A batch file will not run when called from Python - python-3.x

Question

I'm trying to automate some file processing that occurs when you do data analysis on fastq files using STRaitRazor. Briefly, the files themselves are gzipped and the batch file looks into these contents, pulls out necessary information and then stores it in a new folder it creates. This works well manually but when I tried to use Python to call the batch file, the window opens for a split second and then disappears without running.
I've included the basic code I'm using here. There are no error messages but the batch file does not run. I've tried substituting "call" with "Popen" and "run" in the syntax and that also has not worked.
import subprocess
batch = "C:\\STRaitRazor\\Analysis\\fastq\\Data_2\\batchCstr8.bat"
subprocess.call([r"%s"%batch])

Answer 1

First off, I'd recommend calling this script from the command line to see what errors it outputs. But, as a guess, I'm assuming the batch file fails because it's not being run from the directory it expects to be run from, you'll want to change to it's directory first:
import subprocess
import os
batch = "C:\\STRaitRazor\\Analysis\\fastq\\Data_2\\batchCstr8.bat"
# Get the current directory, and change to the directory that batch file is in
previous_dir = os.getcwd()
os.chdir(os.path.dirname(batch))
# Run the batch file (note: don't need the % operator here, also, use check_call
# to raise an exception if calling the batch file fails)
subprocess.check_call([batch])
# Change back to the old working directory, not necessary, but helpful
# if there are any other steps to run after the batch file is done
os.chdir(previous_dir)