Merge branch 'simplify-config-files' of https://github.com/PMBio/deep…

…rvat into simplify-config-files
PMBio · May 29, 2024 · cae5521 · cae5521
2 parents 0dd831d + 64e79bb
commit cae5521
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Showing 2 changed files with 20 additions and 7 deletions.
diff --git a/deeprvat/deeprvat/config.py b/deeprvat/deeprvat/config.py
@@ -119,8 +119,11 @@ def create_main_config(
             )
         )
 
-    if no_pretrain:  
-        if all(key not in input_config["training"] for key in ["pl_trainer", "early_stopping"]):
+    if no_pretrain:
+        if all(
+            key not in input_config["training"]
+            for key in ["pl_trainer", "early_stopping"]
+        ):
             raise KeyError(
                 "Missing keys pl_trainer and/or early_stopping under config['training'] "
                 "Please review DEEPRVAT_DIR/example/config/deeprvat_input_config.yaml for list of keys."
@@ -203,7 +206,9 @@ def create_main_config(
         ]["thresholds"][k] = f"{k} {v}"
     # Results evaluation parameters; alpha parameter for significance threshold
     full_config["evaluation"] = {}
-    full_config["evaluation"]["correction_method"] = input_config["evaluation"]["correction_method"]
+    full_config["evaluation"]["correction_method"] = input_config["evaluation"][
+        "correction_method"
+    ]
     full_config["evaluation"]["alpha"] = input_config["evaluation"]["alpha"]
     # DeepRVAT model
     full_config["n_repeats"] = input_config["n_repeats"]
@@ -215,14 +220,18 @@ def create_main_config(
         # PL trainer
         full_config["training"]["pl_trainer"] = input_config["training"]["pl_trainer"]
         # Early Stopping
-        full_config["training"]["early_stopping"] = input_config["training"]["early_stopping"]
+        full_config["training"]["early_stopping"] = input_config["training"][
+            "early_stopping"
+        ]
         # Training Phenotypes
         full_config["training"]["phenotypes"] = input_config["phenotypes_for_training"]
         # Baseline results
         full_config["baseline_results"]["options"] = input_config["seed_gene_results"][
             "options"
         ]
-        full_config["baseline_results"]["alpha_seed_genes"] = input_config["seed_gene_results"]["alpha_seed_genes"]
+        full_config["baseline_results"]["alpha_seed_genes"] = input_config[
+            "seed_gene_results"
+        ]["alpha_seed_genes"]
     else:
         full_config["model"] = input_config["model"]
 
@@ -324,7 +333,9 @@ def update_config(
             else:
                 logger.info("Not performing EAC filtering of baseline results")
             logger.info(f"  Correcting p-values using {correction_method} method")
-            alpha = config["baseline_results"].get("alpha_seed_genes", config["evaluation"].get("alpha"))
+            alpha = config["baseline_results"].get(
+                "alpha_seed_genes", config["evaluation"].get("alpha")
+            )
             baseline_df = pval_correction(
                 baseline_df, alpha, correction_type=correction_method
             )

diff --git a/deeprvat/deeprvat/train.py b/deeprvat/deeprvat/train.py
@@ -849,7 +849,9 @@ def run_bagging(
 
         # initialize trainer, which will call background functionality
         trainer = pl.Trainer(
-            logger=tb_logger, callbacks=callbacks, **config["training"].get("pl_trainer", {})
+            logger=tb_logger,
+            callbacks=callbacks,
+            **config["training"].get("pl_trainer", {}),
         )
 
         while True: