[ensembl-dev] $transcript->five_prime_utr

[Bert Overduin]

On Fri, Feb 4, 2011 at 7:47 PM, Ryan Giuliany <rgiuliany at bccrc.ca> wrote:
> Hi,
>
> I'm trying to determine if a position is in the 5' or 3' UTR of a
> transcript.  I've tried the following:
>
> my $slice_adaptor = $registry->get_adaptor( 'Human', 'Core', 'Slice' );
> ...
> my $slice = $slice_adaptor->fetch_by_region( 'chromosome', "$chr", $pos,
> $pos);
>    my @transcripts = @{$slice->get_all_Transcripts};
>    foreach my $transcript (@transcripts) {
>        $transcript = $transcript->transform('chromosome');
>        my $fputr = $transcript->five_prime_utr;
>        my $tputr = $transcript->three_prime_utr;
>        if ($pos >= $fputr->start && $pos <= $fputr->end){
> ...
>
> when running this script I get the following error:
>
> Can't locate object method "start" via package "Bio::Seq"
>
> Looking at the docs for Bio::Seq, Seq objects do indeed have a start()
> method.

Where did you see that? In the Pdoc for the Bio::Seq object I don't
see a start method ....

>
> Any tips?
>
> Thanks!
> Ryan
>
>
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-- 
Bert Overduin, Ph.D.
PANDA Coordination & Outreach

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

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