[Bioperl-l] Lineage from GB files

Surya Saha ss2489 at cornell.edu
Tue Jan 31 16:49:37 EST 2012


Hi Adlai,

It really depends on what items are present the Genbank/EMBL. You can use
the NCBI Taxonomy database and Taxonomy
modules<http://search.cpan.org/search?query=taxonomy&mode=all> 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<https://github.com/hyphaltip/mobedac-fungi/blob/master/scripts/taxonomy.pl>
(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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