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#

FlagValuesDefaultDescription--category``all|cardio|cognitive|metabolic|pharma|athletic|traits``allCategory filter--output``text|json|html``textOutput format--output-pathfilepathautoHTML output path--family DIRdirectory 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