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

shalabh sharma shalabh.sharma7 at gmail.com
Thu Nov 10 15:12:09 EST 2011


Hi Anna,
           I think the thread you mentioned was started by me.
That time i wrote few scripts to map gi to taxa, after some time i found
some other efficient ways also. But recently 'Miguel Pignatelli' directed
to some Bio-LITE modules that are really helpful.

These are the modules he mentioned, i found them really easy to use and
very efficient.

Bio-LITE-Taxonomy-0.07
Bio-LITE-Taxonomy-NCBI-0.07
Bio-LITE-Taxonomy-NCBI-**Gi2taxid-0.04

Cheers
Shalabh

On Thu, Nov 10, 2011 at 3:01 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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-- 
Shalabh Sharma
Scientific Computing Professional Associate (Bioinformatics Specialist)
Department of Marine Sciences
University of Georgia
Athens, GA 30602-3636


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