File Path/Global name issue

John Gordon gordon at panix.com
Thu Mar 20 22:31:15 CET 2014


In <2089d20b-aa60-462f-aad0-51109849cf36 at googlegroups.com> roy.snuffles at gmail.com writes:

> I am currently running code for a program called HotNet (https://github.com/raphael-group/hotnet)

> In its simpleRun.py file, there is a place to insert a file path to be run. 

> parser.add_argument('-mf', '--infmat_file', required=True,
>                         help='Path to .mat file containing influence matrix')

> My path file is /home/lai/Downloads/influence_matrix_files/hprd_inf_.mat

You're completely misunderstanding the purpose of this line of code.  Its
intent is to allow you to pass the matrix file location to the script by
using the '-mf' or '--infmat_file' arguments, thus not requiring you to
edit the script at all.

The 'help' parameter provides a message explaining the usage of that
particular argument if the simpleRun.py script is executed with the '-help'
option.

For example, if you were unsure how to use the simpleRun.py script, you
might run this command:

    simpleRun.py -help

And you might see output that looks like this:

    Usage: simpleRun.py [options]

    Options:
      -h, --help            show this help message and exit
      -mf, --infmat_file    Path to .mat file containing influence matrix
      -d, --dance           do a little dance
      -l, --love            make a little love

The help message thus informs you that you can provide the location to an
influence matrix file by using the '-mf' or '--infmat_file' arguments.
There are also -d and -l options that do ... something.

-- 
John Gordon         Imagine what it must be like for a real medical doctor to
gordon at panix.com    watch 'House', or a real serial killer to watch 'Dexter'.




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