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)
# Overriding config
if args.config is not None:
cc = ConfigClient(args.config)
if args.species is not None:
cc.species = args.species
if args.api_version is not None:
cc.version = args.api_version
if args.host is not None:
cc.host = args.host
if args.assembly is not None:
assembly = args.assembly
else:
assembly = _DEFAULT_ASSEMBLY
cbc = CellBaseClient(cc)
if args.which == 'xref':
# Getting available databases
databases = _get_databases_list(cbc, assembly)
# Filtering databases with include and exclude
include = args.include.split(',') if args.include is not None else None
exclude = args.exclude.split(',') if args.exclude is not None else None
databases = _filter_databases(databases, include=include,
exclude=exclude)
# Converting IDs
convert_ids(input_fpath=args.input_fpath,
output_fpath=args.output_fpath,
cellbase_client=cbc,
assembly=assembly,
# Overriding config
if args.config is not None:
cc = ConfigClient(args.config)
if args.species is not None:
cc.species = args.species
if args.api_version is not None:
cc.version = args.api_version
if args.host is not None:
cc.host = args.host
if args.assembly is not None:
assembly = args.assembly
else:
assembly = _DEFAULT_ASSEMBLY
# Setting up pycellbase clients
cbc = CellBaseClient(cc)
xc = cbc.get_xref_client()
# Printing available species and databases lists
if args.list_species:
for species in _get_species_list(cbc, assembly):
print(species)
return
if args.list_databases:
for database in _get_databases_list(xc, assembly):
print(database)
return
# Getting available databases
databases = _get_databases_list(xc, assembly)
# Converting IDs
"rest": {"hosts": [_DEFAULT_HOST]}}
)
if args.config is not None:
cc = ConfigClient(args.config)
if args.species is not None:
cc.species = args.species
if args.api_version is not None:
cc.version = args.api_version
if args.host is not None:
cc.host = args.host
if args.assembly is not None:
assembly = args.assembly
else:
assembly = _DEFAULT_ASSEMBLY
cbc = CellBaseClient(cc)
calculate_hgvs(args.input, args.output_fpath, cbc, args.ref_seq_type,
assembly)
#!/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'])))