Refactoring Tasks

[annaritz]

We will work with the 6 pathway reconstruction methods and the PRAUG framework. Feel free to add more as we think of them.

• [x] Make output files for all pathway reconstruction methods consistent.
• [x] Make one PRAUG function. (needs all output files to be consistent before this can happen).
• [x] Make file prefixes consistent and assembled in one place in the code base.
• [ ] Make one place where all negative files for a pathway live, rather than copy the file in different output directories?
• [x] When PRAUG with a method m is called, first look to see if m has output files.
• [x] Remove the k=500 parameter from PRAUG(PL). If you want to run this we should run main.py with k=500.
• [x] Add optional parameters to command line and also integrate throughout code. Make an args dictionary with all params?
• [ ] Modularize fileIO functions (this has already been started to some extent; also see issue #2

[annaritz]

The refactor branch has major changes. I'm going to merge to annabranch tomorrow, hopefully. In addition, I'm adding the following tasks:

• [ ] Remove unnecessary code
• [ ] Ignore pathways that cannot be run (ID, RAGE, etc.)
• [ ] Make output files for methods write directly to the DEST directory, rather than writing to the current directory and copying them over. This means that there would be no dependencies (other than ALG should be run before PRAUG-ALG).
• [ ] The argument parser is a little less flexible than it was (need to build in flexibility to just compute PR of PRAUG methods instead of calling the --runpraug command.
• [ ] Add data/interactome/etc. directory prefixes as arguments w/ defaults as they are.
• [ ] Use absolute paths for filenames (use os.file.abspath() function)