CODEWITHSUNDEEP
python
An Ignorant Wanderer
An Ignorant Wanderer

Reputation: 1632

Download data from online database in python script

I am trying to download data from UniProt using Python from within a script. If you follow the previous link, you will see a Download button, and then the option of choosing the format of the data. I would like to download the Excel format, compressed. Is there a way to do this within a script?

Upvotes: 0

Views: 598

Answers (1)

Boris Lipschitz
Boris Lipschitz

Reputation: 1641

You can easily see the URL for that if you monitor it in the Firefox "netowork" tab or equivalent. For this page it seems to be https://www.uniprot.org/uniprot/?query=*&format=xlsx&force=true&columns=id,entry%20name,reviewed,protein%20names,genes,organism,length&fil=organism:%22Homo%20sapiens%20(Human)%20[9606]%22%20AND%20reviewed:yes&compress=yes. You should be able to download it using requests or any similar lib.

Example:

import requests

url = "https://www.uniprot.org/uniprot/?query=*&format=xlsx&force=true&columns=id,entry%20name,reviewed,protein%20names,genes,organism,length&fil=organism:%22Homo%20sapiens%20(Human)%20[9606]%22%20AND%20reviewed:yes&compress=yes"
with open("downloaded.xlsx.gz", "wb") as target:
    target.write(requests.get(url).content)

Upvotes: 1

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