#!/usr/bin/env python3
"""
KaKs Analysis Skill - Main Runner
Ka/Ks分析技能主运行脚本

Usage:
    python run.py --cds1 Ft.cds.fa --cds2 Ath.cds.fa --pairs orthologs.txt --output ./kaks
"""

import argparse
import json
import logging
import sys
import re
from datetime import datetime
from pathlib import Path

logging.basicConfig(
    level=logging.INFO,
    format='%(asctime)s - %(levelname)s - %(message)s'
)
logger = logging.getLogger(__name__)


def parse_yn00_output(yn00_file: Path) -> tuple:
    """解析yn00输出文件，提取Ka, Ks, Ka/Ks"""
    ka = ks = kaks = None
    
    with open(yn00_file, 'r') as f:
        content = f.read()
        
        # 查找YN方法的结果
        yn_pattern = r'\d+\.\d+\s+\d+\.\d+\s+\d+\.\d+\s+\d+\.\d+\s+\d+\.\d+\s+\d+\.\d+'
        matches = re.findall(yn_pattern, content)
        
        if matches:
            last_line = matches[-1].split()
            if len(last_line) >= 6:
                ka = float(last_line[0])
                ks = float(last_line[1])
                kaks = float(last_line[2])
    
    return ka, ks, kaks


def main():
    parser = argparse.ArgumentParser(
        description="Ka/Ks Analysis Skill - 非同义/同义替换率分析"
    )
    parser.add_argument(
        "--cds1", "-1", required=True, type=Path,
        help="物种1 CDS FASTA文件"
    )
    parser.add_argument(
        "--cds2", "-2", required=True, type=Path,
        help="物种2 CDS FASTA文件"
    )
    parser.add_argument(
        "--pairs", "-p", required=True, type=Path,
        help="同源基因对列表文件 (TSV格式: gene1\\tgene2)"
    )
    parser.add_argument(
        "--neutral-rate", type=float, default=7.08e-9,
        help="中性替换率 (替换/位点/年), 默认: 7.08e-9 (拟南芥)"
    )
    parser.add_argument(
        "--cpu", type=int, default=8,
        help="CPU线程数, 默认: 8"
    )
    parser.add_argument(
        "--output", "-o", required=True, type=Path,
        help="输出目录"
    )
    
    args = parser.parse_args()
    
    logger.info(f"Starting Ka/Ks analysis...")
    logger.info(f"CDS1: {args.cds1}")
    logger.info(f"CDS2: {args.cds2}")
    logger.info(f"Pairs: {args.pairs}")
    logger.info(f"Output: {args.output}")
    
    # TODO: Implement full analysis pipeline
    logger.info("Ka/Ks analysis completed (placeholder)")


if __name__ == "__main__":
    main()