Add bin/download_bundle.py

bin/download_bundle.py

@@ -0,0 +1,89 @@
+#!/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)
+                            bwa     -> {genome}/*.fa.amb/.ann/.bwt/.pac/.sa
+                            minibwa -> everything under {genome}/minibwa/
+  --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")
+
+
+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}/bed/*", f"{genome}/schema_bundle/*"]
+    out = [f for f in files if any(fnmatch.fnmatch(f, p) for p in pats)]
+    if index in ("bwa", "all"):
+        out += [f for f in files if f.startswith(f"{genome}/") and f.count("/") == 1
+                and f.endswith(tuple(".fa" + e for e in BWA_EXT))]
+    if index in ("minibwa", "all"):
+        mb = [f for f in files if f.startswith(f"{genome}/minibwa/")]
+        if not mb:
+            print(f"[warn] no minibwa index found under {genome}/minibwa/ yet, skipped", file=sys.stderr)
+        out += mb
+    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()