[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 }) {
$count++;
if ($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,
Magali
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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