[ensembl-dev] Getting introns

Andy Yates ayates at ebi.ac.uk
Wed Jun 6 09:38:02 BST 2012

Hi Ben,

There's an get_all_Introns() method available on the Transcript object. The Introns are generated on the fly from the Transcript's Exons. If you need all the unique Introns for a Gene then you'll have to start to do location comparisons but all Feature objects have an equals() and overlaps() method which should help you out



Andrew Yates                   Ensembl Core Software Project Leader
EMBL-EBI                       Tel: +44-(0)1223-492538
Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
Cambridge CB10 1SD, UK         http://www.ensembl.org/

On 5 Jun 2012, at 08:13, Benoît Ballester wrote:

> Hi, 
> I am looking at getting for each genes the list of Introns as features, well at least getting Introns with rank, start, end, strand informations.  I know that there ins't such a method as $gene->get_all_Introns() but I think I vaguely remember that someone mentioned it one day. 
> Could you please advice on how to get this list of introns, or better if you have already have a subroutine ;-)
> Thanks, 
> Ben 
> wx->f
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