47 lines
1.1 KiB
Python
47 lines
1.1 KiB
Python
from __future__ import annotations
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from pathlib import Path
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from typing import Dict
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from ...services.docker_service import DockerRunner
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def run_bttoxin_digger(workspace_root: Path, threads: int, sequence_type: str, scaf_suffix: str, update_db: bool) -> Dict:
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runner = DockerRunner()
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inputs_dir = workspace_root / "inputs"
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results_dir = workspace_root / "results"
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results_dir.mkdir(parents=True, exist_ok=True)
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# 示例命令：根据实际 BtToxin_Digger CLI 调整
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command = [
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"BtToxin_Digger",
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"--threads", str(threads),
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"--seq_type", sequence_type,
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"--scaf_suffix", scaf_suffix,
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"--input", str(inputs_dir),
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"--outdir", str(results_dir),
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]
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if update_db:
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command += ["--update_db"]
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logs = runner.run(
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image=None,
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command=command,
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workdir=Path("/work"),
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mounts={
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workspace_root: "/work",
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},
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env=None,
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platform=None,
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detach=False,
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remove=True,
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)
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return {
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"command": command,
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"logs": logs,
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"results_dir": str(results_dir),
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}
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