Python passing filename through argument

Applications Programming
1

Hello,
A python beginner question on passing filename thru argument. My code is:

#!/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
......

but I always got error as:

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

I was wondering what the right way it is to pass filename thru argument in python. Related lines are highlighted in red.
Thanks a lot!

2

With python, error debuging starts at the bottom - with the 'last' error found
Also, to parse options, you should loop through the arguments, and use a case statement to identify the current option name 'opt' (which was retrieved from arg[v]).

Have a look at: info getopt and continue reading (PGDN).
Also checkout man getopt , to get a possible location for code Examples.

Hope this helps

3

Note also that inputfile is only defined if a -i inputfile option is present on the command line.

Maybe you want to define it with a default value in case that option is not present. Or, if there is no reasonable default, print an error message and exit if no -i option was found while parsing the options.

4

What I expected to have the script working in following command line:

python learnpython01.py -i infile -o outdir -c 500 -e 2

Could not find examples on handling file I/O stream.
I have difficulty to understand string[file] I/O stream here. In the example code, the function prototype is
def get_overlap_data(m4_filename):
and, calling of the function is by
overlap_data, contained_reads = get_overlap_data(inputfile)
where inputfile = arg from argument parsing.
I am not sure what I have missed among the connections, if any stream is involved.
Thanks any way!

5

The inputfile name is defined inside the function main, so it is out of scope when you're calling

overlap_data, contained_reads = get_overlap_data(inputfile)

, so you could just call get_overlap_data from inside of main, after handling all the args.

6

I regret posting this naive questions before I read the book(s). After some more reading and found out one solution:

overlap_data, contained_reads = get_overlap_data(sys.argv[1])

Need more about getopt() and argparse (as Aia pointed out below) in python.
Thanks to all who replied.

7

Try to learn about argparse instead of getopt .
Some documentation why getopt or optparse might not be the right solution.

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