[Bioperl-l] Lineage from GB files

Adlai Burman adlai at refenestration.com
Wed Feb 1 16:43:37 EST 2012


Thanks, Surya.
I'll give it a shot.
Adlai
On Jan 31, 2012, at 10:49 PM, Surya Saha wrote:

> Hi Adlai,
> 
> It really depends on what items are present the Genbank/EMBL. You can use the NCBI Taxonomy database and Taxonomy modules in CPAN to identify the taxonomic hierarchy of an accession, for e.g., you can map the GI to Taxonomy ID and extract the taxonomy using Bio::LITE::Taxonomy::NCBI. 
> 
> Here's a script (not authored by me) on Github that might get you started.
> 
> -Surya
> 
> 
> On Fri, Jan 27, 2012 at 6:27 AM, Adlai Burman <adlai at refenestration.com> wrote:
> Does anyone know if there is a way to batch extract taxa such as class, order in Perl from, e/g/ genbank, EMBL records? I know that genus/species and some of the higher taxa are easy to parse from gb records but the interior are inconsistent strings (e.g. element x sometimes is a subclass and sometimes a family.
> Any help would really be appreciated.
> 
> Thanks.
> Adlai
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