claw-methylation-cycle

Methylation cycle analysis skill for ClawBio. Produces enzymatic activity profiles, Net Methylation Capacity (NMC), BH4 axis estimates, compound heterozygosity detection, and clinician-review genotype findings from raw SNP genotype data.

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Trigger

Fire this skill when:

• The user asks about methylation, MTHFR variants, folate cycle, or homocysteine risk from a genotype file.
• A raw SNP file (23andMe / ADNTRO / Ancestry format) is provided and the clinical question involves methylation, BH4, dopamine/serotonin synthesis capacity, or neurodevelopmental contexts (ADHD, depression, anxiety).
• The upstream workflow (PharmGx Reporter, NutriGx Advisor) has flagged MTHFR or MTRR and the clinician needs the full methylation panel.
• Keywords present: methylation, MTHFR, BH4, folate cycle, metilación, ciclo de metilación, homocysteine, 5-MTHF, methylcobalamin, neurotransmitter synthesis, dopamine upstream.

Do NOT fire this skill when:

• The question is purely about folic acid supplementation without a genotype file.
• The user is asking about MTHFR in the context of thrombophilia/clotting only, use PharmGx Reporter for warfarin/anticoagulation questions.
• Only N-GENE polygenic risk data is available (no raw SNP file), this skill requires genotype-level input; PRS percentiles are not sufficient.
• The SNP file format is VCF, FASTQ, BAM, or PLINK binary, these require preprocessing before this skill can run.
• The clinical question is exclusively pharmacogenomic (CYP enzymes), use PharmGx Reporter instead.

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Workflow

1. Receive input, Accept either a raw genotype file path or a pre-parsed snp_dict. If a file is provided, call parse_genotype_file() to extract the rsID → genotype mapping.