python - 如何使用 Python 从网站链接复制网页的所有文本
问题描述
我需要访问特定部分的 DNA 序列，但是它们太多了，但是我看到了这样的 URL 链接模式
https://www.ncbi.nlm.nih.gov/nuccore/AF193276.1 ?report=fasta&log$= seqview &format=text&from= 1311 &to= 4322
这个链接，我可以从下面的位置 1311 到 4322 访问 HIV（ID：AF193276.1）的 DNA 序列。
>AF193276.1:1311-4322 HIV-1 CRF03_AB isolate KAL153 from Russia, complete genome
TTTTTTAGGGAGAATTTGGCCTTCCAGCAAAGGGAGGCCAGGAAATTTTCCTCAGAGCAGACCAGAGCCA
TCAGCCCCACCAGCAGAAAACTTTGGGATGGGGGAAGAGATAACCCCCTCCCTGAAACAGGAACAGAAGG
ACAGGGAACAGCATCCTCCTTCAATTTCCCTCAAATCACTCTTTGGCGACGACCCCTTGTCACAGTAAGA
ATAGGAGGACAGCTAAAAGAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGACATAAATT
TGCCAGGAAAATGGAAACCAAAAATGATAGGGGGGATTGGAGGTTTTATCAAGGTAAGACAGTATGATCA
GATACTTATAGAAATTTGTGGAAAAAAGGCTATAGGTACGGTATTAGTAGGACCTACCCCTGTCAACATA
ATTGGAAGAAATATGTTGACTCAGCTTGGTTGTACTTTAAATTTTCCAATAAGTCCTATTGAAACTGTAC
CAGTAACATTAAAGCCAGGAATGGATGGCCCAAAGGTTAAACAATGGCCATTAACAGAAGAGAAAATAAA
AGCATTAACAGACATTTGTAAGGAGATGGAAAAGGAAGGAAAAATTTCAAAAATTGGGCCTGAAAATCCA
TACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGGTTTCAGAG
AACTTAATAAGAGAACTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACACCCTGCAGGGTTAAAAAA
GAAAAAATCTGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGATCAAGACTTCAGA
AAGTATACTGCATTTACCATACCTAGTACAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGC
TTCCACAGGGATGGAAAGGATCACCAGCAATTTTCCAAAGTAGCATGACAAAAATCTTAGAGCCTTTTAG
AAAACAAAATCCAGAGATAGTTATCTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAGATA
GGGCAGCATAGAACAGAAATAGAGGAACTGAGAGAACATCTGCTGAGGTGGGGATTTACCACACCAGACA
AAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACTGTACA
GCCTATAGTGTTGCCAGAAAAAGACAGCTGGACTGTCAATGACATACAGAAGCTAGTGGGAAAATTGAAT
TGGGCAAGTCAGATTTATGCAGGGATTAAAGTAAGGCAATTATGTAAACTCCTTAGGGGAGCCAAAGCAC
TAACAGAAGTAATACCACTAACAGCAGAAGCAGAGCTAGAACTGGCAGAAAACAGGGAGATTCTAAAAGA
ACCAGTACATGGAGTGTATTATGACCCATCAAAAGACTTAGTAGCAGAAATACAGAAGCAGGGACAAGGC
CAATGGACATATCAAATTTATCAAGAGCCATTTAAAAATCTGAAAACAGGAAAATATGCAAGACTGAGGG
GTGCCCACACTAATGACGTAAAACAGTTAACAGAGGCAGTGCAAAAAATAGCCACTGAAAGCATAGTAAT
ATGGGGAAAGACTCCTAAATTTAAACTACCCATACAAAAAGAAACATGGGAAACATGGTGGACAGAGTAT
TGGCAAGCCACCTGGATTCCTGAGTGGGAATTTGTCAATACCCCTCCCTTAGTAAAATTATGGTACCAGT
TAGAGAAAGAACCCATAGTAGGAGCAGAAACTTTCTATGTAGATGGAGCAGCTAATAGGGAGACTAAATC
AGGAAAAGCAGGATATGTTACTGACAGAGGAAGACAAAAGGTTGTCTCCCTAACTGACACAACAAATCAG
AAGACTGAGTTACAAGCAATTCATCTAGCTTTGCAGGATTCGGGATTAGAAGTAAACATAGTAACAGACT
CACAATATGCATTAGGAATCATTCAAGCACAACCAGATAAGAGTGAATCAGAGTTAGTCAGTCAAATAAT
AGAGCAGTTGATAAAAAAGGAAAAGGTCTACCTGGCATGGGTACCAGCACACAAAGGAATTGGAGGAAAT
GAACAAGTTGATAAATTAGTCAGTGCTGGAATCAGGGAAGTACTATTTTTAGATGGAATAGATAAGGCAC
AAGAAGAACATGAGAAATATCACGGTAATTGGAGAGCAATGGCTAGTGATTTTAACCTGCCACCTGTGGT
AGCAAAAGAAATAGTAGCCAGCTGTGATAAATGTCAATTAAAAGGAGAAGCCATGCACGGACAAGTAGAC
TGTAGTCCAGGAATATGGCAACTAGATTGTACACATTTAGAAGGAAAAATTATCCTAGTAGCAGTTCATG
TAGCCAGTGGATATATAGAAGCAGAAGTTATTCCAGCAGAAACAGGACAGGAAACAGCATACTTTGTCTT
AAAATTAGCAGGAAGATGGCCAGTAAAAATAATACATACAGACAATGGCAGCAATTTCACCAGTACTGCG
GTTAAGGCTGCCTGTTGGTGGGCAGGGATCAAGCAGGAATTTGGCATTCCCTACAATCCCCAAAGTCAAG
GAGTAGTAGAATCTATGAATAAACAATTAAAGCAAACTATAGGACAGGTAAGAGATCAAGCTGAACATCT
TAAGACAGCAGTACAAATGGCAGTATTCATCCACAATTTTAAAAGAAAAGGGGGGATTGGGGGGTACAGT
GCAGGGGAAAGAATAATAGACATAATAGCAACAGACATACAAACTAAAGAATTACAAAAACAAATTATAA
AAATTCAAAATTTTCGGGTTTATTACAGAGACAGCAGAGATCCAATTTGGAAAGGACCAGCAAAACTACT
CTGGAAAGGTGAAGGGGCAGTGGTAATACAGGACAATAACGATATAAAAGTAGTACCAAGAAGAAAAGCA
AAGATCATTAGGGATTATGGAAAACAGATGGCAGGTGATGATTGTGTGGCAAGTAGACAGGATGAGGATT
AG
我需要这个网页上的所有信息，但有几个菌株。
如果我改变菌株 ID 和 DNA 位置，我想我可以复制所有这些 DNA 序列。
我尝试从将文本从网页复制并粘贴到 txt 文件或 csv 文件
import requests
url = 'https://www.ncbi.nlm.nih.gov/nuccore/AF061641.1?report=fasta&log$=seqview&format=text&from=192&to=1684'
data = requests.get(url)
with open('file.txt','w') as out_f:
out_f.write(str(data.text.encode('utf-8')))
但我得到了这个
b'<?xml version="1.0" encoding="utf-8"?>\n<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">\n<html xmlns="http://www.w3.org/1999/xhtml">\n <head xmlns:xi="http://www.w3.org/2001/XInclude"><meta http-equiv="Content-Type" content="text/html; charset=utf-8" />\n <!-- meta -->\n <meta name="robots" content="index,nofollow,noarchive" />\n<meta name="ncbi_app" content="entrez" /><meta name="ncbi_db" content="nuccore" /><meta name="ncbi_report" content="fasta" /><meta name="ncbi_format" content="text" /><meta name="ncbi_pagesize" content="20" /><meta name="ncbi_sortorder" content="default" /><meta name="ncbi_pageno" content="1" /><meta name="ncbi_resultcount" content="1" /><meta name="ncbi_op" content="retrieve" /><meta name="ncbi_pdid" content="fasta" /><meta name="ncbi_sessionid" content="CE8C1A31EBE79081_2023SID" /><meta name="ncbi_uidlist" content="3403216" /><meta name="ncbi_filter" content="all" /><meta name="ncbi_stat" content="false" /><meta name="ncbi_hitstat" content="false" />\n\n \n <!-- title -->\n <title>HIV-1 isolate HH8793 clone 12.1 from Finland, complete genome - Nucleotide - NCBI</title>\n \n <!-- Common JS and CSS -->\n \n\t\t<script type="text/javascript">\n\t\t var ncbi_startTime = new Date();\n\t\t</script>\n\t\t<style>.async-hide { opacity: 0 !important} </style><script type="text/javascript" src="/core/assets/kis/dist/kis_ga_nuc_protein.js"></script><script type="text/javascript" src="https://static.pubmed.gov/core/jig/1.14.8/js/jig.min.js"></script>\n\t\t\t\t\n\t\t\t<script type="text/javascript" src="/core/ajax_loader/2.1/js/loadingbar.js"></script> \n \t<script type="text/javascript" src="/core/ajax_loader/2.1/js/contentLoader.js"></script>\n \t<link type="text/css" rel="stylesheet" href="/core/ajax_loader/2.1/css/loadingbar.css" />\n\t\t\t\n\t\t\t \n \n <link xmlns="http://www.w3.org/1999/xhtml" type="text/css" rel="stylesheet" href="//static.pubmed.gov/portal/portal3rc.fcgi/4187342/css/3881636/3579733.css" xml:base="http://127.0.0.1/sites/static/header_footer/" /> \n<link rel="shortcut icon" href="//www.ncbi.nlm.nih.gov/favicon.ico" /><meta name="ncbi_phid" content="CE8C1A31EBE6A9A10000000007E703EB.m_11" /><script type="text/javascript"><!--\nvar ScriptPath = \'/portal/\';\nvar objHierarchy = 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现在，我有所有菌株 ID 和位置范围，所以我需要复制这些 DNA 序列进行分析。
先感谢您
解决方案
这是您遇到的可快速纠正的错误。
您所做的基本上称为“Web Scraping”并获得所需的输出，您需要使用另一个包，如“Selenium”或“BeautifulSoup”。
我个人更喜欢 BeautifulSoup 而不是 Selenium，但这只是我的意见。这是一个 BeautifulSoup 实现。
from bs4 import BeautifulSoup
import requests
url = 'https://www.ncbi.nlm.nih.gov/nuccore/AF061641.1?report=fasta&log$=seqview&format=text&from=192&to=1684'
data = requests.get(url)
content = BeautifulSoup(data.content,"html.parser")
这就是一些成品的样子。“内容”变量现在将具有网页的完整 html 结构。剩下要做的就是在 html 结构中找到所需的信息并从中提取。
只剩下一点时间来完成代码，但我无法帮助并完全完成代码，因为我没有所有必需的参数，但你应该能够在阅读 web 抓取大约半小时后完成剩下的部分。
希望这有帮助！:)
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