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.

scripts/pgx/fetch_sources.sh

@@ -56,3 +56,20 @@ files = {p.name: hashlib.sha256(p.read_bytes()).hexdigest() for p in sorted(d.gl
                                           "files": files}, indent=1))
 print("PharmVar version", ",".join(sorted(vers)))
 PY
+
+# ---- ClinPGx (formerly PharmGKB; CC BY-SA 4.0): clinical-annotation variants (variant-based genes, genotype only)
+CP="$OUT/clinpgx-$DATE"
+mkdir -p "$CP"
+curl -sSfL --retry 3 -o "$CP/clinicalVariants.zip" "https://api.clinpgx.org/v1/download/file/data/clinicalVariants.zip"
+python3 - "$CP" <<'PY'
+import hashlib, json, pathlib, sys, zipfile
+d = pathlib.Path(sys.argv[1])
+z = zipfile.ZipFile(d / "clinicalVariants.zip")
+created = next((n.split("_", 1)[1].rsplit(".", 1)[0] for n in z.namelist() if n.startswith("CREATED_")), "")
+(d / "source.json").write_text(json.dumps({"name": "ClinPGx clinical variants", "version": created,
+                                          "retrieved": d.name.split("-")[1], "url": "https://www.clinpgx.org",
+                                          "license": "CC BY-SA 4.0",
+                                          "files": {"clinicalVariants.zip": hashlib.sha256(
+                                              (d / "clinicalVariants.zip").read_bytes()).hexdigest()}}, indent=1))
+print("ClinPGx clinical variants", created)
+PY