def test_parses_prefix(self):
self.assertEqual(
utilities.ProteinSubstitutionEvent("p.Gly2=").prefix, "p")
def test_formats_event_string_correctly(self):
self.assertEqual(
utilities.ProteinSubstitutionEvent("p.Gly2=").event, "Gly2=")
self.assertEqual(
utilities.ProteinSubstitutionEvent("p.Gly2Leu").event, "Gly2Leu")
def test_sets_alt_as_ref_in_silent_variant(self):
self.assertEqual(
utilities.ProteinSubstitutionEvent("p.Gly2=").alt, "Gly")
def test_infers_silent(self):
self.assertEqual(
utilities.ProteinSubstitutionEvent("p.Gly2=").silent, True)
def test_parses_alt_three_letter_aa(self):
self.assertEqual(
utilities.ProteinSubstitutionEvent("p.Gly2Leu").alt, "Leu")
def test_parses_position(self):
self.assertEqual(
utilities.ProteinSubstitutionEvent("p.Gly2Leu").position, 2)
def test_strips_ws(self):
self.assertEqual(
utilities.ProteinSubstitutionEvent(" p.Gly2Leu ").variant,
"p.Gly2Leu")
def test_error_invalid_dna_substitution_syntax(self):
with self.assertRaises(exceptions.InvalidVariantType):
utilities.ProteinSubstitutionEvent("p.100_101delins")
def test_error_set_position_less_than_1(self):
pro = utilities.ProteinSubstitutionEvent("p.Gly4Leu")
with self.assertRaises(ValueError):
pro.position -= 4