Update app.py

app.py

@@ -140,7 +140,7 @@ def run_deep_learning_cascade(dna_sequence):
             
             validation = "High Confidence Regulatory Element" if p_promoter >= 0.50 else "Weak Regulatory Signal"
             final_label += f" | Validation: {validation}"
-            raw_scores[" Promoter Signal"] = p_promoter
+            raw_scores["Promoter Signal"] = p_promoter
 
     return final_label, confidence, raw_scores
 
@@ -150,13 +150,13 @@ def run_deep_learning_cascade(dna_sequence):
 def get_genomic_context(sequence, is_coding):
     feature_type = "CODING" if is_coding else "PROMOTER"
     try:
-        # THE BLAST FIX: Added 'biomol_genomic[PROP]' back to force chromosomal coordinates!
+        # ask blast for 5 hits instead of 1 so we can hunt for the true chromosome
         result_handle = NCBIWWW.qblast(
             "blastn", 
             "nt", 
             sequence, 
             entrez_query="Homo sapiens[Organism] AND biomol_genomic[PROP]", 
-            hitlist_size=1
+            hitlist_size=5
         )
         blast_record = NCBIXML.read(result_handle)
     except Exception as e:
@@ -165,10 +165,17 @@ def get_genomic_context(sequence, is_coding):
     if not blast_record.alignments:
         return {"error": "No human genome match found for this sequence."}
 
-    alignment = blast_record.alignments[0]
+    # Loop through the top hits and grab the first one that is an actual Chromosome
+    alignment = blast_record.alignments[0] # Default to the top hit
+    chrom = None
+    for aln in blast_record.alignments:
+        chrom_match = re.search(r"chromosome\s([0-9XYMT]+)", aln.title, re.IGNORECASE)
+        if chrom_match:
+            alignment = aln
+            chrom = chrom_match.group(1)
+            break # We found the chromosome, stop searching!
+
     hsp = alignment.hsps[0]
-    chrom_match = re.search(r"chromosome\s([0-9XYMT]+)", alignment.title, re.IGNORECASE)
-    chrom = chrom_match.group(1) if chrom_match else None
     location_string = f"Chromosome {chrom}" if chrom else f"Accession {alignment.accession}"
 
     start, end = hsp.sbjct_start, hsp.sbjct_end
@@ -182,7 +189,6 @@ def get_genomic_context(sequence, is_coding):
     search_end = max(start, end) if feature_type == "CODING" else (end + 15000 if is_forward else end)
 
     try:
-        # THE ENSEMBL FIX: Changed 'Content-Type' to 'Accept' for proper JSON retrieval!
         response = requests.get(
             f"https://rest.ensembl.org/overlap/region/human/{chrom}:{search_start}-{search_end}?feature=gene", 
             headers={"Accept": "application/json"}
@@ -210,7 +216,9 @@ def get_genomic_context(sequence, is_coding):
 # ==============================
 def gradio_inference(dna_sequence, run_mapping):
     if len(dna_sequence.strip()) < 10:
-        return ("❌ Sequence too short!", "", "", "⚠️ Please enter at least 10 base pairs.")
+        # Using 'yield' to instantly push updates to the UI
+        yield ("❌ Sequence too short!", "", "", "⚠️ Please enter at least 10 base pairs.")
+        return
 
     # Run AI Models (GPU)
     label, conf, raw_scores = run_deep_learning_cascade(dna_sequence)
@@ -223,34 +231,38 @@ def gradio_inference(dna_sequence, run_mapping):
         else:
             stats_lines.append(f"- {key}: {val}")
 
-    # Run Context Mapping (CPU / Network)
-    context_output = ""
-    if run_mapping:
-        is_coding = "GENE" in label
-        context = get_genomic_context(dna_sequence, is_coding)
-        
-        if "error" in context:
-            context_output = f"❌ Mapping failed: {context['error']}"
-        elif "location" in context:
-            context_lines = [
-                f" Location:     {context['location']}",
-                f" Strand:       {context['strand']}",
-                f" Coordinates:  {context['start']:,} – {context['end']:,}",
-                f" Notes:        {context['metadata']}"
-            ]
-            context_output = "\n".join(context_lines)
-        else:
-            context_output = "⚠️ Could not map sequence."
-    else:
-        context_output = "🗺️ Spatial mapping skipped (Enable checkbox to query NCBI)."
-
     summary = (
         f"✅ Deep Scan Complete\n\n"
-        f"   Final Classification: {label}\n\n"
-        f"   Confidence Score: {conf:.2%}"
+        f"Final Classification: {label}\n"
+        f"Confidence Score: {conf:.2%}"
     )
 
-    return summary, "\n".join(stats_lines), context_output, ""
+    if not run_mapping:
+        yield (summary, "\n".join(stats_lines), "Spatial mapping skipped (Enable checkbox to run BLAST).", "")
+        return
+
+    # 🚨 STREAMING UPDATE: Pushes AI results instantly while showing a loading message for BLAST!
+    yield (summary, "\n".join(stats_lines), "⏳ Querying NCBI BLAST... (This takes 1-3 minutes. Please wait.)", "")
+
+    # Run Context Mapping (CPU / Network)
+    is_coding = "GENE" in label
+    context = get_genomic_context(dna_sequence, is_coding)
+    
+    if "error" in context:
+        context_output = f"❌ Mapping failed: {context['error']}"
+    elif "location" in context:
+        context_lines = [
+            f"Location:    {context['location']}",
+            f"Strand:      {context['strand']}",
+            f"Coordinates: {context['start']:,} – {context['end']:,}",
+            f"Notes:       {context['metadata']}"
+        ]
+        context_output = "\n".join(context_lines)
+    else:
+        context_output = "⚠️ Could not map sequence."
+
+    # 🚨 FINAL UPDATE: Pushes the finished BLAST results!
+    yield (summary, "\n".join(stats_lines), context_output, "")
 
 # --- CUSTOM CSS ---
 custom_css = """
@@ -302,14 +314,21 @@ with gr.Blocks(theme=gr.themes.Soft(), title="🧬 The Genomic Oracle 🧬", css
             submit_btn = gr.Button("🚀 Initialize Deep Scan", elem_id="scan_btn")
 
         with gr.Column(scale=1):
-            output_summary = gr.Textbox(label=" Classification Summary", lines=4)
-            stats_panel = gr.Textbox(label=" Internal Pipeline Statistics", lines=4)
-            mapping_section = gr.Accordion(" Genomic Context (BLAST/Ensembl)", open=False)
+            output_summary = gr.Textbox(label="Classification Summary", lines=4)
+            stats_panel = gr.Textbox(label="Internal Pipeline Statistics", lines=4)
+            mapping_section = gr.Accordion("Genomic Context (BLAST/Ensembl)", open=False)
             with mapping_section:
                 context_output = gr.Textbox(label="Mapping Results", lines=5, placeholder="Results will appear here...")
 
     info_box = gr.Markdown("", elem_id="info_box")
 
+    # 🚨 NEW UX FEATURE: Auto-open the accordion when the user checks the BLAST box!
+    run_mapping_cb.change(
+        fn=lambda is_checked: gr.Accordion(open=is_checked),
+        inputs=[run_mapping_cb],
+        outputs=[mapping_section]
+    )
+
     submit_btn.click(
         fn=lambda seq, map_flag: (
             *gradio_inference(seq, map_flag)[:3],