Opened 4 years ago

Closed 3 years ago

Last modified 3 years ago

#5056 closed enhancement (fixed)

Allow blastprotein command to use a UniProt name or id

Reported by: Tom Goddard Owned by: Zach Pearson
Priority: moderate Milestone:
Component: Sequence Version:
Keywords: Cc: Eric Pettersen, Elaine Meng
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description

Would be convenient if the blastprotein command could take as the first argument a uniprot name

blastprotein MELB_ECOLI

or uniprot id

blastprotein P02921

It could do a web query to fetch the sequence or just run command "open MELB_ECOLI from uniprot".

Change History (3)

comment:1 by Zach Pearson, 3 years ago

Resolution: → fixed
Status: assigned → closed

​This was implemented today, but there is now a little bit of duplicated processing in the AlphaFold and blastprotein bundles. Still, I tested the AlphaFold search command and it is working.

in reply to:  2 ; comment:2 by Tom Goddard, 3 years ago 

I'll look into making the alphafold search command not convert uniprot name to accession code if the blastprotein command is doing it.

in reply to:  3 ; comment:3 by Tom Goddard, 3 years ago 

The alphafold search command does not run the blastprotein command.   Instead it creates a BlastProteinJob directly using the explicit sequence.  So there is no   code duplication to remove unless we want the alphafold search command to invoke the blastprotein command.  I don't plan to do that.
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