Commit e2a2707f authored by Vermaat's avatar Vermaat
Browse files

Fix typo in batch SNP converter

parent f545acd9
......@@ -728,7 +728,7 @@ Mutalyzer batch scheduler""" % download_url)
descriptions = []
descriptions = ncbi.rsid_to_descriptions(rs_id)
descriptions = ncbi.rsid_to_descriptions(cmd)
except ncbi.ServiceError:
O.addMessage(__file__, 4, 'EENTREZ',
'An error occured while communicating with '
......@@ -69,6 +69,36 @@ def test_syntax_checker():
_batch_job_plain_text(variants, expected, 'syntax-checker')
def test_snp_converter():
Simple SNP converter batch job.
snps = ['rs9919552']
expected = [['rs9919552',
# Patch Bio.Entrez.efetch to return dbSNP record for rs9919552.
def mock_efetch(*args, **kwargs):
path = os.path.join(os.path.dirname(os.path.realpath(__file__)),
return bz2.BZ2File(path)
with patch.object(Entrez, 'efetch', mock_efetch):
_batch_job_plain_text(snps, expected, 'snp-converter')
def test_large_input():
Simple batch job with large input.
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