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Soul2DNA Compiler\n\n## Purpose\n\nCompile SOUL.md character profiles into synthetic diploid genomes. Each soul file\ndescribes a historical or fictional figure with trait scores (0.0 to 1.0). The\ncompiler maps these scores to alleles at defined loci using additive, dominant, or\nrecessive inheritance models, producing a `.genome.json` file per character.\n\n## How It Works\n\n1. **Parse SOUL.md** files from `GENOMEBOOK\u002FDATA\u002FSOULS\u002F` extracting identity\n   metadata (name, sex, ancestry, domain, era) and trait scores.\n2. **Load trait registry** (`GENOMEBOOK\u002FDATA\u002Ftrait_registry.json`) which defines\n   loci, alleles, chromosomal positions, dominance models, and effect sizes for\n   each trait.\n3. **Assign genotypes** at each locus based on trait score thresholds:\n   - Additive: \u003C0.33 ref\u002Fref, 0.33-0.66 ref\u002Falt, >0.66 alt\u002Falt\n   - Dominant: \u003C0.40 ref\u002Fref, 0.40-0.75 ref\u002Falt, >0.75 alt\u002Falt\n   - Recessive: \u003C0.50 ref\u002Fref, 0.50-0.80 ref\u002Falt, >0.80 alt\u002Falt\n4. **Write genome** as JSON with full locus detail, trait scores, and metadata.\n\n## Input\n\n- `GENOMEBOOK\u002FDATA\u002FSOULS\u002F*.soul.md` (20 historical figures)\n- `GENOMEBOOK\u002FDATA\u002Ftrait_registry.json`\n\n## Output\n\n- `GENOMEBOOK\u002FDATA\u002FGENOMES\u002F\u003Cname>-g0.genome.json` per character\n\n## CLI Usage\n\n```bash\n# Compile all souls to genomes\npython skills\u002Fsoul2dna\u002Fsoul2dna.py\n\n# Demo mode (shows summary without writing files)\npython skills\u002Fsoul2dna\u002Fsoul2dna.py --demo\n```\n\n## Output Format\n\nEach `.genome.json` contains:\n\n```json\n{\n  \"id\": \"einstein-g0\",\n  \"name\": \"Albert Einstein\",\n  \"sex\": \"Male\",\n  \"sex_chromosomes\": \"XY\",\n  \"ancestry\": \"...\",\n  \"generation\": 0,\n  \"parents\": [null, null],\n  \"loci\": { \"\u003Clocus_id>\": { \"chromosome\": \"...\", \"alleles\": [\"A\",\"G\"], ... } },\n  \"trait_scores\": { \"curiosity\": 0.95, ... }\n}\n```\n\n","# ? Soul2DNA Compiler\n\n## Purpose\n\nCompile SOUL.md character profiles into synthetic diploid genomes. Each soul file\ndescribes a historical or fictional figure with trait scores (0.0 to 1.0). The\ncompiler maps these scores to alleles at defined loci using additive, dominant, or\nrecessive inheritance models, producing a `.genome.json` file per character.\n\n## How It Works\n\n1. **Parse SOUL.md** files from `GENOMEBOOK\u002FDATA\u002FSOULS\u002F` extracting identity\n   metadata (name, sex, ancestry, domain, era) and trait scores.\n2. **Load trait registry** (`GENOMEBOOK\u002FDATA\u002Ftrait_registry.json`) which defines\n   loci, alleles, chromosomal positions, dominance models, and effect sizes for\n   each trait.\n3. **Assign genotypes** at each locus based on trait score thresholds:\n   - Additive: \u003C0.33 ref\u002Fref, 0.33-0.66 ref\u002Falt, >0.66 alt\u002Falt\n   - Dominant: \u003C0.40 ref\u002Fref, 0.40-0.75 ref\u002Falt, >0.75 alt\u002Falt\n   - Recessive: \u003C0.50 ref\u002Fref, 0.50-0.80 ref\u002Falt, >0.80 alt\u002Falt\n4. **Write genome** as JSON with full locus detail, trait scores, and metadata.\n\n## Input\n\n- `GENOMEBOOK\u002FDATA\u002FSOULS\u002F*.soul.md` (20 historical figures)\n- `GENOMEBOOK\u002FDATA\u002Ftrait_registry.json`\n\n## Output\n\n- `GENOMEBOOK\u002FDATA\u002FGENOMES\u002F\u003Cname>-g0.genome.json` per character\n\n## CLI Usage\n\n```bash\n# Compile all souls to genomes\npython skills\u002Fsoul2dna\u002Fsoul2dna.py\n\n# Demo mode (shows summary without writing files)\npython skills\u002Fsoul2dna\u002Fsoul2dna.py --demo\n```\n\n## Output Format\n\nEach `.genome.json` contains:\n\n```json\n{\n  \"id\": \"einstein-g0\",\n  \"name\": \"Albert Einstein\",\n  \"sex\": \"Male\",\n  \"sex_chromosomes\": \"XY\",\n  \"ancestry\": \"...\",\n  \"generation\": 0,\n  \"parents\": [null, null],\n  \"loci\": { \"\u003Clocus_id>\": { \"chromosome\": \"...\", \"alleles\": [\"A\",\"G\"], ... } },\n  \"trait_scores\": { \"curiosity\": 0.95, ... }\n}\n```\n\n",{"name":5,"tags":42,"author":43,"license":15,"version":44,"metadata":45,"description":7},[23,22,21,20],"Manuel 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