| 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", |
| } |
|
|
| 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"] |
|
|
| |
| 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) |
|
|
| |
| cmd_str = " ".join(cmd) |
|
|
| try: |
| |
| process = subprocess.Popen(cmd_str, stdout=subprocess.PIPE, stderr=subprocess.PIPE, shell=True, text=True) |
|
|
| |
| stdout, stderr = process.communicate() |
|
|
| return process.returncode, stdout, stderr |
|
|
| except Exception as e: |
| return -1, "", str(e) |
|
|
