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)

README.md

@@ -140,6 +140,86 @@ tests/output/
 └── BtToxin_Digger.log
 ```
 
+## bttoxin_db更新
+
+BtToxin_Digger 容器内置的数据库版本较旧（2021年8月），建议使用官方 GitHub 仓库的最新数据库。
+
+### 数据库目录结构
+
+```
+external_dbs/bt_toxin/
+├── db/                    # BLAST 索引文件（运行时必需）
+│   ├── bt_toxin.phr
+│   ├── bt_toxin.pin
+│   ├── bt_toxin.psq
+│   ├── bt_toxin.pdb
+│   ├── bt_toxin.pjs
+│   ├── bt_toxin.pot
+│   ├── bt_toxin.ptf
+│   ├── bt_toxin.pto
+│   └── old/
+└── seq/                   # 序列源文件（留档/更新用）
+    ├── bt_toxin20251104.fas
+    └── ...
+```
+
+### 更新步骤
+
+```bash
+mkdir -p external_dbs
+rm -rf external_dbs/bt_toxin tmp_bttoxin_repo
+
+git clone --filter=blob:none --no-checkout https://github.com/liaochenlanruo/BtToxin_Digger.git tmp_bttoxin_repo
+cd tmp_bttoxin_repo
+
+git sparse-checkout init --cone
+git sparse-checkout set BTTCMP_db/bt_toxin
+git checkout master
+
+# 把目录拷贝到你的项目 external_dbs 下
+cd ..
+cp -a tmp_bttoxin_repo/BTTCMP_db/bt_toxin external_dbs/bt_toxin
+
+# 清理临时 repo
+rm -rf tmp_bttoxin_repo
+```
+
+### 验证数据库绑定
+
+```bash
+# 检查数据库文件是否完整
+ls -lh external_dbs/bt_toxin/db/
+
+# 验证容器能正确访问绑定的数据库
+docker run --rm \
+  -v "$(pwd)/external_dbs/bt_toxin:/usr/local/bin/BTTCMP_db/bt_toxin:ro" \
+  quay.io/biocontainers/bttoxin_digger:1.0.10--hdfd78af_0 \
+  bash -lc 'ls -lh /usr/local/bin/BTTCMP_db/bt_toxin/db | head'
+```
+
+输出应显示 `.pin/.psq/.phr` 等文件，且时间戳/大小与宿主机一致，说明绑定成功。
+
+### 使用外部数据库运行 Pipeline
+
+脚本会自动检测 `external_dbs/bt_toxin` 目录，若存在则自动绑定：
+
+```bash
+# 自动使用 external_dbs/bt_toxin（推荐）
+uv run python scripts/run_single_fna_pipeline.py --fna tests/test_data/HAN055.fna
+
+# 或手动指定数据库路径
+uv run python scripts/run_single_fna_pipeline.py \
+  --fna tests/test_data/HAN055.fna \
+  --bttoxin_db_dir /path/to/custom/bt_toxin
+```
+
+### 注意事项
+
+- **db/ 目录是必需的**：运行时 BLAST 只读取 `db/` 下的索引文件
+- **seq/ 目录是可选的**：仅用于留档或重新生成索引
+- **绑定模式为只读 (ro)**：防止容器意外修改宿主机数据库
+- **不需要重新 index**：GitHub 仓库已包含预构建的 BLAST 索引
+
 ## License
 
 MIT License

backend/app/utils/docker_client.py

@@ -151,9 +151,19 @@ class DockerContainerManager:
         sequence_type: str = "nucl",
         scaf_suffix: str = ".fna",
         threads: int = 4,
+        bttoxin_db_dir: Optional[Path] = None,
         **kwargs: Any,
     ) -> Dict[str, Any]:
-        """在容器中运行 BtToxin_Digger 主分析（单目录方案）。"""
+        """在容器中运行 BtToxin_Digger 主分析（单目录方案）。
+
+        Args:
+            bttoxin_db_dir: 外部 bt_toxin 数据库目录路径（可选）。
+                           若提供，将绑定到容器内 /usr/local/bin/BTTCMP_db/bt_toxin，
+                           覆盖容器内置的旧数据库。目录结构应为：
+                           bt_toxin/
+                             ├── db/   (BLAST 索引文件)
+                             └── seq/  (序列源文件)
+        """
 
         # 1) 在宿主输出目录下准备 input_files，并复制输入文件
         work_input_dir = (output_dir / "input_files").resolve()
@@ -239,12 +249,24 @@ class DockerContainerManager:
         if kwargs.get("assemble_only"):
             base_cmd.append("--assemble_only")
 
-        # 2) 只挂载输出目录（含 input_files）与日志目录
+        # 2) 挂载输出目录（含 input_files）、日志目录、以及可选的外部数据库
         volumes = {
             str(output_dir.resolve()): {"bind": "/workspace", "mode": "rw"},
             str(log_dir.resolve()): {"bind": "/data/logs", "mode": "rw"},
         }
 
+        # 绑定外部 bt_toxin 数据库（覆盖容器内置旧库）
+        if bttoxin_db_dir is not None:
+            db_path = Path(bttoxin_db_dir).resolve()
+            if db_path.exists() and (db_path / "db").exists():
+                volumes[str(db_path)] = {
+                    "bind": "/usr/local/bin/BTTCMP_db/bt_toxin",
+                    "mode": "ro",
+                }
+                logger.info(f"绑定外部数据库: {db_path} -> /usr/local/bin/BTTCMP_db/bt_toxin")
+            else:
+                logger.warning(f"外部数据库目录不存在或结构不完整: {bttoxin_db_dir}")
+
         logger.info("开始 BtToxin_Digger 分析...")
 
         final_cmd = base_cmd

external_dbs/bt_toxin/db/bt_toxin.pjs

@@ -0,0 +1,22 @@
+{
+  "version": "1.2",
+  "dbname": "bt_toxin",
+  "dbtype": "Protein",
+  "db-version": 5,
+  "description": "bt_toxin20251104.fas",
+  "number-of-letters": 996368,
+  "number-of-sequences": 1199,
+  "last-updated": "2025-11-04T15:35:00",
+  "number-of-volumes": 1,
+  "bytes-total": 1149077,
+  "bytes-to-cache": 1007264,
+  "files": [
+    "bt_toxin.pdb",
+    "bt_toxin.phr",
+    "bt_toxin.pin",
+    "bt_toxin.pot",
+    "bt_toxin.psq",
+    "bt_toxin.ptf",
+    "bt_toxin.pto"
+  ]
+}

external_dbs/bt_toxin/seq/updateDB.py

@@ -0,0 +1,36 @@
+def get_unique_headers(file_path):
+    """读取文件中以'>'开头的行，返回'>'后面内容的集合"""
+    headers = set()
+    with open(file_path, 'r') as f:
+        for line in f:
+            line = line.strip()
+            if line.startswith('>'):
+                # 提取'>'后面的内容（包括可能的空格和其他字符）
+                header = line[1:]
+                headers.add(header)
+    return headers
+
+# 输入文件路径
+file1 = 'bt_toxin20251104.fas'
+file2 = 'all_app_cry_cyt_gpp_mcf_mpf_mpp_mtx_pra_prb_spp_tpp_txp_vip_vpa_vpb_xpp_fasta_sequences.txt'
+output_file = 'unique_headers.txt'
+
+# 获取两个文件中的header集合
+headers1 = get_unique_headers(file1)
+headers2 = get_unique_headers(file2)
+
+# 计算各自独有的header
+unique_to_file1 = headers1 - headers2
+unique_to_file2 = headers2 - headers1
+
+# 写入输出文件
+with open(output_file, 'w') as out_f:
+    out_f.write(f"### Unique headers in {file1} ###\n")
+    for header in sorted(unique_to_file1):
+        out_f.write(f">{header}\n")
+    
+    out_f.write(f"\n### Unique headers in {file2} ###\n")
+    for header in sorted(unique_to_file2):
+        out_f.write(f">{header}\n")
+
+print(f"处理完成，结果已保存至 {output_file}")

frontend/index.html

@@ -1,12 +0,0 @@
-<!DOCTYPE html>
-<html lang="en">
-<head>
-  <meta charset="UTF-8">
-  <meta name="viewport" content="width=device-width, initial-scale=1.0">
-  <title>BtToxin Pipeline</title>
-</head>
-<body>
-  <div id="app"></div>
-  <script type="module" src="/src/main.js"></script>
-</body>
-</html>

frontend/package.json

@@ -1,22 +0,0 @@
-{
-  "name": "bttoxin-frontend",
-  "version": "1.0.0",
-  "type": "module",
-  "scripts": {
-    "dev": "vite",
-    "build": "vite build",
-    "preview": "vite preview"
-  },
-  "dependencies": {
-    "vue": "^3.5.13",
-    "vue-router": "^4.5.0",
-    "pinia": "^2.3.0",
-    "axios": "^1.7.9",
-    "naive-ui": "^2.40.1",
-    "@vicons/ionicons5": "^0.12.0"
-  },
-  "devDependencies": {
-    "@vitejs/plugin-vue": "^5.2.1",
-    "vite": "^6.0.5"
-  }
-}

frontend/src/App.vue

@@ -1,41 +0,0 @@
-<template>
-  <n-config-provider :theme="darkTheme">
-    <n-layout>
-      <n-layout-header bordered>
-        <n-space align="center" justify="space-between" style="padding: 16px">
-          <n-h2>BtToxin Pipeline</n-h2>
-          <n-menu mode="horizontal" :options="menuOptions" />
-        </n-space>
-      </n-layout-header>
-
-      <n-layout-content style="padding: 24px">
-        <router-view />
-      </n-layout-content>
-
-      <n-layout-footer bordered style="padding: 16px; text-align: center">
-        BtToxin Pipeline © 2025
-      </n-layout-footer>
-    </n-layout>
-  </n-config-provider>
-</template>
-
-<script setup>
-import { darkTheme } from 'naive-ui'
-import { h } from 'vue'
-import { RouterLink } from 'vue-router'
-
-const menuOptions = [
-  {
-    label: () => h(RouterLink, { to: '/' }, { default: () => 'Home' }),
-    key: 'home'
-  },
-  {
-    label: () => h(RouterLink, { to: '/upload' }, { default: () => 'Upload' }),
-    key: 'upload'
-  },
-  {
-    label: () => h(RouterLink, { to: '/jobs' }, { default: () => 'Jobs' }),
-    key: 'jobs'
-  }
-]
-</script>

frontend/src/main.js

@@ -1,14 +0,0 @@
-import { createApp } from 'vue'
-import { createPinia } from 'pinia'
-import naive from 'naive-ui'
-import App from './App.vue'
-import router from './router'
-
-const app = createApp(App)
-const pinia = createPinia()
-
-app.use(pinia)
-app.use(router)
-app.use(naive)
-
-app.mount('#app')

frontend/src/router.js

@@ -1,31 +0,0 @@
-import { createRouter, createWebHistory } from 'vue-router'
-
-const routes = [
-  {
-    path: '/',
-    name: 'Home',
-    component: () => import('./views/Home.vue')
-  },
-  {
-    path: '/upload',
-    name: 'Upload',
-    component: () => import('./views/Upload.vue')
-  },
-  {
-    path: '/jobs',
-    name: 'Jobs',
-    component: () => import('./views/Jobs.vue')
-  },
-  {
-    path: '/jobs/:id',
-    name: 'JobDetail',
-    component: () => import('./views/JobDetail.vue')
-  }
-]
-
-const router = createRouter({
-  history: createWebHistory(),
-  routes
-})
-
-export default router

frontend/src/services/api.js

@@ -1,22 +0,0 @@
-import axios from 'axios'
-
-const api = axios.create({
-  baseURL: '/api/v1',
-  timeout: 30000
-})
-
-export default {
-  createJob(formData) {
-    return api.post('/jobs/create', formData, {
-      headers: { 'Content-Type': 'multipart/form-data' }
-    })
-  },
-
-  getJob(jobId) {
-    return api.get(`/jobs/${jobId}`)
-  },
-
-  getJobProgress(jobId) {
-    return api.get(`/jobs/${jobId}/progress`)
-  }
-}

frontend/src/views/Home.vue

@@ -1,7 +0,0 @@
-<template>
-  <n-space vertical size="large">
-    <n-card title="Welcome to BtToxin Pipeline">
-      <p>Automated Bacillus thuringiensis toxin mining system</p>
-    </n-card>
-  </n-space>
-</template>

frontend/src/views/JobDetail.vue

@@ -1,5 +0,0 @@
-<template>
-  <n-card title="Job Details">
-    <p>Job ID: {{ $route.params.id }}</p>
-  </n-card>
-</template>

frontend/src/views/Jobs.vue

@@ -1,5 +0,0 @@
-<template>
-  <n-card title="Job List">
-    <n-empty description="No jobs yet" />
-  </n-card>
-</template>

frontend/src/views/Upload.vue

@@ -1,7 +0,0 @@
-<template>
-  <n-card title="Upload Genome Files">
-    <n-upload multiple>
-      <n-button>Select Files</n-button>
-    </n-upload>
-  </n-card>
-</template>

frontend/vite.config.js

@@ -1,21 +0,0 @@
-import { defineConfig } from 'vite'
-import vue from '@vitejs/plugin-vue'
-import { fileURLToPath, URL } from 'node:url'
-
-export default defineConfig({
-  plugins: [vue()],
-  resolve: {
-    alias: {
-      '@': fileURLToPath(new URL('./src', import.meta.url))
-    }
-  },
-  server: {
-    port: 3000,
-    proxy: {
-      '/api': {
-        target: 'http://localhost:8000',
-        changeOrigin: true
-      }
-    }
-  }
-})

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"):