[Bioperl-l] Lineage from GB files

Surya Saha ss2489 at cornell.edu
Tue Jan 31 17:07:47 EST 2012


Small world :-)

On Tue, Jan 31, 2012 at 5:02 PM, Chris Fields <cjfields at illinois.edu> wrote:

> 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<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<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<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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>
>
>
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