Question

so I have a python script which takes the filename as a command argument and processes that file. However, because I have 263 files which need the same processing, I was wondering whether the command argument section could be modified with a for loop to consecutively run through all the files in a folder? Cheers, Sat

EDIT:

The code for the system argument is here:

try:
    opt_list, args = getopt.getopt(sys.argv[1:], 'r:vo:A:Cp:U:eM:')

except getopt.GetoptError, msg:
    print 'prepare_receptor4.py: %s' %msg
    usage()
    sys.exit(2)

with ‘r’ being the name of the file needing to be processed and the others are optional arguments. I’m not sure how to modify this with a for loop.

Answer 1

As a practical matter, whatever shell you’re using probably has some syntax that can be easily used for this. In Bash, for example:

for f in *; do python myscript.py $f; done

To actually do this in Python, I’d suggest structuring your program so that the main code is in a function which takes one argument, the filename.

def process(filename):
    ...code goes here...

Then you can invoke this function like so,

for f in os.listdir(folder):
    process(f)

folder could be passed as a command-line argument, or just written into the script (if it’s not something you’d be reusing).

EDIT: In response to your edit, I’d suggest just giving the filenames as regular command-line arguments, without using the -r option, so that they’ll wind up in args. Then you can do

for f in args:
    process(f)

or if you would rather pass the directory name as the command-line argument,

for d in args:
    for f in os.listdir(d):
        process(f)

Alternatively, I suppose you could pass multiple instances of the -r option, and then do

for opt, arg in opt_list:
    if opt == '-r':
        process(arg)