I am trying to access the sequence on this webpage:
https://www.ncbi.nlm.nih.gov/protein/EGW15053.1?report=fasta
The sequence is stored under the div class="seq gbff". Each line is stored under
<span class='ff_line' id='gi_344258949_1"> *line 1 of sequence* </span>
When I try to search for the spans containing the sequence, beautiful soup returns None
. Same problem when I try to look at the children or content of the div
above the spans
.
Here is the code:
import requests
import re
from bs4 import BeautifulSoup
# Create a variable with the url
url = 'https://www.ncbi.nlm.nih.gov/protein/EGW15053.1?report=fasta'
# Use requests to get the contents
r = requests.get(url)
# Get the text of the contents
html_content = r.text
# Convert the html content into a beautiful soup object
soup = BeautifulSoup(html_content, 'html.parser')
div = soup.find_all('div', attrs={'class', 'seq gbff'})
for each in div.children:
print(each)
soup.find_all('span', aatrs={'class', 'ff_line'})
Neither method works and I'd greatly appreciate any help :D
This page uses JavaScript to load data
With DevTools
in Chrome/Firefox I found this url and there are all <span>
https://www.ncbi.nlm.nih.gov/sviewer/viewer.fcgi?id=344258949&db=protein&report=fasta&extrafeat=0&fmt_mask=0&retmode=html&withmarkup=on&tool=portal&log $=seqview&maxdownloadsize=1000000
Now hard part. You have to find this url in HTML because different pages will use different arguments in url. Or you have to compare few urls and find schema so you could generate this url manually.
EDIT: if in url you change retmode=html
to retmode=xml
then you get it as XML
. If you use retmode=text
then you get it as text without HTML
tags. retmode=json
doesn't works.
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