def _tstv(variant, vtype): """Returns a pair of bools indicating Transition, Transversion status.""" if vtype == BIALLELIC_SNP: is_transition = variant_utils.is_transition(variant.reference_bases, variant.alternate_bases[0]) is_transversion = not is_transition else: is_transition = is_transversion = False return is_transition, is_transversion
def test_is_transition_raises_with_bad_args(self): with self.assertRaises(ValueError): variant_utils.is_transition('A', 'A') with self.assertRaises(ValueError): variant_utils.is_transition('A', 'AA') with self.assertRaises(ValueError): variant_utils.is_transition('AA', 'A')
def test_is_transition(self, ordered_alleles, expected): for alleles in [ordered_alleles, reversed(ordered_alleles)]: self.assertEqual(variant_utils.is_transition(*alleles), expected)