[ensembl-dev] Exception when retrieving UTR feature from transcript...

[Andy Yates]

Hey Steve,

Very sorry about this. Yes you are right this code should be checking if there is a coordinate to convert. I've pushed the fix into HEAD and 71. If you update your API you should see a marked improvement. If you cannot update then your solution is the same as what I have had to do.

As for why I believe it's an issue with anything that doesn't have a translation (hence cannot have any kind of 5' or 3' feature). So you can continue in the same vein ATMO

All the best,

Andy

On 15 Apr 2013, at 12:21, Steve Moss <gawbul at gmail.com> wrote:

> Dear EnsEMBL Developers,
> 
> I receive the following exception when trying to retrieve a UTR feature from a transcript object. I have run the code on all 61 genomes of release 70 and I can only see issues with 5'-UTRs, but this is probably due to the data rather than the code and so the 3'-UTR code will likely also be affected too.
> 
> -------------------- EXCEPTION --------------------
> MSG: Must call with start/end
> STACK Bio::EnsEMBL::TranscriptMapper::cdna2genomic /Users/stevemoss/work/ensembl70/ensembl/modules/Bio/EnsEMBL/TranscriptMapper.pm:246
> STACK Bio::EnsEMBL::Transcript::cdna2genomic /Users/stevemoss/work/ensembl70/ensembl/modules/Bio/EnsEMBL/Transcript.pm:2002
> STACK Bio::EnsEMBL::Transcript::five_prime_utr_Feature /Users/stevemoss/work/ensembl70/ensembl/modules/Bio/EnsEMBL/Transcript.pm:1713
> STACK toplevel /Users/stevemoss/Dropbox/PhD/Research/Development/gcat/modules/GCAT/Scripts/get_intron_counts.pl:124
> Date (localtime)    = Mon Apr 15 11:08:05 2013
> Ensembl API version = 70
> ---------------------------------------------------
> 
> The problem seems to be that the five_ and three_prime_utr_Feature method code assigns my $cdna_coding = $self->cdna_coding_start(); (or cda_coding_end for the 3'-UTR) and then assumes a non undef value by then immediately calling my ($genomic_pos) = $self->cdna2genomic($cdna_coding, $cdna_coding);.
> 
> I worked around this by utilising the following code:
> 
> my $_5putr = defined $tr->cdna_coding_start ? $tr->five_prime_utr_Feature : undef;
> my $_3putr = defined $tr->cdna_coding_end ? $tr->three_prime_utr_Feature : undef;
> 
> Perhaps this is due to me parsing non-coding genes? I should perhaps just check the biotype before parsing any further? Any thoughts welcome :)
> 
> Kindest regards,
> 
> Steve Moss
> http://about.me/gawbul
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