一、KEGG數(shù)據(jù)下載
1、先進(jìn)入官網(wǎng)：https://www.kegg.jp/
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2、進(jìn)入KO (KEGG ORTHOLOGY) Database
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3、點擊此處選擇物種
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4、此處以斑馬魚為例，所以選擇dre
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5、下載json文件到本地
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二、json文件的處理
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()
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如果需要gene id 那么需要gtf文件，通過gene name轉(zhuǎn)化即可
注意：json.load(f) 若報錯：AttributeError: 'str' object has no attribute 'load'，那么需要修改名稱，此處的f指向的名稱為json，與import json重復(fù)，覆蓋了此處的名稱。因此會報錯
