Update app.py

app.py

@@ -46,12 +46,13 @@ def design_primers_for_region(sequence, product_size_range, num_to_return=5):
         }
     )
 
-def plot_pcr_product(sequence, primers, num_pairs=5):
-    """Visualize the PCR product based on primer locations."""
+def plot_pcr_product(sequence, primers, feature_length, num_pairs=5):
+    """Visualize the PCR product based on primer locations relative to a feature."""
     import matplotlib.pyplot as plt  # Ensure matplotlib is imported here if not already done
     
-    plt.figure(figsize=(10, 2))
-    plt.plot([0, len(sequence)], [0, 0], 'k-')  # Draw the sequence line
+    # Start 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
     
     for i in range(num_pairs):
         left_key = f'PRIMER_LEFT_{i}_POSITION'  # Correct key for left primer position
@@ -60,16 +61,20 @@ def plot_pcr_product(sequence, primers, num_pairs=5):
         # Check if keys exist before trying to access them
         if left_key in primers and right_key in primers:
             left_pos = primers[left_key]
-            right_pos = primers[right_key] + primers.get(f'PRIMER_RIGHT_{i}_LENGTH', 0)  # Adjust right position by length
-            plt.plot([left_pos, right_pos], [i, i], 'r-')  # Draw the PCR product line
-            plt.text(left_pos, i, f'Pair {i+1}', va='center', ha='right')
+            right_pos = primers[right_key]
+            # Draw lines for primers; left primer above (y=1.2) and right primer below (y=0.8) the feature line
+            plt.plot([left_pos, left_pos], [1.1, 1.3], 'r-', label='Left Primer' if i == 0 else "")  # Red line represents left primer
+            plt.plot([right_pos, right_pos], [0.7, 0.9], 'g-', label='Right Primer' if i == 0 else "")  # Green line represents right primer
+            plt.text(left_pos, 1.4, f'L{i+1}', ha='center')  # Label for left primer
+            plt.text(right_pos, 0.6, f'R{i+1}', ha='center')  # Label for right primer
     
-    plt.yticks([])
-    plt.title('PCR Products Visualization')
+    plt.ylim(0, 2)  # Set the limits of Y-axis to make the plot clearer
+    plt.title('Feature and Primer Positions')
     plt.xlabel('Nucleotide position')
+    plt.legend()
     plt.grid(True)
     
-    # Instead of plt.show(), use st.pyplot() for Streamlit
+    # Use st.pyplot() to display the plot in Streamlit
     st.pyplot(plt)
 
 
@@ -120,6 +125,7 @@ if uploaded_file is not None:
             )
             # Plotting PCR products
             st.write("### Visualization of PCR Products")
-            plot_pcr_product(feature_sequence, primers, num_pairs=5)
+            feature_length = len(feature_sequence)  # Length of the selected feature
+            plot_pcr_product(feature_sequence, primers, feature_length, num_pairs=5)
         else:
             st.error('No primers were found. Please adjust your parameters and try again.')