def parseArguments(self, args):
''' Parse user options and call the correct pipeline'''
# Load the workDirectory
wd_loc = str(os.path.abspath(args.work_directory))
wd = WorkDirectory(wd_loc)
# Set up the logger
self.setup_logger(wd.get_loc('log'))
logging.debug(str(args))
# Call the appropriate workflow
if args.operation == "dereplicate":
self.dereplicate_operation(**vars(args))
if args.operation == "compare":
self.compare_operation(**vars(args))
if args.operation == "filter":
self.filter_operation(**vars(args))
if args.operation == "cluster":
self.cluster_operation(**vars(args))
if args.operation == "analyze":
self.analyze_operation(**vars(args))
if args.operation == "choose":
self.choose_operation(**vars(args))
if args.operation == "adjust":
self.adjust_operation(**vars(args))
if args.operation == "bonus":
self.bonus_operation(**vars(args))
if args.operation == "evaluate":
self.evaluate_operation(**vars(args))
def parseArguments(self, args):
''' Parse user options and call the correct pipeline'''
if args.operation == 'check_dependencies':
drep.d_bonus.check_dependencies(print_out=True)
return
# Load the workDirectory
wd_loc = str(os.path.abspath(args.work_directory))
wd = WorkDirectory(wd_loc)
# Set up the logger
self.setup_logger(wd.get_loc('log'))
logging.debug(str(args))
# Do some testing
if args.run_tertiary_clustering:
if args.operation != "dereplicate":
raise ValueError(
"Can only run tertiary clustering with dereplicate")
# Call the appropriate workflow
if args.operation == "dereplicate":
self.dereplicate_operation(**vars(args))
if args.operation == "compare":
self.compare_operation(**vars(args))