365 lines
12 KiB
Python
Executable File
365 lines
12 KiB
Python
Executable File
#!/usr/bin/env python3
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"""
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Domain Analysis Skill - 蛋白结构域分析技能
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使用HMMER对Pfam数据库进行蛋白结构域分析
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Usage:
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python run.py --input protein.fa --pfam PF03110.hmm --output ./domain
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python run.py --config config.yaml --output ./domain
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python run.py --demo --output ./domain
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"""
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import argparse
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import hashlib
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import json
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import logging
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import os
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import shutil
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import subprocess
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import sys
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from datetime import datetime
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from pathlib import Path
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from typing import Dict, List, Optional
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import yaml
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# 设置日志
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logging.basicConfig(
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level=logging.INFO,
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format='%(asctime)s - %(levelname)s - %(message)s'
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)
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logger = logging.getLogger(__name__)
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class DomainSkill:
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"""蛋白结构域分析技能主类"""
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def __init__(self, config_path: Optional[str] = None):
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self.config = self._load_config(config_path)
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self.commands = [] # 记录所有执行的命令
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self.checksums = {} # 记录文件校验
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def _load_config(self, config_path: Optional[str]) -> Dict:
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"""加载配置文件"""
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if config_path and os.path.exists(config_path):
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with open(config_path) as f:
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return yaml.safe_load(f)
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default_config = Path(__file__).parent / "config.yaml"
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with open(default_config) as f:
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return yaml.safe_load(f)
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def _which(self, cmd: str) -> Optional[str]:
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"""检查命令是否存在"""
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return shutil.which(cmd)
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def _run_command(self, cmd: List[str], description: str):
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"""运行命令并记录"""
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logger.info(f"Running: {description}")
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logger.info(f"Command: {' '.join(cmd)}")
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self.commands.append({
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"description": description,
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"command": " ".join(cmd),
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"timestamp": datetime.now().isoformat()
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})
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subprocess.run(cmd, check=True)
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def _compute_checksum(self, filepath: Path) -> str:
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"""计算文件SHA256校验"""
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sha256 = hashlib.sha256()
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with open(filepath, "rb") as f:
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for chunk in iter(lambda: f.read(8192), b""):
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sha256.update(chunk)
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return sha256.hexdigest()
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def _record_file(self, filepath: Path, file_type: str = "output"):
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"""记录文件信息"""
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if filepath.exists():
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self.checksums[str(filepath)] = {
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"sha256": self._compute_checksum(filepath),
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"size": filepath.stat().st_size,
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"type": file_type
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}
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def run_hmmscan(self, protein_fasta: Path, pfam_hmm: Path,
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output_dir: Path) -> Dict:
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"""运行hmmscan Pfam搜索"""
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params = self.config["parameters"]["hmmscan"]
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cpu = self.config["parameters"]["cpu"]
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hmmscan = self._which("hmmscan")
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if not hmmscan:
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raise RuntimeError("hmmscan not found. Please install HMMER.")
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output_dir.mkdir(parents=True, exist_ok=True)
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prefix = "domain_scan"
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domtblout = output_dir / f"{prefix}.pfam.domtblout"
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tblout = output_dir / f"{prefix}.pfam.tblout"
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hmmscan_out = output_dir / f"{prefix}.pfam.out"
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cmd = [
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"hmmscan",
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"--cpu", str(cpu),
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"--domtblout", str(domtblout),
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"--tblout", str(tblout),
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"-o", str(hmmscan_out),
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]
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if params.get("use_cut_ga"):
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cmd.append("--cut_ga")
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cmd.extend([str(pfam_hmm), str(protein_fasta)])
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self._run_command(cmd, "HMMER hmmscan Pfam搜索")
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self._record_file(domtblout)
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self._record_file(tblout)
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self._record_file(hmmscan_out)
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return {
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"domtblout": str(domtblout),
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"tblout": str(tblout)
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}
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def generate_report(self, output_dir: Path, evalue: float,
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coverage: float) -> Path:
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"""生成分析报告"""
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report_file = output_dir / "report.md"
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report_content = f"""# 蛋白结构域分析报告
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## 基本信息
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- **E-value阈值**: {evalue}
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- **HMM覆盖度阈值**: {coverage}
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- **分析时间**: {datetime.now().strftime("%Y-%m-%d %H:%M:%S")}
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- **技能版本**: {self.config["skill"]["version"]}
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## 分析结果
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| 文件 | 描述 |
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|------|------|
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| domain_scan.pfam.domtblout | Domain表格输出 |
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| domain_scan.pfam.tblout | 表格输出 |
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## 可复现性
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所有分析命令已记录在 `commands.sh` 中，
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环境配置见 `environment.yml`。
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## 校验信息
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文件SHA256校验值见 `checksums.sha256`。
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"""
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with open(report_file, "w") as f:
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f.write(report_content)
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self._record_file(report_file)
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return report_file
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def write_reproducibility_bundle(self, output_dir: Path):
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"""写入可复现性文件包"""
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# commands.sh
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commands_file = output_dir / "commands.sh"
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with open(commands_file, "w") as f:
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f.write("#!/bin/bash\n# 蛋白结构域分析复现命令\n\n")
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for cmd in self.commands:
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f.write(f"# {cmd['description']}\n")
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f.write(f"{cmd['command']}\n\n")
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os.chmod(commands_file, 0o755)
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# environment.yml
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env_file = output_dir / "environment.yml"
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env_config = {
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"name": "domain-analysis",
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"channels": self.config["dependencies"]["conda"]["channels"],
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"dependencies": self.config["dependencies"]["conda"]["packages"]
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}
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with open(env_file, "w") as f:
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yaml.dump(env_config, f, default_flow_style=False)
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# checksums.sha256
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checksums_file = output_dir / "checksums.sha256"
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with open(checksums_file, "w") as f:
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for filepath, info in self.checksums.items():
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f.write(f"{info['sha256']} {filepath}\n")
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def run(self, protein_fasta: Path, pfam_hmm: Path,
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output_dir: Path) -> Dict:
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"""运行完整的蛋白结构域分析流程"""
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logger.info(f"Starting domain analysis")
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# 记录输入文件
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self._record_file(protein_fasta, "input")
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self._record_file(pfam_hmm, "input")
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# 运行hmmscan
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results = self.run_hmmscan(protein_fasta, pfam_hmm, output_dir)
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# 生成报告
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params = self.config["parameters"]["hmmscan"]
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report = self.generate_report(
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output_dir,
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params["evalue"],
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params["coverage"]
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)
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# 写入可复现性文件
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self.write_reproducibility_bundle(output_dir)
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logger.info(f"Domain analysis completed. Report: {report}")
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return {
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"status": "success",
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"output_dir": str(output_dir),
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"report": str(report),
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"domtblout": results["domtblout"]
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}
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def run_demo(self, output_dir: Path) -> Dict:
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"""运行Demo模式"""
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logger.info("Running in demo mode")
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# 创建模拟数据
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demo_dir = output_dir / "demo_data"
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demo_dir.mkdir(parents=True, exist_ok=True)
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# 模拟蛋白质FASTA
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protein_fasta = demo_dir / "demo_proteins.fa"
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with open(protein_fasta, "w") as f:
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f.write(">FtGene001\nMKTLLLPLLLLVLLLLLVQGSISAQ\n"
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">FtGene002\nMKTLLLPLLLLVLLLLLVQGSISAQ\n"
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">AtGene001\nMKTLLLPLLLLVLLLLLVQGSISAQ\n")
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# 模拟PFAM HMM文件
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pfam_hmm = demo_dir / "demo_pfam.hmm"
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pfam_hmm.write_text("HMMER3/f [3.3.2 | ]\n")
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# 创建模拟输出文件
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output_dir.mkdir(parents=True, exist_ok=True)
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# domtblout (模拟)
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domtblout = output_dir / "domain_scan.pfam.domtblout"
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domtblout.write_text("""# --- full sequence --- --- best 1 domain --- --- domain number estimation ---
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# target name accession tlen query name accession qlen E-value score bias c-Evalue i-Evalue score bias from to from to from to acc
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PF03110.16 SBP 383 FtGene001 - 284 1.2e-45 156.8 0.0 1.1e-47 1.2e-45 156.8 0.0 52 376 52 376 1 1 0.89
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PF03110.16 SBP 383 FtGene002 - 284 1.5e-42 148.2 0.0 1.4e-44 1.5e-42 148.2 0.0 55 380 55 380 1 1 0.87
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""")
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# tblout (模拟)
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tblout = output_dir / "domain_scan.pfam.tblout"
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tblout.write_text("""# target name accession tlen query name accession qlen E-value score bias
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PF03110.16 SBP 383 FtGene001 - 284 1.2e-45 156.8 0.0
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PF03110.16 SBP 383 FtGene002 - 284 1.5e-42 148.2 0.0
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""")
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# report.md
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report_file = output_dir / "report.md"
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report_file.write_text(f"""# 蛋白结构域分析报告
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## 基本信息
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- **E-value阈值**: 1e-5 (demo)
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- **HMM覆盖度阈值**: 0.5 (demo)
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- **分析时间**: {datetime.now().strftime("%Y-%m-%d %H:%M:%S")}
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- **技能版本**: {self.config["skill"]["version"]}
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## 分析结果
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| 文件 | 描述 |
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|------|------|
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| domain_scan.pfam.domtblout | Domain表格输出 |
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| domain_scan.pfam.tblout | 表格输出 |
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## 可复现性
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所有分析命令已记录在 `commands.sh` 中，环境配置见 `environment.yml`。
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## 校验信息
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文件SHA256校验值见 `checksums.sha256`。
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""")
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# commands.sh
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commands_file = output_dir / "commands.sh"
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commands_file.write_text("""#!/bin/bash
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# 蛋白结构域分析复现命令 (Demo模式)
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hmmscan --cpu 8 --domtblout domain.pfam.domtblout --tblout domain.pfam.tblout -o domain.pfam.out PF03110.hmm proteins.fa
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""")
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# environment.yml
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env_file = output_dir / "environment.yml"
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env_file.write_text("""name: domain-analysis
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channels:
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- bioconda
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- conda-forge
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dependencies:
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- hmmer=3.3.2
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- biopython=1.81
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""")
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# checksums.sha256
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checksums_file = output_dir / "checksums.sha256"
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for f in [domtblout, tblout, report_file, commands_file, env_file]:
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if f.exists():
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sha256 = hashlib.sha256()
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with open(f, "rb") as fp:
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for chunk in iter(lambda: fp.read(8192), b""):
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sha256.update(chunk)
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checksums_file.write_text(f"{sha256.hexdigest()} {f.name}\n")
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logger.info(f"Domain demo completed. Report: {report_file}")
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return {
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"status": "success",
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"output_dir": str(output_dir),
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"report": str(report_file),
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"domtblout": str(domtblout)
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}
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def main():
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parser = argparse.ArgumentParser(
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description="Domain Analysis Skill - 蛋白结构域分析"
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)
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parser.add_argument("--input", "-i", type=Path, help="蛋白序列FASTA文件")
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parser.add_argument("--pfam", type=Path, help="Pfam HMM模型文件")
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parser.add_argument("--evalue", type=float, help="E-value阈值")
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parser.add_argument("--coverage", type=float, help="HMM覆盖度阈值")
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parser.add_argument("--cpu", type=int, help="CPU线程数")
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parser.add_argument("--output", "-o", type=Path, required=True, help="输出目录")
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parser.add_argument("--config", "-c", type=Path, help="配置文件路径")
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parser.add_argument("--demo", action="store_true", help="运行Demo模式")
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args = parser.parse_args()
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# 初始化技能
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skill = DomainSkill(args.config)
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# 更新配置参数
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if args.evalue:
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skill.config["parameters"]["hmmscan"]["evalue"] = args.evalue
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if args.coverage:
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skill.config["parameters"]["hmmscan"]["coverage"] = args.coverage
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if args.cpu:
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skill.config["parameters"]["cpu"] = args.cpu
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# 运行
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if args.demo:
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result = skill.run_demo(args.output)
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else:
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if not args.input or not args.pfam:
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parser.error("--input and --pfam are required (unless using --demo)")
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result = skill.run(args.input, args.pfam, args.output)
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# 输出结果
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print(json.dumps(result, indent=2, ensure_ascii=False))
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return 0 if result["status"] == "success" else 1
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if __name__ == "__main__":
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sys.exit(main()) |