Update app.py

app.py

@@ -46,48 +46,44 @@ 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."""
-    import matplotlib.pyplot as plt  # Ensure matplotlib is imported here if not already done
-
+def plot_pcr_product_with_df(feature_sequence, primer_df, feature_length):
+    """Visualize the PCR product based on primer information in a DataFrame."""
+    import matplotlib.pyplot as plt
+    
     # Initialize the figure for plotting
     plt.figure(figsize=(10, 3))
-
+    
     # 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_key_pos = f'PRIMER_LEFT_{i}_POSITION'
-        right_key_pos = f'PRIMER_RIGHT_{i}_POSITION'
+    # Extracting primer information from the DataFrame
+    for index, row in primer_df.iterrows():
+        primer_type = "Left" if "Left" in row["Primer"] else "Right"
+        y_position = 1.1 if primer_type == "Left" else 0.9
+        label_y_position = 1.2 if primer_type == "Left" else 0.8
+        color = 'r' if primer_type == "Left" else 'g'
+        
+        # Assuming the start of the feature is the reference point (0)
+        # For demonstration, this simplistic method places primers evenly across the feature length.
+        # This part needs adjustment based on actual primer positions if available.
+        position = (index + 1) * (feature_length // len(primer_df)) 
         
-        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.plot([position, position], [y_position - 0.05, y_position + 0.05], color + '-', lw=2)
+        plt.text(position, label_y_position, f'{primer_type} {index + 1}', ha='center', color=color)
+
     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(axis='x')  # Show only horizontal grid lines for clarity
-
-    # Use st.pyplot() to display the plot in Streamlit
+    plt.grid(axis='x')
+    
     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)
@@ -134,10 +130,9 @@ if uploaded_file is not None:
                 key='download-csv'
             )
             # 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)
+        if st.button(f'Design Primers for selected {feature_type}'):
+            # Assuming primer_df is already created with the required information
+            feature_length = len(feature_sequence)  # Length of the selected feature
+            plot_pcr_product_with_df(feature_sequence, primer_df, feature_length)
         else:
             st.error('No primers were found. Please adjust your parameters and try again.')