Add complete Gene2Text DNA codon explainer tool

app.py

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+import gradio as gr
+from codon_table import translate_dna_to_text, get_example_sequences, CODON_TABLE
+
+def process_dna_sequence(sequence, reading_frame, detailed_mode, example_dropdown):
+    """Process DNA sequence and return explanation"""
+    
+    # If user selected an example, use that
+    if example_dropdown and example_dropdown != "Choose an example...":
+        examples = get_example_sequences()
+        if example_dropdown in examples:
+            sequence = examples[example_dropdown]
+    
+    if not sequence or sequence.strip() == "":
+        return "Please enter a DNA sequence or select an example."
+    
+    try:
+        result = translate_dna_to_text(sequence, reading_frame, detailed_mode)
+        return result
+    except Exception as e:
+        return f"❌ Error processing sequence: {str(e)}\n\nPlease check your input and try again."
+
+def get_genetic_code_table():
+    """Generate a formatted genetic code reference table"""
+    output = ["# 🧬 Genetic Code Reference\n"]
+    output.append("| Codon | Amino Acid | Type | Description |")
+    output.append("|-------|------------|------|-------------|")
+    
+    # Group by amino acid for better organization
+    amino_acid_groups = {}
+    for codon, info in CODON_TABLE.items():
+        aa = info['amino_acid']
+        if aa not in amino_acid_groups:
+            amino_acid_groups[aa] = []
+        amino_acid_groups[aa].append((codon, info))
+    
+    # Sort amino acids, with special codons first
+    special_order = ['Methionine', 'STOP']
+    regular_amino_acids = sorted([aa for aa in amino_acid_groups.keys() if aa not in special_order])
+    
+    for aa in special_order + regular_amino_acids:
+        if aa in amino_acid_groups:
+            for codon, info in sorted(amino_acid_groups[aa]):
+                icon = "🚀" if info['type'] == 'start' else "🛑" if info['type'] == 'stop' else "🔤"
+                output.append(f"| {codon} | {aa} | {icon} | {info['description'][:50]}{'...' if len(info['description']) > 50 else ''} |")
+    
+    return "\n".join(output)
+
+# Create the Gradio interface
+with gr.Blocks(
+    title="Gene2Text: DNA Codon Explainer",
+    theme=gr.themes.Soft(),
+    css="""
+    .gradio-container {
+        max-width: 1200px !important;
+    }
+    .output-markdown {
+        font-family: 'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;
+    }
+    """
+) as app:
+    
+    gr.Markdown("""
+    # 🧬 Gene2Text: Interpretable Codon-by-Codon Describer
+    
+    **Transform DNA sequences into readable explanations!** This tool takes raw DNA sequences and explains what each three-letter codon codes for, making molecular biology accessible to everyone.
+    
+    Perfect for:
+    - 🎓 **Students** learning molecular biology
+    - 👩‍🏫 **Teachers** explaining genetic concepts  
+    - 🔬 **Researchers** quickly interpreting sequences
+    - 🤔 **Anyone curious** about how DNA codes for proteins
+    """)
+    
+    with gr.Row():
+        with gr.Column(scale=2):
+            gr.Markdown("## 📝 Input Your DNA Sequence")
+            
+            # Example dropdown
+            example_dropdown = gr.Dropdown(
+                choices=["Choose an example..."] + list(get_example_sequences().keys()),
+                value="Choose an example...",
+                label="📚 Or select an example sequence:",
+                info="Choose a pre-loaded example to see how the tool works"
+            )
+            
+            # Main input
+            sequence_input = gr.Textbox(
+                label="🧬 DNA Sequence",
+                placeholder="Enter your DNA sequence here (e.g., ATG GCT TAA)\nSpaces and line breaks will be automatically removed.",
+                lines=4,
+                info="Enter nucleotides: A, T, G, C only. Other characters will be filtered out."
+            )
+            
+            with gr.Row():
+                reading_frame = gr.Radio(
+                    choices=[0, 1, 2],
+                    value=0,
+                    label="📍 Reading Frame",
+                    info="Choose which nucleotide to start reading from (0=first, 1=second, 2=third)"
+                )
+                
+                detailed_mode = gr.Checkbox(
+                    value=True,
+                    label="🔍 Detailed Descriptions",
+                    info="Include biological context and amino acid properties"
+                )
+            
+            submit_btn = gr.Button("🔬 Analyze Sequence", variant="primary", size="lg")
+        
+        with gr.Column(scale=3):
+            gr.Markdown("## 📋 Results")
+            output_text = gr.Markdown(
+                value="Enter a DNA sequence to see the codon-by-codon breakdown here...",
+                elem_classes=["output-markdown"]
+            )
+    
+    # Genetic Code Reference (collapsible)
+    with gr.Accordion("📖 Genetic Code Reference Table", open=False):
+        genetic_code_display = gr.Markdown(get_genetic_code_table())
+    
+    # Educational content
+    with gr.Accordion("💡 How It Works", open=False):
+        gr.Markdown("""
+        ### The Genetic Code Explained
+        
+        **DNA → RNA → Protein** is the central dogma of molecular biology:
+        
+        1. **Codons**: DNA is read in groups of 3 nucleotides called codons
+        2. **Translation**: Each codon codes for a specific amino acid (or stop signal)
+        3. **Proteins**: Amino acids chain together to form proteins
+        4. **Reading Frames**: DNA can be read in 3 different frames, giving different results
+        
+        **Special Codons:**
+        - 🚀 **ATG**: Start codon (Methionine) - where protein synthesis begins
+        - 🛑 **TAA, TAG, TGA**: Stop codons - where protein synthesis ends
+        
+        **Why This Matters:**
+        Understanding how DNA codes for proteins helps us comprehend genetics, evolution, 
+        disease mechanisms, and biotechnology applications.
+        """)
+    
+    # Event handlers
+    submit_btn.click(
+        fn=process_dna_sequence,
+        inputs=[sequence_input, reading_frame, detailed_mode, example_dropdown],
+        outputs=output_text
+    )
+    
+    # Auto-update when example is selected
+    example_dropdown.change(
+        fn=process_dna_sequence,
+        inputs=[sequence_input, reading_frame, detailed_mode, example_dropdown],
+        outputs=output_text
+    )
+    
+    # Footer
+    gr.Markdown("""
+    ---
+    **Built with ❤️ for biology education** | Made with [Gradio](https://gradio.app) | 
+    Perfect for classrooms, labs, and curious minds everywhere!
+    """)
+
+# Launch the app
+if __name__ == "__main__":
+    app.launch(
+        share=True,
+        server_name="0.0.0.0",
+        server_port=7860,
+        show_error=True
+    )

codon_table.py

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+# Complete genetic code dictionary with biological context
+CODON_TABLE = {
+    # Start codon
+    'ATG': {'amino_acid': 'Methionine', 'type': 'start', 'description': 'The universal start codon - where protein synthesis begins'},
+    
+    # Stop codons
+    'TAA': {'amino_acid': 'STOP', 'type': 'stop', 'description': 'Amber stop codon - signals end of protein synthesis'},
+    'TAG': {'amino_acid': 'STOP', 'type': 'stop', 'description': 'Ochre stop codon - signals end of protein synthesis'},
+    'TGA': {'amino_acid': 'STOP', 'type': 'stop', 'description': 'Opal stop codon - signals end of protein synthesis'},
+    
+    # Alanine (A)
+    'GCT': {'amino_acid': 'Alanine', 'type': 'regular', 'description': 'Small, hydrophobic amino acid - often found in protein cores'},
+    'GCC': {'amino_acid': 'Alanine', 'type': 'regular', 'description': 'Small, hydrophobic amino acid - often found in protein cores'},
+    'GCA': {'amino_acid': 'Alanine', 'type': 'regular', 'description': 'Small, hydrophobic amino acid - often found in protein cores'},
+    'GCG': {'amino_acid': 'Alanine', 'type': 'regular', 'description': 'Small, hydrophobic amino acid - often found in protein cores'},
+    
+    # Arginine (R)
+    'CGT': {'amino_acid': 'Arginine', 'type': 'regular', 'description': 'Positively charged amino acid - important for protein-DNA interactions'},
+    'CGC': {'amino_acid': 'Arginine', 'type': 'regular', 'description': 'Positively charged amino acid - important for protein-DNA interactions'},
+    'CGA': {'amino_acid': 'Arginine', 'type': 'regular', 'description': 'Positively charged amino acid - important for protein-DNA interactions'},
+    'CGG': {'amino_acid': 'Arginine', 'type': 'regular', 'description': 'Positively charged amino acid - important for protein-DNA interactions'},
+    'AGA': {'amino_acid': 'Arginine', 'type': 'regular', 'description': 'Positively charged amino acid - important for protein-DNA interactions'},
+    'AGG': {'amino_acid': 'Arginine', 'type': 'regular', 'description': 'Positively charged amino acid - important for protein-DNA interactions'},
+    
+    # Asparagine (N)
+    'AAT': {'amino_acid': 'Asparagine', 'type': 'regular', 'description': 'Polar amino acid - often involved in protein folding and stability'},
+    'AAC': {'amino_acid': 'Asparagine', 'type': 'regular', 'description': 'Polar amino acid - often involved in protein folding and stability'},
+    
+    # Aspartic acid (D)
+    'GAT': {'amino_acid': 'Aspartic acid', 'type': 'regular', 'description': 'Negatively charged amino acid - important for enzyme active sites'},
+    'GAC': {'amino_acid': 'Aspartic acid', 'type': 'regular', 'description': 'Negatively charged amino acid - important for enzyme active sites'},
+    
+    # Cysteine (C)
+    'TGT': {'amino_acid': 'Cysteine', 'type': 'regular', 'description': 'Contains sulfur - can form disulfide bonds for protein structure'},
+    'TGC': {'amino_acid': 'Cysteine', 'type': 'regular', 'description': 'Contains sulfur - can form disulfide bonds for protein structure'},
+    
+    # Glutamic acid (E)
+    'GAA': {'amino_acid': 'Glutamic acid', 'type': 'regular', 'description': 'Negatively charged amino acid - common in enzyme active sites'},
+    'GAG': {'amino_acid': 'Glutamic acid', 'type': 'regular', 'description': 'Negatively charged amino acid - common in enzyme active sites'},
+    
+    # Glutamine (Q)
+    'CAA': {'amino_acid': 'Glutamine', 'type': 'regular', 'description': 'Polar amino acid - involved in protein-protein interactions'},
+    'CAG': {'amino_acid': 'Glutamine', 'type': 'regular', 'description': 'Polar amino acid - involved in protein-protein interactions'},
+    
+    # Glycine (G)
+    'GGT': {'amino_acid': 'Glycine', 'type': 'regular', 'description': 'Smallest amino acid - provides flexibility in protein structure'},
+    'GGC': {'amino_acid': 'Glycine', 'type': 'regular', 'description': 'Smallest amino acid - provides flexibility in protein structure'},
+    'GGA': {'amino_acid': 'Glycine', 'type': 'regular', 'description': 'Smallest amino acid - provides flexibility in protein structure'},
+    'GGG': {'amino_acid': 'Glycine', 'type': 'regular', 'description': 'Smallest amino acid - provides flexibility in protein structure'},
+    
+    # Histidine (H)
+    'CAT': {'amino_acid': 'Histidine', 'type': 'regular', 'description': 'Can be positively charged - often found in enzyme active sites'},
+    'CAC': {'amino_acid': 'Histidine', 'type': 'regular', 'description': 'Can be positively charged - often found in enzyme active sites'},
+    
+    # Isoleucine (I)
+    'ATT': {'amino_acid': 'Isoleucine', 'type': 'regular', 'description': 'Hydrophobic amino acid - important for protein core structure'},
+    'ATC': {'amino_acid': 'Isoleucine', 'type': 'regular', 'description': 'Hydrophobic amino acid - important for protein core structure'},
+    'ATA': {'amino_acid': 'Isoleucine', 'type': 'regular', 'description': 'Hydrophobic amino acid - important for protein core structure'},
+    
+    # Leucine (L)
+    'TTA': {'amino_acid': 'Leucine', 'type': 'regular', 'description': 'Hydrophobic amino acid - very common in proteins'},
+    'TTG': {'amino_acid': 'Leucine', 'type': 'regular', 'description': 'Hydrophobic amino acid - very common in proteins'},
+    'CTT': {'amino_acid': 'Leucine', 'type': 'regular', 'description': 'Hydrophobic amino acid - very common in proteins'},
+    'CTC': {'amino_acid': 'Leucine', 'type': 'regular', 'description': 'Hydrophobic amino acid - very common in proteins'},
+    'CTA': {'amino_acid': 'Leucine', 'type': 'regular', 'description': 'Hydrophobic amino acid - very common in proteins'},
+    'CTG': {'amino_acid': 'Leucine', 'type': 'regular', 'description': 'Hydrophobic amino acid - very common in proteins'},
+    
+    # Lysine (K)
+    'AAA': {'amino_acid': 'Lysine', 'type': 'regular', 'description': 'Positively charged amino acid - important for DNA binding'},
+    'AAG': {'amino_acid': 'Lysine', 'type': 'regular', 'description': 'Positively charged amino acid - important for DNA binding'},
+    
+    # Phenylalanine (F)
+    'TTT': {'amino_acid': 'Phenylalanine', 'type': 'regular', 'description': 'Aromatic, hydrophobic amino acid - important for protein structure'},
+    'TTC': {'amino_acid': 'Phenylalanine', 'type': 'regular', 'description': 'Aromatic, hydrophobic amino acid - important for protein structure'},
+    
+    # Proline (P)
+    'CCT': {'amino_acid': 'Proline', 'type': 'regular', 'description': 'Rigid amino acid - creates kinks and turns in protein structure'},
+    'CCC': {'amino_acid': 'Proline', 'type': 'regular', 'description': 'Rigid amino acid - creates kinks and turns in protein structure'},
+    'CCA': {'amino_acid': 'Proline', 'type': 'regular', 'description': 'Rigid amino acid - creates kinks and turns in protein structure'},
+    'CCG': {'amino_acid': 'Proline', 'type': 'regular', 'description': 'Rigid amino acid - creates kinks and turns in protein structure'},
+    
+    # Serine (S)
+    'TCT': {'amino_acid': 'Serine', 'type': 'regular', 'description': 'Polar amino acid - can be phosphorylated for regulation'},
+    'TCC': {'amino_acid': 'Serine', 'type': 'regular', 'description': 'Polar amino acid - can be phosphorylated for regulation'},
+    'TCA': {'amino_acid': 'Serine', 'type': 'regular', 'description': 'Polar amino acid - can be phosphorylated for regulation'},
+    'TCG': {'amino_acid': 'Serine', 'type': 'regular', 'description': 'Polar amino acid - can be phosphorylated for regulation'},
+    'AGT': {'amino_acid': 'Serine', 'type': 'regular', 'description': 'Polar amino acid - can be phosphorylated for regulation'},
+    'AGC': {'amino_acid': 'Serine', 'type': 'regular', 'description': 'Polar amino acid - can be phosphorylated for regulation'},
+    
+    # Threonine (T)
+    'ACT': {'amino_acid': 'Threonine', 'type': 'regular', 'description': 'Polar amino acid - can be phosphorylated for regulation'},
+    'ACC': {'amino_acid': 'Threonine', 'type': 'regular', 'description': 'Polar amino acid - can be phosphorylated for regulation'},
+    'ACA': {'amino_acid': 'Threonine', 'type': 'regular', 'description': 'Polar amino acid - can be phosphorylated for regulation'},
+    'ACG': {'amino_acid': 'Threonine', 'type': 'regular', 'description': 'Polar amino acid - can be phosphorylated for regulation'},
+    
+    # Tryptophan (W)
+    'TGG': {'amino_acid': 'Tryptophan', 'type': 'regular', 'description': 'Largest amino acid - important for protein folding and fluorescence'},
+    
+    # Tyrosine (Y)
+    'TAT': {'amino_acid': 'Tyrosine', 'type': 'regular', 'description': 'Aromatic amino acid - can be phosphorylated for signaling'},
+    'TAC': {'amino_acid': 'Tyrosine', 'type': 'regular', 'description': 'Aromatic amino acid - can be phosphorylated for signaling'},
+    
+    # Valine (V)
+    'GTT': {'amino_acid': 'Valine', 'type': 'regular', 'description': 'Hydrophobic amino acid - common in protein cores'},
+    'GTC': {'amino_acid': 'Valine', 'type': 'regular', 'description': 'Hydrophobic amino acid - common in protein cores'},
+    'GTA': {'amino_acid': 'Valine', 'type': 'regular', 'description': 'Hydrophobic amino acid - common in protein cores'},
+    'GTG': {'amino_acid': 'Valine', 'type': 'regular', 'description': 'Hydrophobic amino acid - common in protein cores'}
+}
+
+def clean_sequence(sequence):
+    """Clean and validate DNA sequence"""
+    # Remove spaces, newlines, and convert to uppercase
+    cleaned = sequence.upper().replace(" ", "").replace("\n", "").replace("\t", "")
+    
+    # Remove any non-DNA characters
+    valid_chars = set('ATGC')
+    cleaned = ''.join(char for char in cleaned if char in valid_chars)
+    
+    return cleaned
+
+def translate_dna_to_text(sequence, reading_frame=0, detailed=True):
+    """
+    Translate DNA sequence to descriptive text
+    
+    Args:
+        sequence (str): DNA sequence
+        reading_frame (int): 0, 1, or 2 for different reading frames
+        detailed (bool): Whether to include detailed descriptions
+    
+    Returns:
+        str: Formatted explanation of the sequence
+    """
+    sequence = clean_sequence(sequence)
+    
+    if len(sequence) == 0:
+        return "❌ No valid DNA sequence found. Please enter a sequence with A, T, G, C characters only."
+    
+    # Adjust for reading frame
+    sequence = sequence[reading_frame:]
+    
+    if len(sequence) < 3:
+        return "❌ Sequence too short. Need at least 3 nucleotides to form a codon."
+    
+    # Split into codons
+    codons = [sequence[i:i+3] for i in range(0, len(sequence), 3)]
+    
+    output = []
+    output.append(f"🧬 **DNA Sequence Analysis** (Reading Frame {reading_frame + 1})")
+    output.append(f"📊 **Sequence Length:** {len(sequence)} nucleotides ({len(codons)} codons)")
+    output.append("")
+    
+    protein_sequence = []
+    
+    for i, codon in enumerate(codons):
+        if len(codon) == 3:
+            codon_info = CODON_TABLE.get(codon)
+            
+            if codon_info:
+                amino_acid = codon_info['amino_acid']
+                codon_type = codon_info['type']
+                description = codon_info['description']
+                
+                # Add to protein sequence
+                if amino_acid == 'STOP':
+                    protein_sequence.append('*')
+                elif amino_acid == 'Methionine':
+                    protein_sequence.append('M')
+                else:
+                    protein_sequence.append(amino_acid[0])
+                
+                # Format output based on codon type
+                if codon_type == 'start':
+                    output.append(f"🚀 **Codon {i+1}: {codon}** → {amino_acid}")
+                elif codon_type == 'stop':
+                    output.append(f"🛑 **Codon {i+1}: {codon}** → {amino_acid}")
+                else:
+                    output.append(f"🔤 **Codon {i+1}: {codon}** → {amino_acid}")
+                
+                if detailed:
+                    output.append(f"   💡 {description}")
+                output.append("")
+            else:
+                output.append(f"❓ **Codon {i+1}: {codon}** → Unknown codon")
+                output.append("")
+        else:
+            output.append(f"⚠️ **Incomplete codon: {codon}** (only {len(codon)} nucleotides)")
+            output.append("")
+    
+    # Add protein sequence summary
+    if protein_sequence:
+        protein_str = ''.join(protein_sequence)
+        output.append("🧪 **Resulting Protein Sequence:**")
+        output.append(f"{protein_str}")
+        output.append("")
+        
+        # Count amino acids
+        start_codons = sum(1 for codon in codons if len(codon) == 3 and CODON_TABLE.get(codon, {}).get('type') == 'start')
+        stop_codons = sum(1 for codon in codons if len(codon) == 3 and CODON_TABLE.get(codon, {}).get('type') == 'stop')
+        
+        output.append(f"📈 **Summary:** {start_codons} start codon(s), {stop_codons}    
+    return "\n".join(output)
+
+def get_example_sequences():
+    """Return example DNA sequences for testing"""
+    return {
+        "Basic Example": "ATG GCT TAA",
+        "Insulin Gene (partial)": "ATG GCC CTG TGG ATG CGC CTC CTG CCC CTG CTG GCG CTG CTG GCC CTG TGG GGG ACC TCG TCG",
+        "Beta-globin (partial)": "ATG GTG CAC CTG ACT CCT GAG GAG AAG TCT",
+        "Green Fluorescent Protein (partial)": "ATG AGC AAG GGC GAG GAG CTG TTC ACC GGG GTG GTG CCC ATC CTG GTG GAG CTG"
+    }

requirements.txt

@@ -0,0 +1 @@
+gradio>=4.0.0