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

Fields, Christopher J cjfields at illinois.edu
Thu Nov 10 15:23:14 EST 2011


Yes, these are probably wrappers around the gi2taxid, and taxonomy data; bioperl lacks the former, whereas the latter is handled by Bio::DB::Taxonomy (the 'flatfile' option).  I did something very similar locally, though I used Bio::DB::Taxonomy for the taxonomy lookups.

chris

On Nov 10, 2011, at 2:12 PM, shalabh sharma wrote:

> 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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