Interacting with R script via Python subprocess

Question

I was wondering how to open an R script and interact with it (for example, send strings, integers etc.). Although I have not used it before, subprocess seemed like a reasonable way to do this.

So far, I have

process = subprocess.Popen(['/path/to/Rscript --no-save path/to/script.R'], stdout=subprocess.PIPE, stdin=subprocess.PIPE, shell=True)

This appears to be successful in opening script.R, however in my script I prompt the user to enter an integer and I cannot quite sort out how to do this. I have tried:

process.communicate(input=1)[0]

But I appear to be barking up the wrong tree. The subprocess closes without appearing to receive this input.

EDIT: Rpy is probably not a good alternative at this point, because users of this script will not necessarily have access to that module and its dependencies.

Right - good question, I should have specified that I see no visible output as a result of process.communicate(input=1) — J R
– J R, Commented Apr 2, 2013 at 14:39

lcgong · Accepted Answer · 2013-04-04 03:07:47Z

2

Try PypeR ?

It is an great interface to use R in python through pipe.

answered Apr 4, 2013 at 3:07

lcgong

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J R Over a year ago

This was really useful, thanks. I was able to send commands through to my scripts using this approach.

User · Accepted Answer · 2013-04-02 14:47:50Z

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EDIT2

What about that?

process = subprocess.Popen(['/path/to/Rscript', '--no-save', 'path/to/script.R'], stdout=subprocess.PIPE, stdin=subprocess.PIPE)

EDIT1

You can only comunicate strings between processes over stdin and stdout.

Does process.communicate("1\n") help you out?

edited Apr 2, 2013 at 14:47

answered Apr 2, 2013 at 14:03

User

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2 Comments

J R Over a year ago

Unfortunately, no. The string vs int distinction does not matter, because the process closes before the input can be passed.

J R Over a year ago

Yes, that seems to help. I can now pipe strings to the subprocess via process.stdin.write('source("script.R")') That's a step forward, thanks!

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