I am trying to run the following code in Python which calls a Bash script file and saves its output to a variable. I am trying to use subprocess.check_output but it raises an error to the effect of "No such file or directory". subprocess.call does not work either. Here is a bit of my code.
answer = subprocess.check_output(['/directory/bashfile.bash -c /directory/file -i input -o output'])
print answer
-c -i and -o are just arguments to the script bashfile.
The problem is that you are passing the entire command string rather than splitting them into args. You either need to pass it as a shell command:
answer = subprocess.check_output('/directory/bashfile.bash -c /directory/file -i input -o output',
shell=True)
print answer
Or you need to tokenize it yourself:
answer = subprocess.check_output(['/directory/bashfile.bash',
'-c', '/directory/file',
'-i', 'input',
'-o', 'output'])
print answer
For more information about subprocess refer to the docs (python 3 version here)! Specifically you will want to read the section about "Frequently used arguments"
