Comments (3)
alexlenail
commented on July 23, 2024
@AmandaKedaigle This is currently lines 18-42. It represents the interface to the script (which is currently called garnet.py (the only file in src/). The help messages are the ones you would get if you did garnet.py --help (and they show up in other places too). Ideally they would be written for maximum clarity for people inside and outside the lab to use. Hopefully they're nice and short, about a sentence.
The description, on the other hand, should be longer, probably about a paragraph. It should mostly explain the weird design decision we made whereby 4 different things can happen depending on what files are passed in. It doesn't need to explain everything that Garnet does in general.
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AmandaKedaigle
commented on July 23, 2024
from garnet.
alexlenail
commented on July 23, 2024
Woo! Thanks!
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Related Issues (20)
- Python version compatability HOT 2
- MotifMap has transfac IDs HOT 1
- MotifMap takes too long to load into RAM -- could we use a database? HOT 1
- Map Motifs to Gene Symbols HOT 2
- TF Regression Error HOT 9
- Include TF "targets" in output HOT 3
- check files exist HOT 1
- What does motif score mean? HOT 14
- Garnet file stuck loading HOT 1
- Bedtools can perform map_peaks function in ~1 min HOT 7
- Comparison: Garnet file generation HOT 1
- TF regression drop duplicates HOT 4
- `TF_regression` not working properly on server (or locally either) HOT 2
- Filter out unreasonable regressions HOT 2
- GarNet File has inconsistent naming convention for record: HOT 5
- mm9, mm10 garnet file construction notebooks HOT 3
- Window optional param HOT 3
- Idea for speed optimization.
- TODO: update garnet construction function HOT 3
- TODO: autofetch reference files HOT 1
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