expr_stats.py

#!/usr/bin/env python

import argparse, sys
from argparse import RawTextHelpFormatter

__author__ = "Author (cchiang@genome.wustl.edu)"
__version__ = "$Revision: 0.0.1 $"
__date__ = "$Date: 2015-07-14 14:31 $"

# --------------------------------------
# define functions

def get_args():
    parser = argparse.ArgumentParser(formatter_class=RawTextHelpFormatter, description="\
expr_stats.py\n\
author: " + __author__ + "\n\
version: " + __version__ + "\n\
description: Basic python script template")
    parser.add_argument('-sr', '--argA', metavar='argA', type=str, required=True, help='description of argument')
    parser.add_argument('-b', '--argB', metavar='argB', required=False, help='description of argument B')
    parser.add_argument('-c', '--flagC', required=False, action='store_true', help='sets flagC to true')
    parser.add_argument('input', nargs='?', type=argparse.FileType('r'), default=None, help='file to read. If \'-\' or absent then defaults to stdin.')

    # parse the arguments
    args = parser.parse_args()

    # if no input, check if part of pipe and if so, read stdin.
    if args.input == None:
        if sys.stdin.isatty():
            parser.print_help()
            exit(1)
        else:
            args.input = sys.stdin

    # send back the user input
    return args

# primary function
def myFunction(argA, argB, flagC, file):
    for line in file:
        print line.rstrip()
    
    return

# --------------------------------------
# main function

def main():
    # parse the command line args
    args = get_args()

    # call primary function
    myFunction(args.argA, args.argB, args.flagC, args.input)

    # close the input file
    args.input.close()

# initialize the script
if __name__ == '__main__':
    try:
        sys.exit(main())
    except IOError, e:
        if e.errno != 32:  # ignore SIGPIPE
            raise