How to use data stream from bash with subprocess in python

Question

I am trying to call a process in linux bash using data stream signal '<' to use a file as input to an application.

However, this application do not receives its input from the file. I am using this:

#the application do not receives data stream from file

command = './grid < /home/felipe/Documents/proteins/grid.in'.split(' ')

p = subprocess.Popen(command,stdout=subprocess.PIPE)

But it does not work such as os.system(), that did what I want to do with subprocess:

#works
command = './grid < /home/felipe/Documents/proteins/grid.in'.split(' ')

os.system(command)

How can I use data stream signal '<' with subprocess module to get input to an application?

No. `<` is a *shell* operator. In subprocess you should open the file yourself and pass it to `Popen` as `stdin`. — iBug, Jan 21 '19 at 13:06
@iBug thanks a lot. There is a more detailed answer below that shows a example of how to do it :D — Guilherme Barsoti, Jan 21 '19 at 15:26

score 1 · Accepted Answer · answered Jan 21 '19 at 14:06

1

If you just wanted to use Python as a shell wrapper, you would have to launch your (sub)process with shell=True. But since you're already using Python, you may want to rely on Python more and on shell less, you could do the following:

with open('/home/felipe/Documents/proteins/grid.in') as in_file:
    p = subprocess.Popen('./grid', stdin=in_file)

This opens your input file as in_file and feeds it into standard input of ./grid just like shell redirection would do.

answered Jan 21 '19 at 14:06

Ondrej K.

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Thanks a lot. I think that is the best way to do what I need. I will try it soon to the result. This application runs in an sever that I can't access right now. Soon I will let you know if it worked to me. :) – Guilherme Barsoti Jan 21 '19 at 15:23
It really work to me. Once more, thanks for your help. – Guilherme Barsoti Feb 06 '19 at 18:47

How to use data stream from bash with subprocess in python

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