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:
