Create app.py

app.py

@@ -0,0 +1,59 @@
+import streamlit as st
+import primer3
+from Bio.Seq import Seq
+
+# Streamlit app layout
+st.title('PCR Primer Design Tool')
+st.write('Enter your DNA sequence and target region to design PCR primers.')
+
+# User input for DNA sequence and target region
+user_sequence = st.text_area("Enter DNA sequence:", height=150)
+target_start = st.number_input("Target start position:", min_value=0, value=0, step=1)
+target_length = st.number_input("Target length:", min_value=1, value=20, step=1)
+
+if st.button('Design Primers'):
+    if user_sequence:
+        # Convert user input into the format expected by Primer3
+        target = [(target_start, target_length)]
+        sequence = str(Seq(user_sequence).upper())  # Ensure uppercase sequence
+
+        # Set basic primer design parameters (customize as needed)
+        primer_params = {
+            'SEQUENCE_TEMPLATE': sequence,
+            'SEQUENCE_TARGET': target,
+            'PRIMER_OPT_SIZE': 20,
+            'PRIMER_MIN_SIZE': 18,
+            'PRIMER_MAX_SIZE': 25,
+            '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,
+        }
+
+        # Design primers
+        primers = primer3.bindings.designPrimers(
+            {
+                'SEQUENCE_TEMPLATE': primer_params['SEQUENCE_TEMPLATE'],
+                'SEQUENCE_TARGET': primer_params['SEQUENCE_TARGET'],
+            },
+            {
+                'PRIMER_OPT_SIZE': primer_params['PRIMER_OPT_SIZE'],
+                'PRIMER_MIN_SIZE': primer_params['PRIMER_MIN_SIZE'],
+                'PRIMER_MAX_SIZE': primer_params['PRIMER_MAX_SIZE'],
+                'PRIMER_OPT_TM': primer_params['PRIMER_OPT_TM'],
+                'PRIMER_MIN_TM': primer_params['PRIMER_MIN_TM'],
+                'PRIMER_MAX_TM': primer_params['PRIMER_MAX_TM'],
+                'PRIMER_MIN_GC': primer_params['PRIMER_MIN_GC'],
+                'PRIMER_MAX_GC': primer_params['PRIMER_MAX_GC'],
+            }
+        )
+
+        # Display the results
+        st.subheader('Designed Primers:')
+        st.write(f"Left Primer (5'-3'): {primers.get('PRIMER_LEFT_0_SEQUENCE', 'Not available')}")
+        st.write(f"Right Primer (5'-3'): {primers.get('PRIMER_RIGHT_0_SEQUENCE', 'Not available')}")
+        st.write(f"Left Primer Tm: {primers.get('PRIMER_LEFT_0_TM', 'Not available')}")
+        st.write(f"Right Primer Tm: {primers.get('PRIMER_RIGHT_0_TM', 'Not available')}")
+    else:
+        st.error('Please input a valid DNA sequence.')