[Bioperl-l] taxonomy db flatfile: get taxon from gi?

Bernd Web bernd.web at gmail.com
Thu Nov 10 15:51:13 EST 2011


Hi Anna,

Jason changed his example script from using hashes to using SQLite:
bp_classify_hits_kingdom - classify BLAST hits by taxonomic kingdom

See
https://github.com/bioperl/bioperl-live/blob/master/scripts/taxa/bp_classify_hits_kingdom.pl

It's an example script that shows how to do the tax to gi mapping for
blast reports.


Bernd

On Thu, Nov 10, 2011 at 9:01 PM, Anna Friedlander <anna.fr at gmail.com> wrote:
> Hi all
>
> Does anyone know if there is a way to get a Taxonomy node and/or
> taxonid from a gi number using the flatfile with taxonomy db?
>
> I have blast output that I want to append taxonomic information to. I
> have hundreds of thousands of items to do this for, so it's not
> practical to use entrez to query the NCBI database.
>
> I have the GI->taxid file from the taxonomy ftp but it's 3.2GB so I
> think much too large to put into a hash!
>
> This was also discussed in 2009:
> http://bioperl.org/pipermail/bioperl-l/2009-April/029751.html but I
> don't think there was a conclusion?
>
> Thanks for your help
> Anna Friedlander
>
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