Python passing filename through argument Post: 302951770

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Top Forums Programming Python passing filename through argument Post 302951770 by yifangt on Monday 10th of August 2015 01:53:24 PM

08-10-2015

Registered User

Python passing filename through argument

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

Code:

#!/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:

Code:

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!

yifangt

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set_color

set_color(1)							       fish							      set_color(1)

NAME

       set_color - set_color - set the terminal color

set_color - set the terminal color
   Synopsis
       set_color [-v --version] [-h --help] [-b --background COLOR] [COLOR]

   Description
       Change the foreground and/or background color of the terminal. COLOR is one of black, red, green, brown, yellow, blue, magenta, purple,
       cyan, white and normal.

       o -b, --background Set the background color

       o -c, --print-colors Prints a list of all valid color names

       o -h, --help Display help message and exit

       o -o, --bold Set bold or extra bright mode

       o -u, --underline Set underlined mode

       o -v, --version Display version and exit

       Calling set_color normal will set the terminal color to whatever is the default color of the terminal.

       Some terminals use the --bold escape sequence to switch to a brighter color set. On such terminals, set_color white will result in a grey
       font color, while set_color --bold white will result in a white font color.

       Not all terminal emulators support all these features. This is not a bug in set_color but a missing feature in the terminal emulator.

       set_color uses the terminfo database to look up how to change terminal colors on whatever terminal is in use. Some systems have old and
       incomplete terminfo databases, and may lack color information for terminals that support it. Download and install the latest version of
       ncurses and recompile fish against it in order to fix this issue.

Version 1.23.1							  Sun Jan 8 2012						      set_color(1)

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