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)