Update app.py

app.py

@@ -48,34 +48,46 @@ def design_primers_for_region(sequence, product_size_range, num_to_return=5):
 
 def plot_pcr_product(sequence, primers, feature_length, num_pairs=5):
     """Visualize the PCR product based on primer locations relative to a feature."""
-    # Debugging: Print primer positions to check if they're being correctly extracted
-    for i in range(num_pairs):
-        print(f"Left Primer {i} Position: {primers.get(f'PRIMER_LEFT_{i}_POSITION', 'N/A')}")
-        print(f"Right Primer {i} Position: {primers.get(f'PRIMER_RIGHT_{i}_POSITION', 'N/A')}")
+    import matplotlib.pyplot as plt  # Ensure matplotlib is imported here if not already done
 
-    # Start the figure for plotting
+    # Initialize the figure for plotting
     plt.figure(figsize=(10, 3))
-    plt.plot([0, feature_length], [1, 1], 'b-', label='Selected Feature')  # Blue line represents the selected feature
-    
+
+    # Plot the selected feature line in the middle
+    plt.plot([0, feature_length], [1, 1], 'b-', lw=2, label='Selected Feature')
+
+    # Iterate over the number of expected primer pairs
     for i in range(num_pairs):
-        left_pos = primers.get(f'PRIMER_LEFT_{i}_POSITION', -1)
-        right_pos = primers.get(f'PRIMER_RIGHT_{i}_POSITION', -1)
-        if left_pos != -1 and right_pos != -1:
-            plt.plot([left_pos, left_pos], [1.1, 1.3], 'r-', label=f'Left Primer {i+1}' if i == 0 else "")  # Draw the left primer position
-            plt.plot([right_pos, right_pos], [0.7, 0.9], 'g-', label=f'Right Primer {i+1}' if i == 0 else "")  # Draw the right primer position
-            plt.text(left_pos, 1.35, f'L{i+1}', ha='center')  # Label for left primer
-            plt.text(right_pos, 0.65, f'R{i+1}', ha='center')  # Label for right primer
-
-    plt.ylim(0, 2)  # Set the limits of Y-axis to make the plot clearer
+        left_key_pos = f'PRIMER_LEFT_{i}_POSITION'
+        right_key_pos = f'PRIMER_RIGHT_{i}_POSITION'
+        
+        if left_key_pos in primers and right_key_pos in primers:
+            # Fetch positions for left and right primers
+            left_pos = primers[left_key_pos]
+            right_pos = primers[right_key_pos]
+
+            # Plotting the left primer above the feature line
+            plt.plot([left_pos, left_pos], [1.05, 1.15], 'r-', label=f'Left Primer {i+1}' if i == 0 else "")
+            plt.text(left_pos, 1.17, f'L{i+1}', ha='center', color='red')
+            
+            # Plotting the right primer below the feature line
+            plt.plot([right_pos, right_pos], [0.85, 0.95], 'g-', label=f'Right Primer {i+1}' if i == 0 else "")
+            plt.text(right_pos, 0.83, f'R{i+1}', ha='center', color='green')
+
+    # Adjusting the plot
+    plt.ylim(0.75, 1.25)
+    plt.xlim(0, feature_length)
     plt.title('Feature and Primer Positions')
     plt.xlabel('Nucleotide position')
+    plt.yticks([])
     plt.legend()
-    plt.grid(True)
+    plt.grid(axis='x')  # Show only horizontal grid lines for clarity
 
     # Use st.pyplot() to display the plot in Streamlit
     st.pyplot(plt)
 
 
+
 if uploaded_file is not None:
     genbank_content = StringIO(uploaded_file.getvalue().decode("utf-8"))
     features, record = extract_features_from_genbank(genbank_content)
@@ -123,6 +135,8 @@ if uploaded_file is not None:
             )
             # Plotting PCR products
             st.write("### Visualization of PCR Products")
+        if st.button(f'Design Primers for selected {feature_type}'):
+            # Your primer design logic and data preparation
             feature_length = len(feature_sequence)
             plot_pcr_product(feature_sequence, primers, feature_length, num_pairs=5)
         else: