motif mode should not be part of learn_decoy_implementation branch

[biodataganache]

The motif mode is part of a separate branch effort but there are references to it here. For example in the demo

https://github.com/PNNL-CompBio/Snekmer/blob/learn_decoy_implementation/resources/tutorial/demo_example/run_demo.sh

So this needs to be removed from this branch (it doesn't function here)

[biodataganache]

This is a bit more of a question than an issue: I know Tara had been working on actual analysis that might go in to a paper, etc. using motif mode. It's not clear to me that we should be lumping these in with the decoy scoring and updates to l/a - or maybe they need to be?

[christinehc]

The demo hasn't been updated since we added motif mode and reflects testing of motif mode, hence why it is the way it is.

I wonder if we should split the demo per mode (i.e. separate .sh files)? Functionally may be more useful to new users