Using R to run Python with command line arguments

Question

I'm trying to use R to run a Python script. I'm creating an R script that calls my Python script. I need to do this from the command prompt and pass along 3 arguments (latitude, longitude, and year) in integer form. Below is my R script:

args <- commandArgs(trailingOnly = TRUE)
lat_desired = args[1]
lon_desired = args[2]
year_desired = args[3]
system('/home/ "import sys; sys.stdout.write(file(\'python_file\', \'r\').read());"; python python_file lat_desired, lon_desired, year_desired')

My python script reads the lat_desired/lon_desired/year_desired arguments and converts them to integers (shown below):

line4 > lat_desired = int(sys.argv[1])
line5 > lon_desired = int(sys.argv[2])
line6 > year_desired = int(sys.argv[3])

When I run all of this in the command prompt I get this: Error: invalid literal for int() with base 10. Any ideas on how to pass along command line arguments from my R script to my Python script?

Perhaps you should print sys.argv from your python script to see what it's getting. — Steven Rumbalski
– Steven Rumbalski, Commented Dec 3, 2015 at 21:29
Maybe try running things from a batch file and call the commands there. Maybe have the R script write a csv that python will open. I've used this method to link several programs for modeling purposes. — CCurtis
– CCurtis, Commented Dec 3, 2015 at 21:54

doicomehereoften1 · Accepted Answer · 2015-12-03 22:33:31Z

2

In system() you're passing the strings "lat_desired", "lon_desired", and "year_desired". You need to do a little bit of text processing before passing all of this into system(). You can also make it a little bit more compact.

args <- commandArgs(trailingOnly = TRUE)
command <- sprintf(
    '/home/ "import sys; sys.stdout.write(file(\'python_file\', \'r\').read());"; python python_file %s, %s, %s',
    args[1], args[2], args[3])
system(command)

Also, you could just convert these to integers in R if you're going to be continuing to work with them in R.

args <- as.integer(commandArgs(trailingOnly = TRUE))

answered Dec 3, 2015 at 22:33

doicomehereoften1

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