lingyuzeng/bttoxin-pipeline
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feat(scripts): add protein file (.faa) support to pipeline\n\n- Add detect_sequence_type() function for automatic file type detection\n- Rename run_single_fna_pipeline() to run_single_file_pipeline()\n- Add backward compatibility alias for existing callers\n- Add --input CLI argument (preferred over --fna)\n- Support .faa protein files alongside .fna/.fa/.fasta genome files\n- Auto-detect sequence type and pass correct suffix to BtToxin_Digger\n- Update documentation with protein file examples\n\nCo-Authored-By: Claude <noreply@anthropic.com>

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zly
2026-01-13 23:45:34 +08:00
parent 7379c98fac
commit 80e7d1ffb6
1 changed files with 116 additions and 28 deletions
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144
scripts/run_single_fna_pipeline.py
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@@ -1,7 +1,9 @@
#!/usr/bin/env python3
"""Run a single-fna BtToxin_Digger -> Shotter -> Plots pipeline.
"""Run a single-file BtToxin_Digger -> Shotter -> Plots pipeline.
- Input: one .fna file (nucleotide scaffold)
Supports both genome (.fna/.fa) and protein (.faa) files.
- Input: one .fna/.fa file (nucleotide scaffold) OR one .faa file (protein)
- Steps:
1) Stage this single file, run BtToxin_Digger via PixiRunner (pixi environment)
2) Run Shotter scoring on Digger's All_Toxins.txt via pixi run -e pipeline
@@ -18,21 +20,28 @@ Notes
- 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）。
Example
Example (Genome file):
python scripts/run_single_fna_pipeline.py \\
--fna tests/test_data/HAN055.fna \\
--input 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
Example (Protein file):
python scripts/run_single_fna_pipeline.py \\
--input tests/test_data/proteins.faa \\
--toxicity_csv Data/toxicity-data.csv \\
--out_root runs/proteins_run \\
--min_identity 0.50 --min_coverage 0.60
# 使用自定义数据库路径
python scripts/run_single_fna_pipeline.py \\
--fna tests/test_data/HAN055.fna \\
--input tests/test_data/HAN055.fna \\
--bttoxin_db_dir /path/to/custom/bt_toxin
# 使用 pixi 任务运行
pixi run pipeline --fna tests/test_data/HAN055.fna
pixi run pipeline --input tests/test_data/HAN055.fna
"""
from __future__ import annotations
@@ -51,6 +60,32 @@ sys.path.insert(0, str(Path(__file__).parent))
from pixi_runner import PixiRunner, build_shotter_command, build_plot_command
# Supported file extensions
GENOME_EXTENSIONS = {".fna", ".fa", ".fasta"}
PROTEIN_EXTENSIONS = {".faa"}
ALL_EXTENSIONS = GENOME_EXTENSIONS | PROTEIN_EXTENSIONS
def detect_sequence_type(file_path: Path) -> tuple[str, str]:
"""
检测文件类型并返回 (sequence_type, suffix)。
Returns:
(sequence_type, suffix): where sequence_type is "nucl" or "prot",
and suffix is the file extension (e.g., ".fna", ".faa")
"""
ext = file_path.suffix.lower()
if ext in PROTEIN_EXTENSIONS:
return "prot", ext
elif ext in GENOME_EXTENSIONS:
return "nucl", ext
else:
raise ValueError(
f"Unsupported file extension: {ext}. "
f"Supported: genome {GENOME_EXTENSIONS}, protein {PROTEIN_EXTENSIONS}"
)
def _shell(cmd: list[str]) -> subprocess.CompletedProcess:
return subprocess.run(cmd, text=True)
@@ -72,8 +107,8 @@ def _read_first_strain(strain_scores_tsv: Path) -> str:
return ""
def run_single_fna_pipeline(
fna_path: Path,
def run_single_file_pipeline(
input_path: Path,
out_root: Path,
toxicity_csv: Path = Path("Data/toxicity-data.csv"),
min_identity: float = 0.0,
@@ -83,11 +118,13 @@ def run_single_fna_pipeline(
lang: str = "zh",
bttoxin_db_dir: Path | None = None,
threads: int = 4,
sequence_type: str | None = None,
file_suffix: str | None = None,
) -> Dict[str, Any]:
"""运行单个 fna 文件的完整 pipeline（使用 pixi 环境）。
"""运行单个文件（基因组或蛋白）的完整 pipeline（使用 pixi 环境）。
Args:
fna_path: 输入 .fna 文件路径
input_path: 输入文件路径（.fna/.fa/.fasta 或 .faa）
out_root: 输出根目录
toxicity_csv: 毒性数据 CSV 文件路径
min_identity: 最小 identity 阈值
@@ -98,11 +135,23 @@ def run_single_fna_pipeline(
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。
threads: 线程数
sequence_type: 序列类型 ("nucl" 或 "prot")，若为 None 则自动检测
file_suffix: 文件后缀，若为 None 则自动检测
"""
fna_path = fna_path.resolve()
input_path = input_path.resolve()
out_root = out_root.resolve()
out_root.mkdir(parents=True, exist_ok=True)
# 自动检测序列类型
if sequence_type is None or file_suffix is None:
detected_type, detected_suffix = detect_sequence_type(input_path)
sequence_type = sequence_type or detected_type
file_suffix = file_suffix or detected_suffix
seq_type_label = "protein" if sequence_type == "prot" else "genome"
print(f"[pipeline] Input file: {input_path.name}")
print(f"[pipeline] Detected type: {seq_type_label} ({sequence_type}), suffix: {file_suffix}")
# 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"
@@ -120,20 +169,30 @@ def run_single_fna_pipeline(
d.mkdir(parents=True, exist_ok=True)
# Stage single input file
staged_fna = stage_dir / fna_path.name
shutil.copy2(fna_path, staged_fna)
staged_file = stage_dir / input_path.name
shutil.copy2(input_path, staged_file)
# 1) Run BtToxin_Digger via PixiRunner (pixi digger environment)
runner = PixiRunner(env_name="digger")
result = runner.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=threads,
bttoxin_db_dir=bttoxin_db_dir,
)
# 构建参数：根据序列类型使用不同的参数名
digger_params = {
"input_dir": stage_dir,
"output_dir": digger_dir,
"log_dir": logs_dir,
"sequence_type": sequence_type,
"threads": threads,
"bttoxin_db_dir": bttoxin_db_dir,
}
# 根据序列类型添加相应的后缀参数
if sequence_type == "prot":
digger_params["prot_suffix"] = file_suffix
else:
digger_params["scaf_suffix"] = file_suffix
result = runner.run_bttoxin_digger(**digger_params)
if not result.get("success"):
return {
"ok": False,
@@ -151,7 +210,7 @@ def run_single_fna_pipeline(
shotter_dir.mkdir(parents=True, exist_ok=True)
scripts_dir = Path(__file__).resolve().parents[0]
pixi_project_dir = Path(__file__).resolve().parents[1]
shoter_cmd = build_shotter_command(
pixi_project_dir=pixi_project_dir,
script_path=scripts_dir / "bttoxin_shoter.py",
@@ -205,12 +264,23 @@ def run_single_fna_pipeline(
"bundle": str(bundle),
"all_toxins": str(all_toxins),
"strain": strain_for_plot,
"sequence_type": sequence_type,
}
def main() -> int:
ap = argparse.ArgumentParser(description="Run single-fna Digger -> Shotter pipeline (pixi-based)")
ap.add_argument("--fna", type=Path, required=True, help="Path to a single .fna file")
ap = argparse.ArgumentParser(
description="Run single-file Digger -> Shotter pipeline (pixi-based). "
"Supports genome (.fna/.fa/.fasta) and protein (.faa) files."
)
ap.add_argument(
"--input",
type=Path,
required=True,
help="Path to input file (genome: .fna/.fa/.fasta, protein: .faa). "
"Deprecated: --fna still works for backward compatibility."
)
ap.add_argument("--fna", type=Path, default=None, help=argparse.SUPPRESS) # Hidden backward compat
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("--min_identity", type=float, default=0.0)
@@ -223,13 +293,26 @@ def main() -> int:
ap.add_argument("--threads", type=int, default=4, help="线程数")
args = ap.parse_args()
# Backward compatibility: --fna flag
input_file = args.input if args.input is not None else args.fna
if input_file is None:
print("[pipeline] Error: --input argument is required")
return 1
# 验证文件扩展名
if input_file.suffix.lower() not in ALL_EXTENSIONS:
print(f"[pipeline] Error: Unsupported file extension: {input_file.suffix}")
print(f"[pipeline] Supported: genome {GENOME_EXTENSIONS}, protein {PROTEIN_EXTENSIONS}")
return 1
# derive per-run default out_root using file stem
if str(args.out_root) == "runs/single_run":
stem = args.fna.stem
stem = input_file.stem
args.out_root = Path("runs") / f"{stem}_run"
res = run_single_fna_pipeline(
fna_path=args.fna,
res = run_single_file_pipeline(
input_path=input_file,
out_root=args.out_root,
toxicity_csv=args.toxicity_csv,
min_identity=args.min_identity,
@@ -249,6 +332,7 @@ def main() -> int:
return 1
print("[pipeline] ✓ Done")
print(f" Input type: {res.get('sequence_type', 'unknown')}")
print(f" Digger: {res['digger_dir']}")
print(f" Shotter: {res['shotter_dir']}")
print(f" Bundle: {res['bundle']}")
@@ -256,5 +340,9 @@ def main() -> int:
return 0
# Backward compatibility alias
run_single_fna_pipeline = run_single_file_pipeline
if __name__ == "__main__":
raise SystemExit(main())