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?
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1If you want to summon Darth Vader riding Donald Trump to fight Velociraptors with lasers strapped to their heads, there's definitely a way to do that in Python. What code do you have?Enzo Ferber– Enzo Ferber2020-03-25 04:34:27 +00:00Commented Mar 25, 2020 at 4:34
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1 Answer
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)
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