File size: 3,715 Bytes
3e51a60 bbb4495 3e51a60 bbb4495 3e51a60 8609330 3e51a60 bbb4495 3e51a60 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 | #!/usr/bin/env python3
"""
Download the SchemaBio reference bundle (hg19 or hg38) from Hugging Face.
Always downloaded:
- reference genome (*.fa.gz, *.fai)
- bed/
- schema_bundle/
- VEP cache tarball (homo_sapiens_merged_vep_*.tar.gz)
Optional:
--index bwa|minibwa|all aligner index (default: none)
matched by file suffix under {genome}/:
bwa -> .amb .ann .bwt .pac .sa
minibwa -> .l2b .mbw (incl. .meth.mbw)
--extract-vep extract the VEP cache into <outdir>/vep (default: no)
Examples:
python download_bundle.py -g hg38 -o /data/database
python download_bundle.py -g hg19 -o /data/database --index bwa --extract-vep
Requires: pip install huggingface_hub
Set HF_ENDPOINT=https://hf-mirror.com to use a mirror.
"""
import argparse, fnmatch, os, sys, tarfile
REPO = "pzweuj/SchemaBio_Bundle"
BWA_EXT = (".amb", ".ann", ".bwt", ".pac", ".sa")
MINIBWA_EXT = (".l2b", ".mbw")
def select(files, genome, index):
pats = [f"{genome}/Homo_sapiens.*.fa.gz", f"{genome}/Homo_sapiens.*.fa.fai",
f"{genome}/homo_sapiens_merged_vep_*.tar.gz", f"{genome}/{genome}_default.bed",
f"{genome}/bed/*", f"{genome}/schema_bundle/*"]
out = [f for f in files if any(fnmatch.fnmatch(f, p) for p in pats)]
gfiles = [f for f in files if f.startswith(f"{genome}/")]
for name, ext in (("bwa", BWA_EXT), ("minibwa", MINIBWA_EXT)):
if index in (name, "all"):
hit = [f for f in gfiles if f.endswith(ext)]
if not hit:
print(f"[warn] no {name} index ({' '.join(ext)}) found for {genome}, skipped", file=sys.stderr)
out += hit
return sorted(set(out))
def main():
ap = argparse.ArgumentParser(description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter)
ap.add_argument("-g", "--genome", required=True, choices=["hg19", "hg38"])
ap.add_argument("-o", "--outdir", default=".", help="output directory (default: .)")
ap.add_argument("--index", default="none", choices=["none", "bwa", "minibwa", "all"],
help="aligner index to download (default: none)")
ap.add_argument("--extract-vep", action="store_true", help="extract VEP cache after download")
ap.add_argument("--revision", default="main")
ap.add_argument("--dry-run", action="store_true", help="only list files")
a = ap.parse_args()
try:
from huggingface_hub import HfApi, hf_hub_download
except ImportError:
sys.exit("huggingface_hub not installed: pip install huggingface_hub")
files = [f.path for f in HfApi().list_repo_tree(REPO, repo_type="dataset", recursive=True,
revision=a.revision) if hasattr(f, "size")]
todo = select(files, a.genome, a.index)
print(f"{len(todo)} files to download for {a.genome} (index={a.index})")
for f in todo:
print(" " + f)
if a.dry_run:
return
os.makedirs(a.outdir, exist_ok=True)
for i, f in enumerate(todo, 1):
print(f"[{i}/{len(todo)}] {f}", flush=True)
hf_hub_download(REPO, f, repo_type="dataset", revision=a.revision, local_dir=a.outdir)
if a.extract_vep:
for f in todo:
if os.path.basename(f).startswith("homo_sapiens_merged_vep_"):
src = os.path.join(a.outdir, f)
dst = os.path.join(a.outdir, a.genome, "vep")
os.makedirs(dst, exist_ok=True)
print(f"extracting {src} -> {dst}", flush=True)
with tarfile.open(src) as t:
t.extractall(dst)
print("done")
if __name__ == "__main__":
main()
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