Update app.py

app.py

@@ -7,66 +7,71 @@ from io import StringIO
 st.title('PCR Primer Design Tool')
 st.write('Upload a FASTA file with your DNA sequence to design PCR primers.')
 
-# User input for DNA sequence via file upload
+# User inputs
 fasta_file = st.file_uploader("Upload DNA sequence (FASTA format):", type=['fasta', 'fa'])
-
-# Input for target region
+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=1, value=20, 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)
 
 if st.button('Design Primers'):
-    if fasta_file and target_length > 0:
+    if fasta_file:
         # Read the sequence from the FASTA file
         sequence_data = StringIO(fasta_file.getvalue().decode("utf-8"))
         record = next(SeqIO.parse(sequence_data, "fasta"))
-        user_sequence = str(record.seq).upper()  # Ensure sequence is uppercase
-
-        # Remove non-sequence characters (e.g., spaces, line breaks)
-        clean_sequence = ''.join(user_sequence.split())
-
-        # 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)]
+        sequence = str(record.seq).upper()  # Ensure sequence is uppercase
 
-            # 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,
-            }
+        # 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)))
 
-            # 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']}
-                )
+        # 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]],
+                }
+            )
 
-                # 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}")
+            # Display the results
+            st.subheader('Designed Primers:')
+            for i in range(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')}")
+        except Exception as e:
+            st.error(f"An error occurred while designing primers: {e}")
     else:
-        st.error('Please upload a valid FASTA file and specify a target region.')
+        st.error('Please upload a valid FASTA file.')