Closed rvinas closed 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.
Merging #48 (a223817) into graphein-api (6c946d9) will decrease coverage by
1.89%
. The diff coverage is0.43%
.
@@ 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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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:
datasets/<name of database>
.root_dir = os.path.dirname(os.path.realpath("../"))
. Perhaps there's a better way to achieve this?-p
and-/-
mean exactly. I am mapping them to the unknown class?
.