Open rafwiewiora opened 8 years ago
Yikes!
Does ensembler offer a way to retrieve by accession number?
For reproducibility, we can still let you search by uniprot ID but it could generate an input file where these are translated into accession numbers.
Yep, definitely use accession numbers if you need to use persistent IDs.
The --query
argument is passed directly to the UniProt search API, which
allows you to search by accession number as follows:
--query 'accession:Q9NQR1'
http://ensembler.readthedocs.io/en/latest/examples.html#example-using-the-main-pipeline-functions
On Mon, Jun 27, 2016 at 8:35 PM, John Chodera notifications@github.com wrote:
Yikes!
Does ensembler offer a way to retrieve by accession number?
For reproducibility, we can still let you search by uniprot ID but it could generate an input file where these are translated into accession numbers.
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Thanks Danny, exactly what I needed!
A word of caution about using Uniprot IDs.
I have come back to my Ensembler set-up from a few months ago, to find that:
no longer work. It's already not reproducible!
Uniprot appears to have changed the ID from SETD8_HUMAN to KMT5A_HUMAN. I've now learnt that I should be using the accession number (AC), not IDs - ACs never change (http://www.uniprot.org/help/difference_accession_entryname).