Update app.py

app.py

@@ -87,8 +87,8 @@ def simulate_digest_and_plot_gradio(plasmid_seq_record, enzyme_name, plasmid_lab
     ax.set_xticks([])
     ax.tick_params(axis='y', labelsize=8)
 
-    well_top_y = ax.get_ylim()[0]
-    well_line_y = well_top_y * 1.01
+    well_top_y = ax.get_ylim()[0] 
+    well_line_y = well_top_y * 1.01 
     well_depth_y = well_top_y * 0.98
 
     ax.plot([lane_center - band_width/1.5, lane_center + band_width/1.5], [well_line_y, well_line_y], 
@@ -103,12 +103,15 @@ def simulate_digest_and_plot_gradio(plasmid_seq_record, enzyme_name, plasmid_lab
 
 def analyze_plasmids_gradio(file1_path, file2_path, current_plasmid_choice_for_plot):
     """
-    Analyzes two plasmid files to find unique restriction enzymes.
-    Returns status messages, plasmid data, lists of unique enzyme names,
+    Analyzes two plasmid files to find unique restriction enzymes and
+    enzymes that cut both plasmids but with different fragmentation patterns.
+    Returns status messages, plasmid data, lists of enzyme names,
     and an update for the enzyme selection dropdown.
     """
     initial_enzyme_dd_update = gr.update(choices=["Analyze plasmids first"], value="Analyze plasmids first", interactive=False)
-    
+    empty_return_for_error = ["", "", "", None, None, [], [], [], initial_enzyme_dd_update]
+
+
     # Check if example files exist if paths match example paths
     example_file_error_msg = ""
     if file1_path == EXAMPLE_PLASMID1_PATH and not os.path.exists(EXAMPLE_PLASMID1_PATH):
@@ -117,11 +120,11 @@ def analyze_plasmids_gradio(file1_path, file2_path, current_plasmid_choice_for_p
         example_file_error_msg += f"Example file not found: {EXAMPLE_PLASMID2_PATH}. Please create it in the '{EXAMPLE_DIR}' directory.\n"
     
     if example_file_error_msg:
-         return example_file_error_msg, "", "", None, None, [], [], initial_enzyme_dd_update
+          return example_file_error_msg, *empty_return_for_error
 
 
     if file1_path is None or file2_path is None:
-        return "Error: Please upload or load both plasmid files.", "", "", None, None, [], [], initial_enzyme_dd_update
+        return "Error: Please upload or load both plasmid files.", *empty_return_for_error
 
     try:
         def read_plasmid(filepath, filename_for_error):
@@ -140,7 +143,7 @@ def analyze_plasmids_gradio(file1_path, file2_path, current_plasmid_choice_for_p
         plasmid2_seq_rec = read_plasmid(file2_path, p2_orig_filename)
 
     except Exception as e:
-        return str(e), "", "", None, None, [], [], initial_enzyme_dd_update
+        return str(e), *empty_return_for_error
 
     valid_enzyme_objects = []
     for enz_name in AllEnzymes.elements():
@@ -152,17 +155,17 @@ def analyze_plasmids_gradio(file1_path, file2_path, current_plasmid_choice_for_p
                  valid_enzyme_objects.append(enzyme_obj)
 
     if not valid_enzyme_objects:
-         return "Error: Could not load any restriction enzymes from Biopython.", "", "", None, None, [], [], initial_enzyme_dd_update
+        return "Error: Could not load any restriction enzymes from Biopython.", *empty_return_for_error
 
     enzymes_batch = RestrictionBatch(valid_enzyme_objects)
     analysis1 = Analysis(enzymes_batch, plasmid1_seq_rec.seq, linear=False)
     analysis2 = Analysis(enzymes_batch, plasmid2_seq_rec.seq, linear=False)
 
-    enzymes_cutting_p1 = set(analysis1.with_sites().keys())
-    enzymes_cutting_p2 = set(analysis2.with_sites().keys())
+    enzymes_cutting_p1_obj = set(analysis1.with_sites().keys())
+    enzymes_cutting_p2_obj = set(analysis2.with_sites().keys())
 
-    unique_to_1_obj = sorted(list(enzymes_cutting_p1 - enzymes_cutting_p2), key=lambda e: str(e))
-    unique_to_2_obj = sorted(list(enzymes_cutting_p2 - enzymes_cutting_p1), key=lambda e: str(e))
+    unique_to_1_obj = sorted(list(enzymes_cutting_p1_obj - enzymes_cutting_p2_obj), key=lambda e: str(e))
+    unique_to_2_obj = sorted(list(enzymes_cutting_p2_obj - enzymes_cutting_p1_obj), key=lambda e: str(e))
 
     unique_to_1_names = [str(e) for e in unique_to_1_obj]
     unique_to_2_names = [str(e) for e in unique_to_2_obj]
@@ -173,9 +176,32 @@ def analyze_plasmids_gradio(file1_path, file2_path, current_plasmid_choice_for_p
     msg1 = f"Enzymes cutting only {p1_display_label} ({len(unique_to_1_names)}):\n" + ", ".join(unique_to_1_names) if unique_to_1_names else f"No unique enzymes found for {p1_display_label}."
     msg2 = f"Enzymes cutting only {p2_display_label} ({len(unique_to_2_names)}):\n" + ", ".join(unique_to_2_names) if unique_to_2_names else f"No unique enzymes found for {p2_display_label}."
     
+    # New: Find enzymes cutting both but with different fragments
+    common_enzymes_obj = enzymes_cutting_p1_obj.intersection(enzymes_cutting_p2_obj)
+    common_diff_fragments_enzymes_names = []
+    for enzyme_obj in common_enzymes_obj:
+        try:
+            fragments1_seqs = enzyme_obj.catalyse(plasmid1_seq_rec.seq)
+            fragments2_seqs = enzyme_obj.catalyse(plasmid2_seq_rec.seq)
+            
+            lengths1 = sorted([len(f) for f in fragments1_seqs])
+            lengths2 = sorted([len(f) for f in fragments2_seqs])
+            
+            if lengths1 != lengths2:
+                common_diff_fragments_enzymes_names.append(str(enzyme_obj))
+        except Exception as e_cat_common:
+            print(f"Warning: Error during catalysis comparison for common enzyme {str(enzyme_obj)}: {e_cat_common}")
+            # Optionally skip this enzyme or log more formally
+            
+    common_diff_fragments_enzymes_names = sorted(list(set(common_diff_fragments_enzymes_names)))
+    
+    msg_common_diff = f"Enzymes cutting BOTH plasmids with DIFFERENT fragments ({len(common_diff_fragments_enzymes_names)}):\n" + \
+                      ", ".join(common_diff_fragments_enzymes_names) if common_diff_fragments_enzymes_names \
+                      else "No enzymes found that cut both plasmids with different fragment patterns."
+
     status = "Analysis complete."
-    if not unique_to_1_names and not unique_to_2_names:
-        status += " No enzymes found that uniquely cut only one of the plasmids."
+    if not unique_to_1_names and not unique_to_2_names and not common_diff_fragments_enzymes_names:
+        status += " No differentiating enzymes found."
     
     dd_choices = []
     if current_plasmid_choice_for_plot == "Plasmid 1":
@@ -185,11 +211,12 @@ def analyze_plasmids_gradio(file1_path, file2_path, current_plasmid_choice_for_p
 
     if (current_plasmid_choice_for_plot == "Plasmid 1" and unique_to_1_names) or \
        (current_plasmid_choice_for_plot == "Plasmid 2" and unique_to_2_names):
-        initial_enzyme_dd_update = gr.update(choices=["Select an enzyme"] + dd_choices, value="Select an enzyme", interactive=True)
+        current_dd_update = gr.update(choices=["Select an enzyme"] + dd_choices, value="Select an enzyme", interactive=True)
     else:
-        initial_enzyme_dd_update = gr.update(choices=dd_choices, value=dd_choices[0], interactive=False if not dd_choices or "No unique" in dd_choices[0] else True)
+        current_dd_update = gr.update(choices=dd_choices, value=dd_choices[0], interactive=False if not dd_choices or "No unique" in dd_choices[0] else True)
         
-    return status, msg1, msg2, plasmid1_seq_rec, plasmid2_seq_rec, unique_to_1_names, unique_to_2_names, initial_enzyme_dd_update
+    return status, msg1, msg2, msg_common_diff, plasmid1_seq_rec, plasmid2_seq_rec, \
+           unique_to_1_names, unique_to_2_names, common_diff_fragments_enzymes_names, current_dd_update
 
 def plot_selected_digest_controller(plasmid_choice_label, enzyme_name, p1_data, p2_data):
     """
@@ -217,8 +244,8 @@ def plot_selected_digest_controller(plasmid_choice_label, enzyme_name, p1_data,
             return fig_placeholder
         target_plasmid_rec = p1_data
         target_label = "Plasmid 1"
-        if hasattr(p1_data, 'name') and p1_data.name: target_label += f" ({p1_data.name})"
-        elif hasattr(p1_data, 'id') and p1_data.id: target_label += f" ({p1_data.id})"
+        if hasattr(p1_data, 'name') and p1_data.name and p1_data.name !="<unknown name>": target_label += f" ({p1_data.name})"
+        elif hasattr(p1_data, 'id') and p1_data.id and p1_data.id !="<unknown id>": target_label += f" ({p1_data.id})"
     elif plasmid_choice_label == "Plasmid 2":
         if p2_data is None:
             ax_placeholder.clear()
@@ -227,8 +254,8 @@ def plot_selected_digest_controller(plasmid_choice_label, enzyme_name, p1_data,
             return fig_placeholder
         target_plasmid_rec = p2_data
         target_label = "Plasmid 2"
-        if hasattr(p2_data, 'name') and p2_data.name: target_label += f" ({p2_data.name})"
-        elif hasattr(p2_data, 'id') and p2_data.id: target_label += f" ({p2_data.id})"
+        if hasattr(p2_data, 'name') and p2_data.name and p2_data.name !="<unknown name>": target_label += f" ({p2_data.name})"
+        elif hasattr(p2_data, 'id') and p2_data.id and p2_data.id !="<unknown id>": target_label += f" ({p2_data.id})"
     else:
         ax_placeholder.clear()
         ax_placeholder.text(0.5, 0.5, "Invalid plasmid selection.", ha='center', va='center', wrap=True, color='red')
@@ -256,67 +283,70 @@ def load_examples_and_auto_process():
     Loads example files, triggers analysis, and then attempts to auto-plot.
     """
     # Step 1: Perform analysis with example files
-    # Default to "Plasmid 1" for initial dropdown population logic within analyze_plasmids_gradio
-    status, msg1, msg2, p1_rec, p2_rec, p1_enz_names, p2_enz_names, enz_dd_update = \
+    status, msg1, msg2, msg_common_diff, p1_rec, p2_rec, p1_enz_names, p2_enz_names, \
+    _common_diff_list_ignore, enz_dd_update_from_analysis = \
         analyze_plasmids_gradio(EXAMPLE_PLASMID1_PATH, EXAMPLE_PLASMID2_PATH, "Plasmid 1")
 
     # If analysis failed (e.g., files not found), p1_rec or p2_rec might be None
     if p1_rec is None or p2_rec is None :
-         # Create a placeholder plot for error
         fig_error, ax_error = plt.subplots(figsize=(6,8))
-        ax_error.text(0.5, 0.5, "Error during example analysis.\nCheck file paths and content.", ha='center', va='center', color='red', wrap=True)
+        ax_error.text(0.5, 0.5, f"Error during example analysis:\n{status}", ha='center', va='center', color='red', wrap=True) # Display actual error
         ax_error.set_xticks([]); ax_error.set_yticks([])
         plt.tight_layout()
-        return status, msg1, msg2, p1_rec, p2_rec, p1_enz_names, p2_enz_names, \
+        # Ensure all expected output values are provided
+        return status, msg1, msg2, msg_common_diff, None, None, [], [], \
                gr.update(choices=["Error"], value="Error", interactive=False), \
-               gr.update(value="Plasmid 1"), fig_error # Default radio to P1, show error plot
+               gr.update(value="Plasmid 1"), fig_error
 
-    # Step 2: Determine auto-plot parameters
+    # Step 2: Determine auto-plot parameters and update dropdown based on analysis
     auto_plot_plasmid_label = None
     auto_plot_enzyme_name = None
     auto_plot_plasmid_data = None
-    final_radio_choice = "Plasmid 1" # Default if P1 has unique enzymes
+    final_radio_choice = "Plasmid 1" # Default
+    final_enz_dd_update = enz_dd_update_from_analysis # Use directly from analysis initially
 
     if p1_enz_names:
         auto_plot_plasmid_label = "Plasmid 1"
         auto_plot_enzyme_name = p1_enz_names[0]
         auto_plot_plasmid_data = p1_rec
         final_radio_choice = "Plasmid 1"
-        # Update enzyme dropdown for P1
-        enz_dd_update = gr.update(choices=["Select an enzyme"] + p1_enz_names, value=auto_plot_enzyme_name, interactive=True)
-
+        final_enz_dd_update = gr.update(choices=["Select an enzyme"] + p1_enz_names, value=auto_plot_enzyme_name, interactive=True)
     elif p2_enz_names:
         auto_plot_plasmid_label = "Plasmid 2"
         auto_plot_enzyme_name = p2_enz_names[0]
         auto_plot_plasmid_data = p2_rec
         final_radio_choice = "Plasmid 2"
-        # Update enzyme dropdown for P2
-        enz_dd_update = gr.update(choices=["Select an enzyme"] + p2_enz_names, value=auto_plot_enzyme_name, interactive=True)
-    else:
-        # No unique enzymes for auto-plotting, update dropdown to reflect current choice (P1 default)
+        final_enz_dd_update = gr.update(choices=["Select an enzyme"] + p2_enz_names, value=auto_plot_enzyme_name, interactive=True)
+    else: # No unique enzymes for either, dropdown should reflect current radio choice (P1 default from analyze call)
         if final_radio_choice == "Plasmid 1":
-             enz_dd_update = gr.update(choices=[f"No unique enzymes for Plasmid 1 ({os.path.basename(EXAMPLE_PLASMID1_PATH)})"], value=f"No unique enzymes for Plasmid 1 ({os.path.basename(EXAMPLE_PLASMID1_PATH)})", interactive=False)
-        # (No need to handle P2 here as P1 is checked first for default)
-
+             final_enz_dd_update = gr.update(choices=[f"No unique enzymes for P1 ({os.path.basename(EXAMPLE_PLASMID1_PATH)})"], 
+                                             value=f"No unique enzymes for P1 ({os.path.basename(EXAMPLE_PLASMID1_PATH)})", interactive=False)
+        # No explicit else for P2 needed here as P1 is the default for initial dropdown population
 
     # Step 3: Generate plot if possible
     if auto_plot_enzyme_name and auto_plot_plasmid_data:
-        gel_fig = simulate_digest_and_plot_gradio(auto_plot_plasmid_data, auto_plot_enzyme_name, auto_plot_plasmid_label)
+        # Use the actual name from p1_data or p2_data for the label if available
+        plot_label_detail = ""
+        if auto_plot_plasmid_label == "Plasmid 1":
+            if hasattr(p1_rec, 'name') and p1_rec.name and p1_rec.name != "<unknown name>": plot_label_detail = f" ({p1_rec.name})"
+            elif hasattr(p1_rec, 'id') and p1_rec.id and p1_rec.id != "<unknown id>": plot_label_detail = f" ({p1_rec.id})"
+        elif auto_plot_plasmid_label == "Plasmid 2":
+            if hasattr(p2_rec, 'name') and p2_rec.name and p2_rec.name != "<unknown name>": plot_label_detail = f" ({p2_rec.name})"
+            elif hasattr(p2_rec, 'id') and p2_rec.id and p2_rec.id != "<unknown id>": plot_label_detail = f" ({p2_rec.id})"
+        
+        gel_fig = simulate_digest_and_plot_gradio(auto_plot_plasmid_data, auto_plot_enzyme_name, f"{auto_plot_plasmid_label}{plot_label_detail}")
     else:
-        # Create a placeholder plot if no auto-plot target
         fig_placeholder, ax_placeholder = plt.subplots(figsize=(6, 8))
         ax_placeholder.text(0.5, 0.5, "No unique enzymes found for automatic plotting.", ha='center', va='center', wrap=True)
         ax_placeholder.set_xticks([]); ax_placeholder.set_yticks([])
         plt.tight_layout()
         gel_fig = fig_placeholder
-        # Ensure dropdown reflects that no enzyme was selected for plotting
-        if not p1_enz_names and not p2_enz_names: # If truly no unique enzymes for either
-            enz_dd_update = gr.update(choices=["No unique enzymes found"], value="No unique enzymes found", interactive=False)
-
+        if not p1_enz_names and not p2_enz_names:
+             final_enz_dd_update = gr.update(choices=["No unique enzymes found"], value="No unique enzymes found", interactive=False)
 
     # Return all updates
-    return status, msg1, msg2, p1_rec, p2_rec, p1_enz_names, p2_enz_names, \
-           enz_dd_update, gr.update(value=final_radio_choice), gel_fig
+    return status, msg1, msg2, msg_common_diff, p1_rec, p2_rec, p1_enz_names, p2_enz_names, \
+           final_enz_dd_update, gr.update(value=final_radio_choice), gel_fig
 
 
 # --- Gradio Interface Definition ---
@@ -325,10 +355,13 @@ with gr.Blocks(theme=gr.themes.Default()) as demo:
     gr.Markdown(
         "**Instructions:**\n"
         "1. Upload two plasmid sequence files (GenBank `.gb`/`.gbk` or FASTA `.fasta`/`.fna`/`.fa` format) OR click 'Load Example Files'.\n"
-        "2. If uploading manually, click `Analyze Plasmids`. Results will show enzymes that uniquely cut one plasmid but not the other.\n"
-        "3. Select which plasmid's unique enzymes you want to consider for plotting.\n"
+        "2. If uploading manually, click `Analyze Uploaded Plasmids`. Results will show:\n"
+        "    a. Enzymes that uniquely cut only Plasmid 1.\n"
+        "    b. Enzymes that uniquely cut only Plasmid 2.\n"
+        "    c. Enzymes that cut **both** plasmids but produce different fragment patterns.\n"
+        "3. Select which plasmid's **unique** enzymes you want to consider for plotting.\n"
         "4. Choose a specific enzyme from the dropdown list.\n"
-        "5. Click `Generate Gel Plot` to visualize the digestion pattern.\n"
+        "5. Click `Generate Gel Plot` to visualize the digestion pattern for the selected plasmid and enzyme.\n"
         f"Note: For 'Load Example Files', ensure `plasmid1_example.gb` and `plasmid2_example.gb` are in a folder named `{EXAMPLE_DIR}` next to this script."
     )
 
@@ -336,6 +369,7 @@ with gr.Blocks(theme=gr.themes.Default()) as demo:
     plasmid2_data_state = gr.State()
     p1_unique_enzymes_list_state = gr.State([])
     p2_unique_enzymes_list_state = gr.State([])
+    # common_diff_enzymes_list_state = gr.State([]) # Not strictly needed as state if only displayed
 
     with gr.Row():
         with gr.Column(scale=1):
@@ -343,16 +377,17 @@ with gr.Blocks(theme=gr.themes.Default()) as demo:
             file_p1 = gr.File(label="Plasmid 1 File (e.g., .gb, .fasta)", type="filepath", file_types=[".gb", ".gbk", ".fasta", ".fna", ".fa"])
             file_p2 = gr.File(label="Plasmid 2 File (e.g., .gb, .fasta)", type="filepath", file_types=[".gb", ".gbk", ".fasta", ".fna", ".fa"])
             
-            _current_plasmid_choice_for_plot_hidden = gr.Textbox(value="Plasmid 1", visible=False)
+            _current_plasmid_choice_for_plot_hidden = gr.Textbox(value="Plasmid 1", visible=False) # For analysis logic with dropdown
 
-            analyze_btn = gr.Button("Analyze Uploaded Plasmids", variant="secondary") # Changed variant
+            analyze_btn = gr.Button("Analyze Uploaded Plasmids", variant="secondary")
             example_btn = gr.Button("Load Example Files & Auto-Analyze/Plot", variant="primary", elem_id="example_button")
         
         with gr.Column(scale=2):
             gr.Markdown("### Analysis Results")
-            status_message_txt = gr.Textbox(label="Status", interactive=False, lines=1, max_lines=3) # Increased max_lines for error messages
+            status_message_txt = gr.Textbox(label="Status", interactive=False, lines=1, max_lines=3)
             unique_enzymes_p1_txt = gr.Textbox(label="Enzymes cutting only Plasmid 1", interactive=False, lines=3, max_lines=6)
             unique_enzymes_p2_txt = gr.Textbox(label="Enzymes cutting only Plasmid 2", interactive=False, lines=3, max_lines=6)
+            common_diff_enzymes_txt = gr.Textbox(label="Enzymes cutting BOTH plasmids (different fragments)", interactive=False, lines=3, max_lines=6) # New Textbox
 
     gr.Markdown("---")
     gr.Markdown("### 2. Visualize Digestion on Virtual Gel")
@@ -361,18 +396,18 @@ with gr.Blocks(theme=gr.themes.Default()) as demo:
         with gr.Column(scale=1):
             plasmid_to_plot_choice_radio = gr.Radio(
                 choices=["Plasmid 1", "Plasmid 2"], 
-                label="Select Plasmid for Gel Visualization",
+                label="Select Plasmid for Gel Visualization (of its unique enzymes)",
                 value="Plasmid 1",
                 interactive=True
             )
             
             enzyme_for_plot_dropdown = gr.Dropdown(
-                label="Select Unique Enzyme", 
+                label="Select Unique Enzyme for Chosen Plasmid", 
                 choices=["Analyze plasmids first"], 
                 value="Analyze plasmids first",
                 interactive=False
             )
-            plot_btn = gr.Button("Generate Gel Plot for Selection", variant="secondary", elem_id="plot_button") # Changed variant
+            plot_btn = gr.Button("Generate Gel Plot for Selection", variant="secondary", elem_id="plot_button")
 
         with gr.Column(scale=2):
             gel_plot_output = gr.Plot(label="Virtual Agarose Gel")
@@ -385,30 +420,33 @@ with gr.Blocks(theme=gr.themes.Default()) as demo:
     plasmid_to_plot_choice_radio.change(
         fn=lambda x: x, 
         inputs=[plasmid_to_plot_choice_radio], 
-        outputs=[_current_plasmid_choice_for_plot_hidden]
+        outputs=[_current_plasmid_choice_for_plot_hidden] # Keep this to inform analyze_plasmids_gradio logic for initial dd
     )
     
     analyze_btn.click(
         fn=analyze_plasmids_gradio,
-        inputs=[file_p1, file_p2, _current_plasmid_choice_for_plot_hidden],
+        inputs=[file_p1, file_p2, _current_plasmid_choice_for_plot_hidden], # Pass the hidden value
         outputs=[
             status_message_txt, unique_enzymes_p1_txt, unique_enzymes_p2_txt,
+            common_diff_enzymes_txt, # New output for the new textbox
             plasmid1_data_state, plasmid2_data_state,
             p1_unique_enzymes_list_state, p2_unique_enzymes_list_state, 
+            gr.State(), # Placeholder for common_diff_fragments_enzymes_names list (returned but not stored in state)
             enzyme_for_plot_dropdown
         ]
     )
 
     example_btn.click(
         fn=load_examples_and_auto_process,
-        inputs=[], # No direct inputs, uses hardcoded paths
+        inputs=[], 
         outputs=[
             status_message_txt, unique_enzymes_p1_txt, unique_enzymes_p2_txt,
+            common_diff_enzymes_txt, # New output
             plasmid1_data_state, plasmid2_data_state,
             p1_unique_enzymes_list_state, p2_unique_enzymes_list_state,
-            enzyme_for_plot_dropdown, # Update dropdown based on auto-selected enzyme
-            plasmid_to_plot_choice_radio, # Update radio based on auto-selected plasmid
-            gel_plot_output # Display the auto-generated plot
+            enzyme_for_plot_dropdown, 
+            plasmid_to_plot_choice_radio, 
+            gel_plot_output 
         ]
     )
 
@@ -425,11 +463,13 @@ with gr.Blocks(theme=gr.themes.Default()) as demo:
     )
 
 if __name__ == '__main__':
-    # Create eg_files directory if it doesn't exist (optional, good for local testing)
     if not os.path.exists(EXAMPLE_DIR):
         os.makedirs(EXAMPLE_DIR)
-        print(f"Created directory: {EXAMPLE_DIR}. Please add example plasmid files to it.")
-        # You might want to add a check here to see if files exist and guide the user
-        # For Hugging Face Spaces, you'd typically upload the eg_files directory with the files.
+        print(f"Created directory: {EXAMPLE_DIR}. Please add example plasmid files (plasmid1_example.gb, plasmid2_example.gb) to it for the example button to work.")
+    
+    # Check for example files and print a message if they are missing
+    if not os.path.exists(EXAMPLE_PLASMID1_PATH) or not os.path.exists(EXAMPLE_PLASMID2_PATH):
+        print(f"Warning: Example files (plasmid1_example.gb, plasmid2_example.gb) not found in '{EXAMPLE_DIR}'. The 'Load Example Files' button might not work as expected.")
+        print("You can create dummy GenBank or FASTA files with these names for testing if needed.")
 
     demo.launch()