Python 用类似于之后的下一个词更改 fasta 标题

(交叉发布到Biostar:https://www.biostars.org/p/9562110/)

我有一个FASTA文件，我想在&gt；之后的第一个位置添加‘similar to’

>_Anouracaudifer_00017283-RA transcript Name:"Similar to Chid1 Chitinase domain-containing protein 1 (Rattus norvegicus OX=10116)" offset:0 AED:0.30 eAED:0.30 QI:0|0|0|1|1|1|12|0|393
ATGAAGGCGCTCCTGCATGTGCTCTGGCTCACTCTGGCCTGCGGCTCTGCTCACACCACCCTGTCGAAGTCGGATGCCAAGAAGTCTGCCTCCAAGACACTGCAGGAGAAGACTCAGCTCTCAGAGACACCTGTGCAGGACCGGGGTCTGGTGGTAACAGACCCCCGAGCCGAGGACG

我希望输出是这样的

>Chid1_Anouracaudifer_00017283-RA transcript Name:"Similar to Chid1 Chitinase domain-containing protein 1 (Rattus norvegicus OX=10116)" offset:0 AED:0.30 eAED:0.30 QI:0|0|0|1|1|1|12|0|393
ATGAAGGCGCTCCTGCATGTGCTCTGGCTCACTCTGGCCTGCGGCTCTGCTCACACCACCCTGTCGAAGTCGGATGCCAAGAAGTCTGCCTCCAAGACACTGCAGGAGAAGACTCAGCTCTCAGAGACACCTGTGCAGGACCGGGGTCTGGTGGTAACAGACCCCCGAGCCGAGGACG

我该怎么做呢？ 我已经试过了

sed -E 's/(Similar to )(\w+)/>CHIA_\2\1\2/' file.txt > new_file_2.txt个

并将其存储在一个新文件中，并try 将其粘贴到标题中，但它不起作用，你有什么 idea 吗？

并且还使用了一个python脚本

def extract_similar_to_word(line):
    words = line.split()
    for i, word in enumerate(words):
        if word == "Similar":
            similar_to_word = words[i + 2].strip('""')
            if i + 3 < len(words) and words[i + 3].strip('""')[0].isupper():
                similar_to_word = words[i + 1].strip('""') + words[i + 2].strip('""')
            return similar_to_word
    return None

def modify_fasta_headers(input_file, output_file):
    with open(input_file, "r") as in_file, open(output_file, "w") as out_file:
        for line in in_file:
            if line.startswith(">"):
                similar_to_word = extract_similar_to_word(line)
                if similar_to_word:
                    # Find the first space in the line, then insert the similar_to_word
                    first_space_index = line.find(" ")
                    line = ">" + similar_to_word + "_" + line[1:first_space_index] + line[first_space_index:]
            out_file.write(line)



input_file = "all_chias.fasta"
output_file = "modified_output_fasta_v1.fasta"

modify_fasta_headers(input_file, output_file)