非模式物种KEGG富集数据库准备(二)
一、KEGG数据下载
1、先进入官网:https://www.kegg.jp/
2、进入KO (KEGG ORTHOLOGY) Database
3、点击此处选择物种
4、此处以斑马鱼为例,所以选择dre
5、下载json文件到本地
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:
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
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