Passing multiple arguments from python to R

Question

I have a python script that calls to multiple R scripts, so far I can successfully pass single and multiple variables, ask R to read and execute it. My current method is very crude and it is only effective when passing strings and fails with numbers. Is there an efficient way to accomplish this task?

#### Python Code
import subprocess

def rscript():
    r_path = "C:/.../R/R-3.3.2/bin/x64/Rscript"
    script = "C:/.../test.R" 

    #The separators are not recognized in R script so commas are added for splitting text
    a_list = ["C:/SomeFolder,", "abc,", "25"] 

    subprocess.call ([r_path, script, a_list], shell = True)
    print 'Script Complete'

#Execute R Function
rscript()

#### R Code
options(echo=TRUE)
args <- commandArgs(trailingOnly = TRUE)

print(args)

args1 <- strsplit(args,",") #split the string argument with ','
args1 <- as.data.frame(args1)

print(args1)

path <- as.character(args1[1,])
abc <- as.character(args1[2,])
number <- as.numeric(args1[3,])

print (path)
print (abc)
print (number)

write.table(path, file = "C:/path.txt", row.names = FALSE)
write.table(abc, file = "C:/abc.txt", row.names = FALSE)
write.table(number, file = "C:/number.txt", row.names = FALSE)

#### R - Output
> print (path)
[1] "C:/SomeFolder"
> print (abc)
[1] "abc"
> print (number)
[1] 1

Jean · Accepted Answer · 2017-03-16 02:18:32Z

5

You should concatenate [r_path, script] with a_list to produce a flat list.

script.R

options(echo=TRUE)
args <- commandArgs(trailingOnly = TRUE)
print(args)

Python repl

>>> commands = ["rscript", "script.R"]
>>> args = ["C:/SomeFolder", "abc", "25"]
>>> subprocess.call(commands + args, shell=True)
> args <- commandArgs(trailingOnly = TRUE)
>
> print(args)
[1] "C:/SomeFolder" "abc"           "25"

answered Mar 16, 2017 at 2:18

Jean

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1 Comment

cpt_python Over a year ago

Worked beautifully. I didn't even think about the list syntax for the subprocess.call().

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