Update app.py

app.py

@@ -785,6 +785,60 @@ def run_pipeline(dna_input, similarity_score=95.0, build_ml_tree=False):
         return error_msg, "", "", "", "", None, None, None, None, error_msg, error_msg
 
 
+def run_pipeline(dna_sequence: str, similarity_threshold: float, do_phylogeny: bool):
+    try:
+        # Step 1: F Gene Extraction
+        f_gene_seq = boundary_model.predict_sequence(dna_sequence)
+        if not f_gene_seq:
+            return "❌ No F gene found", "", "", "", "F gene extraction failed", None, None, None, None, "", ""
+        
+        # Step 2: F Gene Validation
+        is_valid = keras_model.validate_sequence(f_gene_seq)
+        keras_result = "✅ Valid F gene" if is_valid else "❌ Not an F gene"
+
+        # Step 3: Save input to temp FASTA
+        temp_fasta_path = os.path.join(BASE_DIR, "input_temp.fasta")
+        SeqIO.write(SeqRecord(Seq(f_gene_seq), id="query", description=""), temp_fasta_path, "fasta")
+
+        # Step 4: Phylogenetic Placement (if enabled)
+        tree_result = ""
+        analysis_status = ""
+        summary_text = ""
+        align_file = tree_file = html_file = report_file = None
+        tree_html = report_html = "<div style='color:gray'>Skipped</div>"
+
+        if do_phylogeny:
+            # Run analyzer (wraps MAFFT + IQ-TREE + HTML visualizer)
+            outputs = analyzer.analyze(
+                input_fasta=temp_fasta_path,
+                similarity=similarity_threshold / 100.0,
+                output_dir=BASE_DIR
+            )
+            tree_result = outputs["tree_info"]
+            analysis_status = outputs["tree_status"]
+            summary_text = outputs["summary"]
+            align_file = outputs["alignment"]
+            tree_file = outputs["tree"]
+            html_file = outputs["tree_html"]
+            report_file = outputs["report"]
+            tree_html = Path(html_file).read_text() if html_file else tree_html
+            report_html = Path(report_file).read_text() if report_file else report_html
+
+        return f_gene_seq, keras_result, tree_result, analysis_status, summary_text, align_file, tree_file, html_file, report_file, tree_html, report_html
+
+    except Exception as e:
+        logging.error(f"Pipeline Error: {e}")
+        return "❌ Error during processing", "", "", "", f"Error: {e}", None, None, None, None, "", ""
+
+def run_pipeline_from_file(fasta_path, similarity_threshold: float, do_phylogeny: bool):
+    try:
+        seq_record = next(SeqIO.parse(fasta_path, "fasta"))
+        dna_sequence = str(seq_record.seq)
+        return run_pipeline(dna_sequence, similarity_threshold, do_phylogeny)
+    except Exception as e:
+        logging.error(f"File Pipeline Error: {e}")
+        return "❌ Invalid FASTA", "", "", "", f"Error: {e}", None, None, None, None, "", ""
+
 # --- Gradio Interface ---
 def create_interface():
     """Create and configure the Gradio interface"""