Add two step classifier

alphadia/constants/default.yaml

@@ -225,6 +225,7 @@ fdr:
   keep_decoys: false
   channel_wise_fdr: false
   inference_strategy: "heuristic"
+  enable_two_step_classifier: false
 
 search_output:
   peptide_level_lfq: false

alphadia/fdr.py

@@ -10,6 +10,8 @@
 import pandas as pd
 import sklearn
 
+import alphadia.fdrexperimental as fdrx
+
 # alphadia imports
 # alpha family imports
 from alphadia import fragcomp
@@ -168,6 +170,23 @@ def perform_fdr(
     return psm_df
 
 
+def perform_fdr_new(
+    classifier: fdrx.Classifier,
+    available_columns: list[str],
+    df: pd.DataFrame,
+    group_columns,
+    **kwargs,
+):
+    df.dropna(subset=available_columns, inplace=True)
+    psm_df = classifier.fit_predict(
+        df,
+        available_columns + ["score"],
+        "decoy",
+        group_columns,
+    )
+    return psm_df
+
+
 def keep_best(
     df: pd.DataFrame,
     score_column: str = "proba",