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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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LEARN ABOUT DEBIAN

colorgccrc

COLORGCCRC(5)							File Formats Manual						     COLORGCCRC(5)

NAME

       colorgccrc - configuration file for colorgcc

DESCRIPTION

       A colorgccrc configuration file is used to configure the highlighting of the compiler output from colorgcc.

SYNTAX

       Each  line  consists  of  a  keyword  designating  a configuration variable.  The keyword is followed by `:' and then one or several values
       (depending on the keyword).  Lines beginning with a hash mark `#' are comments.

CONFIGURATION VARIABLES

       g++ | gcc | c++ | cc | g77 | gcj | gnat | gpc
	      Specifies the paths to the compilers.  Takes one value; a path to the compiler.

       nocolor
	      Specifies what terminal types colorization should be disabled on.  Takes one or several values, separated by whitespace.

       srcColor
	      Specifies the highlighting attributes source-code should be given.  Takes one or several color attributes.  See  the  section  COLOR
	      ATTRIBUTES for more information.

       introColor
	      Specifies  the  highlighting  attributes	for normal compiler output.  Takes one or several color attributes.  See the section COLOR
	      ATTRIBUTES for more information.

       warningFileNameColor | errorFileNameColor
	      Specifies the highlighting attributes for the filename in a  warning  or	an  error,  respectively.   Takes  one	or  several  color
	      attributes.  See the section COLOR ATTRIBUTES for more information.

       warningNumberColor | errorNumberColor
	      Specifies  the  highlighting  attributes	for  the  line-number  in a warning or an error, respectively.	Takes one or several color
	      attributes.  See the section COLOR ATTRIBUTES for more information.

       warningMessageColor | errorMessageColor
	      Specifies the highlighting attributes for the message-text in a warning or an error,  respectively.   Takes  one	or  several  color
	      attributes.  See the section COLOR ATTRIBUTES for more information.

COLOR ATTRIBUTES

       The following attributes are valid for highlighting.

       clear, reset

       bold, underline, underscore, blink, reverse, concealed

       black, red, green, yellow, blue, magenta, cyan, white

       on_black, on_red, on_green, on_yellow, on_blue, on_magenta, on_cyan, on_white

SEE ALSO

       gcc(1), colorgcc(1)

HISTORY

       Jan 15 2003: Initial version of this manual-page.

REPORTING BUGS

       Report bugs to <jmoyers@geeks.com>

AUTHORS

       Jamie Moyers <jmoyers@geeks.com> is the author of colorgcc.

       This  manual  page  was	written  by Joe Wreschnig <piman@sacredchao.net>, and modified by David Weinehall <tao@debian.org>, for the Debian
       GNU/Linux system (but may be used by others).

COPYRIGHT

       Copyright (C) 2003 Jamie Moyers
       This is free software; see the source for copying conditions.  There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICU-
       LAR PURPOSE.

								   Jan 15, 2003 						     COLORGCCRC(5)

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