| |
| """ |
| 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() |
|
|
