[ensembl-dev] Get transcripts for a given exon

[Kieron Taylor]

Dear Luke,

You have quite justifiably not noticed the TranscriptAdaptor->fetch_all_by_exon_stable_id() method. That is provided you have the Ensembl stable IDs…

You might do something like:

my $adaptor = $registry->get_adaptor($species,’core’,Transcript);
foreach my $exon (@list_of_exons) {
  my $transcripts = $adaptor->fetch_all_by_exon_stable_id($exon->stable_id);
  … act on transcript list here
}


Regards,

Kieron

Kieron Taylor PhD.
Ensembl Core senior software developer

EMBL, European Bioinformatics Institute

> On 4 Mar 2015, at 15:25, Luke Goodsell <Luke.Goodsell at ogt.com> wrote:
> 
> Hi,
> 
> I would like to be able to retrieve all the transcript objects to which a given exon object belongs. The only way that I can see, is to get all overlapping genes, get the transcripts for those genes, get the exons for those transcripts and check if the exon of interest is returned.
> 
> Is there a more elegant way that I've overlooked?
> 
> Kind regards,
> Luke
> 
> <winmail.dat>_______________________________________________
> Dev mailing list    Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/