Update app.py

app.py

@@ -7,53 +7,58 @@ 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)
+user_sequence = st.text_area("Enter DNA sequence:", height=150).upper()  # Ensure sequence is uppercase
 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
+    if user_sequence and target_length > 0:
+        # Remove non-sequence characters (e.g., spaces, line breaks)
+        clean_sequence = ''.join(user_sequence.split())
 
-        # 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,
-        }
+        # Validate DNA sequence
+        if not all(nucleotide in 'ATCG' for nucleotide in clean_sequence):
+            st.error('Invalid DNA sequence: please ensure it contains only A, T, C, and G.')
+        else:
+            # Define target region based on user input
+            target = [(target_start, target_length)]
 
-        # 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'],
+            # Set basic primer design parameters (customize as needed)
+            primer_params = {
+                'SEQUENCE_TEMPLATE': clean_sequence,
+                'SEQUENCE_TARGET': target,
+                'PRIMER_OPT_SIZE': 20,  # Optimum primer size, change as needed
+                '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,
             }
-        )
 
-        # 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')}")
+            # Design primers using Primer3
+            try:
+                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')}")
+            except Exception as e:
+                st.error(f"An error occurred while designing primers: {e}")
     else:
-        st.error('Please input a valid DNA sequence.')
+        st.error('Please input a valid DNA sequence and specify a target region.')