[ensembl-dev] exon rank in transcript

mag mr6 at ebi.ac.uk
Fri Jul 25 14:52:36 BST 2014

Hi David,

I am afraid we do not provide a direct way to get this information from 
the exon.

If you know the transcript stable identifier for which you want the exon 
rank, you could use the following:

my $count = 0;
foreach my $exon (@{ $transcript->get_all_Exons }) {
   if ($exon->stable_id eq $input_exon->stable_id) {
     print "Found " . $exon->stable_id . " at rank $count\n";

I admit this is not an ideal way, we will look into implementing a rank 
function for the Exon object.
It would need the transcript as argument, working similarly to the 
current peptide method.

Hope that helps,

On 25/07/2014 14:36, David Salgado wrote:
> Dear developers,
> Is there a way, from an exon stable identifier, to get its rank within 
> a particular transcript using the Ensembl Core API , without comparing 
> start and end positions?
> Many thanks in advance for any tips,
> David
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