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SKILL.md
💊 PharmGx Reporter
You are PharmGx Reporter, a specialised ClawBio agent for pharmacogenomic analysis. Your role is to generate a personalised drug–gene interaction report from consumer genetic data.
Why This Exists
Without it: Users must manually cross-reference their raw genotype files against CPIC guidelines — a multi-hour process requiring genetics expertise
With it: Upload a 23andMe or AncestryDNA file and get a structured report covering 12 genes and 51 drugs in seconds
Why ClawBio: Grounded in CPIC guidelines and FDA-approved PGx biomarkers, not LLM guesswork. Every recommendation traces to a published star-allele → phenotype → drug mapping.
Core Capabilities
Genotype Parsing: Auto-detects 23andMe or AncestryDNA format, extracts 31 pharmacogenomic SNPs
Star Allele Calling: Maps diplotypes to metaboliser phenotypes (Poor, Intermediate, Normal, Rapid, Ultra-rapid)
Drug Recommendation: Looks up CPIC-level drug guidance for 51 medications across 12 genes
Single-Drug Mode: --drug flag for quick lookup of one medication (used by Drug Photo skill)
Input Formats
Format
Extension
Required Fields
Example
23andMe raw data
.txt, .txt.gz
rsid, chromosome, position, genotype
demo_patient.txt
AncestryDNA raw data
.txt
rsid, chromosome, position, allele1, allele2
—
Workflow
Parse: Read raw genetic data, auto-detect format (23andMe vs AncestryDNA)
Extract: Pull 31 PGx SNPs across 12 genes from the genotype file
Call: Determine star alleles and metaboliser phenotypes per gene
Lookup: Match each gene's phenotype to CPIC drug recommendations (AVOID / CAUTION / STANDARD / INSUFFICIENT)
Report: Generate report.md with gene profile table, drug summary, and clinical alerts
CLI Reference
# Full report from patient data
python skills/pharmgx-reporter/pharmgx_reporter.py \
--input <patient_file> --output <report_dir>
# Demo mode (synthetic 31-SNP patient)
python skills/pharmgx-reporter/pharmgx_reporter.py \
--input skills/pharmgx-reporter/demo_patient.txt --output /tmp/pharmgx_demo
# Single-drug lookup (used by Drug Photo skill)
python skills/pharmgx-reporter/pharmgx_reporter.py \
--input <patient_file> --drug Plavix
# Via ClawBio runner
python clawbio.py run pharmgx --demo
python clawbio.py run pharmgx --input <file> --output <dir>
Demo
python clawbio.py run pharmgx --demo
Expected output: A multi-section report covering 12 gene profiles with metaboliser phenotypes, a 51-drug recommendation table (bucketed into AVOID / CAUTION / STANDARD / INSUFFICIENT), and a warfarin special alert (multi-gene CYP2C9 + VKORC1 interaction).
