Improve Programmatic Invokation: native python inputs

[rwnx]

Is your feature request related to a problem? Please describe. The current interface is based on the CLI, so it only accepts filepaths (or stdin). Really that should be extended to support python file inputs. There are other options that could benefit from being made pythonic.

Describe the solution you'd like I like the way this is handled in the click-style CLIs, where all files are abstracted into a readable interface. This might pose some problems with the existing gzip reading scenario, but i'm convinced we can get this in as a minimum.