Question

我目前正在尝试从ncbi蛋白质数据库中删除蛋白质序列。此时，用户可以搜索蛋白质，我可以获得数据库吐出的第一个结果的链接。然而，当我通过美丽的汤来运行时，汤与铬检查元素不匹配，也没有完全顺序。

这是我目前的代码：

import string
import requests
from bs4 import BeautifulSoup

def getSequence():
    searchProt = input("Enter a Protein Name!:")
    if searchProt != '':
        searchString = "https://www.ncbi.nlm.nih.gov/protein/?term=" + searchProt
        page = requests.get(searchString)
        soup = BeautifulSoup(page.text, 'html.parser')
        soup = str(soup)
        accIndex = soup.find("a")
        accessionStart = soup.find('<dd>',accIndex)
        accessionEnd = soup.find('</dd>', accessionStart + 4)
        accession = soup[accessionStart + 4: accessionEnd]
        newSearchString = "https://www.ncbi.nlm.nih.gov/protein/" + accession
        try:
            newPage = requests.get(newSearchString)
            #This is where it fails
            newSoup = BeautifulSoup(newPage.text, 'html.parser')
            aaList = []
            spaceCount = newSoup.count("ff_line")
            print(spaceCount)
            for i in range(spaceCount):
                startIndex = newSoup.find("ff_line")
                startIndex = newSoup.find(">", startIndex) + 2
                nextAA = newSoup[startIndex]
                while nextAA in string.ascii_lowercase:
                    aaList.append(nextAA)
                    startIndex += 1
                    nextAA = newSoup[startIndex]
            return aaList        
         except:
            print("Please Enter a Valid Protein")

我一直试图用搜索'p53'来运行它并且已经到了链接：here

我在这个网站上查看过一系列网页搜索条目并尝试了很多方面，包括安装selenium和使用不同的解析器。我仍然对这些不匹配的原因感到困惑。（对不起，如果这是一个重复的问题，我对webscraping很新，目前有一个脑震荡，所以我正在寻找一些个案反馈）

Answer 1

此代码将使用Selenium提取您想要的蛋白质序列。我修改了您的原始代码，为您提供所需的结果。

from bs4 import BeautifulSoup
from selenium import webdriver
import requests

driver = webdriver.Firefox()

def getSequence():
    searchProt = input("Enter a Protein Name!:")
    if searchProt != '':
        searchString = "https://www.ncbi.nlm.nih.gov/protein/?term=" + searchProt
        page = requests.get(searchString)
        soup = BeautifulSoup(page.text, 'html.parser')
        soup = str(soup)
        accIndex = soup.find("a")
        accessionStart = soup.find('<dd>',accIndex)
        accessionEnd = soup.find('</dd>', accessionStart + 4)
        accession = soup[accessionStart + 4: accessionEnd]
        newSearchString = "https://www.ncbi.nlm.nih.gov/protein/" + accession
        try:
            driver.get(newSearchString)
            html = driver.page_source
            newSoup = BeautifulSoup(html, "lxml")
            ff_tags = newSoup.find_all(class_="ff_line")
            aaList = []
            for tag in ff_tags:
                aaList.append(tag.text.strip().replace(" ",""))
            protSeq = "".join(aaList)
            return protSeq
        except:
            print("Please Enter a Valid Protein")

sequence = getSequence()
print(sequence)

为“p53”的输入产生以下输出：

meepqsdlsielplsqetfsdlwkllppnnvlstlpssdsieelflsenvtgwledsggalqgvaaaaastaedpvtetpapvasapatpwplsssvpsyktfqgdygfrlgflhsgtaksvtctyspslnklfcqlaktcpvqlwvnstpppgtrvramaiykklqymtevvrrcphherssegdslappqhlirvegnlhaeylddkqtfrhsvvvpyeppevgsdcttihynymcnsscmggmnrrpiltiitledpsgnllgrnsfevricacpgrdrrteeknfqkkgepcpelppksakralptntssspppkkktldgeyftlkirgherfkmfqelnealelkdaqaskgsedngahssylkskkgqsasrlkklmikregpdsd

在Python webscraping中，beautifulSoup与chrome inspect不匹配

1 个答案: