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self._tfbs_client = None
self._regulation_client = None
self._species_client = None
self._meta_client = None
# Setting up config params
if config_client is not None:
if isinstance(config_client, ConfigClient):
self._configuration = config_client
else:
msg = ('CellBaseClient configuration not properly set.' +
' "pycellbase.config.ConfigClient" object is needed as' +
' parameter')
raise ValueError(msg)
else:
self._configuration = ConfigClient()
#!/usr/bin/python
# Loading CellBase and configuration clients
from pycellbase.cbconfig import ConfigClient
from pycellbase.cbclient import CellBaseClient
# Initializing CellBaseClient
cc = ConfigClient("../conf/client-configuration.yml")
cbc = CellBaseClient(cc)
# Initializing gene client
gc = cbc.get_gene_client()
# Retrieving transcription factor binding sites (TFBS) for a gene list
gene_list = ['BRCA1', 'BRCA2', 'LDLR']
tfbs_responses = gc.get_tfbs(gene_list, include='id')
# Printing the number of TFBS found for each gene
for response in tfbs_responses:
print('Number of TFBS for "%s": %d' % (response['id'], len(response['result'])))
self._transcript_client = None
self._protein_client = None
self._variation_client = None
self._xref_client = None
self._region_client = None
self._variant_client = None
self._genome_sequence_client = None
self._clinical_client = None
self._tfbs_client = None
self._regulation_client = None
self._species_client = None
self._meta_client = None
# Setting up config params
if config_client is not None:
if isinstance(config_client, ConfigClient):
self._configuration = config_client
else:
msg = ('CellBaseClient configuration not properly set.' +
' "pycellbase.config.ConfigClient" object is needed as' +
' parameter')
raise ValueError(msg)
else:
self._configuration = ConfigClient()