def test_rna_del(self): statement = 'var(r.1653_1655delcuu)' expected = hgvs('r.1653_1655delcuu') result = self.parser.parseString(statement) self.assertEqual(expected, result.asDict())
def test_protein_trunc_legacy(self): statement = 'var(p.65*)' result = self.parser.parseString(statement) expected = hgvs('p.65*') self.assertEqual(expected, result.asDict())
def test_chromosome_1(self): statement = 'variant(g.117199646_117199648delCTT)' expected = hgvs('g.117199646_117199648delCTT') result = self.parser.parseString(statement) self.assertEqual(expected, result.asDict())
def test_chromosome_2(self): statement = 'var(c.1521_1523delCTT)' expected = hgvs('c.1521_1523delCTT') result = self.parser.parseString(statement) self.assertEqual(expected, result.asDict())
def test_unspecified(self): statement = 'var(=)' expected = hgvs('=') result = self.parser.parseString(statement) self.assertEqual(expected, result.asDict())
def test_frameshift(self): statement = 'variant(p.Thr1220Lysfs)' expected = hgvs('p.Thr1220Lysfs') result = self.parser.parseString(statement) self.assertEqual(expected, result.asDict())
def test_protein_mut(self): statement = 'var(p.Gly576Ala)' expected = hgvs('p.Gly576Ala') result = self.parser.parseString(statement) self.assertEqual(expected, result.asDict())
def test_trunc_1(self): statement = 'trunc(40)' result = self.parser.parseString(statement) expected = hgvs('p.40*') self.assertEqual(expected, result.asDict())
def test_protein_del_quoted(self): statement = 'variant("p.Phe508del")' expected = hgvs('p.Phe508del') result = self.parser.parseString(statement) self.assertEqual(expected, result.asDict())
def test_gsub(self): statement = 'sub(G,308,A)' result = self.parser.parseString(statement) expected_dict = hgvs('c.308G>A') self.assertEqual(expected_dict, result.asDict())
def test_psub_2(self): statement = 'sub(Ala, 127, Tyr)' result = self.parser.parseString(statement) expected_list = hgvs('p.Ala127Tyr') self.assertEqual(expected_list, result.asDict())