CODEWITHSUNDEEP
pythonpandasbeautifulsoup
Slowat_Kela
Slowat_Kela

Reputation: 1511

Why is there a table when I scrape with beautifulSoup, but not pandas

Trying to scrape entries on this page into a tab-delimited format (mainly pulling out the sequence and UniProt accession number).

When I run:

url = 'www.signalpeptide.de/index.php?sess=&m=listspdb_bacteria&s=details&id=1000&listname='    
table = pd.read_html(url)
print(table)

I get:

Traceback (most recent call last):
  File "scrape_signalpeptides.py", line 7, in <module>
    table = pd.read_html(url)
  File "/Users/ION/anaconda3/lib/python3.7/site-packages/pandas/io/html.py", line 1094, in read_html
    displayed_only=displayed_only)
  File "/Users/ION/anaconda3/lib/python3.7/site-packages/pandas/io/html.py", line 916, in _parse
    raise_with_traceback(retained)
  File "/Users/ION/anaconda3/lib/python3.7/site-packages/pandas/compat/__init__.py", line 420, in raise_with_traceback
    raise exc.with_traceback(traceback)
ValueError: No tables found

So then I tried the beautiful soup method:

import requests
import pandas as pd
import json
from pandas.io.json import json_normalize
from bs4 import BeautifulSoup

url = 'http://www.signalpeptide.de/index.php?sess=&m=listspdb_bacteria&s=details&id=1000&listname='
res = requests.get(url)
soup = BeautifulSoup(res.content, "lxml")
print(soup)

and I can see there is data there. Does anyone have an idea why can I not parse this page with pandas.read_html? Edit 1: Based on suggestion below I ran this:

from bs4 import BeautifulSoup
import requests
s = requests.session()
s.headers['User-Agent'] = 'Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_2) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/34.0.1847.131 Safari/537.36'
res = s.get('https://www.signalpeptide.de/index.php?sess=&m=listspdb_bacteria&s=details&id=2&listname=')
print(res)

....I changed the URL to all of www,http and https; and for all I get errors relating to connection errors, e.g.

urllib3.exceptions.NewConnectionError: <urllib3.connection.VerifiedHTTPSConnection object at 0x1114f0898>: Failed to establish a new connection: [Errno 61] Connection refused

urllib3.exceptions.MaxRetryError: HTTPSConnectionPool(host='www.signalpeptide.de', port=443): Max retries exceeded with url: /index.php?sess=&m=listspdb_bacteria&s=details&id=2&listname= (Caused by NewConnectionError('<urllib3.connection.VerifiedHTTPSConnection object at 0x1114f0898>: Failed to establish a new connection: [Errno 61] Connection refused'

ConnectionRefusedError: [Errno 61] Connection refused

Upvotes: 2

Views: 597

Answers (3)

ravinder kumar
ravinder kumar

Reputation: 1

If you find table in soup but not while parsing using read_html, the reason could be that specific table is hidden. So you can use below snap:

import bs4
import pandas

# open file available at file_path
with open(file_path, encoding='utf-8') as fobj:
    soup = bs4.BeautifulSoup(fobj, 'html5lib')

# provide your table's class_name
tables = soup.find_all('table', attrs={'class': 'class_name'})


for table in tables:
    filtered_lines = list()
    data_frame = pandas.read_html(str(table), displayed_only=False)

Note: Option displayed_only in read_html will allow you to parse hidden tables also.

Upvotes: 0

Reedinationer
Reedinationer

Reputation: 5774

The url variable is different between your scripts.

Side by side for comparison:

url = 'www.signalpeptide.de/index.php?sess=&m=listspdb_bacteria&s=details&id=1000&listname=' # pandas
url = 'http://www.signalpeptide.de/index.php?sess=&m=listspdb_bacteria&s=details&id=1000&listname=' # BeautifulSoup

I suspect that the http:// bit is important for pandas to recognize it as a URL as opposed to the HTML itself. After all, pandas.read_html interprets the argument dynamically as described in the documentation

A URL, a file-like object, or a raw string containing HTML. Note that lxml only accepts the http, ftp and file url protocols. If you have a URL that starts with 'https' you might try removing the 's'.

Where specifically the part If you have a URL that starts with 'https' you might try removing the 's' leads me to believe the http:// is important for it to know it is a link as opposed to a "file-like object" or raw HTML.

If the error is exceeding max retries, you probably need to implement a requests.session with headers. A previous code I've done with this looked like:

import requests

s = requests.session()
s.headers['User-Agent'] = 'Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_2) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/34.0.1847.131 Safari/537.36'

res = s.get('your_url')

At which point you should be able to interpret the res object the same way you would a normal requests.get() object (you can call methods like .text and such). I'm not too sure how the s.headers work, it was just from another SO post that I copied and fixed my script!

update

Part of the error message from your last code block is

ssl.CertificateError: hostname 'www.signalpeptide.de' doesn't match either of 'www.kg13.art', 'www.thpr.net'

Which means their SSL certificate is not valid, and https probably won't work because the host cannot be verified. I adjusted it to http and to show the resulting HTML:

from bs4 import BeautifulSoup
import requests
s = requests.session()
s.headers['User-Agent'] = 'Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_2) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/34.0.1847.131 Safari/537.36'
res = s.get('http://www.signalpeptide.de/index.php?sess=&m=listspdb_bacteria&s=details&id=2&listname=')
print(res.text)

Results in:

C:\Users\rparkhurst\PycharmProjects\Workspace\venv\Scripts\python.exe C:/Users/rparkhurst/PycharmProjects/Workspace/new_workspace.py
<!doctype html>
<html class="no-js" lang="en">
<head>
 <meta charset="utf-8"/>
 <meta name="viewport" content="width=device-width, initial-scale=1.0"/>
 <title>Signal Peptide Database</title>
 <link rel="stylesheet" href="css/foundation.css">
 <link href='http://cdnjs.cloudflare.com/ajax/libs/foundicons/3.0.0/foundation-icons.css' rel='stylesheet' type='text/css'>
 <link href="css/custom.css" rel="stylesheet" type="text/css">
</head>
<body>
<div class="top-bar">
 <div class="row">
  <div class="top-bar-left">
   <div class="top-bar-title">
    <span data-responsive-toggle="responsive-menu" data-hide-for="medium">
     <span class="menu-icon dark" data-toggle></span>
    </span>
    <a href="./"><img src="img/logo.jpg" alt="logo" id="logo"></a>
   </div>
  </div>
 <div class="top-bar-right">
  <h3 class="hide-for-small">Signal Peptide Website</h3>
  <div id="responsive-menu">
   <ul class="dropdown menu" data-dropdown-menu>
    <li><a href="./?m=myprotein">Search my Protein</a></li>
    <li><a href="./?m=searchspdb">Advanced Search</a></li>
    <li><a href="./?m=listspdb">Database Search</a></li>
    <li><a href="./?m=references">References</a></li>
    <li><a href="./?m=hints">Hints</a></li>
    <li><a href="./?m=links">Links</a></li>
    <li><a href="./?m=imprint">Imprint</a></li>
    </ul>
   </div>
  </div>
 </div>
</div>
<br>
<div class="row columns">
<div class="content">
<span class="headline">Signal Peptide Database - Bacteria</span><br><br>
<form action="index.php" method="post"><input type="hidden" name="sess" value="">
<input type="hidden" name="m" value="listspdb_bacteria">
<input type="hidden" name="id" value="2">
<input type="hidden" name="a" value="save">
<table cellspacing="2" cellpadding="2" border="0">
<tr>
<td colspan="3" class="tabhead">&nbsp;<b>Entry Details</b></td></tr>
<tr height="23">
<td class="highlight">ID</td>
<td class="highlight" width="50">&nbsp;</td>
<td class="highlight">2</td>
</tr>
<tr height="23">
<td class="highlight">Source Database</td>
<td class="highlight" width="50">&nbsp;</td>
<td class="highlight">UniProtKB/Swiss-Prot</td>
</tr>
<tr height="23">
<td class="highlight">UniProtKB/Swiss-Prot Accession Number</td>
<td class="highlight" width="50">&nbsp;</td>
<td class="highlight">A6X5T5&nbsp;&nbsp;&nbsp;&nbsp;(Created: 2009-01-20 Updated: 2009-01-20)</td>
</tr>
<tr height="23">
<td class="highlight">UniProtKB/Swiss-Prot Entry Name</td>
<td class="highlight" width="50">&nbsp;</td>
<td class="highlight"><a target="_new" class="bblack" href="http://www.uniprot.org/uniprot/14KL_OCHA4">14KL_OCHA4</a></td>
</tr>
<tr height="23">
<td class="highlight">Protein Name</td>
<td class="highlight" width="50">&nbsp;</td>
<td class="highlight">Lectin-like protein BA14k</td>
</tr>
<tr height="23">
<td class="highlight">Gene</td>
<td class="highlight" width="50">&nbsp;</td>
<td class="highlight">Oant_3884</td>
</tr>
<tr height="23">
<td class="highlight">Organism Scientific</td>
<td class="highlight" width="50">&nbsp;</td>
<td class="highlight">Ochrobactrum anthropi (strain ATCC 49188 / DSM 6882 / NCTC 12168)</td>
</tr>
<tr height="23">
<td class="highlight">Organism Common</td>
<td class="highlight" width="50">&nbsp;</td>
<td class="highlight"></td>
</tr>
<tr height="23">
<td class="highlight">Lineage</td>
<td class="highlight" width="50">&nbsp;</td>
<td class="highlight">Bacteria<br>&nbsp;&nbsp;Proteobacteria<br>&nbsp;&nbsp;&nbsp;&nbsp;Alphaproteobacteria<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Rhizobiales<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Brucellaceae<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Ochrobactrum<br></td>
</tr>
<tr height="23">
<td class="highlight">Protein Length [aa]</td>
<td class="highlight" width="50">&nbsp;</td>
<td class="highlight">151</td>
</tr>
<tr height="23">
<td class="highlight">Protein Mass [Da]</td>
<td class="highlight" width="50">&nbsp;</td>
<td class="highlight">17666</td>
</tr>
<tr height="23">
<td class="highlight">Features</td>
<td class="highlight" width="50">&nbsp;</td>
<td class="highlight"><table><tr><td><b>Type</b></td><td><b>Description</b></td><td><b>Status</b></td><td><b>Start</b></td><td><b>End</b></td></tr><tr><td class="w"><font color="red">signal peptide</font>&nbsp;&nbsp;&nbsp;</td><td class="w"><font color="red"></font>&nbsp;&nbsp;&nbsp;</td><td class="w"><font color="red">potential</font>&nbsp;&nbsp;&nbsp;</td><td class="w"><font color="red">1</font>&nbsp;&nbsp;&nbsp;</td><td class="w"><font color="red">26</font></td></tr><tr><td class="w"><font color="blue">chain</font>&nbsp;&nbsp;&nbsp;</td><td class="w"><font color="blue">Lectin-like protein BA14k</font>&nbsp;&nbsp;&nbsp;</td><td class="w"><font color="blue"></font>&nbsp;&nbsp;&nbsp;</td><td class="w"><font color="blue">27</font>&nbsp;&nbsp;&nbsp;</td><td class="w"><font color="blue">151</font></td></tr><tr><td class="w"><font color="green">transmembrane region</font>&nbsp;&nbsp;&nbsp;</td><td class="w"><font color="green"></font>&nbsp;&nbsp;&nbsp;</td><td class="w"><font color="green">potential</font>&nbsp;&nbsp;&nbsp;</td><td class="w"><font color="green">83</font>&nbsp;&nbsp;&nbsp;</td><td class="w"><font color="green">103</font></td></tr></table></td>
</tr>
<tr height="23">
<td class="highlight">SP Length</td>
<td class="highlight" width="50">&nbsp;</td>
<td class="highlight">26</td>
</tr>
<tr valign="top">
<td class="highlight"></td><td class="highlight" width="50">&nbsp;</td><td class="highlightfixed">----+----1----+----2----+----3----+----4----+----5</td></tr><tr valign="top">
<td class="highlight">Signal Peptide</td><td class="highlight" width="50">&nbsp;</td><td class="highlightfixed">MNIFKQTCVGAFAVIFGATSIAPTMA</td></tr><tr valign="top">
<td class="highlight">
Sequence</td><td class="highlight" width="50">&nbsp;</td><td class="highlightfixed"><font color="red">MNIFKQTCVGAFAVIFGATSIAPTMA</font><font color="blue">APLNLERPVINHNVEQVRDHRRPP<br>RHYNGHRPHRPGYWNGHRGYRHYRHGYRRYND</font><font color="green">GWWYPLAAFGAGAIIGGA<br>VSQ</font><font color="blue">PRPVYRAPRMSNAHVQWCYNRYKSYRSSDNTFQPYNGPRRQCYSPYS<br>R</td></tr><tr valign="top">
<td class="highlight">
Original</td><td class="highlight" width="50">&nbsp;</td><td class="highlightfixed">MNIFKQTCVGAFAVIFGATSIAPTMAAPLNLERPVINHNVEQVRDHRRPP<br>RHYNGHRPHRPGYWNGHRGYRHYRHGYRRYNDGWWYPLAAFGAGAIIGGA<br>VSQPRPVYRAPRMSNAHVQWCYNRYKSYRSSDNTFQPYNGPRRQCYSPYS<br>R</td></tr><tr valign="top">
<td class="highlight"></td><td class="highlight" width="50">&nbsp;</td><td class="highlightfixed">----+----1----+----2----+----3----+----4----+----5</td></tr><tr height="23">
<td class="highlight">Hydropathies</td>
<td class="highlight" width="50">&nbsp;</td>
<td class="highlight"><a href="./hydropathy/hydropathy.php?id=2" target="_new"><img src="./hydropathy/hydropathy.php?id=2" border="0" width="600"></a></td>
</tr>
<tr>
<td colspan="3" class="nohighlight">&nbsp;</td>
</tr>
<tr>
<td colspan="3" class="tabhead" align="center"><input class="button" type="reset" value="Back" onclick="history.back(-1);"></td>
</tr>
</table>
</form></div>
<hr>
<div class="row">
 <div class="small-4 medium-3 columns"><a href="./">Home</a>&nbsp;&nbsp;&nbsp;<a href="./?m=imprint">Imprint</a></div>
 <div class="small-8 medium-9 columns text-right">
 &copy; 2007-2017 <a href="mailto:[email protected]">Katja Kapp</a>, Dresden &amp; <a href="http://www.thpr.net/">thpr.net e. K.</a>, Dresden, Germany, last update 2010-06-11
 </div>
</div><br><br>
<script src="js/vendor/jquery.js"></script>
<script src="js/foundation.js"></script>
<script>
 $(document).foundation();
</script>
</body>
</html>


Process finished with exit code 0

So it seems this solves your issues.

Upvotes: 1

Jack Fleeting
Jack Fleeting

Reputation: 24940

Try this:

from bs4 import BeautifulSoup as bs
import requests
import pandas as pd

url = 'http://www.signalpeptide.de/index.php?sess=&m=listspdb_bacteria&s=details&id=1000&listname='    
r = requests.get(url)

tabs = soup.find_all('table')
my_tab = pd.read_html(str(tabs[0]))
my_tab[0].drop(my_tab[0].columns[1], axis=1).drop(my_tab[0].index[0])

This should output the main table on the page beginning with 'id 1000'.

Upvotes: 1

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