CODEWITHSUNDEEP
pythonhtmlpandasbeautifulsoup
lmml
lmml

Reputation: 79

Possible to retain line breaks in pandas read_html when making data frame from html table?

I'm trying to convert a scraped HTML table into a dataframe in python using pandas read_html. The problem is that read_html brings in a column of my data without breaks, which makes the content of those cells hard to parse. In the original HTML, each "word" in the column is separated by a break. Is there a way to keep this formatting or otherwise keep the "words" separated when converting to a data frame?

import requests
from bs4 import BeautifulSoup
import pandas as pd

url="https://www.who.int/en/activities/tracking-SARS-CoV-2-variants/"
html_content = requests.get(url).text

# Parse the html content
soup = BeautifulSoup(html_content, "lxml")

voc_html = soup.find("table")

#convert to dataframe
voc_df = pd.read_html(str(voc_html))[0]

#retain list of variants
voc_list=voc_df['Pango lineages']

example from voc_list where separate items are smushed together: voc_list[1]

`B.1.351\xa0B.1.351.2B.1.351.3`

what I would like it to look like: B.1.3510 B.1.351.2 B.1.351.3 (or have each item on its own row)

excerpt from original html version which includes breaks:

<td style="width:13%;background-color:#69d4ef;text-align:left;vertical-align:middle;">Beta <br/></td><td style="width:12.9865%;background-color:#69d4ef;text-align:left;"><p>B.1.351 <br/>B.1.351.2<br/>B.1.351.3</p></td>

Thanks for any guidance!

Upvotes: 3

Views: 2674

Answers (1)

MDR
MDR

Reputation: 2670

Maybe...

import pandas as pd
import requests

url = r'https://www.who.int/en/activities/tracking-SARS-CoV-2-variants/'

page = requests.get(url)
table = pd.read_html(page.text.replace('<br />',' '))
df = table[0]

Outputs:

  WHO label               Pango lineages GISAID clade Nextstrain clade  \
0     Alpha                      B.1.1.7          GRY         20I (V1)   
1      Beta  B.1.351 B.1.351.2 B.1.351.3   GH/501Y.V2         20H (V2)   
2     Gamma              P.1 P.1.1 P.1.2   GR/501Y.V3         20J (V3)   
3     Delta          B.1.617.2 AY.1 AY.2    G/478K.V1              21A   

  Additional amino acid changes monitored* Earliest documented samples  \
0                          +S:484K +S:452R    United Kingdom, Sep-2020   
1                                  +S:L18F      South Africa, May-2020   
2                                  +S:681H            Brazil, Nov-2020   
3                                  +S:417N             India, Oct-2020   

                Date of designation  
0                       18-Dec-2020  
1                       18-Dec-2020  
2                       11-Jan-2021  
3  VOI: 4-Apr-2021 VOC: 11-May-2021 
    print(df)

Equally you could replace the <br /> with \n.

Upvotes: 8

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