Update to Synthetic Networks

[ntalluri]

Added code to make synthetic data SPRAS compatible
Added code to make the threshold interactomes with uniprot accession ids
Added code to make combined networks with pathways and threshold interactomes
Added code to do overlap analytics between the pathways and threshold interactomes

Updated TF file to use reviewed/unreviewed uniprot accession ids
Updated organization of code
Updated existing code to make easier to use

In progress of updating instructions on how to use code

Removed unused code and files

[ntalluri]

@agitter The synthetic networks are be ready to use and ready for a first pass review.

• this work builds off of oliver and altaf's branches.

[tristan-f-r]

Closed in favor of #22. (I built on top of your work by Snakemake-ifying this entire script process, and converting that R script to python 👍)

[ntalluri]

@tristan-f-r This still needed to reviewed in general for how everything was being made. If that is going to be done in #22, that is fine, otherwise this should stay open.

[tristan-f-r]

Since #22 still PRs these changes, I suspect that that will be done in #22. [Unless we had a different merge strategy for #22.]

[ntalluri]

@tristan-f-r Okay, please make a note that in #22 that the code and data for this PR #11 (and I suspect #5 as well) still needs to be fully reviewed. Whoever reviews #22 can decide on the way to break down how to review the code.