[Bioperl-l] Lineage from GB files

Chris Fields cjfields at illinois.edu
Tue Jan 31 17:02:18 EST 2012


Funny, the script you link to is hyphaltip's, a.k.a. Jason Stajich :)

chris

On 01/31/2012 03:49 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<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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