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a/workflow/rules/features/alphagenome.smk b/workflow/rules/features/alphagenome.smk index 093c335..e1386d1 100644 --- a/workflow/rules/features/alphagenome.smk +++ b/workflow/rules/features/alphagenome.smk @@ -6,3 +6,25 @@ rule run_vep_alphagenome: threads: workflow.cores shell: "python workflow/scripts/vep_alphagenome.py {input} {output} --num_workers {threads}" + + +rule alphagenome_aggregate_assay: + input: + "results/dataset/{dataset}/features/AlphaGenome_L2.parquet", + output: + "results/dataset/{dataset}/features/AlphaGenome_L2_{operation,max|mean|L2}.parquet", + run: + operation = wildcards.operation + df = pd.read_parquet(input[0]) + col_assay = df.columns.str.split("-").str[0] + assays = ["all"] + col_assay.unique().tolist() + result = {} + for assay in assays: + df_assay = df if assay == "all" else df.loc[:, col_assay == assay] + if operation == "max": + result[assay] = df_assay.max(axis=1) + elif operation == "mean": + result[assay] = df_assay.mean(axis=1) + elif operation 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