parse_input.py

# Functions for parsing command line arguments (YAML file) for HDIprep
# Developer: Joshua M. Hess, BSc
# Developed at the Vaccine & Immunotherapy Center, Mass. General Hospital

# Import external modules
import argparse


def ParseCommandYAML():
    """Function for parsing command line arguments for input to YAML HDIprep"""

    # if __name__ == '__main__':
    parser = argparse.ArgumentParser()
    parser.add_argument("--im", nargs='*')
    parser.add_argument("--pars")
    parser.add_argument("--out_dir")
    args = parser.parse_args()
    # Create a dictionary object to pass to the next function
    dict = {"im": args.im, "pars": args.pars, "out_dir": args.out_dir}
    # Print the dictionary object
    print(dict)
    # Return the dictionary
    return dict