[ensembl-dev] Core API : Exon is_coding method

[Premanand Achuthan]

Hi Bhavana

Thanks for pointing it out. We will get it fixed in release 91.

Best Regards
Prem (Ensembl Core Team)

On 06/10/2017 09:49, Bhavana Harsha wrote:
> Hello,
>
> I’m looking at the exons for the human gene CEBPA ENST00000498907.2.
> http://grch37.ensembl.org/Homo_sapiens/Transcript/Exons?db=core;g=ENSG00000245848;r=19:33790840-33793470;t=ENST00000498907
>
> It turns out that it has one exon (with UTR sequences on either side 
> of it) and it is protein-coding.
>
> However, when I use the API like this:
>
> my $transcript = 
> $transcript_adaptor->fetch_by_stable_id(‘ENST00000498907’);
> my $exon = $transcript->get_all_Exons()->[0];
> $exon->is_coding($transcript);
>
> returns 0.
>
> This is because neither of the conditions in the $exon->is_coding() 
> method evaluate to true.
>
> if ($transcript->coding_region_start < $self->start && $self->start < 
> $transcript->coding_region_end) { return 1; }
> if ($transcript->coding_region_end > $self->end && $self->end > 
> $transcript->coding_region_start) { return 1; }
>
> I realise this happens for transcripts which have only one exon (e.g. 
> FOXL2).
>
> Do you think that the exon->start and exon->end should be changed to 
> exon->coding_region_start and exon->coding_region_end respectively?
>
> I’m using API version 89.
>
>
>
> Regards,
> Bhavana
>
>
>
>
>
>
> ---------------------------------------------
> Bhavana Harsha
> Bioinformatician
> COSMIC
> Wellcome Trust Sanger Institute
> Hinxton, UK
> CB10 1SA
>
>
>
>
>
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