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"
@@ -14,8 +13,8 @@ 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}
@@ -24,8 +23,9 @@ 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(
         {
@@ -45,122 +45,52 @@ 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:
-    # 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'])
+    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
+    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':
                 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"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)
+                primer_data.append(primer_info)
 
-                    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.')
+        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.')