#!/usr/bin/env python
# -*- encoding: utf-8 -*-
'''
@file               :main.py
@Description:       : foldseek quick search for protein structure alignment
@Date               :2024/03/11 15:17:21
@Author             :lyzeng
@Email              :pylyzeng@gmail.com
@version            :1.0
'''


import subprocess
from pathlib import Path
import pandas as pd
import shutil
import attrs
import argparse
from typing import Optional

@attrs.define
class FoldseekComparer:
    pdb_file: Path = attrs.field(converter=Path, validator=attrs.validators.instance_of(Path))  # 指定的PDB文件
    pdb_dir: Path = attrs.field(converter=Path, validator=attrs.validators.instance_of(Path))  # 包含PDB文件的目录
    output_dir: Path = attrs.field(factory=lambda: Path('compare_out'), validator=attrs.validators.instance_of(Path))
    output_format: str = attrs.field(default='xlsx', validator=attrs.validators.in_(['xlsx', 'csv']))

    def __attrs_post_init__(self):
        """
        Create the output directory if it doesn't exist.
        """
        self.output_dir.mkdir(parents=True, exist_ok=True)

    @staticmethod
    def check_foldseek_path() -> Optional[str]:
        """
        Check if Foldseek is available in the system PATH.
        """
        foldseek_path = shutil.which("foldseek")
        if foldseek_path is None:
            raise FileNotFoundError("Foldseek is not found in the system PATH. Please install Foldseek and add it to the PATH environment variable.")
        return foldseek_path

    def compare_with_directory(self) -> None:
        """
        Compare the specified PDB file with all PDB files in the specified directory.
        """
        foldseek_path = self.check_foldseek_path()

        for target_pdb in self.pdb_dir.glob('*.pdb'):
            # Skip the comparison if the target PDB is the same as the specified PDB
            if target_pdb.resolve() == self.pdb_file.resolve():
                continue

            oup = self.output_dir / f"{self.pdb_file.stem}_vs_{target_pdb.stem}"

            cmd = f"{foldseek_path} easy-search '{self.pdb_file}' '{target_pdb}' '{oup}' tmp --format-output query,target,fident,alnlen,mismatch,gapopen,qstart,qend,tstart,tend,evalue,bits,prob,lddt,alntmscore"

            result = subprocess.run(cmd, shell=True, capture_output=True, text=True)

            if result.returncode != 0:
                print(f"Error executing foldseek: {result.stderr}")
                continue

            output_file = f"{oup}"
            if Path(output_file).exists():
                col_names = 'query,target,fident,alnlen,mismatch,gapopen,qstart,qend,tstart,tend,evalue,bits,prob,lddt,alntmscore'.split(',')
                df_aln = pd.read_table(output_file, names=col_names)

                if self.output_format == 'xlsx':
                    df_aln.to_excel(f"{oup}.xlsx", index=False, engine='openpyxl')
                elif self.output_format == 'csv':
                    df_aln.to_csv(f"{oup}.csv", index=False)
            else:
                print(f"Expected output file not found: {output_file}")

if __name__ == "__main__":
    parser = argparse.ArgumentParser(description='Compare a specified PDB file with all PDB files in a directory.')
    parser.add_argument('pdb_file', type=Path, help='Path to the specified PDB file to compare')
    parser.add_argument('pdb_dir', type=Path, help='Path to the directory containing PDB files for comparison')
    parser.add_argument('-o', '--output_dir', type=Path, default=Path('compare_out'), help='Path to the output directory (default: compare_out)')
    parser.add_argument('-f', '--format', choices=['xlsx', 'csv'], default='xlsx', help='Output file format (default: xlsx)')

    args = parser.parse_args()

    comparer = FoldseekComparer(pdb_file=args.pdb_file, pdb_dir=args.pdb_dir, output_dir=args.output_dir, output_format=args.format)
    comparer.compare_with_directory()