fix: updating config paths and fine-mapping methods #725
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ireneisdoomed
approved these changes
Aug 8, 2024
| @@ -40,7 +41,7 @@ def __init__( | |||
| credible_set = ( | |||
| StudyLocus.from_parquet( | |||
| session, credible_set_path, recursiveFileLookup=True | |||
| ).filter(col("finemappingMethod") == "SuSie") | |||
| ).filter(col("finemappingMethod").isin("SuSie", "SuSiE-inf")) | |||
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Ideally we want to have all finemapping methods inside a directory so that we could import them and not hard code these values. We did something similar for coloc https://github.com/opentargets/gentropy/blob/bc1a1124b0744895f2ce246c23b62861ea600288/src/gentropy/colocalisation.py For the future
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Sure - I've just done this as a temporary fix. After this release we'll probably put together fine-mapping dictionary which includes all the different methods and the parameters for them.
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✨ Context
🛠 What does this PR implement
Updating the config paths for variant-to-gene in locus-to-gene-train/predict.
Also included SuSiE-inf as a possible option when filtering by fine mapping method for colocalisation step.
🙈 Missing
🚦 Before submitting
devbranch?make test)?poetry run pre-commit run --all-files)?