usalign_runner.py

import subprocess
import os
from typing import List, Optional
from pathlib import Path
import yaml

class USalignRunner:
    def __init__(self, config_path: str = "config.yaml"):
        """
        Initialize USalignRunner with parameters from config file.
        
        Args:
            config_path (str): Path to the configuration file
        """
        with open(config_path, 'r',encoding="utf-8") as f:
            config = yaml.safe_load(f)
        
        self.usalign_path = Path(config['USalign']['path'])
        self.default_params = {
            'tmscore': config['USalign']['tmscore'],
            'outfmt': config['USalign']['outfmt'],
            'mol': 'protein'  # Default to protein alignment
        }
        
        if not self.usalign_path.exists():
            raise FileNotFoundError(f"USalign executable not found at {self.usalign_path}")

    def run_alignment(
        self,
        target_dir: str,
        pdb_list_file: str,
        tmscore: Optional[float] = None,
        outfmt: Optional[int] = None,
    ) -> tuple[int, str, str]:
        tmscore = tmscore if tmscore is not None else self.default_params['tmscore']
        outfmt = outfmt if outfmt is not None else self.default_params['outfmt']
        
        # Create the command
        cmd = [
            str(self.usalign_path),
            "-mol", self.default_params['mol'],
            "-dir", str(target_dir),
            pdb_list_file,
            "-TMscore", str(tmscore),
            "-outfmt", str(outfmt)
        ]
        print(cmd)
        
        # Convert command list to string
        cmd_str = "  ".join(cmd)
        
        try:
            # Execute the command
            process = subprocess.Popen(
                cmd_str,
                stdout=subprocess.PIPE,
                stderr=subprocess.PIPE,
                shell=True,
                text=True
            )
            
            # Get output
            stdout, stderr = process.communicate()
            
            return process.returncode, stdout, stderr
            
        except Exception as e:
            return -1, "", str(e)