def parse_args(): # setup the parser add_subparsers() parser = base.get_parser() subpars = base.get_subparser() subpars.required = True args = parser.parse_args() # parse directory file list # (requires input_directory_parser to be included) try: args.find_files(args) except AttributeError: pass # protect file names protect = ['summary', 'root_dir', 'data_dir'] for p in protect: try: setattr(args, p, path.protect(getattr(args, p))) except TypeError: pass # arg might not be set (is None) return args
def add_subparsers(): '''Use this function to add subparsers from modules''' subparser = base.get_subparser() fastq_parser = FastqScripted(subparser) fastq_parser.setup()
def main(): pass if __name__ == '__main__': # setup logger import logging from remsci.lib.utility import customLogging customLogging.config() log = logging.getLogger(__name__) # setup the parser add_subparsers() parser = base.get_parser() subpars = base.get_subparser() subpars.required = True args = parser.parse_args() # parse directory file list # (requires input_directory_parser to be included) try: args.find_files(args) except AttributeError: pass # call the default function try: file_list = args.func(args) except AttributeError: