新浪博客

下载kegg代谢通路图以及对应的html文件

2018-09-04 11:10阅读：

http://blog.sina.cn/dpool/blog/u/2214034580

# coding:utf-8
# Email:fanyucai1@126.com
# 2018.3.15


import subprocess
import os
import sys


if len(sys.argv) !=3:
sys.stderr.write('This script is used to download KEGG pathway maps.')
sys.stderr.write('usage:python %s hsa hsa/' %(sys.argv[0]))
sys.exit(1)


abb=sys.argv[1]
outdir=sys.argv[2]
pathway = 'http://rest.kegg.jp/list/pathway/'
pathway+=abb
FONT>
os.chdir(outdir)


def ko(pathway,abb):
subprocess.check_call('curl -s %s -o ID.list' % (pathway), shell=True)
subprocess.check_call('awk \'{print $1}\' ID.list|awk -F':' \'{print $2}\'|sort -u >abb_ID.list && mv abb_ID.list ID.list',shell=True)
file = open('ID.list', 'r')
for line in file:
line = line.strip()
if not os.path.exists('%s.png' %(line)):
subprocess.check_call('curl http://rest.kegg.jp/get/%s/image -o %s.png' % (line, line),shell=True)
if not os.path.exists('%s.html' %(line)):
subprocess.check_call('curl https://www.kegg.jp/kegg-bin/show_pathway?%s -o %s.html' % (line,line), shell=True)
file.close()


if __name__ =='__main__':
ko(pathway, abb)

我的更多文章

下载客户端阅读体验更佳

APP专享