kemal
cc89e9b334
- 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.
76 lines
4.1 KiB
Bash
76 lines
4.1 KiB
Bash
#!/usr/bin/env bash
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# Download the public PGx sources for `simurg pgx db build` (spec PGX-001) into a dated folder.
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# bash scripts/pgx/fetch_sources.sh [OUT_DIR] (default data/pgx/sources)
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# CPIC (CC0): tables from the CPIC API (https://api.cpicpgx.org, PostgREST) as JSON; the newest change-log date is
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# recorded as the data version. PharmVar (https://www.pharmvar.org; cite Gaedigk et al. 2018 CPT 103:399): per-gene
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# zips (haplotype VCFs, GRCh37/GRCh38) for the star-allele genes CPIC does not define. Never committed (data/ is
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# ignored); the DB records each source's version and file hashes.
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set -euo pipefail
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OUT=${1:-data/pgx/sources}
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DATE=$(date -u +%Y%m%d)
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D="$OUT/cpic-$DATE"
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mkdir -p "$D"
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API=https://api.cpicpgx.org/v1
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for t in gene allele allele_definition allele_location_value sequence_location gene_result gene_result_lookup \
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gene_result_diplotype population change_log; do
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curl -sSf --retry 3 -H "Accept: application/json" "$API/$t" -o "$D/$t.json"
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python3 -c "import json,sys; print(sys.argv[1], len(json.load(open(sys.argv[2]))))" "$t" "$D/$t.json"
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done
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python3 - "$D" <<'PY'
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import hashlib, json, pathlib, sys
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d = pathlib.Path(sys.argv[1])
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log = json.loads((d / "change_log.json").read_text())
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ver = max(e["date"] for e in log if e.get("date"))
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files = {p.name: hashlib.sha256(p.read_bytes()).hexdigest() for p in sorted(d.glob("*.json")) if p.name != "source.json"}
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(d / "source.json").write_text(json.dumps({"name": "CPIC", "version": ver, "retrieved": d.name.split("-")[1],
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"url": "https://api.cpicpgx.org/v1", "license": "CC0-1.0",
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"files": files}, indent=1))
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print("CPIC data version", ver)
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PY
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# ---- PharmVar: star-allele genes without CPIC definitions
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PV="$OUT/pharmvar-$DATE"
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mkdir -p "$PV"
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PV_GENES=${PV_GENES:-"CYP1A2 CYP2A6 CYP2A13 CYP2C8 CYP3A4"} # the PharmVar genes CPIC does not define (2026-09)
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for g in $PV_GENES; do
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if curl -sSf --retry 3 -o "$PV/$g.zip" \
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"https://www.pharmvar.org/get-download-file?name=$g&refSeq=ALL&fileType=zip&version=current"; then
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echo "PharmVar $g $(unzip -l "$PV/$g.zip" | awk 'NR==4{print $4}' | cut -d/ -f1)"
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else
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echo "PharmVar $g: not available"; rm -f "$PV/$g.zip"
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fi
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done
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python3 - "$PV" <<'PY'
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import hashlib, json, pathlib, re, sys, zipfile
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d = pathlib.Path(sys.argv[1])
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vers = set()
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for z in sorted(d.glob("*.zip")):
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top = zipfile.ZipFile(z).namelist()[0].split("/")[0]
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m = re.search(r"-(\d+\.\d+\.\d+)$", top)
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if m:
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vers.add(m.group(1))
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files = {p.name: hashlib.sha256(p.read_bytes()).hexdigest() for p in sorted(d.glob("*.zip"))}
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(d / "source.json").write_text(json.dumps({"name": "PharmVar", "version": ",".join(sorted(vers)),
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"retrieved": d.name.split("-")[1], "url": "https://www.pharmvar.org",
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"license": "PharmVar terms of use (cite Gaedigk et al. 2018)",
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"files": files}, indent=1))
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print("PharmVar version", ",".join(sorted(vers)))
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PY
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# ---- ClinPGx (formerly PharmGKB; CC BY-SA 4.0): clinical-annotation variants (variant-based genes, genotype only)
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CP="$OUT/clinpgx-$DATE"
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mkdir -p "$CP"
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curl -sSfL --retry 3 -o "$CP/clinicalVariants.zip" "https://api.clinpgx.org/v1/download/file/data/clinicalVariants.zip"
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python3 - "$CP" <<'PY'
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import hashlib, json, pathlib, sys, zipfile
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d = pathlib.Path(sys.argv[1])
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z = zipfile.ZipFile(d / "clinicalVariants.zip")
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created = next((n.split("_", 1)[1].rsplit(".", 1)[0] for n in z.namelist() if n.startswith("CREATED_")), "")
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(d / "source.json").write_text(json.dumps({"name": "ClinPGx clinical variants", "version": created,
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"retrieved": d.name.split("-")[1], "url": "https://www.clinpgx.org",
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"license": "CC BY-SA 4.0",
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"files": {"clinicalVariants.zip": hashlib.sha256(
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(d / "clinicalVariants.zip").read_bytes()).hexdigest()}}, indent=1))
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print("ClinPGx clinical variants", created)
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PY
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