genome-report

# Genome Report Analyze 23andMe v5 raw data files and generate health/trait reports with risk scoring. ## Usage ```bash python3 skills/genome-report/scripts/genome_report.py <genome_file.txt> [options] ``` ### Options | Flag | Values | Default | Description | |------|--------|---------|-------------| | `--category` | `all\|cardio\|cognitive\|metabolic\|pharma\|athletic\|traits` | `all` | Category filter | | `--output` | `text\|json\|html` | `text` | Output format | | `--output-path` | filepath | auto | HTML output path | | `--family DIR` | directory path | — | Family comparison mode | ### Examples ```bash # Full report to console python3 skills/genome-report/scripts/genome_report.py ~/my_genome.txt # HTML report for one category python3 skills/genome-report/scripts/genome_report.py ~/my_genome.txt --category cardio --output html # Family comparison python3 skills/genome-report/scripts/genome_report.py --family ~/genomes/ --output html ``` ## Input Format 23andMe v5 raw data (tab-separated): `rsid chromosome position genotype` Lines starting with `#` are skipped. Genotypes marked `--` (no-call) are excluded. ## Output - **Text**: Console output with risk bars and color-coded SNP details - **JSON**: Structured data with scores and per-SNP results - **HTML**: Styled report with risk score cards and color-coded tables ## Categories & Coverage ~55 curated SNPs across 6 categories: - **Cardiovascular** — blood pressure, cholesterol, cardiac rhythm, CAD risk - **Cognitive** — memory, dopamine, BDNF, social cognition, brain volume - **Metabolic** — diabetes risk, MTHFR, lactose, alcohol, iron metabolism - **Pharmacogenomics** — warfarin, clopidogrel, CYP2D6, CYP2C19 drug metabolism - **Athletic** — muscle fiber type, endurance, recovery, injury risk - **Traits** — eye color, hair color, earwax, bitter taste, asparagus smell ## SNP Database The SNP reference data lives in `references/snp_database.json`. Edit this file to add/update SNPs without changing the script. Each entry has: rsid, gene, category, trait, risk_allele, and genotype-specific effect descriptions. ## Constraints - Pure Python 3.9+ — no external dependencies - **Not medical advice** — educational/informational only