[ensembl-dev] 5 prime UTR coordinates

[Andy Yates]

Hi Nick,

The method five_prime_utr() returns a Bio::Seq object & is meant to be a way of accessing the sequence data not the coordinates. Take a look at this script hosted at GitHub's gist:

https://gist.github.com/1237394

It should give you all the information you need to extract the coordinates you need

All the best,

Andy

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 9 Mar 2012, at 10:51, Nick Fankhauser wrote:

> Hi!
> 
> I'm trying to get the coordinates of the 5' UTRs of all transcripts of a
> given gene. But the "start" method can't be located for the UTR object.
> Is there a different approach that makes it possible to retrieve the
> UTR's coordinates?
> 
> This is what I tried:
> 
> foreach my $transcript ( @{ $gene->get_all_Transcripts() } ) {
> 	my $utr5	= $transcript->five_prime_utr();
> 	next if not defined $utr5;
> 	my $start5      = $utr5->start();
> 	my $end5        = $utr5->end();
> }
> 
> Thanks!
> 
> 
> Nick Fankhauser
> ---
> http://www.ccspmd.ethz.ch/people/fniklaus
> 
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