--- name: pharmgx-reporter description: Pharmacogenomic report from DTC genetic data (23andMe/AncestryDNA) β€” 12 genes, 31 SNPs, 51 drugs license: MIT metadata: version: 0.1.0 author: Manuel Corpas tags: - pharmacogenomics - CPIC - DTC-genetics - precision-medicine openclaw: requires: bins: - python3 always: false emoji: πŸ’Š homepage: https://github.com/ClawBio/ClawBio os: - darwin - linux trigger_keywords: - pharmacogenomics - drug interactions - 23andMe medications - CYP2D6 - CYP2C19 - warfarin - CPIC --- # πŸ’Š 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 β€” 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 β†’ phenotype β†’ drug mapping. ## Core Capabilities 1. **Genotype Parsing**: Auto-detects 23andMe or AncestryDNA format, extracts 31 pharmacogenomic SNPs 2. **Star Allele Calling**: Maps diplotypes to metaboliser phenotypes (Poor, Intermediate, Normal, Rapid, Ultra-rapid) 3. **Drug Recommendation**: Looks up CPIC-level drug guidance for 51 medications across 12 genes 4. **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 | β€” | ## Workflow 1. **Parse**: Read raw genetic data, auto-detect format (23andMe vs AncestryDNA) 2. **Extract**: Pull 31 PGx SNPs across 12 genes from the genotype file 3. **Call**: Determine star alleles and metaboliser phenotypes per gene 4. **Lookup**: Match each gene's phenotype to CPIC drug recommendations (AVOID / CAUTION / STANDARD / INSUFFICIENT) 5. **Report**: Generate `report.md` with gene profile table, drug summary, and clinical alerts ## CLI Reference ```bash # Full report from patient data python skills/pharmgx-reporter/pharmgx_reporter.py \ --input --output # 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 --drug Plavix # Via ClawBio runner python clawbio.py run pharmgx --demo python clawbio.py run pharmgx --input --output ``` ## Demo ```bash 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). ## Genes Covered CYP2C19, CYP2D6, CYP2C9, VKORC1, SLCO1B1, DPYD, TPMT, UGT1A1, CYP3A5, CYP2B6, NUDT15, CYP1A2 ## Drug Classes Antiplatelet, opioids, statins, anticoagulants, PPIs, antidepressants (TCAs, SSRIs, SNRIs), antipsychotics, NSAIDs, oncology, immunosuppressants, antivirals ## Output Structure ``` output_directory/ β”œβ”€β”€ report.md # Full pharmacogenomic report β”œβ”€β”€ result.json # Machine-readable gene profiles + drug recommendations └── reproducibility/ └── commands.sh # Exact command to reproduce ``` ## Dependencies **Required**: - Python 3.10+ (standard library only β€” no external packages) ## Safety - **Local-first**: Genetic data never leaves the machine - **Disclaimer**: Every report includes the ClawBio medical disclaimer - **CPIC-grounded**: All gene–drug mappings trace to published CPIC guidelines - **No hallucinated associations**: Only the 31 validated SNPs are used ## Integration with Bio Orchestrator **Trigger conditions** β€” the orchestrator routes here when: - User mentions pharmacogenomics, drug interactions, medications, CYP genes, warfarin, CPIC - User provides a 23andMe or AncestryDNA file and asks about drugs **Chaining partners**: - `drug-photo`: Single-drug mode powers the photo β†’ dosage card pipeline - `profile-report`: PharmGx results feed into the unified genomic profile - `clinpgx`: ClinPGx provides deeper gene-drug lookup when the user wants more detail ## Citations - [CPIC Guidelines](https://cpicpgx.org/) β€” Clinical Pharmacogenetics Implementation Consortium - [FDA Table of Pharmacogenomic Biomarkers](https://www.fda.gov/drugs/science-and-research-drugs/table-pharmacogenomic-biomarkers-drug-labeling) β€” FDA-approved PGx drug labels --- Source attribution: ClawBio Original project: https://github.com/ClawBio/ClawBio License: MIT License information: https://opensource.org/license/mit Original upstream instructions; downloaded from Mega AI Hub. ## Upstream license notice MIT License Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. # Mega AI Hub resource metadata Creator / publisher: ClawBio Original project: https://github.com/ClawBio/ClawBio Attribution basis: Exact package in biomedical source index and publisher source table Fields of work: Healthcare & Life Sciences Roles: Clinical Research, Health Informatics, Medical Writer Specialties: Specialty not specified Tools: Python3 Country applicability: Country not specified Classification basis: Source catalog labels Instruction SHA-256: 6efd795cacbf065cf6b6fc255029a238e7053466d3d00362feef2d6ba9433388 Metadata reviewed: 2026-10-27 This metadata supersedes earlier Mega AI Hub catalog attribution. Original instruction and supporting files are preserved.