import os fasta_file = "E:\泛基因组分析\ORF\ORF_xml\PRRSV.fasta" new_id_file = "E:\泛基因组分析\ORF\ORF_xml\prr.txt" if not os.path.exists(fasta_file): print("Error: Fasta file does not exist!") exit() if not os.path.exists(new_id_file): print("Error: New id file does not exist!") exit() try: with open(new_id_file, "r",encoding="utf-8") as f: new_ids = [line.strip() for line in f] except: print("Error: Failed to read new id file!") exit() try: with open(fasta_file, "r",encoding="utf-8") as f: lines = f.readlines() except: print("Error: Failed to read fasta file!") exit() new_lines = [] for line in lines: if line.startswith(">"): # 获取当前id在新id列表中的索引 id_str = line.strip().lstrip(">") if id_str.isdigit(): index = int(id_str) - 1 else: try: index = new_ids.index(id_str) except ValueError: print("Error: Id not found in new id file! ({})".format(id_str)) exit() # 替换为新id new_lines.append(">{}\n".format(new_ids[index])) else: new_lines.append(line) # 将替换后的fasta文件写入新文件 with open("E:\泛基因组分析\ORF\ORF_xml\1.fasta", "w") as f: f.writelines(new_lines)

这个代码看起来已经很完整了，不过还是有一些可以改进的地方：

1. 在文件路径中使用“\\”或者“/”代替“\”，因为“\”是转义字符，容易出现错误。

2. 可以添加一些输入输出路径的提示信息，方便用户操作。

3. 可以添加一个函数来判断文件是否存在，避免代码重复。

4. 可以将代码分解成多个函数，提高代码的可读性和可维护性。

下面是一个改进版本的代码，你可以参考一下：

import os


def check_file(file_path):
    if not os.path.exists(file_path):
        print("Error: File does not exist! ({})".format(file_path))
        return False
    return True


def read_file(file_path):
    try:
        with open(file_path, "r", encoding="utf-8") as f:
            lines = f.readlines()
        return lines
    except:
        print("Error: Failed to read file! ({})".format(file_path))
        return None


def replace_seq_id(fasta_file, new_id_file, output_file):
    if not check_file(fasta_file):
        exit()
    if not check_file(new_id_file):
        exit()
    new_ids = read_file(new_id_file)
    if new_ids is None:
        exit()
    lines = read_file(fasta_file)
    if lines is None:
        exit()
    new_lines = []
    for line in lines:
        if line.startswith(">"):
            # 获取当前id在新id列表中的索引
            id_str = line.strip().lstrip(">")
            if id_str.isdigit():
                index = int(id_str) - 1
            else:
                try:
                    index = new_ids.index(id_str)
                except ValueError:
                    print("Error: Id not found in new id file! ({})".format(id_str))
                    exit()
            # 替换为新id
            new_lines.append(">{}\n".format(new_ids[index].strip()))
        else:
            new_lines.append(line)
    # 将替换后的fasta文件写入新文件
    with open(output_file, "w") as f:
        f.writelines(new_lines)


if __name__ == "__main__":
    fasta_file = input("Please input fasta file path: ")
    new_id_file = input("Please input new id file path: ")
    output_file = input("Please input output file path: ")
    replace_seq_id(fasta_file, new_id_file, output_file)

这个版本的代码中，添加了三个函数分别用来检查文件是否存在、读取文件内容和替换序列ID。在主函数中，通过输入文件路径来执行替换操作。