From 120968f45288905b10dba990ed438e30ddc61695 Mon Sep 17 00:00:00 2001
From: Eva Holtkamp <eva.holtkamp@gmx.de>
Date: Thu, 12 Oct 2023 16:51:16 +0200
Subject: [PATCH] require MAF column argument

---
 deeprvat/seed_gene_discovery/seed_gene_discovery.py | 9 ++-------
 pipelines/seed_gene_discovery.snakefile             | 1 +
 2 files changed, 3 insertions(+), 7 deletions(-)

diff --git a/deeprvat/seed_gene_discovery/seed_gene_discovery.py b/deeprvat/seed_gene_discovery/seed_gene_discovery.py
index c0518310..933c3577 100644
--- a/deeprvat/seed_gene_discovery/seed_gene_discovery.py
+++ b/deeprvat/seed_gene_discovery/seed_gene_discovery.py
@@ -469,7 +469,7 @@ def update_config(
     simulated_phenotype_file: str,
     variant_type: Optional[str],
     rare_maf: Optional[float],
-    maf_column: Optional[str],
+    maf_column: str,
     new_config_file: str,
 ):
     with open(old_config_file) as f:
@@ -479,12 +479,7 @@ def update_config(
         config["data"]["dataset_config"][
             "sim_phenotype_file"
         ] = simulated_phenotype_file
-    if maf_column is None:
-        annotations = config["data"]["dataset_config"]["annotations"]
-        af_pattern = re.compile(r".*(_MAF|_AF|MAF)\b")
-        rare_maf_col = [s for s in annotations if af_pattern.match(s)]
-        assert len(rare_maf_col) == 1
-        maf_column = rare_maf_col[0]
+    logger.info(f'Reading MAF column from column {maf_column}')
 
     if phenotype is not None:
         config["data"]["dataset_config"]["y_phenotypes"] = [phenotype]
diff --git a/pipelines/seed_gene_discovery.snakefile b/pipelines/seed_gene_discovery.snakefile
index 0aa03d97..7a93ac26 100644
--- a/pipelines/seed_gene_discovery.snakefile
+++ b/pipelines/seed_gene_discovery.snakefile
@@ -261,6 +261,7 @@ rule config:
         "seed_gene_pipeline update-config "
                     + "--phenotype {wildcards.phenotype} "
                     + "--variant-type {wildcards.vtype} "
+                    + "--maf-column MAF "
                     + "--rare-maf "
                     + "{params.rare_maf}"
                     + " {input.config} "