNone(b)
self.assertEqual(c, ["expected_error_centroid"])
def test_cmalign(self, callMock):
self.func_args['prediction_method'] = 'rfam-Rc'
a, b, c = repredict_structures_for_homol_seqs(**self.func_args)
self.assertIsNone(a)
self.assertIsNone(b)
self.assertEqual(c, ["expected_error_cmalign"])
def test_rnafold(self, callMock):
self.func_args['prediction_method'] = 'rnafold'
a, b, c = repredict_structures_for_homol_seqs(**self.func_args)
self.assertIsNone(a)
self.assertIsNone(b)
self.assertEqual(c, ['expected_error_rnafold'])