Update app.py

app.py

@@ -244,7 +244,7 @@ def create_kmer_shap_csv(kmers, shap_values):
     temp_path = os.path.join(temp_dir, f"kmer_shap_values_{os.urandom(4).hex()}.csv")
     kmer_df.to_csv(temp_path, index=False)
     
-    return temp_path
+    return temp_path, "kmer_shap_values.csv"
 
 def analyze_sequence(file_obj, top_kmers=10, fasta_text="", window_size=500):
     if fasta_text.strip():
@@ -1000,11 +1000,12 @@ def load_example_fasta():
         return example_text
     except Exception as e:
         return f">example_sequence\nACGTACGT...\n\n(Note: Could not load example.fasta: {str(e)})"
-        
+
 ###############################################################################
 # 14. BUILD GRADIO INTERFACE
 ###############################################################################
 
+
 css = """
 .gradio-container {
     font-family: 'IBM Plex Sans', sans-serif;
@@ -1031,37 +1032,42 @@ with gr.Blocks(css=css) as iface:
                 file_input = gr.File(label="Upload FASTA file", file_types=[".fasta", ".fa", ".txt"], type="filepath")
                 text_input = gr.Textbox(label="Or paste FASTA sequence", placeholder=">sequence_name\nACGTACGT...", lines=5)
                 
+                # Add example FASTA button in a row
                 with gr.Row():
                     example_btn = gr.Button("Load Example FASTA", variant="secondary")
                 
                 top_k = gr.Slider(minimum=5, maximum=30, value=10, step=1, label="Number of top k-mers to display")
                 win_size = gr.Slider(minimum=100, maximum=5000, value=500, step=100, label="Window size for 'most pushing' subregions")
                 analyze_btn = gr.Button("Analyze Sequence", variant="primary")
+            
             with gr.Column(scale=2):
                 results_box = gr.Textbox(label="Classification Results", lines=12, interactive=False)
                 kmer_img = gr.Image(label="Top k-mer SHAP")
                 genome_img = gr.Image(label="Genome-wide SHAP Heatmap (Blue=neg, White=0, Red=pos)")
                 
-                with gr.Row():
-                    download_kmer_shap = gr.File(label="Download k-mer SHAP Values (CSV)", visible=True)
-                    download_results = gr.File(label="Download Results", visible=False, elem_classes="download-button")
+                # Make both download buttons visible
+                download_kmer_shap = gr.File(label="Download k-mer SHAP Values (CSV)", visible=True)
+                download_results = gr.File(label="Download Results", visible=True, elem_classes="download-button")
         
         seq_state = gr.State()
         header_state = gr.State()
 
         # Event handlers
+        # Connect the example button
         example_btn.click(
             load_example_fasta,
             inputs=[],
             outputs=[text_input]
         )
         
+        # Important: Make sure we have 7 outputs to match the 7 values returned by analyze_sequence
         analyze_btn.click(
             analyze_sequence,
             inputs=[file_input, top_k, text_input, win_size],
             outputs=[results_box, kmer_img, genome_img, seq_state, header_state, download_results, download_kmer_shap]
         )
 
+
     with gr.Tab("2) Subregion Exploration"):
         gr.Markdown("""
         **Subregion Analysis**