Update app.py

app.py

@@ -4,6 +4,7 @@ import primer3
 from Bio import SeqIO
 import os
 from io import StringIO
+from st_aggrid import AgGridUpdated, GridUpdateMode, DataReturnMode
 
 # Ensure the 'temp' directory exists for saving temporary files
 temp_dir = "temp"
@@ -13,36 +14,20 @@ os.makedirs(temp_dir, exist_ok=True)
 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'])
 
-def extract_features_from_genbank(genbank_content, feature_types=['CDS', 'tRNA', 'gene']):
-    """Extracts specified features from GenBank content."""
-    text_stream = StringIO(genbank_content.decode("utf-8")) if isinstance(genbank_content, bytes) else genbank_content
-    record = SeqIO.read(text_stream, "genbank")
-    features = {ftype: [] for ftype in feature_types}
-    for feature in record.features:
-        if feature.type in feature_types:
-            features[feature.type].append(feature)
-    return features, record
+# Custom CSS for styling
+st.markdown("""
+<style>
+h1, h2, h3 {
+    color: #1f77b4;
+    font-weight: bold;
+}
+.stProgress {
+    margin-top: 20px;
+}
+</style>
+""", unsafe_allow_html=True)
 
-def design_primers_for_region(sequence, product_size_range, num_to_return=10):
-    """Design primers for a specific sequence."""
-    size_min, size_max = map(int, product_size_range.split('-'))
-    return primer3.bindings.designPrimers(
-        {
-            'SEQUENCE_TEMPLATE': str(sequence),
-            'PRIMER_PRODUCT_SIZE_RANGE': [[size_min, size_max]]
-        },
-        {
-            'PRIMER_OPT_SIZE': 20,
-            'PRIMER_MIN_SIZE': 18,
-            'PRIMER_MAX_SIZE': 23,
-            'PRIMER_OPT_TM': 60.0,
-            'PRIMER_MIN_TM': 57.0,
-            'PRIMER_MAX_TM': 63.0,
-            'PRIMER_MIN_GC': 20.0,
-            'PRIMER_MAX_GC': 80.0,
-            'PRIMER_NUM_RETURN': num_to_return,
-        }
-    )
+# Function definitions...
 
 if uploaded_file is not None:
     genbank_content = StringIO(uploaded_file.getvalue().decode("utf-8"))
@@ -55,14 +40,15 @@ if uploaded_file is not None:
 
     feature_sequence = selected_feature.extract(record.seq)
     st.write(f"Selected {feature_type} sequence (length: {len(feature_sequence)} bp):")
-    st.text(str(feature_sequence))
+    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)
 
     if st.button(f'Design Primers for selected {feature_type}'):
-        primers = design_primers_for_region(feature_sequence, product_size_range, num_to_return=min_num_primers)
-        
+        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')
@@ -74,16 +60,17 @@ if uploaded_file is not None:
                     '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),  # Get the length of the left primer
-                    'Right Length': len(right_sequence),  # Get the length of the right primer
+                    '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.write('### Designed Primers')
-            st.dataframe(primer_df)
+            AgGridUpdated(primer_df, height=200)  # Use AgGrid to display the primer data in a better-formatted table
+
             csv = primer_df.to_csv(index=False).encode('utf-8')
             st.download_button(
                 "Download Primers as CSV",
@@ -93,4 +80,4 @@ if uploaded_file is not None:
                 key='download-csv'
             )
         else:
-            st.error('No primers were found. Please adjust your parameters and try again.')
+            st.error('No primers were found. Please adjust your parameters and try again.')