a-r-j / graphein

Protein Graph Library
https://graphein.ai/
MIT License
1.03k stars 131 forks source link

Add GRN support #48

Closed rvinas closed 3 years ago

rvinas commented 3 years ago

This PR constructs GRNs networks by downloading data from public databases. Currently, it supports TRRUST and RegNetwork, but others can be added in the future. I tried to follow the coding conventions from PPI networks. It would be great to double-check the following:

a-r-j commented 3 years ago

Hey @rvinas will review this now. I had a look at the docs for RegNetwork. I think -/- means the directionality is unknown. I can't make sense of -p and it happens infrequently enough that it's probably safe to assign to unknown.

codecov-io commented 3 years ago

Codecov Report

Merging #48 (a223817) into graphein-api (6c946d9) will decrease coverage by 1.89%. The diff coverage is 0.43%.

Impacted file tree graph

@@               Coverage Diff                @@
##           graphein-api      #48      +/-   ##
================================================
- Coverage         19.33%   17.43%   -1.90%     
================================================
  Files                25       33       +8     
  Lines              1583     1870     +287     
================================================
+ Hits                306      326      +20     
- Misses             1277     1544     +267     
Impacted Files Coverage Δ
graphein/grn/config.py 0.00% <0.00%> (ø)
graphein/grn/edges.py 0.00% <0.00%> (ø)
graphein/grn/features/node_features.py 0.00% <0.00%> (ø)
graphein/grn/graphs.py 0.00% <0.00%> (ø)
graphein/grn/parse_regnetwork.py 0.00% <0.00%> (ø)
graphein/grn/parse_trrust.py 0.00% <0.00%> (ø)
graphein/utils.py 31.03% <25.00%> (ø)
... and 5 more

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