[ensembl-dev] 5 prime UTR coordinates

[Nick Fankhauser]

Hi Andy

thanks for your helpful reply!

But when I try this example script, it only works on the first two
transcripts:

5' UTR 248790491-248790430 | 3' UTR 248789478-248789420
5' UTR 249120832-249119135 | 3' UTR 249106098-249104650
5' UTR 0-0 | 3' UTR 0-0

For the last one, it doesn't seem to work. Is this method maybe not
compatible with the current version of the API?

Yours,
Nick

On 09/03/12 16:55, Andy Yates wrote:
> 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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> 
> 
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