Update app.py

app.py

@@ -124,21 +124,21 @@ if st.session_state.get("is_genbank"):
         st.warning("No features found. Using full sequence.")
         target_sequence = record.seq
 
-# Show sequence preview
+# Step 3: Sequence Preview
 if target_sequence:
     st.subheader("Sequence Preview")
     st.code(str(target_sequence), language="text")
 
-# Step 3: Primer Design
+# Step 4: Primer Design
 if target_sequence:
-    st.subheader("Step 3: Primer Design")
+    st.subheader("Step 4: Primer Design")
     size_range = st.slider("PCR product size (bp)", 100, len(target_sequence), (100, min(500, len(target_sequence))), step=10)
     primer_count = st.number_input("Number of primer pairs", 1, 20, 5)
     hp_thresh = st.number_input("Max hairpin Tm (°C)", 0.0, 100.0, 45.0)
     dim_thresh = st.number_input("Max dimer Tm (°C)", 0.0, 100.0, 45.0)
 
     if st.button("Design Primers"):
-        with st.spinner("Designing primers and checking structure..."):
+        with st.spinner("Designing primers and checking structures..."):
             res = design_primers(target_sequence, f"{size_range[0]}-{size_range[1]}", primer_count)
             rows = []
             for i in range(primer_count):
@@ -161,8 +161,12 @@ if target_sequence:
                     })
             df = pd.DataFrame(rows)
             df_unique = df.drop_duplicates(subset=["Left Seq","Right Seq"]).reset_index(drop=True)
-            df_filtered = df_unique[(df_unique["Left HP Tm (°C)"]<=hp_thresh)&(df_unique["Right HP Tm (°C)"]<=hp_thresh)&(df_unique["Dimer Tm (°C)"]<=dim_thresh)]
-            st.session_state['primer_df']=df_filtered
+            df_filtered = df_unique[
+                (df_unique["Left HP Tm (°C)"] <= hp_thresh) &
+                (df_unique["Right HP Tm (°C)"] <= hp_thresh) &
+                (df_unique["Dimer Tm (°C)"] <= dim_thresh)
+            ]
+            st.session_state['primer_df'] = df_filtered
 
     # Display and annotate results
     if 'primer_df' in st.session_state and not st.session_state['primer_df'].empty:
@@ -181,20 +185,22 @@ if target_sequence:
 - **Left HP Tm (°C)**: Hairpin melting temp for forward primer.  
 - **Right HP Tm (°C)**: Hairpin melting temp for reverse primer.  
 - **Dimer Tm (°C)**: Heterodimer melting temp between primers.
-"""
-)
+""")
 
         csv = df.to_csv(index=False).encode('utf-8')
-        st.download_button("Download Primer Table", csv, "primers.csv", "text/csv")("Download Primer Table", csv, "primers.csv", "text/csv")
+        st.download_button("Download Primer Table", csv, "primers.csv", "text/csv")
 
         selected = st.selectbox("Select Primer Pair to View", df["Pair"], key="viz_pair")
-        row = df[df["Pair"]==selected].iloc[0]
+        row = df[df["Pair"] == selected].iloc[0]
+        # retrieve positions for visualization
+        left_pos = res.get(f'PRIMER_LEFT_{selected-1}')[0]
+        left_len = res.get(f'PRIMER_LEFT_{selected-1}')[1]
+        right_pos = res.get(f'PRIMER_RIGHT_{selected-1}')[0]
+        right_len = res.get(f'PRIMER_RIGHT_{selected-1}')[1]
         fig = plot_primer_binding(
             len(target_sequence),
-            row["L_Pos"] if "L_Pos" in row else 0,
-            res[f'PRIMER_LEFT_{selected-1}'][1] if f'PRIMER_LEFT_{selected-1}' in res else 0,
-            row["R_Pos"] if "R_Pos" in row else len(target_sequence),
-            res[f'PRIMER_RIGHT_{selected-1}'][1] if f'PRIMER_RIGHT_{selected-1}' in res else 0,
+            left_pos, left_len,
+            right_pos, right_len,
             row["Product Size (bp)"]
         )
         st.pyplot(fig)