Update app.py

app.py

@@ -4,6 +4,7 @@ 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"
@@ -13,8 +14,8 @@ 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'])
 
+# Function to extract features from GenBank content
 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}
@@ -23,9 +24,8 @@ def extract_features_from_genbank(genbank_content, feature_types=['CDS', 'tRNA',
             features[feature.type].append(feature)
     return features, record
 
+# Function to design primers for a specific sequence
 def design_primers_for_region(sequence, product_size_range, num_to_return=5):
-    """Design primers for a specific sequence."""
-    # Parse the product size range
     size_min, size_max = map(int, product_size_range.split('-'))
     return primer3.bindings.designPrimers(
         {
@@ -45,52 +45,122 @@ def design_primers_for_region(sequence, product_size_range, num_to_return=5):
         }
     )
 
+# Function to display primer design results
+def display_primer_results(primer_df):
+    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'
+    )
+
+# Main application logic
 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'])
+    # Option for Batch Primer Design
+    batch_design = st.checkbox("Batch Primer Design")
+
+    if not batch_design:
+        # Design primers for a single feature
+        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'])
 
-    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]
+        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]
 
-    feature_sequence = selected_feature.extract(record.seq)
-    st.write(f"Selected {feature_type} sequence (length: {len(feature_sequence)} bp):")
-    st.text(str(feature_sequence))
+        feature_sequence = selected_feature.extract(record.seq)
+        st.write(f"Selected {feature_type} sequence (length: {len(feature_sequence)} bp):")
+        st.text(str(feature_sequence))
 
-    product_size_range = st.text_input("Enter desired PCR product size range (e.g., 150-500):", value="150-500")
+        product_size_range = st.text_input("Enter desired PCR product size range (e.g., 150-500):", value="150-500")
 
-    if st.button(f'Design Primers for selected {feature_type}'):
-        primers = design_primers_for_region(feature_sequence, product_size_range, num_to_return=5)
-        
-        primer_data = []
-        for i in range(5):  # Collect data for 5 primer pairs
-            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':
+        if st.button(f'Design Primers for selected {feature_type}'):
+            primers = design_primers_for_region(feature_sequence, product_size_range, num_to_return=5)
+            
+            primer_data = []
+            for i in range(5):  # Collect data for 5 primer pairs
                 primer_info = {
                     'Primer Pair': i + 1,
-                    'Left Sequence': left_sequence,
-                    'Right Sequence': right_sequence,
+                    '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')
                 }
-                primer_data.append(primer_info)
+                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)
+                    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"Right {i+1}"
+                        primer_data.append(primer_info)
+
+            if primer_data:
+                primer_df = pd.DataFrame(primer_data)
+                display_primer_results(primer_df)
+            else:
+                st.error('No primers were found. Please adjust your parameters and try again.')
+    else:
+        # Design primers for multiple features
+        uploaded_features = st.file_uploader("Upload a file containing multiple sequences (FASTA format)", type=['fasta'])
+        if uploaded_features is not None:
+            feature_records = list(SeqIO.parse(uploaded_features, "fasta"))
+            st.write(f"Number of sequences uploaded: {len(feature_records)}")
+
+            # Iterate over each sequence and design primers
+            for index, record in enumerate(feature_records):
+                st.write(f"### Sequence {index + 1}: {record.id} (length: {len(record.seq)})")
+                product_size_range = st.text_input("Enter desired PCR product size range (e.g., 150-500):", value="150-500")
+
+                if st.button(f'Design Primers for Sequence {index + 1}'):
+                    primers = design_primers_for_region(record.seq, product_size_range, num_to_return=5)
+                    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)
+                            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"Right {i+1}"
+                                primer_data.append(primer_info)
 
-        if primer_data:
-            primer_df = pd.DataFrame(primer_data)
-            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.error('No primers were found. Please adjust your parameters and try again.')
+                    if primer_data:
+                        primer_df = pd.DataFrame(primer_data)
+                        display_primer_results(primer_df)
+                    else:
+                        st.error(f'No primers were found for Sequence {index + 1}. Please adjust your parameters and try again.')