include shell command into program python

Question

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I'm currently trying to implement a program that includes the following shell command:

/home/myfolder/ParZu/parzu -l tagged < /home/myfolder/raw_text_de/raw_text_de0.txt >/home/myfolder/raw_text_de0_parsed.txt

/home/myfolder/ParZu/parzu is the program I want to run, -l and tagged are options to go with the program and I want to feed in my raw_text_de0.txt and write the result into another file raw_text_de0_parsed.txt.

The thing is, that I have to do this more than 400 times (for file raw_text_de1.txt, raw_text_de2.txt....), which is why I really want to automatize it.

I tried several things that have been suggested here on Stackoverflow, but none seems to work. My current attempt looks as follows:

path_texts = '/home/myfolder/raw_text_de'
filename = os.listdir(path_texts)

##create list of filenames ('/home/myfolder/raw_text_de/raw_text_de0.txt', ...)
infile_list = []
for fname in filename: 
    new_filename = '/home/myfolder/raw_text_de/' + fname
    infile_list.append(new_filename)

##go through the files in the infile_list and include it in shell command
for item in infile_list: 
    p = subprocess.call(['/home/myfolder/ParZu/parzu', '-l', 'tagged', '<', item, '>', item + 'parsed.txt'])

However, this doesn't work. It apparently calls the program, but then gets stuck. I know that it is difficult to answer this question without being able to try it, but I hope someone has an idea about what could be wrong or missing.

wouldn't os.commandline() work?

sshashank124
– sshashank124

2014-03-18 10:08:18 +00:00
Commented Mar 18, 2014 at 10:08 — sshashank124
– sshashank124, Commented Mar 18, 2014 at 10:08

Logan Ding · Accepted Answer · 2014-03-18 10:18:38Z

1

subprocess.call has two arguments: stdin and stdout. Take advantage of them instead of putting the redirection operators > and < in the arguments.

In your case:

for item in infile_list: 
    infile = file(item)
    outfile = file(item + 'parsed.txt','w')
    p = subprocess.call(['/home/myfolder/ParZu/parzu', '-l', 'tagged'], stdin=infile, stdout=outfile)
    infile.close()
    outfile.close()

answered Mar 18, 2014 at 10:18

Logan Ding

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QuestionEverything · Accepted Answer · 2014-03-18 10:16:30Z

It would have been better if you could print some of your outputs of that call here.

However, I guess the problem is in your parameters of that call.

Here is the proper argument list of subprocess.call()

subprocess.call(args, *, stdin=None, stdout=None, stderr=None, shell=False)
subprocess.call(["ls", "-l"])

And you can check the return result of your call individually just to make sure it's working fine.

subprocess.check_call(args, *, stdin=None, stdout=None, stderr=None, shell=False)
subprocess.check_call(["ls", "-l"])

subprocess.check_output(args, *, stdin=None, stderr=None, shell=False, universal_newlines=False)
subprocess.check_output(["echo", "Hello World!"])

Details could be found here:

subprocess doc

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