usalign_runner.py

import subprocess
from pathlib import Path
from typing import Optional

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
        }

    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)