Update app.py

app.py

@@ -4,7 +4,6 @@ import primer3
 from Bio import SeqIO
 import os
 from io import StringIO
-import matplotlib.pyplot as plt
 
 # Ensure the 'temp' directory exists for saving temporary files
 temp_dir = "temp"
@@ -46,38 +45,6 @@ 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."""
-    
-    plt.figure(figsize=(10, 3))
-    
-    # Plot the selected feature
-    plt.plot([0, feature_length], [1, 1], 'b-', lw=2, label='Selected Feature')
-    
-    # Assuming primer positions are not directly available and using the index for demonstration
-    for index, row in primer_df.iterrows():
-        # 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([index * feature_length // len(primer_df)]*2, y_pos, 'r-')
-
-    plt.ylim(0.8, 1.2)
-    plt.xlim(0, feature_length)
-    plt.title('Feature and Primer Positions')
-    plt.xlabel('Nucleotide position')
-    plt.legend()
-    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)
@@ -98,32 +65,20 @@ if uploaded_file is not None:
         
         primer_data = []
         for i in range(5):  # Collect data for 5 primer pairs
-            primer_info = {
-                'Primer Pair': i + 1,
-                'Left Sequence': primers.get(f'PRIMER_LEFT_{i}_SEQUENCE', 'N/A'),
-                'Right Sequence': primers.get(f'PRIMER_RIGHT_{i}_SEQUENCE', 'N/A'),
-                'Left TM (°C)': primers.get(f'PRIMER_LEFT_{i}_TM', 'N/A'),
-                'Right TM (°C)': primers.get(f'PRIMER_RIGHT_{i}_TM', 'N/A'),
-                'Left Length': primers.get(f'PRIMER_LEFT_{i}_SIZE', 'N/A'),
-                'Right Length': primers.get(f'PRIMER_RIGHT_{i}_SIZE', 'N/A'),
-                'PCR Product Size (bp)': primers.get(f'PRIMER_PAIR_{i}_PRODUCT_SIZE', 'N/A')
-            }
-            if primer_info['Left Sequence'] != 'N/A' and primer_info['Right Sequence'] != 'N/A':
-                primer_info['Primer'] = f"Left {i+1}"
-                primer_data.append(primer_info)
+            left_sequence = primers.get(f'PRIMER_LEFT_{i}_SEQUENCE', 'N/A')
+            right_sequence = primers.get(f'PRIMER_RIGHT_{i}_SEQUENCE', 'N/A')
+            if left_sequence != 'N/A' and right_sequence != 'N/A':
                 primer_info = {
                     'Primer Pair': i + 1,
-                    'Left Sequence': primers.get(f'PRIMER_LEFT_{i}_SEQUENCE', 'N/A'),
-                    'Right Sequence': primers.get(f'PRIMER_RIGHT_{i}_SEQUENCE', 'N/A'),
+                    'Left Sequence': left_sequence,
+                    'Right Sequence': right_sequence,
                     'Left TM (°C)': primers.get(f'PRIMER_LEFT_{i}_TM', 'N/A'),
                     'Right TM (°C)': primers.get(f'PRIMER_RIGHT_{i}_TM', 'N/A'),
                     'Left Length': primers.get(f'PRIMER_LEFT_{i}_SIZE', 'N/A'),
                     'Right Length': primers.get(f'PRIMER_RIGHT_{i}_SIZE', 'N/A'),
                     'PCR Product Size (bp)': primers.get(f'PRIMER_PAIR_{i}_PRODUCT_SIZE', 'N/A')
                 }
-                if primer_info['Left Sequence'] != 'N/A' and primer_info['Right Sequence'] != 'N/A':
-                    primer_info['Primer'] = f"Right {i+1}"
-                    primer_data.append(primer_info)
+                primer_data.append(primer_info)
 
         if primer_data:
             primer_df = pd.DataFrame(primer_data)
@@ -137,10 +92,5 @@ if uploaded_file is not None:
                 "text/csv",
                 key='download-csv'
             )
-            # Plotting PCR products
-            st.write("### Visualization of PCR Products")
-            # Your primer design logic and data preparation
-            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.')