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Uniprot API change #24

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yaccos opened this issue Jun 29, 2023 · 1 comment

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yaccos commented Jun 29, 2023 •

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From my understanding, Uniprot's web API has changed from the time autoPACMEN was created and I used it. For this reason the Uniprot ID -> Protein mass mapping no longer works (https://github.com/klamt-lab/autopacmen/blob/cb828391d4cbb17e50ba9752cc974d78775d836d/autopacmen/submodules/get_protein_mass_mapping.py#L116C8-L116C105). However, I one of my group members have come up with a suggested solution; this is: Replace

uniprot_query_url = f"https://www.uniprot.org/uniprot/?query={query}&format=tab&columns=id,mass"

with

uniprot_query_url = f"https://rest.uniprot.org/uniprotkb/search?query=accession:{query}&format=tsv&fields=accession,mass"

I have tested both approaches in the web browser and can confirm that the old query string does no longer work, whereas the newly suggested one does.

yaccos mentioned this issue

UniProt API Update #25

Merged

Member

Paulocracy commented Jul 6, 2023

Fixed thanks to @yaccos as per #25 :-)

Paulocracy closed this as completed

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