Update app.py

app.py

@@ -1,63 +1,84 @@
 import streamlit as st
-import primer3
+import pandas as pd
 from Bio import SeqIO
-from io import StringIO
-
-# Streamlit app layout
-st.title('PCR Primer Design Tool')
-st.write('Upload a FASTA file with your DNA sequence and specify the desired product size range for PCR primer design.')
+from Bio.SeqFeature import SeqFeature, FeatureLocation
+import primer3
+import os
+from collections import Counter
 
-# User inputs
-fasta_file = st.file_uploader("Upload DNA sequence (FASTA format):", type=['fasta', 'fa'])
-product_size_range = st.text_input("Product Size Range (format: min-max, e.g. 150-250):", value="150-250")
+# Ensure the 'temp' directory exists for saving temporary files
+temp_dir = "temp"
+os.makedirs(temp_dir, exist_ok=True)
 
-if st.button('Design Primers'):
-    if fasta_file and product_size_range:
-        # Read the sequence from the FASTA file
-        sequence_data = StringIO(fasta_file.getvalue().decode("utf-8"))
-        record = next(SeqIO.parse(sequence_data, "fasta"))
-        sequence = str(record.seq).upper()  # Ensure sequence is uppercase
+# 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'])
 
-        # Convert product size range from string to list of tuples
-        size_range = [tuple(map(int, range_pair.split('-'))) for range_pair in product_size_range.split(',')]
+def extract_features(genbank_path, feature_type='CDS'):
+    """Extracts features from a GenBank file."""
+    with open(genbank_path, 'r') as file:
+        record = SeqIO.read(file, "genbank")
+        features = [feature for feature in record.features if feature.type == feature_type]
+        return features, record
 
-        # Set basic primer design parameters (based on defaults provided)
-        primer_params = {
-            'PRIMER_TASK': 'generic',
+def design_primers_for_feature(feature, sequence, num_to_return=5):
+    """Design primers for a specific feature."""
+    start, end = int(feature.location.start), int(feature.location.end)
+    sequence_template = str(sequence)
+    target = [start, end - start]
+    primer_design_results = primer3.bindings.designPrimers(
+        {
+            'SEQUENCE_ID': feature.qualifiers.get('gene', [''])[0],
+            'SEQUENCE_TEMPLATE': sequence_template,
+            'SEQUENCE_TARGET': target,
+        },
+        {
             'PRIMER_OPT_SIZE': 20,
             'PRIMER_MIN_SIZE': 18,
             'PRIMER_MAX_SIZE': 23,
+            'PRIMER_OPT_TM': 60.0,
             'PRIMER_MIN_TM': 57.0,
-            'PRIMER_OPT_TM': 59.0,
-            'PRIMER_MAX_TM': 62.0,
-            'PRIMER_MIN_GC': 30.0,
-            'PRIMER_OPT_GC_PERCENT': 50.0,
-            'PRIMER_MAX_GC': 70.0,
-            'PRIMER_MAX_POLY_X': 4,
-            'PRIMER_SALT_MONOVALENT': 50.0,
-            'PRIMER_SALT_DIVALENT': 1.5,
-            'PRIMER_DNTP_CONC': 0.6,
-            'PRIMER_NUM_RETURN': 5,
-            'PRIMER_PRODUCT_SIZE_RANGE': size_range
+            'PRIMER_MAX_TM': 63.0,
+            'PRIMER_MIN_GC': 20.0,
+            'PRIMER_MAX_GC': 80.0,
+            'PRIMER_NUM_RETURN': num_to_return,
         }
+    )
+    return primer_design_results
+
+if uploaded_file is not None:
+    temp_gb_path = os.path.join(temp_dir, uploaded_file.name)
+    with open(temp_gb_path, 'wb') as f:
+        f.write(uploaded_file.getvalue())
+
+    features, record = extract_features(temp_gb_path)
+    gene_names = [feature.qualifiers.get('gene', ['N/A'])[0] for feature in features]
+    selected_gene = st.selectbox('Select a gene to design primers for:', gene_names)
+
+    if st.button('Design Primers'):
+        selected_feature = next(feature for feature in features if feature.qualifiers.get('gene', [''])[0] == selected_gene)
+        primers = design_primers_for_feature(selected_feature, record.seq)
+        primer_df = pd.DataFrame({
+            'Primer': ['Left Primer', 'Right Primer'] * len(primers) // 2,
+            'Sequence': [primers[f'PRIMER_LEFT_{i}_SEQUENCE'] for i in range(len(primers) // 2)] +
+                        [primers[f'PRIMER_RIGHT_{i}_SEQUENCE'] for i in range(len(primers) // 2)],
+            'Tm (°C)': [primers[f'PRIMER_LEFT_{i}_TM'] for i in range(len(primers) // 2)] +
+                       [primers[f'PRIMER_RIGHT_{i}_TM'] for i in range(len(primers) // 2)],
+            'Length': [primers[f'PRIMER_LEFT_{i}_SIZE'] for i in range(len(primers) // 2)] +
+                      [primers[f'PRIMER_RIGHT_{i}_SIZE'] for i in range(len(primers) // 2)],
+            'GC%': [primers[f'PRIMER_LEFT_{i}_GC_PERCENT'] for i in range(len(primers) // 2)] +
+                   [primers[f'PRIMER_RIGHT_{i}_GC_PERCENT'] for i in range(len(primers) // 2)],
+        })
 
-        # Design primers using Primer3
-        try:
-            primers = primer3.bindings.designPrimers(
-                {'SEQUENCE_ID': record.id, 'SEQUENCE_TEMPLATE': sequence},
-                primer_params
-            )
-
-            # Display the results
-            st.subheader('Designed Primers:')
-            for i in range(primer_params['PRIMER_NUM_RETURN']):
-                st.write(f"Primer Pair {i+1}:")
-                st.write(f"Left Primer (5'-3'): {primers.get(f'PRIMER_LEFT_{i}_SEQUENCE', 'Not available')}")
-                st.write(f"Right Primer (5'-3'): {primers.get(f'PRIMER_RIGHT_{i}_SEQUENCE', 'Not available')}")
-                st.write(f"Left Primer Tm: {primers.get(f'PRIMER_LEFT_{i}_TM', 'Not available')}")
-                st.write(f"Right Primer Tm: {primers.get(f'PRIMER_RIGHT_{i}_TM', 'Not available')}")
-                st.write(f"Product Size: {primers.get(f'PRIMER_PAIR_{i}_PRODUCT_SIZE', 'Not available')}")
-        except Exception as e:
-            st.error(f"An error occurred while designing primers: {e}")
-    else:
-        st.error('Please upload a valid FASTA file and specify a product size range.')
+        st.write('### Designed Primers')
+        st.dataframe(primer_df)
+        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.warning("Please upload a GenBank file.")