open file in Python using "python scriptname.py filename"

Question

I am a novice to python scripting. I have a script that I am hoping to run on all files in a directory. I found very helpful advice in this thread. However, I am having difficulty in determining how to format the actual script so that it retrieves the filename of the file that I want to run the script on in the command prompt, i.e. "python script.py filename.*" I've tried my best at looking through the Python documentation and the forums in this site and have come up empty (I probably just don't know what keywords I should be searching).

I am currently able to run my script on one file at a time, and output it with a new file extension using the following code, but this way I can only do one file at a time. I'd like to be able to iterate over the whole directory using 'GENE.*':

InFileName = 'GENE.303'

InFile = open(InFileName, 'r') #opens a pipeline to the file to be read line by line

OutFileName = InFile + '.phy'

OutFile = open(OutFileName, 'w')

What can I do to the code to allow myself to use an iteration through the directory similar to what is done in this case? Thank you!

NPE · Accepted Answer · 2013-01-15 14:50:37Z

1

You are looking for:

import sys
InFileName = sys.argv[1]

See the documentation.

For something more sophisticated, take a look at the optparse and argparse modules (the latter is preferable but is only available in newer versions of Python).

answered Jan 15, 2013 at 14:50

NPE

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moooeeeep · Accepted Answer · 2013-01-15 15:02:51Z

0

You have quite a few options to process a list of files using Python:

You can use the shell expansion facilities of your command line to pass more filenames to your script and then iterate the command line arguments:

import sys

def process_file(fname):
    with open(fname) as f:
        for line in f:
            # TODO: implement
            print line

for fname in sys.argv[1:]:
    process_file(fname)

and call it like:

python my_script.py * # expands to all files in the directory

You can also use the glob module to do this expansion:

import glob

for fname in glob.glob('*'):
    process_file(fname)

edited Jan 15, 2013 at 15:02

answered Jan 15, 2013 at 14:56

moooeeeep

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