hotwa
1c0e8f90a5
- 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)
263 lines
9.2 KiB
Python
263 lines
9.2 KiB
Python
#!/usr/bin/env python3
|
||
"""Run a single-fna BtToxin_Digger -> Shotter -> Plots pipeline.
|
||
|
||
- Input: one .fna file (nucleotide scaffold)
|
||
- Steps:
|
||
1) Stage this single file, run BtToxin_Digger via DockerContainerManager
|
||
2) Run Shotter scoring on Digger's All_Toxins.txt
|
||
3) Render heatmaps + paper-style report
|
||
4) Organize outputs under one root folder:
|
||
<out_root>/
|
||
├─ digger/ (container outputs)
|
||
├─ shotter/ (Shotter TSV/JSON + plots + report)
|
||
└─ pipeline_results.tar.gz (bundle)
|
||
|
||
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/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
|
||
|
||
import argparse
|
||
import os
|
||
import shutil
|
||
import subprocess
|
||
import sys
|
||
import tarfile
|
||
from pathlib import Path
|
||
from typing import Dict, Any
|
||
|
||
# import DockerContainerManager from backend
|
||
sys.path.append(str(Path(__file__).resolve().parents[1] / "backend"))
|
||
from app.utils.docker_client import DockerContainerManager # type: ignore
|
||
|
||
|
||
def _shell(cmd: list[str]) -> subprocess.CompletedProcess:
|
||
return subprocess.run(cmd, text=True)
|
||
|
||
|
||
def _read_first_strain(strain_scores_tsv: Path) -> str:
|
||
try:
|
||
with strain_scores_tsv.open("r", encoding="utf-8") as f:
|
||
header = f.readline().strip().split("\t")
|
||
idx_strain = header.index("Strain")
|
||
# next non-empty line
|
||
for line in f:
|
||
if not line.strip():
|
||
continue
|
||
parts = line.rstrip("\n").split("\t")
|
||
if len(parts) > idx_strain:
|
||
return parts[idx_strain]
|
||
except Exception:
|
||
pass
|
||
return ""
|
||
|
||
|
||
def run_single_fna_pipeline(
|
||
fna_path: Path,
|
||
out_root: Path,
|
||
toxicity_csv: Path = Path("Data/toxicity-data.csv"),
|
||
image: str = "quay.io/biocontainers/bttoxin_digger:1.0.10--hdfd78af_0",
|
||
platform: str = "linux/amd64",
|
||
min_identity: float = 0.0,
|
||
min_coverage: float = 0.0,
|
||
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"
|
||
stage_dir = out_root / "stage"
|
||
for d in (digger_dir, shotter_dir, logs_dir, stage_dir):
|
||
d.mkdir(parents=True, exist_ok=True)
|
||
|
||
# Stage single input file
|
||
staged_fna = stage_dir / fna_path.name
|
||
shutil.copy2(fna_path, staged_fna)
|
||
|
||
# 1) Run BtToxin_Digger via DockerContainerManager
|
||
mgr = DockerContainerManager(image=image, platform=platform)
|
||
result = mgr.run_bttoxin_digger(
|
||
input_dir=stage_dir,
|
||
output_dir=digger_dir,
|
||
log_dir=logs_dir,
|
||
sequence_type="nucl",
|
||
scaf_suffix=fna_path.suffix or ".fna",
|
||
threads=4,
|
||
bttoxin_db_dir=bttoxin_db_dir,
|
||
)
|
||
if not result.get("success"):
|
||
return {
|
||
"ok": False,
|
||
"stage": "digger",
|
||
"error": result.get("error") or f"Digger failed (exit={result.get('exit_code')})",
|
||
"logs": (logs_dir / "digger_execution.log").read_text(encoding="utf-8") if (logs_dir / "digger_execution.log").exists() else "",
|
||
}
|
||
|
||
toxins_dir = digger_dir / "Results" / "Toxins"
|
||
all_toxins = toxins_dir / "All_Toxins.txt"
|
||
if not all_toxins.exists():
|
||
return {"ok": False, "stage": "digger", "error": f"Missing All_Toxins.txt at {all_toxins}"}
|
||
|
||
# 2) Run Shotter scoring
|
||
shotter_dir.mkdir(parents=True, exist_ok=True)
|
||
py = sys.executable
|
||
shoter_cmd: list[str] = [
|
||
py,
|
||
str(Path(__file__).resolve().parents[0] / "bttoxin_shoter.py"),
|
||
"--toxicity_csv",
|
||
str(toxicity_csv),
|
||
"--all_toxins",
|
||
str(all_toxins),
|
||
"--output_dir",
|
||
str(shotter_dir),
|
||
]
|
||
if min_identity and min_identity > 0:
|
||
shoter_cmd += ["--min_identity", str(min_identity)]
|
||
if min_coverage and min_coverage > 0:
|
||
shoter_cmd += ["--min_coverage", str(min_coverage)]
|
||
if not allow_unknown_families:
|
||
shoter_cmd += ["--disallow_unknown_families"]
|
||
if require_index_hit:
|
||
shoter_cmd += ["--require_index_hit"]
|
||
|
||
r1 = _shell(shoter_cmd)
|
||
if r1.returncode != 0:
|
||
return {"ok": False, "stage": "shotter", "error": f"Shotter failed: {' '.join(shoter_cmd)}"}
|
||
|
||
strain_scores = shotter_dir / "strain_target_scores.tsv"
|
||
toxin_support = shotter_dir / "toxin_support.tsv"
|
||
species_scores = shotter_dir / "strain_target_species_scores.tsv"
|
||
|
||
# 3) Plot & report
|
||
strain_for_plot = _read_first_strain(strain_scores)
|
||
plot_cmd: list[str] = [
|
||
py,
|
||
str(Path(__file__).resolve().parents[0] / "plot_shotter.py"),
|
||
"--strain_scores",
|
||
str(strain_scores),
|
||
"--toxin_support",
|
||
str(toxin_support),
|
||
"--species_scores",
|
||
str(species_scores),
|
||
"--out_dir",
|
||
str(shotter_dir),
|
||
"--merge_unresolved",
|
||
"--report_mode",
|
||
"paper",
|
||
"--lang",
|
||
lang,
|
||
]
|
||
if strain_for_plot:
|
||
plot_cmd += ["--per_hit_strain", strain_for_plot]
|
||
|
||
r2 = _shell(plot_cmd)
|
||
if r2.returncode != 0:
|
||
# plotting/report optional; continue
|
||
pass
|
||
|
||
# 4) Bundle
|
||
bundle = out_root / "pipeline_results.tar.gz"
|
||
with tarfile.open(bundle, "w:gz") as tar:
|
||
tar.add(digger_dir, arcname="digger")
|
||
tar.add(shotter_dir, arcname="shotter")
|
||
|
||
return {
|
||
"ok": True,
|
||
"digger_dir": str(digger_dir),
|
||
"shotter_dir": str(shotter_dir),
|
||
"bundle": str(bundle),
|
||
"all_toxins": str(all_toxins),
|
||
"strain": strain_for_plot,
|
||
}
|
||
|
||
|
||
def main() -> int:
|
||
ap = argparse.ArgumentParser(description="Run single-fna Digger -> Shotter pipeline")
|
||
ap.add_argument("--fna", type=Path, required=True, help="Path to a single .fna file")
|
||
ap.add_argument("--toxicity_csv", type=Path, default=Path("Data/toxicity-data.csv"))
|
||
ap.add_argument("--out_root", type=Path, default=Path("runs/single_run"))
|
||
ap.add_argument("--image", type=str, default="quay.io/biocontainers/bttoxin_digger:1.0.10--hdfd78af_0")
|
||
ap.add_argument("--platform", type=str, default="linux/amd64")
|
||
ap.add_argument("--min_identity", type=float, default=0.0)
|
||
ap.add_argument("--min_coverage", type=float, default=0.0)
|
||
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
|
||
if str(args.out_root) == "runs/single_run":
|
||
stem = args.fna.stem
|
||
args.out_root = Path("runs") / f"{stem}_run"
|
||
|
||
res = run_single_fna_pipeline(
|
||
fna_path=args.fna,
|
||
out_root=args.out_root,
|
||
toxicity_csv=args.toxicity_csv,
|
||
image=args.image,
|
||
platform=args.platform,
|
||
min_identity=args.min_identity,
|
||
min_coverage=args.min_coverage,
|
||
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"):
|
||
print(f"[pipeline] FAILED at stage={res.get('stage')}: {res.get('error')}")
|
||
logs = res.get("logs")
|
||
if logs:
|
||
print(logs[:2000])
|
||
return 1
|
||
|
||
print("[pipeline] ✓ Done")
|
||
print(f" Digger: {res['digger_dir']}")
|
||
print(f" Shotter: {res['shotter_dir']}")
|
||
print(f" Bundle: {res['bundle']}")
|
||
print(f" Strain: {res.get('strain','')}")
|
||
return 0
|
||
|
||
|
||
if __name__ == "__main__":
|
||
raise SystemExit(main())
|