def test_ens2sym(self):
client=SmartClient()
id_types=['gene_ensembl','gene_symbol']
key='2'.join(id_types)
cache_path=client._get_cache_path(id_types)
client.load(id_types)
self.assertTrue(os.path.exists(cache_path)) # newly created
self.assertIn(key, client.tables, 'no %s in tables' % key)
ens2sym=client.get_map(*id_types)
self.assertEqual(ens2sym['ENSG00000011021'],'CLCN6')
def test_ens2sym(self):
client=SmartClient()
id_types=['gene_ensembl','gene_symbol']
key='2'.join(id_types)
cache_path=client._get_cache_path(id_types)
print 'deleting %s' % cache_path
try: os.unlink(cache_path)
except OSError: pass
client.load(id_types)
self.assertTrue(os.path.exists(cache_path)) # newly created
self.assertIn(key, client.tables, 'no %s in tables' % key)
self.assertTrue(hasattr(client, key))
f=getattr(client,key)
self.assertTrue(callable(f), 'client.%s not callable (%s)' % (key, type(f)))
self.assertTrue(hasattr(client, 'tables'), 'client has no attr "tables"')
self.assertEqual(type(getattr(client, 'tables')), type({}))
self.assertEqual(client.gene_ensembl2gene_symbol('ENSG00000011021'),'CLCN6')
def get_output_map(output_type):
client=SmartClient()
client.load(['gene_known',output_type])
return client.get_map('gene_known', output_type)