create_examples.py

"""
Script to generate example cancer mutation FASTA files
Run this to create sample data for testing the DNA sonification platform
"""

from pathlib import Path

def create_example_fasta_files():
    """Create example FASTA files for common cancer mutations"""
    
    # Create examples directory
    examples_dir = Path("examples")
    examples_dir.mkdir(exist_ok=True)
    
    # TP53 R273H mutation (hotspot in DNA-binding domain)
    tp53_wt = """>TP53_wildtype DNA-binding domain
ATGGAGGAGCCGCAGTCAGATCCTAGCGTCGAGCCCCCTCTGAGTCAGGAAACATTTTCA
GACCTATGGAAACTACTTCCTGAAAACAACGTTCTGTCCCCCTTGCCGTCCCAAGCAATG
GATGATTTGATGCTGTCCCCGGACGATATTGAACAATGGTTCACTGAAGACCCAGGTCCA
GATGAAGCTCCCAGAATGCCAGAGGCTGCTCCCCCCGTGGCCCCTGCACCAGCAGCTCCT
ACACCGGCGGCCCCTGCACCAGCCCCCTCCTGGCCCCTGTCATCTTCT"""
    
    tp53_mut = """>TP53_R273H_mutant DNA-binding domain with R273H mutation
ATGGAGGAGCCGCAGTCAGATCCTAGCGTCGAGCCCCCTCTGAGTCAGGAAACATTTTCA
GACCTATGGAAACTACTTCCTGAAAACAACGTTCTGTCCCCCTTGCCGTCCCAAGCAATG
GATGATTTGATGCTGTCCCCGGACGATATTGAACAATGGTTCACTGAAGACCCAGGTCCA
GATGAAGCTCCCAGAATGCCAGAGGCTGCTCCCCGCGTGGCCCCTGCACCAGCAGCTCCT
ACACCGGCGGCCCCTGCACCAGCCCCCTCCTGGCCCCTGTCATCTTCT"""
    
    # KRAS G12D mutation (codon 12 mutation)
    kras_wt = """>KRAS_wildtype codon 12 region
ATGACTGAATATAAACTTGTGGTAGTTGGAGCTGGTGGCGTAGGCAAGAGTGCCTTGACG
ATACAGCTAATTCAGAATCATTTTGTGGACGAATATGATCCAACAATAGAGGATTCCTAC
AGGAAGCAAGTAGTAATTGATGGAGAAACCTGTCTCTTGGATATTCTCGACACAGCAGGT
CAAGAGGAGTACAGTGCAATGAGGGACCAGTACATGAGGACTGGGGAGGGCTTTCTTTGT
GTATTTGCCATAAATAATACTAAATCATTTGAAGATATTCACCATTATAGAGAACAAATT
AAAAGAGTTAAGGACTCTGAAGATGTACCTATGGTCCTAGTAGGAAATAAATGTGATTTG"""
    
    kras_mut = """>KRAS_G12D_mutant codon 12 G12D activating mutation
ATGACTGAATATAAACTTGTGGTAGTTGGAGCTGGTGGCGTAGGCAAGAGTGCCTTGACG
ATACAGCTAATTCAGAATCATTTTGTGGACGAATATGATCCAACAATAGAGGATTCCTAC
AGGAAGCAAGTAGTAATTGATGGAGAAACCTGTCTCTTGGATATTCTCGACACAGCAGGT
CAAGAGGAGTACAGTGCAATGAGGGACCAGTACATGAGGACTGGGGAGGGCTTTCTTTGT
GTATTTGCCATAAATAATACTAAATCATTTGAAGATATTCACCATTATAGAGAACAAATT
AAAAGAGTTAAGGACTCTGAAGATGTACCTATGGTCCTAGTAGGAAATAAATGTGATTTG"""
    
    # BRAF V600E mutation (common in melanoma)
    braf_wt = """>BRAF_wildtype V600 region kinase domain
ATGAAGACCTCACAGTAAAAATAGGTGATTTTGGTCTAGCTACAGTGAAATCTCGATGGA
GTGGGTCCCATCAGTTTGAACAGTTGTCTGGATCCATTTTGTGGATGGTAAGAATTGAGG
CTATTTTTCCACTGATTAAATTTTTGGCCCTGAGATGCTGCTGAGTTACTAGAAAGTCAT
TTATGAGGACTTGGATATTTTATTTGGTGACTGATATTAGCATTCAGAATGAGTTGCAAC
TAGAAATTATAAGAGAATTCAGATACATTTCTTGATTGAAGACTTAAAATTCTTTCTAAC
TCTTCAGGCATGAAGGTACTCAGCAATGGTTACACAGACCTAGCAGATATTGTTGAAGAC"""
    
    braf_mut = """>BRAF_V600E_mutant V600E activating mutation
ATGAAGACCTCACAGTAAAAATAGGTGATTTTGGTCTAGCTACAGTGAAATCTCGATGGA
GTGGGTCCCATCAGTTTGAACAGTTGTCTGGATCCATTTTGTGGATGGTAAGAATTGAGG
CTATTTTTCCACTGATTAAATTTTTGGCCCTGAGATGCTGCTGAGTTACTAGAAAGTCAT
TTATGAGGACTTGGATATTTTATTTGGTGACTGATATTAGCATTCAGAATGAGTTGCAAC
TAGAAATTATAAGAGAATTCAGATACATTTCTTGATTGAAGACTTAAAATTCTTTCTAAC
TCTTCAGGCATGAAGGTACTCAGCAATGGTTACACAGACCTAGAAGATATTGTTGAAGAC"""
    
    # EGFR L858R mutation (non-small cell lung cancer)
    egfr_wt = """>EGFR_wildtype L858 region tyrosine kinase domain
ATCAAGAATCAGGAGAAAGCTGCCAGCGCCTTCTCAAGCCTCTATGCCTTGGCCAACAGG
CCCCAGATGCTCAATTCCATCATGGACCCGCCATACTCGGAGGCCAAGGTGGGCTTTGGG
GACATCCTGCAGGCCCGCTGCTCCCAGTGCCGGGATGCGGTCCCCCCCAGTGTCGTGAAG
GCGGAGGATGTCCTGGAGAAGGAGATCCTGCCCCAGTGGGTCAGCGTGCTGCGGGCCATC
TATGAGAACCGGAGTGACACGCTGGATGCTGAGGAGACCCTGCAGCGGCTGGGGCCCTTT"""
    
    egfr_mut = """>EGFR_L858R_mutant L858R activating mutation
ATCAAGAATCAGGAGAAAGCTGCCAGCGCCTTCTCAAGCCTCTATGCCTTGGCCAACAGG
CCCCAGATGCTCAATTCCATCATGGACCCGCCATACTCGGAGGCCAAGGTGGGCTTTGGG
GACATCCTGCAGGCCCGCTGCTCCCAGTGCCGGGATGCGGTCCCCCCCAGTGTCGTGAAG
GCGGAGGATGTCCTGGAGAAGGAGATCCTGCCCCAGTGGGTCAGCGTGCTGCGGGCCATC
TATGAGAACCGGAGTGACACGCTGGATGCTGAGGAGACCAGACAGCGGCTGGGGCCCTTT"""
    
    # PIK3CA H1047R mutation (breast cancer)
    pik3ca_wt = """>PIK3CA_wildtype H1047 region helical domain
ATGAAAGCAACTCAGCAATCAGCCCATACAGGTTATTGGCCATTTTTGGTCCAATGATGC
TTGGCTCTGGAATGCCAGAACTACAATCTTTTGAAGGAAATGAATGATGCACATCATGGT
GGCTGGACAACAAAAGGGCAATCAGTTACTTTTCTCCACAGATATCATTGCAAATAGTCA
AGAGTATTGGCTTATGGATTTACAACATATTGATTGTGCATTGATGGCATGGTATATTCA
TGATGCAGAGACGATTGATTTGTGGAAATTGGCTTGGGCACTTACATTGCTGAAGTGAAA"""
    
    pik3ca_mut = """>PIK3CA_H1047R_mutant H1047R gain-of-function mutation
ATGAAAGCAACTCAGCAATCAGCCCATACAGGTTATTGGCCATTTTTGGTCCAATGATGC
TTGGCTCTGGAATGCCAGAACTACAATCTTTTGAAGGAAATGAATGATGCACATCATGGT
GGCTGGACAACAAAAGGGCAATCAGTTACTTTTCTCCACAGATATCATTGCAAATAGTCA
AGAGTATTGGCTTATGGATTTACAACATATTGATTGTGCATTGATGGCATGGTATATTCA
TGATGCAGAGACGATTGATTTGTGGAAATTGGCTTGGGCGCTTACATTGCTGAAGTGAAA"""
    
    # Write files
    files = {
        "TP53_wildtype.fasta": tp53_wt,
        "TP53_R273H_mutant.fasta": tp53_mut,
        "KRAS_wildtype.fasta": kras_wt,
        "KRAS_G12D_mutant.fasta": kras_mut,
        "BRAF_wildtype.fasta": braf_wt,
        "BRAF_V600E_mutant.fasta": braf_mut,
        "EGFR_wildtype.fasta": egfr_wt,
        "EGFR_L858R_mutant.fasta": egfr_mut,
        "PIK3CA_wildtype.fasta": pik3ca_wt,
        "PIK3CA_H1047R_mutant.fasta": pik3ca_mut
    }
    
    for filename, content in files.items():
        filepath = examples_dir / filename
        with open(filepath, 'w') as f:
            f.write(content)
        print(f"Created: {filepath}")
    
    # Create a README
    readme = """# Cancer Mutation Example FASTA Files

This directory contains example DNA sequences for common cancer-related mutations:

## TP53 (Tumor Suppressor)
- **TP53_wildtype.fasta**: Normal DNA-binding domain
- **TP53_R273H_mutant.fasta**: R273H hotspot mutation (CGC→CAC, Arg→His)
  - Common in colorectal, lung, and breast cancers
  - Loss of tumor suppressor function

## KRAS (Oncogene)
- **KRAS_wildtype.fasta**: Normal codon 12 region
- **KRAS_G12D_mutant.fasta**: G12D activating mutation (GGT→GAT, Gly→Asp)
  - Common in pancreatic, colorectal, and lung cancers
  - Constitutive activation of signaling

## BRAF (Oncogene)
- **BRAF_wildtype.fasta**: Normal V600 region
- **BRAF_V600E_mutant.fasta**: V600E activating mutation (GTG→GAG, Val→Glu)
  - Common in melanoma and thyroid cancer
  - Constitutive kinase activation

## EGFR (Receptor Tyrosine Kinase)
- **EGFR_wildtype.fasta**: Normal L858 region
- **EGFR_L858R_mutant.fasta**: L858R activating mutation (CTG→CGG, Leu→Arg)
  - Common in non-small cell lung cancer
  - Increased kinase activity

## PIK3CA (Oncogene)
- **PIK3CA_wildtype.fasta**: Normal H1047 region
- **PIK3CA_H1047R_mutant.fasta**: H1047R gain-of-function mutation (CAT→CGT, His→Arg)
  - Common in breast, colorectal, and endometrial cancers
  - Enhanced PI3K pathway activation

## Usage
Upload pairs of wildtype and mutant files to the DNA Sonification Platform to:
1. Visualize sequence alignments
2. Hear mutations as distinct sound patterns
3. Analyze functional impact with AI
"""
    
    readme_path = examples_dir / "README.md"
    with open(readme_path, 'w', encoding='utf-8') as f:
        f.write(readme)
    print(f"\nCreated: {readme_path}")
    
    print(f"\n✓ Created {len(files)} FASTA files in {examples_dir}/")
    print("These files are ready to use with the DNA Sonification Platform!")


if __name__ == "__main__":
    create_example_fasta_files()