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# Check arguments
args = _check_arguments(args)
# Setting up logging system
_set_logger(args.verbosity)
# Setting up PyCellBase clients
cc = ConfigClient(
{"species": _DEFAULT_SPECIES, "version": _DEFAULT_API_VERSION,
"rest": {"hosts": [_DEFAULT_HOST]}}
)
# 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
def main():
"""The main function"""
# Getting args
args = _parse_arguments()
# Check arguments
args = _check_arguments(args)
# Setting up logging system
_set_logger(args.verbosity)
# Setting up PyCellBase clients
cc = ConfigClient(
{"species": _DEFAULT_SPECIES, "version": _DEFAULT_API_VERSION,
"rest": {"hosts": [_DEFAULT_HOST]}}
)
# 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:
def main():
# Getting args
args = _parse_arguments()
# Check arguments
args = _check_arguments(args)
# Setting up logging system
_set_logger(args.verbosity)
# Setting up PyCellBase clients
cc = ConfigClient(
{"species": _DEFAULT_SPECIES, "version": _DEFAULT_API_VERSION,
"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
# Check arguments
args = _check_arguments(args)
# Setting up logging system
_set_logger(args.verbosity)
# Setting up PyCellBase clients
cc = ConfigClient(
{"species": _DEFAULT_SPECIES, "version": _DEFAULT_API_VERSION,
"rest": {"hosts": [_DEFAULT_HOST]}}
)
# 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)
args = _parse_arguments()
# Check arguments
args = _check_arguments(args)
# Setting up logging system
_set_logger(args.verbosity)
# Setting up PyCellBase clients
cc = ConfigClient(
{"species": _DEFAULT_SPECIES, "version": _DEFAULT_API_VERSION,
"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)
def main():
"""The main function"""
# Getting args
args = _parse_arguments()
# Check arguments
args = _check_arguments(args)
# Setting up logging system
_set_logger(args.verbosity)
# Setting up PyCellBase clients
cc = ConfigClient(
{"species": _DEFAULT_SPECIES, "version": _DEFAULT_API_VERSION,
"rest": {"hosts": [_DEFAULT_HOST]}}
)
# 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: