Update app.py

app.py

@@ -48,42 +48,36 @@ def design_primers_for_region(sequence, product_size_range, num_to_return=5):
 
 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
+    # Plot the selected feature
     plt.plot([0, feature_length], [1, 1], 'b-', lw=2, label='Selected Feature')
-
-    # Extracting primer information from the DataFrame
+    
+    # Assuming primer positions are not directly available and using the index for demonstration
     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)) 
+        # Determine if it's a left or right primer and set the position accordingly
+        if 'Left' in row['Primer']:
+            # Position the left primer slightly above the feature line
+            y_pos = [1.05, 1.10]
+            plt.text(index * feature_length // len(primer_df), 1.15, f"L{index+1}", horizontalalignment='center')
+        else:
+            # Position the right primer slightly below the feature line
+            y_pos = [0.90, 0.95]
+            plt.text(index * feature_length // len(primer_df), 0.85, f"R{index+1}", horizontalalignment='center')
         
-        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.plot([index * feature_length // len(primer_df)]*2, y_pos, 'r-')
 
-    plt.ylim(0.75, 1.25)
+    plt.ylim(0.8, 1.2)
     plt.xlim(0, feature_length)
     plt.title('Feature and Primer Positions')
     plt.xlabel('Nucleotide position')
-    plt.yticks([])
     plt.legend()
-    plt.grid(axis='x')
+    plt.grid(True)
     
     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)
@@ -132,7 +126,7 @@ if uploaded_file is not None:
             # Plotting PCR products
             st.write("### Visualization of PCR Products")
             # Your primer design logic and data preparation
-            feature_length = len(feature_sequence)  # Length of the selected feature
+            feature_length = len(feature_sequence)  # Obtain the 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.')