python的requests爬取Uniprot中蛋白序列和N-糖基化位点

最新推荐文章于 2023-01-17 15:04:12 发布

@ZyuanZhang

最新推荐文章于 2023-01-17 15:04:12 发布

阅读量1k

点赞数 3

分类专栏： Python3 文章标签： python 正则表达式

本文链接：https://blog.csdn.net/weixin_44065416/article/details/127900713

版权

Python3 专栏收录该内容

9 篇文章 1 订阅

订阅专栏

1. 目的：

从Uniprot中下载某个蛋白 (以 P05067 为例) 对应的N-糖基化位点以及该蛋白的序列。

2. python3脚本：

import requests
import re
from requests.adapters import HTTPAdapter
#import time


class Get_Nglyco_Seq(object):
    def __init__(self,uniprot_id):
        self.uniprot_id = uniprot_id

    def __parse_xml_page(self,content_xml): ## 正则表达式匹配xml中N-糖基化和序列对应的部分
        patt_gly = re.compile(
            '\s+<feature type="glycosylation site" description="N-linked.+'
            '\s+<location>'
            '\s+<position position="(\d+)"/>'
            '\s+</location>',
            re.MULTILINE)
        patt_seq = re.compile('<sequence length[\w\s="-]+>([A-Z]+)</sequence>',re.MULTILINE)
        match_gly = patt_gly.findall(content_xml)
        match_seq = patt_seq.findall(content_xml)
        return match_gly, match_seq

    def get_xml_page(self): ## 获取uniprot_id对应的xml网页
        s = requests.Session()
        s.mount('https://', HTTPAdapter(max_retries=2))
        headers = {"User-Agent": "Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/54.0.2840.99 Safari/537.36"}
        response = s.get('https://rest.uniprot.org/uniprotkb/'+self.uniprot_id+'.xml',headers=headers)
        content_xml = response.text
        glyco_pos, sequ = self.__parse_xml_page(content_xml=content_xml)
        return glyco_pos, sequ


def main(uniprot_id):
    try:
        Nglyco_Seq = Get_Nglyco_Seq(uniprot_id)
        glyco_pos, sequ = Nglyco_Seq.get_xml_page()
        if len(glyco_pos) == 0:
            print('Uniprot ID: %s\nN-Glyco Pos: %s\nSequence: %s' % (uniprot_id,'No',sequ[0]))
        else:
            print('Uniprot ID: %s\nN-Glyco Pos: %s\nSequence: %s' % (uniprot_id,glyco_pos,sequ[0]))
    except Exception as e:
        print('Error: %s\t%s' % (uniprot_id,e))
    #time.sleep(random.randint(1,3))
    

if __name__ == '__main__':
	""" 以蛋白 P05067 为例，获取该蛋白的 N-糖基化位点和序列"""
	main('P05067')

3. 测试结果：

P05067的N-糖基化位点和序列结果如下：

Uniprot ID: P05067
N-Glyco Pos: ['542', '571']
Sequence: MLPGLALLLLAAWTARALEVPTDGNAGLLAEPQIAMFCGRLNMHMNVQNGKWDSDPSGTKTCIDTKEGILQYCQEVYPELQITNVVEANQPVTIQNWCKRGRKQCKTHPHFVIPYRCLVGEFVSDALLVPDKCKFLHQERMDVCETHLHWHTVAKETCSEKSTNLHDYGMLLPCGIDKFRGVEFVCCPLAEESDNVDSADAEEDDSDVWWGGADTDYADGSEDKVVEVAEEEEVAEVEEEEADDDEDDEDGDEVEEEAEEPYEEATERTTSIATTTTTTTESVEEVVREVCSEQAETGPCRAMISRWYFDVTEGKCAPFFYGGCGGNRNNFDTEEYCMAVCGSAMSQSLLKTTQEPLARDPVKLPTTAASTPDAVDKYLETPGDENEHAHFQKAKERLEAKHRERMSQVMREWEEAERQAKNLPKADKKAVIQHFQEKVESLEQEAANERQQLVETHMARVEAMLNDRRRLALENYITALQAVPPRPRHVFNMLKKYVRAEQKDRQHTLKHFEHVRMVDPKKAAQIRSQVMTHLRVIYERMNQSLSLLYNVPAVAEEIQDEVDELLQKEQNYSDDVLANMISEPRISYGNDALMPSLTETKTTVELLPVNGEFSLDDLQPWHSFGADSVPANTENEVEPVDARPAADRGLTTRPGSGLTNIKTEEISEVKMDAEFRHDSGYEVHHQKLVFFAEDVGSNKGAIIGLMVGGVVIATVIVITLVMLKKKQYTSIHHGVVEVDAAVTPEERHLSKMQQNGYENPTYKFFEQMQN