将每条染色体拆分成400-500Mb，然后批量运行

# 将每个序列（每条染色体）拆分为单独的文件
seqkit split -i -O split_by_chr genome.fasta
python chaifen.py Tgrandis.Chr.only.part_Chr3.fa 500000000 #chaifen.py脚本在下面
然后运行一下脚本：nohup bash piliang.sh &
cat piliang.sh
#!/bin/bash

# 遍历所有以 Chr1.part_ 开头的 fa 文件
for fa in Chr2.part_*.fa; do

  # 生成日志名
  log=${fa%.fa}.log

  echo "开始运行: $fa"
  echo "日志: $log"

  # 运行 EDTA
  docker run \
    -v $PWD:/in \
    -w /in \
    quay.io/biocontainers/edta:1.9.6--hdfd78af_2 \
    EDTA.pl \
      --genome $fa \
      --species others \
      --sensitive 0 \
      --anno 0 \
      --threads 10 \
      --cds Tgrandis.cds \
      > $log 2>&1

  echo "完成: $fa"
  echo "-----------------------------------------"
done

下面是chaifen.py脚本

cat chaifen.py
#!/usr/bin/env python3
import sys

def split_fasta_into_chunks(input_fasta, chunk_size_bp):
    """将单条序列的FASTA文件按指定长度切分"""
    with open(input_fasta, 'r') as infile:
        # 读取第一行作为序列标题
        header = infile.readline().strip()
        # 移除标题行开头的 '>'
        if header.startswith('>'):
            header = header[1:]
        else:
            print("错误：输入文件不是有效的FASTA格式")
            return

        # 读取剩余的序列内容，并移除换行符
        sequence_lines = [line.strip() for line in infile]
        full_sequence = ''.join(sequence_lines)

    seq_len = len(full_sequence)
    num_chunks = (seq_len + chunk_size_bp - 1) // chunk_size_bp

    print(f"总长度: {seq_len:,} bp")
    print(f"将切分为 {num_chunks} 个片段 (~{chunk_size_bp:,} bp/片段)\n")

    for i in range(num_chunks):
        start = i * chunk_size_bp
        end = min((i+1) * chunk_size_bp, seq_len)
        chunk_seq = full_sequence[start:end]

        # 按80字符一行进行换行，保持FASTA格式整洁
        fasta_lines = [chunk_seq[j:j+80] for j in range(0, len(chunk_seq), 80)]
        # 构建新序列的标题
        new_header = f">{header}_part_{i+1} [{start+1}-{end}]"

        out_filename = f"{header}.part_{i+1:03d}.fa"
        with open(out_filename, 'w') as outfile:
            outfile.write(new_header + '\n')
            outfile.write('\n'.join(fasta_lines))
            if i < num_chunks - 1:
                outfile.write('\n')  # 确保文件间有换行分隔
        print(f"已创建: {out_filename}")

if __name__ == "__main__":
    if len(sys.argv) != 3:
        print("Usage: python script.py input.fasta chunk_size_bp")
        print("例如: python split_fasta.py Tgrandis.Chr1.fa 400000000")
        sys.exit(1)

    input_file = sys.argv[1]
    try:
        chunk_size = int(sys.argv[2])
    except ValueError:
        print("错误: chunk_size_bp 必须是一个整数。")
        sys.exit(1)

    split_fasta_into_chunks(input_file, chunk_size)