From 09251b693dd001425879ca7340c2ed2527260f23 Mon Sep 17 00:00:00 2001 From: Jakob Peder Pettersen Date: Mon, 3 Jul 2023 18:45:29 +0200 Subject: [PATCH] Updated autoPACMEN with new UniProt API --- autopacmen/submodules/get_protein_mass_mapping.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/autopacmen/submodules/get_protein_mass_mapping.py b/autopacmen/submodules/get_protein_mass_mapping.py index 2d622b6..1c13cc6 100644 --- a/autopacmen/submodules/get_protein_mass_mapping.py +++ b/autopacmen/submodules/get_protein_mass_mapping.py @@ -113,7 +113,7 @@ def get_protein_mass_mapping(model: cobra.Model, project_folder: str, project_na # With 'OR', all given IDs are searched, and subsequently in this script, # the right associated masses are being picked. query = " OR ".join(batch) - uniprot_query_url = f"https://www.uniprot.org/uniprot/?query={query}&format=tab&columns=id,mass" + uniprot_query_url = f"https://rest.uniprot.org/uniprotkb/search?query=accession:{query}&format=tsv&fields=accession,mass" print(f"UniProt batch search for: {query}") # Call UniProt's API :-)