Update app.py

app.py

@@ -5,73 +5,59 @@ from io import StringIO
 
 # Streamlit app layout
 st.title('PCR Primer Design Tool')
-st.write('Upload a FASTA file with your DNA sequence to design PCR primers.')
+st.write('Upload a FASTA file with your DNA sequence and specify the desired product size range for PCR primer design.')
 
 # User inputs
 fasta_file = st.file_uploader("Upload DNA sequence (FASTA format):", type=['fasta', 'fa'])
-sequence_id = st.text_input("Sequence ID:", value="")
-target_start = st.number_input("Target start position:", min_value=0, value=0, step=1)
-target_length = st.number_input("Target length:", min_value=0, value=100, step=1)
-excluded_regions = st.text_input("Excluded Regions (format: start,length start,length ...):", value="")
-included_region_start = st.number_input("Included Region Start:", min_value=0, value=20, step=1)
-included_region_length = st.number_input("Included Region Length:", min_value=0, value=400, step=1)
-primer_num_return = st.number_input("Number of Primer Pairs to Return:", min_value=1, value=5, step=1)
+product_size_range = st.text_input("Product Size Range (format: min-max, e.g. 150-250):", value="150-250")
 
 if st.button('Design Primers'):
-    if fasta_file:
+    if fasta_file and product_size_range:
         # Read the sequence from the FASTA file
         sequence_data = StringIO(fasta_file.getvalue().decode("utf-8"))
         record = next(SeqIO.parse(sequence_data, "fasta"))
         sequence = str(record.seq).upper()  # Ensure sequence is uppercase
 
-        # Prepare excluded regions format for Primer3
-        excluded_regions_list = excluded_regions.split()
-        excluded_regions_formatted = []
-        for region in excluded_regions_list:
-            start, length = region.split(',')
-            excluded_regions_formatted.append((int(start), int(length)))
+        # Convert product size range from string to list of tuples
+        size_range = [tuple(map(int, range_pair.split('-'))) for range_pair in product_size_range.split(',')]
+
+        # Set basic primer design parameters (based on defaults provided)
+        primer_params = {
+            'PRIMER_TASK': 'generic',
+            'PRIMER_OPT_SIZE': 20,
+            'PRIMER_MIN_SIZE': 18,
+            'PRIMER_MAX_SIZE': 23,
+            'PRIMER_MIN_TM': 57.0,
+            'PRIMER_OPT_TM': 59.0,
+            'PRIMER_MAX_TM': 62.0,
+            'PRIMER_MIN_GC': 30.0,
+            'PRIMER_OPT_GC_PERCENT': 50.0,
+            'PRIMER_MAX_GC': 70.0,
+            'PRIMER_MAX_POLY_X': 4,
+            'PRIMER_SALT_MONOVALENT': 50.0,
+            'PRIMER_SALT_DIVALENT': 1.5,
+            'PRIMER_DNTP_CONC': 0.6,
+            'PRIMER_NUM_RETURN': 5,
+            'PRIMER_PRODUCT_SIZE_RANGE': size_range
+        }
 
         # Design primers using Primer3
         try:
             primers = primer3.bindings.designPrimers(
-                {
-                    'SEQUENCE_ID': sequence_id,
-                    'SEQUENCE_TEMPLATE': sequence,
-                    'SEQUENCE_TARGET': [(target_start, target_length)],
-                    'SEQUENCE_EXCLUDED_REGION': excluded_regions_formatted,
-                    'SEQUENCE_INCLUDED_REGION': (included_region_start, included_region_length),
-                },
-                {
-                    'PRIMER_TASK': 'generic',
-                    'PRIMER_PICK_LEFT_PRIMER': 1,
-                    'PRIMER_PICK_INTERNAL_OLIGO': 0,
-                    'PRIMER_PICK_RIGHT_PRIMER': 1,
-                    'PRIMER_OPT_SIZE': 20,
-                    'PRIMER_MIN_SIZE': 18,
-                    'PRIMER_MAX_SIZE': 23,
-                    'PRIMER_OPT_TM': 59.0,
-                    'PRIMER_MIN_TM': 57.0,
-                    'PRIMER_MAX_TM': 62.0,
-                    'PRIMER_MIN_GC': 30.0,
-                    'PRIMER_MAX_GC': 70.0,
-                    'PRIMER_MAX_POLY_X': 4,
-                    'PRIMER_SALT_MONOVALENT': 50.0,
-                    'PRIMER_SALT_DIVALENT': 1.5,
-                    'PRIMER_DNTP_CONC': 0.6,
-                    'PRIMER_NUM_RETURN': primer_num_return,
-                    'PRIMER_PRODUCT_SIZE_RANGE': [[150,250], [100,300], [301,400], [401,500], [501,600], [601,700], [701,850], [851,1000]],
-                }
+                {'SEQUENCE_ID': record.id, 'SEQUENCE_TEMPLATE': sequence},
+                primer_params
             )
 
             # Display the results
             st.subheader('Designed Primers:')
-            for i in range(primer_num_return):
+            for i in range(primer_params['PRIMER_NUM_RETURN']):
                 st.write(f"Primer Pair {i+1}:")
                 st.write(f"Left Primer (5'-3'): {primers.get(f'PRIMER_LEFT_{i}_SEQUENCE', 'Not available')}")
                 st.write(f"Right Primer (5'-3'): {primers.get(f'PRIMER_RIGHT_{i}_SEQUENCE', 'Not available')}")
                 st.write(f"Left Primer Tm: {primers.get(f'PRIMER_LEFT_{i}_TM', 'Not available')}")
                 st.write(f"Right Primer Tm: {primers.get(f'PRIMER_RIGHT_{i}_TM', 'Not available')}")
+                st.write(f"Product Size: {primers.get(f'PRIMER_PAIR_{i}_PRODUCT_SIZE', 'Not available')}")
         except Exception as e:
             st.error(f"An error occurred while designing primers: {e}")
     else:
-        st.error('Please upload a valid FASTA file.')
+        st.error('Please upload a valid FASTA file and specify a product size range.')