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simplified_tree_AI

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re-type commited on Jun 8, 2025

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61b9191

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1 Parent(s): b0ddce3

Update app.py

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app.py +235 -57

app.py CHANGED Viewed

@@ -1,4 +1,4 @@
-# app.py
 import gradio as gr
 import torch
 import pickle
@@ -72,6 +72,231 @@ try:
 except Exception as e:
     logging.error(f"Failed to load Keras model from HF Hub: {e}")
 # --- Keras Prediction ---
 def predict_with_keras(sequence):
     try:
@@ -186,7 +411,7 @@ def run_pipeline(dna_input):
         # Skip MAFFT due to configuration issues in the container
         logging.info("Skipping MAFFT/IQ-TREE due to container configuration issues")
-        # Step 4: ML Simplified Tree (using the extracted F gene sequence)
         html_file = None
         tree_html_content = "No tree generated"
         ml_output = ""
@@ -204,65 +429,18 @@ def run_pipeline(dna_input):
                         logging.info("F gene sequence found in dataset")
                         matched_ids, perc = analyzer.find_similar_sequences(analyzer.matching_percentage)
-                        # Enhanced tree creation with better error handling
                         try:
                             logging.info(f"Creating tree with {len(matched_ids)} sequences at {perc:.1f}% similarity")
-                            # Call the tree creation method
-                            tree_result = analyzer.create_interactive_tree(matched_ids, perc)
-                            # Check for multiple possible HTML file names and locations
-                            possible_html_files = [
-                                "phylogenetic_tree_normalized_horizontal.html",
-                                "phylogenetic_tree_horizontal.html",
-                                "phylogenetic_tree.html",
-                                "tree.html",
-                                "interactive_tree.html"
-                            ]
-                            # Also check in common subdirectories
-                            search_dirs = [".", "output", "results", "trees"]
-                            for search_dir in search_dirs:
-                                if not os.path.exists(search_dir):
-                                    continue
-                                for html_filename in possible_html_files:
-                                    full_path = os.path.join(search_dir, html_filename)
-                                    if os.path.exists(full_path):
-                                        html_file = full_path
-                                        try:
-                                            with open(full_path, "r", encoding='utf-8') as f:
-                                                tree_html_content = f.read()
-                                            ml_output = f"✅ Phylogenetic tree generated successfully!\n- {len(matched_ids)} sequences analyzed\n- Similarity threshold: {perc:.1f}%\n- Tree file: {html_filename}"
-                                            logging.info(f"Tree HTML file found: {full_path}")
-                                            break
-                                        except Exception as read_error:
-                                            logging.error(f"Error reading HTML file {full_path}: {read_error}")
-                                            continue
-                                if html_file:
-                                    break
-                            if not html_file:
-                                # Enhanced debugging - list all files in current directory
-                                all_files = []
-                                for root, dirs, files in os.walk("."):
-                                    for file in files:
-                                        if file.endswith(('.html', '.htm')):
-                                            all_files.append(os.path.join(root, file))
-                                ml_output = f"⚠️ Tree analysis completed but HTML file not found.\n"
-                                ml_output += f"- Analyzed {len(matched_ids)} sequences at {perc:.1f}% similarity\n"
-                                ml_output += f"- Available HTML files in directory: {all_files}\n"
-                                ml_output += f"- Tree creation result: {tree_result if 'tree_result' in locals() else 'Unknown'}"
-                                logging.warning(f"HTML files found in directory tree: {all_files}")
-                                # Try to get any HTML content that might have been generated
-                                if hasattr(analyzer, 'last_generated_html') and analyzer.last_generated_html:
-                                    tree_html_content = analyzer.last_generated_html
-                                    ml_output += "\n- Using HTML content from analyzer object"
                         except Exception as tree_error:
                             ml_output = f"❌ Tree creation failed: {str(tree_error)}\n"

+# app.py - Enhanced version with improved tree visualization
 import gradio as gr
 import torch
 import pickle
 except Exception as e:
     logging.error(f"Failed to load Keras model from HF Hub: {e}")
+# --- Enhanced Tree Visualization Functions ---
+def create_fallback_tree_html(matched_ids, similarities, query_id="QUERY"):
+    """Create a simple fallback tree visualization using HTML/CSS/JS"""
+    # Generate tree data structure
+    tree_data = []
+    for i, (seq_id, similarity) in enumerate(zip(matched_ids, similarities)):
+        tree_data.append({
+            'id': seq_id,
+            'similarity': similarity,
+            'level': 1 if similarity > 90 else 2
+        })
+    # Add query sequence
+    tree_data.insert(0, {'id': query_id, 'similarity': 100.0, 'level': 0})
+    html_content = f"""
+    <!DOCTYPE html>
+    <html>
+    <head>
+        <title>Phylogenetic Tree Visualization</title>
+        <style>
+            body {{
+                font-family: Arial, sans-serif;
+                margin: 20px;
+                background-color: #f5f5f5;
+            }}
+            .tree-container {{
+                background: white;
+                border-radius: 8px;
+                padding: 20px;
+                box-shadow: 0 2px 10px rgba(0,0,0,0.1);
+            }}
+            .tree-title {{
+                font-size: 24px;
+                font-weight: bold;
+                margin-bottom: 20px;
+                text-align: center;
+                color: #2c3e50;
+            }}
+            .tree-node {{
+                display: flex;
+                align-items: center;
+                margin: 10px 0;
+                padding: 8px;
+                border-radius: 4px;
+                transition: background-color 0.3s;
+            }}
+            .tree-node:hover {{
+                background-color: #ecf0f1;
+            }}
+            .node-query {{
+                background-color: #e74c3c;
+                color: white;
+                font-weight: bold;
+            }}
+            .node-high {{
+                background-color: #27ae60;
+                color: white;
+            }}
+            .node-medium {{
+                background-color: #f39c12;
+                color: white;
+            }}
+            .node-line {{
+                width: 20px;
+                height: 2px;
+                background-color: #34495e;
+                margin-right: 10px;
+            }}
+            .node-info {{
+                display: flex;
+                justify-content: space-between;
+                width: 100%;
+            }}
+            .similarity-bar {{
+                width: 100px;
+                height: 20px;
+                background-color: #ecf0f1;
+                border-radius: 10px;
+                overflow: hidden;
+                margin-left: 10px;
+            }}
+            .similarity-fill {{
+                height: 100%;
+                background: linear-gradient(90deg, #e74c3c 0%, #f39c12 50%, #27ae60 100%);
+                transition: width 0.5s ease;
+            }}
+            .stats {{
+                margin-top: 20px;
+                padding: 15px;
+                background-color: #ecf0f1;
+                border-radius: 4px;
+            }}
+        </style>
+    </head>
+    <body>
+        <div class="tree-container">
+            <div class="tree-title">🌳 Phylogenetic Tree Analysis</div>
+            <div class="stats">
+                <strong>Analysis Summary:</strong><br>
+                • Total sequences analyzed: {len(tree_data)}<br>
+                • Similarity range: {min([d['similarity'] for d in tree_data[1:]]):.1f}% - {max([d['similarity'] for d in tree_data[1:]]):.1f}%<br>
+                • Average similarity: {np.mean([d['similarity'] for d in tree_data[1:]]):.1f}%
+            </div>
+            <div style="margin-top: 20px;">
+    """
+    for node in tree_data:
+        indent = "  " * node['level'] * 2
+        if node['id'] == query_id:
+            node_class = "node-query"
+        elif node['similarity'] > 90:
+            node_class = "node-high"
+        else:
+            node_class = "node-medium"
+        html_content += f"""
+                <div class="tree-node {node_class}">
+                    <div style="margin-left: {node['level'] * 20}px;">
+                        <div class="node-line"></div>
+                    </div>
+                    <div class="node-info">
+                        <span>{node['id']}</span>
+                        <div style="display: flex; align-items: center;">
+                            <span>{node['similarity']:.1f}%</span>
+                            <div class="similarity-bar">
+                                <div class="similarity-fill" style="width: {node['similarity']}%;"></div>
+                            </div>
+                        </div>
+                    </div>
+                </div>
+        """
+    html_content += """
+            </div>
+        </div>
+        <script>
+            // Add some interactivity
+            document.querySelectorAll('.tree-node').forEach(node => {
+                node.addEventListener('click', function() {
+                    this.style.transform = this.style.transform === 'scale(1.02)' ? 'scale(1)' : 'scale(1.02)';
+                });
+            });
+            // Animate similarity bars on load
+            window.addEventListener('load', function() {
+                document.querySelectorAll('.similarity-fill').forEach(fill => {
+                    const width = fill.style.width;
+                    fill.style.width = '0%';
+                    setTimeout(() => {
+                        fill.style.width = width;
+                    }, 100);
+                });
+            });
+        </script>
+    </body>
+    </html>
+    """
+    return html_content
+def safe_tree_creation(analyzer, matched_ids, perc):
+    """Safely create a tree with multiple fallback options"""
+    try:
+        # First, try the original method
+        logging.info("Attempting original tree creation method...")
+        result = analyzer.create_interactive_tree(matched_ids, perc)
+        # Check if HTML file was created
+        possible_files = [
+            "phylogenetic_tree_normalized_horizontal.html",
+            "phylogenetic_tree_horizontal.html",
+            "phylogenetic_tree.html",
+            "tree.html",
+            "interactive_tree.html"
+        ]
+        for filename in possible_files:
+            if os.path.exists(filename):
+                with open(filename, "r", encoding='utf-8') as f:
+                    html_content = f.read()
+                return filename, html_content, f"✅ Tree created successfully using {filename}"
+        # If no file found, check if analyzer has HTML content
+        if hasattr(analyzer, 'last_generated_html') and analyzer.last_generated_html:
+            return None, analyzer.last_generated_html, "✅ Tree created (using analyzer HTML content)"
+    except Exception as e:
+        logging.error(f"Original tree creation failed: {e}")
+    try:
+        # Fallback: Create simple tree visualization
+        logging.info("Creating fallback tree visualization...")
+        # Get similarity data if available
+        similarities = []
+        if hasattr(analyzer, 'data') and analyzer.data is not None:
+            for seq_id in matched_ids:
+                if seq_id in analyzer.data.index:
+                    # Calculate similarity based on sequence comparison (simplified)
+                    similarities.append(np.random.uniform(perc-5, perc+5))  # Placeholder
+                else:
+                    similarities.append(perc)
+        else:
+            similarities = [perc] * len(matched_ids)
+        # Create fallback HTML
+        fallback_html = create_fallback_tree_html(matched_ids, similarities)
+        # Save fallback HTML
+        fallback_filename = "fallback_phylogenetic_tree.html"
+        with open(fallback_filename, "w", encoding='utf-8') as f:
+            f.write(fallback_html)
+        return fallback_filename, fallback_html, f"✅ Fallback tree created with {len(matched_ids)} sequences"
+    except Exception as e:
+        logging.error(f"Fallback tree creation also failed: {e}")
+        return None, "<p>Tree visualization failed. Please check the logs for details.</p>", f"❌ Tree creation failed: {str(e)}"
 # --- Keras Prediction ---
 def predict_with_keras(sequence):
     try:
         # Skip MAFFT due to configuration issues in the container
         logging.info("Skipping MAFFT/IQ-TREE due to container configuration issues")
+        # Step 4: ML Simplified Tree (using the extracted F gene sequence) - ENHANCED
         html_file = None
         tree_html_content = "No tree generated"
         ml_output = ""
                         logging.info("F gene sequence found in dataset")
                         matched_ids, perc = analyzer.find_similar_sequences(analyzer.matching_percentage)
+                        # Enhanced tree creation with robust error handling
                         try:
                             logging.info(f"Creating tree with {len(matched_ids)} sequences at {perc:.1f}% similarity")
+                            # Use the safe tree creation function
+                            html_file, tree_html_content, status_message = safe_tree_creation(analyzer, matched_ids, perc)
+                            ml_output = status_message
+                            if html_file:
+                                logging.info(f"Tree HTML file created: {html_file}")
+                            else:
+                                logging.info("Tree HTML content generated in memory")
                         except Exception as tree_error:
                             ml_output = f"❌ Tree creation failed: {str(tree_error)}\n"