#!/usr/bin/python

import sys, getopt
import os

def main(argv):
    try:
        opts, args = getopt.getopt(sys.argv[1:],"hi:o:ce", ["help", "inputfile", "outputdir", "containment", "error_tolerance"])
    except getopt.GetoptError:
        usage()
        print("Usage: %s -i inputfile -o outputdirectory -c containment -e error_tolerance" % sys.argv[0])
        sys.exit(2)

    for opt, arg in opts:
        if opt == '-h':
           print 'this_script.py -i <inputfile> -o <outputdir> -c <containment> -e <error_tolerance>'
           sys.exit()
        elif opt in ("-i", "--infile"):
           inputfile = arg    #Is this the right way to pass filename thru argument?
        elif opt in ("-o", "--outdir"):
           outputdir = arg
        elif opt == '-c':
           containment = arg
        elif opt == '-e':
           error_pct = arg

if __name__ == '__main__':
    main(sys.argv[1])


def get_overlap_data(m4_filename):
    containment_tolerance = containment
    permitted_error_pct = error_pct
    overlap_data = {}
    contained_reads = set()
    with open(m4_filename) as m4_f:
        for l in m4_f:
            # ......omitted
    return overlap_data, contained_reads

overlap_data, contained_reads = get_overlap_data(inputfile)   #This line always gave error
......

Traceback (most recent call last):
  File "learnpython01.py", line 123, in <module>
    overlap_data, contained_reads = get_overlap_data(inputfile)
NameError: name 'inputfile' is not defined