根据Knumbers注释爬取KEGG对应KO号和pathway

背景

手头有KEGG对应各个基因的注释文件（注释可以参考KAAS注释流程)，但没有对应的KO号，需要得到相应的KO号做富集分析

Python script

用selenium+xpath爬取，试了下发现KEGG最大接受的输入knumbers数量为7000左右，所以分割数据进行爬取（这里没有用线程池爬，要加速可以用多线程),注意脚本中chrome driver改成自己的地址即可。
参数三个，分别为-kn,对应你的用换行符分割的knumbers文件；-k2ko，对应爬取的kn对应ko关系的文件保存地址；-t2n,对应爬取的ko号和pathway name描述的文件保存地址。
得到文件后就可以很方便的用R整理数据，以及超几何检验/现成R包(例如ClusterProfiler)进行富集

from selenium import webdriver
# No visual interface
from selenium.webdriver.chrome.options import Options
# Avoid test
from selenium.webdriver import ChromeOptions
from lxml import etree
import os
import argparse


def setoption():
    """
    Google Chrome's anti-anti-crawler parameter settings
    """
    # No visual interface
    chrome_options = Options()
    chrome_options.add_experimental_option(
        'excludeSwitches', ['enable-logging'])
    chrome_options.add_argument("--headless")
    chrome_options.add_argument("--disable-gpu")
    # Avoid test
    option = ChromeOptions()
    option.add_experimental_option("excludeSwitches",
                                   ["enable-automation"])
    return chrome_options, option


def mapkn2ko(knsearch, k2kopath, term2namepath):
    """
    main process to map kn to ko
    :param knsearch: kn string
    :param k2kopath: path to save k2ko file
    :param term2namepath: path to save term2name file
    """
    chrome_options, option = setoption()
    bro = webdriver.Chrome(executable_path=r"/YourPathTo/chromedriver.exe",
                               chrome_options=chrome_options,
                               options=option)
    bro.get("https://www.genome.jp/kegg/ko.html")
    search_input = bro.find_element_by_xpath('//*[@id="content"]/div[2]/div[1]/form/table/tbody/tr[2]/td/textarea')
    search_input.send_keys(knsearch)
    btn = bro.find_element_by_xpath('//*[@id="content"]/div[2]/div[1]/form/table/tbody/tr[3]/td/input[3]')
    btn.click()
    bro.switch_to_window(bro.window_handles[1])
    page_text = bro.page_source
    tree = etree.HTML(page_text)
    li_list = tree.xpath('/html/body/div[2]/li')
    for li in li_list:
        ko = li.xpath('./a[1]/text()')[0]
        ko_name =  li.xpath('./text()')[0].split(" (")[0]
        kn_list = li.xpath('./div/a//text()')
        with open(k2kopath, "a") as k2ko:
            for kn in kn_list:
                k2ko.write(kn.split(":")[1]+"\t"+ko+"\n")
        with open(term2namepath, "a") as term2name:
            term2name.write(ko+"\t"+ko_name+"\n")
    bro.quit()


def kninput(knfile):
    knstring_all = []
    knstring_7000 = []
    with open(knfile, "rt") as knf:
        while True:
            try:
                if len(knstring_7000) <= 7000:
                    knstring_7000.append(next(knf))
                else:
                    knstring_all.append("".join(knstring_7000))
                    knstring_7000 = []
            except StopIteration:
                knstring_all.append("".join(knstring_7000))
                break
    return knstring_all


def getoptions():
    """
    Get options from command line
    :return: knfilepath, k2kofilepath, t2nfilepath
    """
    parser = argparse.ArgumentParser(description="Get k2ko and term2name by inputting a file including knumbers")
    parser.add_argument("-kn", "--knumber", help="Path to knumbers file")
    parser.add_argument("-k2ko", "--knumber2pathway",
                        help="File path to save the relationship between knumbers and pathway names")
    parser.add_argument("-t2n", "--term2name", help="File paht to save the pathway name and corresponding description")
    args = parser.parse_args()
    if not args.knumber:
        raise TypeError("Missing option '-kn', please check your input")
    if not args.knumber2pathway:
        raise TypeError("Missing option '-k2ko', please check your input")
    if not args.term2name:
        raise TypeError("Missing option '-t2n', please check your input")
    return args.knumber, args.knumber2pathway, args.term2name


def mainprocess():
    """
    Pipeline to execute program.
    """
    knfile, k2kofile, t2nfile = getoptions()
    if os.path.isfile(k2kofile):
        os.remove(k2kofile)
    if os.path.isfile(t2nfile):
        os.remove(t2nfile)
    knstring_all = kninput(knfile)
    for knstring in knstring_all:
        mapkn2ko(knstring, k2kofile, t2nfile)


if __name__ == "__main__":
    mainprocess()

富集分析可以参考：
https://www.jianshu.com/p/8ee9a71d056e?utm_campaign=maleskine...