PGx: ClinPGx variant-based genes (PGX-008) and --guideline dpwg (PGX-025)
- fetch_sources.sh downloads ClinPGx clinicalVariants (CC BY-SA 4.0); pgx db build adds genotype-only variant-based genes (levels 1A-2B, level 3 for the parity list), rsIDs resolved from the manifest's probes: 70 genes in the DB. - pgx phenotype --guideline dpwg: CPIC mappings for CPIC genes (as ClinPGx curates DPWG), no phenotype for DPWG-only genes (flags dpwg_via_cpic_mapping / dpwg_mapping_not_available). K-029 updated.
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@@ -18,6 +18,7 @@ used only as external subprocess oracles and are not copied or linked.
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| [CPIC](https://cpicpgx.org) database via the CPIC API (allele definitions, allele function, diplotype→phenotype tables) | CC0 1.0 | downloaded by `scripts/pgx/fetch_sources.sh` into `data/` (never committed); `simurg pgx db build` derives the local PGx DB from it; source version and file hashes are recorded in the DB `meta` table |
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| [PharmVar](https://www.pharmvar.org) haplotype definitions (Gaedigk et al. 2018 CPT 103:399) | PharmVar terms of use (attribution) | per-gene zips downloaded by `scripts/pgx/fetch_sources.sh` into `data/` (never committed); `simurg pgx db build` derives core-allele definitions for genes CPIC does not define |
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| [GeT-RM](https://www.cdc.gov/lab-quality/php/get-rm/reference-materials.html) consolidated PGx/HLA table (CDC) | US government work | validation truth only (`scripts/pgx/getrm_truth.py`), not redistributed |
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| [ClinPGx](https://www.clinpgx.org) (formerly PharmGKB) clinical-annotation variants | CC BY-SA 4.0 (attribution: ClinPGx, https://www.clinpgx.org/page/citingClinpgx) | `clinicalVariants.zip` downloaded by `scripts/pgx/fetch_sources.sh` into `data/` (never committed); rsIDs become genotype-only variant-based genes in the local PGx DB |
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## BSD-2-Clause (BeadArrayFiles, verbatim from its README)
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