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!

Answer 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).