从html文件python中提取文本

Question

I have write down a code to extract some text from the html file, This code extract the requested line from the webpage now I want to extract sequence data.Unfortunately I am not able to extract the text, its showing some error.

import urllib2
from HTMLParser import HTMLParser
import nltk 
from bs4 import BeautifulSoup

# Proxy information were removed  
# from these two lines 

proxyOpener = urllib2.build_opener(proxyHandler)
urllib2.install_opener(proxyOpener)

response = urllib2.urlopen('http://tuberculist.epfl.ch/quicksearch.php?gene+name=Rv0470c')

################## BS Block ################################

soup = BeautifulSoup(response)
text = soup.get_text()
print text 

##########################################################

html = response.readline()

for l in html:
    if "|Rv0470c|" in l:
        print l       # code is running successfully till here 

raw = nltk.clean_html(html) 
print raw

How can I run this code successfully? I have already checked all the available threads and solution, but nothing is working.

i want to extract this part:

M. tuberculosis H37Rv|Rv0470c|pcaA
MSVQLTPHFGNVQAHYDLSDDFFRLFLDPTQTYSCAYFERDDMTLQEAQIAKIDLALGKLNLEPGMTLLDIGCGWGATMRRAIEKYDVNVVGLTLSENQAGHVQKMFDQMDTPRSRRVLLEGWEKFDEPVDRIVSIGAFEHFGHQRYHHFFEVTHRTLPADGKMLLHTIVRPTFKEGREKGLTLTHELVHFTKFILAEIFPGGWLPSIPTVHEYAEKVGFRVTAVQSLQLHYARTLDMWATALEANKDQAIAIQSQTVYDRYMKYLTGCAKLFRQGYTDVDQFTLEK

Answer 1

i am able to extract desired text after writing down this code: which works without any dependencies accept "urllib2" and for my case it works like a charm.

import urllib2

httpProxy = {'username': '------', '-----': '-------', 'host': '------', 'port': '-----'}
proxyHandler = urllib2.ProxyHandler({'http': 'http://'+httpProxy['username']+':'+httpProxy['password']+'@'+httpProxy['host']+':'+httpProxy['port']})
proxyOpener = urllib2.build_opener(proxyHandler)
urllib2.install_opener(proxyOpener)



response = urllib2.urlopen('http://tuberculist.epfl.ch/quicksearch.php?gene+name=Rv0470c')

html = response.readlines()

f = open("/home/zebrafish/Desktop/output.txt",'w')


for l in html:
    if "|Rv0470c|" in l:
        l =  l.split("</small>")[0].split("<TR><TD><small style=font-family:courier>")[1]
        l = l.split("<br />")
        ttl =  l[:1]
        seq =  "".join(l[1:])
        f.write("".join(ttl))
        f.write(seq)
f.close()

Answer 2

I'm not quite sure about what exactly you are requesting as a whole, but here's my ad hoc take on your problem (similar to yours actually) which does retrieve the part of the html you request. Maybe you can get some ideas. (adjust for Python2)

import requests
from bs4 import BeautifulSoup

url = 'http://tuberculist.epfl.ch/quicksearch.php?gene+name=Rv0470c'
r = requests.get(url)
html = r.content
soup = BeautifulSoup(html, "lxml")
for n in soup.find_all('tr'):
    if "|Rv0470c|" in n.text:
        nt = n.text
        while '\n' in nt:
            nt.replace('\n','\t')
        nt=nt.split('\t')
        nt = [x for x in nt if "|Rv0470c|" in x][0].strip()  
        print (nt.lstrip('>'))