Update app.py

app.py

@@ -208,7 +208,7 @@ def check_tool_availability():
 
 # --- Pipeline Functions ---
 def phylogenetic_placement(sequence: str, mafft_cmd: str, iqtree_cmd: str):
-    query_fasta = None
+    query_fasta = None  # Predefine to avoid scoping issues
     try:
         if len(sequence.strip()) < 100:
             return False, "Sequence too short (<100 bp).", None, None
@@ -235,11 +235,10 @@ def phylogenetic_placement(sequence: str, mafft_cmd: str, iqtree_cmd: str):
             return False, "IQ-TREE placement failed.", aligned_with_query, None
         success_msg = f"Placement completed!\nQuery ID: {query_id}\nAlignment: {os.path.basename(aligned_with_query)}\nTree: {os.path.basename(treefile)}"
         return True, success_msg, aligned_with_query, treefile
-    except Exception as e:
-        logger.error(f"Phylogenetic placement failed: {e}", exc_info=True)
-        return False, f"Error: {str(e)}", None, None
+    except Exception as main_error:  # Renamed from 'e' to avoid scoping issues
+        logger.error(f"Phylogenetic placement failed: {main_error}", exc_info=True)
+        return False, f"Error: {str(main_error)}", None, None
     finally:
-        # FIXED: Properly handle cleanup with specific exception handling
         if query_fasta and os.path.exists(query_fasta):
             try:
                 os.unlink(query_fasta)