Update app.py

app.py

@@ -649,7 +649,7 @@ def run_pipeline(dna_input, similarity_score=95.0, build_ml_tree=False):
         else:
             ml_tree_output = "Phylogenetic placement skipped (not requested)"
 
-        # Step 4: NEW Simplified Tree Analysis (using the new analyzer API)
+               # Step 4: NEW Simplified Tree Analysis (using the new analyzer API)
         html_file = None
         tree_html_content = "No tree generated"
         simplified_ml_output = ""
@@ -673,13 +673,13 @@ def run_pipeline(dna_input, similarity_score=95.0, build_ml_tree=False):
                    with open(html_filename, 'r', encoding='utf-8') as f:
                        tree_html_content = f.read()
             
-                  simplified_ml_output = tree_result
-                  logging.info(f"Tree analysis completed successfully. HTML saved to: {html_filename}")
+                   simplified_ml_output = tree_result
+                   logging.info(f"Tree analysis completed successfully. HTML saved to: {html_filename}")
                else:
                  simplified_ml_output = tree_result or "❌ Failed to generate tree visualization"
                  logging.warning("Tree analysis failed or no HTML output generated")
             
-            except Exception as e:
+           except Exception as e:
                 simplified_ml_output = f"❌ Simplified ML tree analysis failed: {str(e)}"
                 logging.error(f"Simplified ML tree analysis failed: {e}")
         elif not analyzer:
@@ -687,7 +687,7 @@ def run_pipeline(dna_input, similarity_score=95.0, build_ml_tree=False):
         elif len(processed_sequence) < 10:
              simplified_ml_output = "❌ Sequence too short for tree analysis (minimum 10 bp)"
         else:
-             simplified_ml_output = "Tree analysis skipped"
+             simplified_ml_output = "Tree analysis skipped" 
         # Prepare final outputs
         final_boundary_output = f"F gene sequence ({len(processed_sequence)} bp):\n{boundary_output}"
         final_keras_output = f"F gene validation: {keras_output}"