how to call python script from R with arguments

Question

I have a python script which takes some 5 arguments( a filename, 3 int values and 2 float values). I need to call this python script from R. How can I do that. I am trying to use rPython, but it doesnt allow me to pass the argument

library("rPython")
python.load("python scriptname")

I dont know how to pass the arguments

from command line, i run my python script like:

python scriptname filename 10 20 0.1 5000 30

What does example(python.load) or ?python.load tell you? — Oliver Frost
– Oliver Frost, Commented Jan 13, 2017 at 16:01
Check if this is relevant stackoverflow.com/questions/40667328/… — Ronak Shah
– Ronak Shah, Commented Jan 13, 2017 at 16:05

Stefan Avey · Accepted Answer · 2017-12-18 22:12:42Z

36

You can invoke a system command

system('python scriptname')

To run the script asynchronously you can set the wait flag to false.

system('python scriptname filename 10 20 0.1 5000 30', wait=FALSE)

The arguments that get passed as they would in command line. You will have to use sys.argv in the python code to access the variables

#test.py
import sys

arg1 = sys.argv[1]
arg2 = sys.argv[2]
print arg1, arg2

The R command below would output 'hello world'

system('python test.py hello world', wait=FALSE)

edited Dec 18, 2017 at 22:12

Stefan Avey

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answered Jan 13, 2017 at 15:59

badger0053

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6 Comments

user1631306 Over a year ago

great. but system commands waits for the python program to get completed. is there any way it wont wait,

badger0053 Over a year ago

@user1631306 yes, Documentation is here. add wait=False

AHegde Over a year ago

So using this I'd have to manually type in the entire path to a file if I'm passing a text file as an argument. Is there a way to instead give it a variable name that has the path stored in it? This way I can automate my R script for any input text file.

AHegde Over a year ago

Never mind, I found the "system2" command in R with a bit of Googling: mango-solutions.com/blog/…

Peter.k Over a year ago

> system('python --version') Warning message: running command 'python --version' had status 127

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Andrii · Accepted Answer · 2017-08-27 20:10:15Z

9

There is a small typo in the great previous answer. The right code is the following:

 system('python test.py hello world', wait = FALSE)

where wait is FALSE (not wait=Flase or wait=False)

answered Aug 27, 2017 at 20:10

Andrii

3,11332 silver badges37 bronze badges

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