一、KEGG数据下载

1、先进入官网：https://www.kegg.jp/

image.png
2、进入KO (KEGG ORTHOLOGY) Database image.png
3、点击此处选择物种 image.png
4、此处以斑马鱼为例，所以选择dre image.png
5、下载json文件到本地 image.png

二、json文件的处理

import json
import re
K_ko_dict = {}
with open(json, "r")as f:
    K_ko_file_content = json.load(f) 
for children_info in K_ko_file_content.get("children"):
    for next_children_info in children_info.get("children"):
        for third_children_info in next_children_info.get("children"):
            name_info = third_children_info.get("name")
            pathway_id = re.findall(r'PATH:(.*)]', name_info)
            pathway_name = re.findall(r'\d+\s(.*)\s\[', name_info)
            if pathway_id and pathway_name:
                K_ko_dict[pathway_id[0]+"\t"+pathway_name[0]] = []
                if third_children_info.get("children"):
                    for fourth_children_info in third_children_info.get("children"):
                        K_name = fourth_children_info.get("name").split(" ")[0]
                        gene_name = fourth_children_info.get("name").split(" ")[1]
                        gene_name=re.sub(';','',gene_name)
                        K_ko_dict[pathway_id[0]+"\t"+pathway_name[0]].append(K_name+'\t'+gene_name)
out=open(outfile,'w+')
out.write("pathway_gene_id\tgene_name\tpathway_id\tpathway_name\n")
key1=sorted(K_ko_dict.keys())
for key in key1:
    K_ko_dict[key].sort()
    for i in K_ko_dict[key]:
        out.write(i+'\t'+key+'\n')
out.close()

处理后的文件： image.png

如果需要gene id 那么需要gtf文件，通过gene name转化即可

注意：json.load(f) 若报错：AttributeError: 'str' object has no attribute 'load'，那么需要修改名称，此处的f指向的名称为json，与import json重复，覆盖了此处的名称。因此会报错