pharmgx-reporter

What problem does it solve?

Many users of consumer genetic tests cannot quickly translate raw 23andMe or AncestryDNA genotype files into actionable, evidence-backed drug guidance; this Skill automates that mapping so clinicians and individuals can see drug–gene recommendations in seconds without manual cross-referencing.

Core Features & Use Cases

• Genotype parsing: Auto-detects 23andMe and AncestryDNA formats and extracts the pharmacogenomic SNPs required for analysis.
• Star allele calling & phenotyping: Converts observed variants into diplotypes and metabolizer phenotypes across 12 clinically relevant genes.
• CPIC-based drug lookup: Maps phenotypes to CPIC-informed recommendations for 51 drugs (AVOID / CAUTION / STANDARD / INSUFFICIENT), including a warfarin multi-gene assessment.
• Outputs & reproducibility: Produces human-readable Markdown/HTML reports, machine-readable JSON results, and a reproducibility bundle (commands and checksums).
• Privacy-first integration: Runs locally with a Python 3.10+ CLI and API, suitable for research, clinical support workflows, or embedding in other ClawBio skills like drug-photo and profile-report.

Quick Start

Generate a pharmacogenomic report from my 23andMe raw data file demo_patient.txt and save the Markdown, JSON, and reproducibility bundle into a local output directory.