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
import docopt
from text2gene.api import LVG, GoogleQuery
__doc__ = """googlequery
Usage:
googlequery <hgvs>
googlequery --help
Options:
-h, --help Show this screen.
"""
lex = LVG("NM_000014.5:c.2998A>G")
def googlequery(hgvs_text):
gq = GoogleQuery(lex)
return gq
def gq_cli(args):
print('Using Google to find sources for ', args['<hgvs>'])
print(googlequery(args['<hgvs>']))
def main():
args = docopt.docopt(__doc__)
gq_cli(args)
print()
print('PUBTATOR')
print()
print('%i HGVS examples found in ClinVarDB.samples' % len(hgvs_examples))
print()
def dmesg(hgvs_text, msg):
print('[%s] <%i> %s' % (hgvs_text, time.time(), msg))
for entry in hgvs_examples:
hgvs_text = entry['HGVS']
dmesg(hgvs_text,
'processing in PubTator (test case) and ClinVar (identity case)')
lex = LVG(hgvs_text)
#try:
pmids = PubtatorHgvs2Pmid(lex)
dmesg(hgvs_text, 'Pubtator PMIDs: %r' % pmids)
#except Exception as error:
# dmesg(hgvs_text, '%r' % error)
#try:
pmids = ClinvarHgvs2Pmid(lex)
dmesg(hgvs_text, 'ClinVar PMIDs: %r' % pmids)
#except Exception as error:
# dmesg(hgvs_text, '%r' % error)
dmesg(hgvs_text, 'done')
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)