Update app.py

app.py

@@ -11,7 +11,26 @@ os.makedirs(temp_dir, exist_ok=True)
 
 # Streamlit UI setup
 st.set_page_config(page_title="PCR Primer Design", page_icon="🧬", layout="wide")
-uploaded_file = st.file_uploader("Upload a GenBank file", type=['gb', 'gbk'])
+
+# User Documentation
+st.sidebar.header("User Guide")
+st.sidebar.info(
+    """
+    This application allows you to design PCR primers for specific features within a GenBank file. 
+    Follow these steps:
+    1. Upload a GenBank file.
+    2. Select a feature type and then a specific feature.
+    3. Enter the desired PCR product size range and the minimum number of primer pairs.
+    4. Click 'Design Primers' to generate your primers.
+    """
+)
+
+# File uploader with additional help
+uploaded_file = st.file_uploader(
+    "Upload a GenBank file", 
+    type=['gb', 'gbk'],
+    help="Upload a GenBank (.gb or .gbk) file containing the DNA sequence from which to design primers."
+)
 
 # Custom CSS for styling
 st.markdown("""
@@ -60,52 +79,73 @@ def design_primers_for_region(sequence, product_size_range, num_to_return=10):
 if uploaded_file is not None:
     genbank_content = StringIO(uploaded_file.getvalue().decode("utf-8"))
     features, record = extract_features_from_genbank(genbank_content)
-    feature_type = st.selectbox('Select feature type:', ['CDS', 'tRNA', 'gene'])
+    
+    st.write("## Feature Selection")
+    feature_type = st.selectbox(
+        'Select feature type:', 
+        ['CDS', 'tRNA', 'gene'],
+        help="Choose the type of genomic feature for which you want to design primers."
+    )
 
-    feature_options = [f"{feature.qualifiers.get('gene', [''])[0]} ({feature.location})" for feature in features[feature_type]]
-    selected_index = st.selectbox(f'Select a {feature_type}:', options=range(len(feature_options)), format_func=lambda x: feature_options[x])
-    selected_feature = features[feature_type][selected_index]
+    if features[feature_type]:
+        feature_options = [f"{feature.qualifiers.get('gene', [''])[0]} ({feature.location})" for feature in features[feature_type]]
+        selected_index = st.selectbox(
+            f'Select a {feature_type}:', 
+            options=range(len(feature_options)), 
+            format_func=lambda x: feature_options[x],
+            help="Select a specific feature based on its gene name and location."
+        )
+        selected_feature = features[feature_type][selected_index]
 
-    feature_sequence = selected_feature.extract(record.seq)
-    st.write(f"Selected {feature_type} sequence (length: {len(feature_sequence)} bp):")
-    st.code(str(feature_sequence), language="text")  # Display sequence in code format
+        feature_sequence = selected_feature.extract(record.seq)
+        st.write(f"Selected {feature_type} sequence (length: {len(feature_sequence)} bp):")
+        st.code(str(feature_sequence), language="text")  # Display sequence in code format
 
-    product_size_range = st.text_input("Enter desired PCR product size range (e.g., 150-500):", value="150-500")
-    min_num_primers = st.number_input("Enter minimum number of primer pairs to return:", min_value=5, value=5, step=1)
+        st.write("## Primer Design Parameters")
+        product_size_range = st.text_input(
+            "Enter desired PCR product size range (e.g., 150-500):", 
+            value="150-500",
+            help="Specify the range of the desired PCR product size in base pairs (e.g., 150-500)."
+        )
+        min_num_primers = st.number_input(
+            "Enter minimum number of primer pairs to return:", 
+            min_value=5, value=5, step=1,
+            help="Determine the minimum number of primer pairs to generate."
+        )
 
-    if st.button(f'Design Primers for selected {feature_type}'):
-        with st.spinner('Designing primers...'):  # Show a spinner while primers are being designed
-            primers = design_primers_for_region(feature_sequence, product_size_range, num_to_return=min_num_primers)
+        if st.button(f'Design Primers for selected {feature_type}'):
+            with st.spinner('Designing primers...'):  # Show a spinner while primers are being designed
+                primers = design_primers_for_region(feature_sequence, product_size_range, num_to_return=min_num_primers)
 
-        primer_data = []
-        for i in range(min_num_primers):
-            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': 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': len(left_sequence),
-                    'Right Length': len(right_sequence),
-                    'PCR Product Size (bp)': primers.get(f'PRIMER_PAIR_{i}_PRODUCT_SIZE', 'N/A')
-                }
-                primer_data.append(primer_info)
+            primer_data = []
+            for i in range(min_num_primers):
+                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': 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': len(left_sequence),
+                        'Right Length': len(right_sequence),
+                        'PCR Product Size (bp)': primers.get(f'PRIMER_PAIR_{i}_PRODUCT_SIZE', 'N/A')
+                    }
+                    primer_data.append(primer_info)
 
-        if primer_data:
-            st.subheader('Designed Primers')
-            primer_df = pd.DataFrame(primer_data)
-            st.table(primer_df)  # Use st.table to display the primer data
+            if primer_data:
+                st.subheader('Designed Primers')
+                primer_df = pd.DataFrame(primer_data)
+                st.table(primer_df)  # Use st.table to display the primer data
 
-            csv = primer_df.to_csv(index=False).encode('utf-8')
-            st.download_button(
-                "Download Primers as CSV",
-                csv,
-                "primers.csv",
-                "text/csv",
-                key='download-csv'
-            )
-        else:
-            st.error('No primers were found. Please adjust your parameters and try again.')
+                csv = primer_df.to_csv(index=False).encode('utf-8')
+                st.download_button(
+                    "Download Primers as CSV",
+                    csv,
+                    "primers.csv",
+                    "text/csv",
+                    key='download-csv'
+                )
+            else:
+                st.error('No primers were found. Please adjust your parameters and try again.')