mokapot: Fix writing of FlashLFQ output when PSMList run field is empty

compomics · Apr 7, 2024 · ed6423b · ed6423b
1 parent c5677a3
commit ed6423b
Showing 1 changed file with 4 additions and 0 deletions.
diff --git a/ms2rescore/rescoring_engines/mokapot.py b/ms2rescore/rescoring_engines/mokapot.py
@@ -171,6 +171,10 @@ def convert_psm_list(
     feature_df.columns = [f"feature:{f}" for f in feature_df.columns]
     combined_df = pd.concat([psm_df[required_columns], feature_df], axis=1)
 
+    # Ensure filename for FlashLFQ txt output
+    if not combined_df["run"].notnull().all():
+        combined_df["run"] = "ms_run"
+
     feature_names = [f"feature:{f}" for f in feature_names] if feature_names else None
 
     lin_psm_data = LinearPsmDataset(