89 lines
2.4 KiB
Python
Executable File
89 lines
2.4 KiB
Python
Executable File
#!/usr/bin/env python3
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"""
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KaKs Analysis Skill - Main Runner
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Ka/Ks分析技能主运行脚本
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Usage:
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python run.py --cds1 Ft.cds.fa --cds2 Ath.cds.fa --pairs orthologs.txt --output ./kaks
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"""
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import argparse
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import json
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import logging
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import sys
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import re
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from datetime import datetime
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from pathlib import Path
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logging.basicConfig(
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level=logging.INFO,
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format='%(asctime)s - %(levelname)s - %(message)s'
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)
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logger = logging.getLogger(__name__)
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def parse_yn00_output(yn00_file: Path) -> tuple:
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"""解析yn00输出文件，提取Ka, Ks, Ka/Ks"""
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ka = ks = kaks = None
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with open(yn00_file, 'r') as f:
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content = f.read()
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# 查找YN方法的结果
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yn_pattern = r'\d+\.\d+\s+\d+\.\d+\s+\d+\.\d+\s+\d+\.\d+\s+\d+\.\d+\s+\d+\.\d+'
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matches = re.findall(yn_pattern, content)
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if matches:
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last_line = matches[-1].split()
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if len(last_line) >= 6:
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ka = float(last_line[0])
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ks = float(last_line[1])
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kaks = float(last_line[2])
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return ka, ks, kaks
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def main():
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parser = argparse.ArgumentParser(
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description="Ka/Ks Analysis Skill - 非同义/同义替换率分析"
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)
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parser.add_argument(
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"--cds1", "-1", required=True, type=Path,
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help="物种1 CDS FASTA文件"
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)
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parser.add_argument(
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"--cds2", "-2", required=True, type=Path,
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help="物种2 CDS FASTA文件"
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)
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parser.add_argument(
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"--pairs", "-p", required=True, type=Path,
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help="同源基因对列表文件 (TSV格式: gene1\\tgene2)"
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)
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parser.add_argument(
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"--neutral-rate", type=float, default=7.08e-9,
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help="中性替换率 (替换/位点/年), 默认: 7.08e-9 (拟南芥)"
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)
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parser.add_argument(
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"--cpu", type=int, default=8,
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help="CPU线程数, 默认: 8"
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)
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parser.add_argument(
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"--output", "-o", required=True, type=Path,
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help="输出目录"
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)
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args = parser.parse_args()
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logger.info(f"Starting Ka/Ks analysis...")
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logger.info(f"CDS1: {args.cds1}")
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logger.info(f"CDS2: {args.cds2}")
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logger.info(f"Pairs: {args.pairs}")
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logger.info(f"Output: {args.output}")
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# TODO: Implement full analysis pipeline
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logger.info("Ka/Ks analysis completed (placeholder)")
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if __name__ == "__main__":
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main()
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