feat: 支持绑定外部 bt_toxin 数据库 (2025-11-04 更新)

- docker_client.py: run_bttoxin_digger() 新增 bttoxin_db_dir 参数，支持挂载外部数据库
- run_single_fna_pipeline.py: 新增 --bttoxin_db_dir 参数，自动检测 external_dbs/bt_toxin
- README.md: 添加 bttoxin_db 更新说明和 Docker 绑定文档
- external_dbs/bt_toxin: 添加 2025-11-04 版本数据库文件

测试验证: HAN055 样本毒素命名版本号变化 (Cry2Aa9→22, Cry2Ab35→41, Cry1Ia40→42, Vip3Aa7→79)

scripts/run_single_fna_pipeline.py

@@ -16,14 +16,20 @@ Notes
 - Digger is executed in a container (root in container); files may be owned by root on host.
   We write everything into <out_root>/digger to keep permissions/locality predictable.
 - This script exposes CLI flags for Shotter filters to allow strict/loose runs.
+- 默认使用 external_dbs/bt_toxin 作为外部数据库（若存在），覆盖容器内置旧库。
 
 Example
-  python scripts/run_single_fna_pipeline.py \
-    --fna tests/test_data/C15.fna \
-    --toxicity_csv Data/toxicity-data.csv \
-    --out_root runs/C15_run \
-    --min_identity 0.50 --min_coverage 0.60 \
+  python scripts/run_single_fna_pipeline.py \\
+    --fna tests/test_data/HAN055.fna \\
+    --toxicity_csv Data/toxicity-data.csv \\
+    --out_root runs/HAN055_run \\
+    --min_identity 0.50 --min_coverage 0.60 \\
     --disallow_unknown_families --require_index_hit --lang zh
+
+  # 使用自定义数据库路径
+  python scripts/run_single_fna_pipeline.py \\
+    --fna tests/test_data/HAN055.fna \\
+    --bttoxin_db_dir /path/to/custom/bt_toxin
 """
 from __future__ import annotations
 
@@ -73,11 +79,27 @@ def run_single_fna_pipeline(
     allow_unknown_families: bool = True,
     require_index_hit: bool = False,
     lang: str = "zh",
+    bttoxin_db_dir: Path | None = None,
 ) -> Dict[str, Any]:
+    """运行单个 fna 文件的完整 pipeline。
+
+    Args:
+        bttoxin_db_dir: 外部 bt_toxin 数据库目录。若为 None，则自动检测
+                       项目根目录下的 external_dbs/bt_toxin。
+    """
     fna_path = fna_path.resolve()
     out_root = out_root.resolve()
     out_root.mkdir(parents=True, exist_ok=True)
 
+    # 自动检测外部数据库
+    if bttoxin_db_dir is None:
+        default_db = Path(__file__).resolve().parents[1] / "external_dbs" / "bt_toxin"
+        if default_db.exists() and (default_db / "db").exists():
+            bttoxin_db_dir = default_db
+            print(f"[pipeline] 使用外部数据库: {bttoxin_db_dir}")
+        else:
+            print("[pipeline] 未找到外部数据库，将使用容器内置数据库（可能较旧）")
+
     digger_dir = out_root / "digger"
     shotter_dir = out_root / "shotter"
     logs_dir = out_root / "logs"
@@ -98,6 +120,7 @@ def run_single_fna_pipeline(
         sequence_type="nucl",
         scaf_suffix=fna_path.suffix or ".fna",
         threads=4,
+        bttoxin_db_dir=bttoxin_db_dir,
     )
     if not result.get("success"):
         return {
@@ -197,6 +220,8 @@ def main() -> int:
     ap.add_argument("--disallow_unknown_families", action="store_true", default=False)
     ap.add_argument("--require_index_hit", action="store_true", default=False)
     ap.add_argument("--lang", type=str, choices=["zh", "en"], default="zh")
+    ap.add_argument("--bttoxin_db_dir", type=Path, default=None,
+                    help="外部 bt_toxin 数据库目录路径（默认自动检测 external_dbs/bt_toxin）")
     args = ap.parse_args()
 
     # derive per-run default out_root using file stem
@@ -215,6 +240,7 @@ def main() -> int:
         allow_unknown_families=not args.disallow_unknown_families,
         require_index_hit=args.require_index_hit,
         lang=args.lang,
+        bttoxin_db_dir=args.bttoxin_db_dir,
     )
 
     if not res.get("ok"):