Update app.py

app.py

@@ -48,19 +48,29 @@ 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."""
+    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
+    
     for i in range(num_pairs):
-        left_pos = primers.get(f'PRIMER_LEFT_{i}', {}).get('position', -1)
-        right_pos = primers.get(f'PRIMER_RIGHT_{i}', {}).get('position', -1)
-        if left_pos != -1 and right_pos != -1:
+        left_key = f'PRIMER_LEFT_{i}_POSITION'  # Correct key for left primer position
+        right_key = f'PRIMER_RIGHT_{i}_POSITION'  # Correct key for right primer position
+        
+        # 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'{i+1}', va='bottom', ha='right')
+            plt.text(left_pos, i, f'Pair {i+1}', va='center', ha='right')
+    
     plt.yticks([])
-    plt.title('PCR Products')
+    plt.title('PCR Products Visualization')
     plt.xlabel('Nucleotide position')
+    plt.grid(True)
     plt.show()
 
+
 if uploaded_file is not None:
     genbank_content = StringIO(uploaded_file.getvalue().decode("utf-8"))
     features, record = extract_features_from_genbank(genbank_content)