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Duplicate score_column in predict.py #235

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nttg8100 opened this issue Aug 27, 2024 · 1 comment
Open

Duplicate score_column in predict.py #235

nttg8100 opened this issue Aug 27, 2024 · 1 comment

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@nttg8100
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This one is already defined in the argument of the command line, I think if the hic file does not exist, it will return the "" for hic params.
https://github.com/broadinstitute/ABC-Enhancer-Gene-Prediction/blob/main/workflow/rules/predictions.smk#L10C3-L10C41

@mayasheth
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Looking at the code actually making predictions, it appears this argument is not actually ever used-- it was initially used in to allow users to binarize predictions that were generated when Hi-C data is provided (in which case ABC.Score uses Hi-C for contact and powerlaw.Score uses the power law to estimate contact) by either score column.

We modified the code for downstream applications so that when no Hi-C file is provided, the ABC.Score column is identical to powerlaw.Score. Therefore, it is always recommended to filter by ABC.Score.

Thanks for flagging this redundancy.

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