A few style changes, autopep, and adding a get_patient_id function

Changes are:

- Ran autopep8 on these files
- Did some manual line-length fixes
- Added get_patient_id function
- Added --debug-patient-id flag (which processes all input, but then post-filters to keep only a specific patient ID)
is this supposed to be an example command wrapped over two lines? should probably add a backslash if so, I thought you were showing a second command here that I couldn't parse