Hi, I have many lists of EC numbers, that look like this:
ec:1.13.11.1; ec:1.14.12.10; ec:1.14.12.13; ec:1.14.13.50; ec:1.21.1.2; ec:1.3.1.25; ec:1.3.1.32; ec:3.1.1.45; ec:3.5.5.6; ec:3.8.1.7; ec:4.2.1.84; ec:5.5.1.1; ec:5.5.1.7; ec:6.2.1.33
And I'd like to download all the corresponding sequences from UniProt (it could be another database, but I like the annotation quality of SwissProt). I've looking for a way to batch download these, but I couldn't find any. It's really easy to do it via website, but it gets annoying when you have many EC numbers.
Is there any script or tool to do it automatically?
Thank you!
I found a way to do with BASH:
while read line; do
wget "http://www.uniprot.org/uniprot/?sort=&desc=&compress=no&query="$line"&fil=&format=fasta&force=yes"
done < "list.txt"
But I don't know if there's another, more efficient way to do it
Yes, this RESTful programmatic access is an approach we would have recommended at the UniProt helpdesk. See also
in case you hadn't noticed these documents yet.
I think you may find useful infos here Convert kegg ids to uniprot ids
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