Executing an R script in python via subprocess.Popen

Question

When I execute the script in R, it is:

$ R --vanilla --args test_matrix.csv < hierarchical_clustering.R > out.txt

In Python, it works if

Answer 1

A couple of ideas:

1. You might want to consider using the Rscript frontend, which makes running scripts easier; you can pass the script filename directly as a parameter, and do not need to read the script in through standard input.
2. You don't need the shell for just redirecting standard output to a file, you can do that directly with subprocess.Popen.

Example:

import subprocess

output_name = 'something'
script_filename = 'hierarchical_clustering.R'
param_filename = '%s_DM_Instances_R.csv' % output_name
result_filename = '%s_out.txt' % output_name
with open(result_filename, 'wb') as result:
    process = subprocess.Popen(['Rscript', script_filename, param_filename],
                               stdout=result);
    process.wait()