This script is an example for using argparse and logging module in one script!

bare_logging_argparse_example.py

#!/usr/bin/env python

# File created by Tabea Kischka at Mon Aug  1 2016


import sys
import os
import argparse
import logging

script_description = """This is an example for using logging and argparse module.
"""

# MAIN
if __name__ == "__main__":
    # parse arguments
    parser = argparse.ArgumentParser(description=script_description)
    parser.add_argument('infile',
                        help="input vcf file with SnpEff annotation",
                        nargs='?',
                        type=argparse.FileType('r'),
                        default=sys.stdin)
    parser.add_argument("-d",
                        help="run in debug mode, print lots of information",
                        action="store_const",
                        dest="loglevel",
                        const=logging.DEBUG,
                        default=logging.WARNING)
    parser.add_argument("-v",
                        help="run in verbose mode, print some more information",
                        action="store_const",
                        dest="loglevel",
                        const=logging.INFO,
                        default=logging.WARNING)
    args = parser.parse_args()

    # set up logging module
    logging.basicConfig(format='[%(asctime)s - %(levelname)s] %(message)s',
                        datefmt='%Y-%m-%d %H:%M:%S',
                        level=args.loglevel)
    logger = logging.getLogger(__name__)
    logger.debug("logging set up!")
    logger.debug("All arguments: %s" % args)
    logger.info("Script starts!")

    convert_vcf(args.infile)


def convert_vcf(infile):
    """
    Runs the conversion
    """
    logger.debug("Will use file %s" % infile)