[Bioperl-l] Lineage from GB files
ss2489 at cornell.edu
Tue Jan 31 16:49:37 EST 2012
It really depends on what items are present the Genbank/EMBL. You can use
the NCBI Taxonomy database and Taxonomy
CPAN to identify the taxonomic hierarchy of an accession, for e.g., you can
map the GI to Taxonomy ID and extract the taxonomy
Here's a script<https://github.com/hyphaltip/mobedac-fungi/blob/master/scripts/taxonomy.pl>
authored by me) on Github that might get you started.
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.
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