Update app.py

app.py

@@ -4,6 +4,10 @@ import primer3
 from Bio import SeqIO
 import os
 from io import StringIO
+
+# Install required libraries
+import subprocess
+subprocess.run(["pip", "install", "st_aggrid"])
 from st_aggrid import AgGridUpdated, GridUpdateMode, DataReturnMode
 
 # Ensure the 'temp' directory exists for saving temporary files
@@ -27,7 +31,36 @@ h1, h2, h3 {
 </style>
 """, unsafe_allow_html=True)
 
-# Function definitions...
+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
+
+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,
+        }
+    )
 
 if uploaded_file is not None:
     genbank_content = StringIO(uploaded_file.getvalue().decode("utf-8"))