Update app.py

app.py

@@ -217,6 +217,11 @@ def phylogenetic_placement(sequence: str, mafft_cmd: str, iqtree_cmd: str):
         aligned_with_query = os.path.join(QUERY_OUTPUT_DIR, f"{query_id}_aligned.fa")
         output_prefix = os.path.join(QUERY_OUTPUT_DIR, f"{query_id}_placed_tree")
         if not os.path.exists(ALIGNMENT_PATH) or not os.path.exists(TREE_PATH):
+            if query_fasta and os.path.exists(query_fasta):  # Cleanup before return
+                try:
+                    os.unlink(query_fasta)
+                except Exception as cleanup_error:
+                    logger.warning(f"Failed to clean up {query_fasta}: {cleanup_error}")
             return False, "Reference alignment or tree not found.", None, None
         query_record = SeqRecord(Seq(sequence.upper()), id=query_id, description="")
         SeqIO.write([query_record], query_fasta, "fasta")
@@ -225,6 +230,11 @@ def phylogenetic_placement(sequence: str, mafft_cmd: str, iqtree_cmd: str):
                 mafft_cmd, "--add", query_fasta, "--reorder", ALIGNMENT_PATH
             ], stdout=output_file, stderr=subprocess.PIPE, text=True, timeout=600, check=True)
         if not os.path.exists(aligned_with_query) or os.path.getsize(aligned_with_query) == 0:
+            if query_fasta and os.path.exists(query_fasta):  # Cleanup before return
+                try:
+                    os.unlink(query_fasta)
+                except Exception as cleanup_error:
+                    logger.warning(f"Failed to clean up {query_fasta}: {cleanup_error}")
             return False, "MAFFT alignment failed.", None, None
         subprocess.run([
             iqtree_cmd, "-s", aligned_with_query, "-g", TREE_PATH,
@@ -232,19 +242,27 @@ def phylogenetic_placement(sequence: str, mafft_cmd: str, iqtree_cmd: str):
         ], capture_output=True, text=True, timeout=1200, check=True)
         treefile = f"{output_prefix}.treefile"
         if not os.path.exists(treefile):
+            if query_fasta and os.path.exists(query_fasta):  # Cleanup before return
+                try:
+                    os.unlink(query_fasta)
+                except Exception as cleanup_error:
+                    logger.warning(f"Failed to clean up {query_fasta}: {cleanup_error}")
             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)}"
+        if query_fasta and os.path.exists(query_fasta):  # Cleanup before return
+            try:
+                os.unlink(query_fasta)
+            except Exception as cleanup_error:
+                logger.warning(f"Failed to clean up {query_fasta}: {cleanup_error}")
         return True, success_msg, aligned_with_query, treefile
-    except Exception as main_error:  # Renamed from 'e' to avoid scoping issues
+    except Exception as main_error:  # Renamed from 'e'
         logger.error(f"Phylogenetic placement failed: {main_error}", exc_info=True)
-        return False, f"Error: {str(main_error)}", None, None
-    finally:
-        if query_fasta and os.path.exists(query_fasta):
+        if query_fasta and os.path.exists(query_fasta):  # Cleanup in except
             try:
                 os.unlink(query_fasta)
             except Exception as cleanup_error:
                 logger.warning(f"Failed to clean up {query_fasta}: {cleanup_error}")
-def analyze_sequence_for_tree(sequence: str, matching_percentage: float):
+        return False, f"Error: {str(main_error)}", None, Nonedef analyze_sequence_for_tree(sequence: str, matching_percentage: float):
     try:
         logger.debug("Starting tree analysis...")
         if not analyzer: