[Bioperl-l] extract information with Bio::DB::GFF3 from gff3 file

Scott Cain cain.cshl at gmail.com
Wed Jul 18 09:10:40 EDT 2007


Hi Xianran Li,

Assuming $gene is a Bio::DB::GFF::Feature object (there is no such thing
as Bio::DB::GFF3), then you can use the attributes method to get
anything in the ninth column:

  my ($name) = $gene->attributes('Name');

The parenthesis are needed around $name because the attributes method
returns a list and the parens capture the first item of the list into
$name.

Scott


On Wed, 2007-07-18 at 13:55 +0800, Xianran Li wrote:
> Hi,
> 
> I want to extract some infomation  from the gff3 file like:
> 
> 12001 . gene 854759 857385 . - . ID=12001.t00153;Name=receptor kinase ORK10, putative
>    
> The gene position can be reterived as $gene->start, but how can I get the annotation infomatin (receptor kinase ORK10) ?
> 
> Thanks for your help.
> 
> 
> Xianran Li
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                         cain at cshl.edu
GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
Cold Spring Harbor Laboratory
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