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))