def test_simple_substitution_case(self): var_c = Variant(hgvs_c['SUB']) lex = LVG(var_c) query = GoogleQuery(lex) assert query.startswith( '"SCN5A" ("4786T>A"|"T4786A"|"4786T-->A"|"4786T/A"|"4786T->A"') assert query.find('4732T->A') > -1 assert query.find('4783T-->A') > -1
def googlequery(hgvs_text): gq = GoogleQuery(lex) return gq
def test_no_duplicate_terms_in_query(self): hgvs_text = "NM_000722.2:c.355-5dupT" lex = LVG(hgvs_text) query = GoogleQuery(lex) posedits = query.strip('"CACNA2D1" (').strip(')').split('|') assert len(posedits) == len(set(posedits))
def test_dup_intronic(self): hgvs_text = "NM_000722.2:c.355-5dupT" lex = LVG(hgvs_text) query = GoogleQuery(lex) assert query.startswith( '"CACNA2D1" ("355-5dupT"|"355-5dup"|"355-14dupT"|"355-14dup"')
def test_ins_case(self): var_c = Variant(hgvs_c['INS']) lex = LVG(var_c) query = GoogleQuery(lex)
def test_dup_case(self): var_c = Variant(hgvs_c['DUP']) lex = LVG(var_c) query = GoogleQuery(lex)
def test_frameshift_case(self): var_c = Variant(hgvs_c['FS']) lex = LVG(var_c) query = GoogleQuery(lex)
def test_deletion_case(self): var_c = Variant(hgvs_c['DEL']) lex = LVG(var_c) query = GoogleQuery(lex)
def setUp(self): self.test_lex = LVGEnriched('NM_000125.3:c.1339_1340delTGinsGC') self.test_gq = GoogleQuery(self.test_lex)
class TestGoogleQuery(unittest.TestCase): def setUp(self): self.test_lex = LVGEnriched('NM_000125.3:c.1339_1340delTGinsGC') self.test_gq = GoogleQuery(self.test_lex) def tearDown(self): pass def test_query_c(self): assert self.test_gq.query_c( ) == '"ESR1" ("1339_1340delTGinsGC"|"1345_1346delTGinsGC"|"1336_1337delTGinsGC")' def test_query_g(self): assert self.test_gq.query_g( ) == '"ESR1" ("152382229_152382230delTGinsGC")' def test_query_p(self): assert self.test_gq.query_p( ) == '"ESR1" ("Cys447Ala"|"C447A"|"Cys446Ala"|"C446A"|"Cys449Ala"|"C449A")' def test_query_n(self): assert self.test_gq.query_n( ) == '"ESR1" ("1600_1601delTGinsGC"|"1557_1558delTGinsGC"|"1573_1574delTGinsGC"|"1563_1564delTGinsGC"|"1709_1710delTGinsGC"|"1554_1555delTGinsGC")' def test_simple_substitution_case(self): var_c = Variant(hgvs_c['SUB']) lex = LVG(var_c) query = GoogleQuery(lex) assert query.startswith( '"SCN5A" ("4786T>A"|"T4786A"|"4786T-->A"|"4786T/A"|"4786T->A"') assert query.find('4732T->A') > -1 assert query.find('4783T-->A') > -1 #assert query.find( def test_deletion_case(self): var_c = Variant(hgvs_c['DEL']) lex = LVG(var_c) query = GoogleQuery(lex) def test_frameshift_case(self): var_c = Variant(hgvs_c['FS']) lex = LVG(var_c) query = GoogleQuery(lex) def test_indel_case(self): var_c = Variant(hgvs_c['INDEL']) lex = LVG(var_c) query = GoogleQuery(lex) def test_dup_case(self): var_c = Variant(hgvs_c['DUP']) lex = LVG(var_c) query = GoogleQuery(lex) def test_ins_case(self): var_c = Variant(hgvs_c['INS']) lex = LVG(var_c) query = GoogleQuery(lex) def test_dup_intronic(self): hgvs_text = "NM_000722.2:c.355-5dupT" lex = LVG(hgvs_text) query = GoogleQuery(lex) assert query.startswith( '"CACNA2D1" ("355-5dupT"|"355-5dup"|"355-14dupT"|"355-14dup"') def test_no_duplicate_terms_in_query(self): hgvs_text = "NM_000722.2:c.355-5dupT" lex = LVG(hgvs_text) query = GoogleQuery(lex) posedits = query.strip('"CACNA2D1" (').strip(')').split('|') assert len(posedits) == len(set(posedits))