[ensembl-dev] $transcript->five_prime_utr

Ryan Giuliany rgiuliany at bccrc.ca
Fri Feb 4 19:47:44 GMT 2011


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", $pos, 
     my @transcripts = @{$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() 

Any tips?


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