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greenelab / core-accessory-interactome

Investigating the functional relationship between P. aeruginosa core and accessory genes.
BSD 3-Clause "New" or "Revised" License
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Refactor #43

Closed ajlee21 closed 3 years ago

ajlee21 commented 3 years ago

This PR refactors the repository. The following changes were made:

  1. Rename and organize directories so that the flow of analysis makes sense
  2. Update Readme
  3. Archive old files
  4. Pull out functions from notebooks and put into scripts

Main files to look at are:

  1. Readme: README.md
  2. Script files: annotations.py, gene_relationships.py

Note: There are many files changed only because I wanted to rerun all the notebooks to verify that everything ran correctly. So most files can be ignored since they were already reviewed previously. Only the ones highlighted above need a review.