调整基因组中序列的顺序，名称和方向

依赖biopyhon包
pip install biopython

首先获得当前基因组文件的序列名,以便后续编辑。注意，生成的list.txt文件原编辑为等下提到的三列格式。
seqkit fx2tab -n genome.fa > list.txt

import argparse
from Bio import SeqIO
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord

# 创建命令行参数解析器
parser = argparse.ArgumentParser(description="Adjust sequence order and direction based on a list file.")

# 添加命令行参数
parser.add_argument("-g", "--genome", help="Path to the genome.fa file", required=True)
parser.add_argument("-l", "--list", help="Path to the list.txt file", required=True)
parser.add_argument("-o", "--output", help="Output file name", required=True)

# 添加使用帮助
parser.epilog = """
Example usage:
  python adjust_sequence.py -g genome.fa -l list.txt -o adjusted_genome_modified.fa
"""

# 解析命令行参数
args = parser.parse_args()

# 读取genome.fa文件
genome_records = SeqIO.to_dict(SeqIO.parse(args.genome, "fasta"))

# 读取list.txt文件
with open(args.list, "r") as file:
    listed_sequences = []
    for line in file:
        line = line.strip().split("\t")
        seq_name = line[0]
        direction = int(line[1])
        new_seq_name = line[2]
        
        # 获取序列
        seq = genome_records[seq_name].seq
        
        # 根据方向调整序列
        if direction == 2:
            seq = seq.reverse_complement()
        
        # 创建新的序列记录
        new_record = SeqRecord(seq, id=new_seq_name, description="")
        
        # 将新的序列记录添加到字典中
        genome_records[new_seq_name] = new_record
        
        # 记录已列出的序列
        listed_sequences.append(new_seq_name)

    # 将未列出的序列附加在列出序列的后面
    for seq_name, record in genome_records.items():
        if seq_name not in listed_sequences:
            genome_records[new_seq_name] = record

# 保存调整后的序列到新的fasta文件
SeqIO.write(genome_records.values(), args.output, "fasta")

用法

python adjust_sequence.py -g genome.fa -l list.txt -o adjusted_genome_modified.fa

其中list.txt分三列，第一列原序列名；第二列，如果是1就原方向，2就变为反向互补；第三列，新序列名。以制表符分隔
如
B04 2 B01
B08 2 B02
B07 1 B03
B06 2 B04
B02 2 B05
B05 1 B06
B01 2 B07
B03 2 B08