Thanks for the discussion. I ended up doing something similar to the code snippet Christian posted, except I also had a second try/except FileNotFoundError within the original finally block to catch the case that David pointed out.

In retrospect, I probably should have used TemporaryDirectory since I am using Python 3.5 and because the file I was creating with NamedTemporaryFile was only being used as an output file, not an input file, to the subprocess command.