Recombination step: Add input flexibility

[dominiquesydow]

Hi Paula,

Thanks a lot for the detailed README instructing the user how to run your code - and I really like the intuitive way of using the CLI!

Procedure

I tried to run the recombination step directly after the fragmentation step, i.e. without doing the fragment analysis step where you produce cluster centroids -- no worries, I am using only a few input ligands here :).

Observation

Apparently, it is currently not possible to run the recombination with the full set of fragments, but only with these cluster centroids.

Questions

• Could we make the recombination step more generic, so that one can run the full or reduced fragment library?
• In any case, could you specify in the README which notebooks need to be run in order to produce the output needed for the recombination step? Currently, it only says:

Fragment analysis: Jupyter notebooks for analyzing the fragment library are stored in kinase_focused_fragment_library/analysis/fragment_analysis/.

I am posting this issue for us to discuss on Friday.

[dominiquesydow]

Change input paths (fragment library) in kinase_focused_fragment_library/recombination/cli.py and in associated files.