[ensembl-dev] 5 prime UTR coordinates

[Bert Overduin]

Hello Nick,

That is because the third transcript does not have any UTRs annotated:

http://www.ensembl.org/Homo_sapiens/Transcript/Summary?g=ENSG00000177275;r=1:248097071-248098057;t=ENST00000318244

Cheers,
Bert

On Tue, Mar 13, 2012 at 11:12 AM, Nick Fankhauser <lists at nyk.ch> wrote:
> 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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-- 
Bert Overduin, Ph.D.
Vertebrate Genomics Team

EMBL - European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton, Cambridge CB10 1SD
United Kingdom

http://www.ebi.ac.uk/~bert

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