[ensembl-dev] Question regarding UTR retrieval from database

[Duarte Molha]

Thanks Kieron

I understand your point of view... but I still think there is a case for a
couple of methods to be implemented in the transcript object:
@{$transcript->get_coding_regions} and
@{$transcript->get_noncoding_regions}

Both returning feature objects. Am I the only one to find these useful? I
hope not :)

Thanks

Duarte



=========================
     Duarte Miguel Paulo Molha
         http://about.me/duarte
=========================

On 16 April 2015 at 16:19, Kieron Taylor <ktaylor at ebi.ac.uk> wrote:

> Hi Duarte,
>
> The coordinates you’re getting back are pre-splicing. The method you’re
> calling is from the Transcript class, hence the response is with reference
> to that object. If you’re after exon coordinates, you should be attempting
> to work with exon objects, such as fetching the exons of the transcript and
> asking them for coding_region_start($transcript) until numbers start
> appearing. Your workaround is also a valid approach.
>
> My explanation isn’t very satisfactory, but we try to avoid writing
> methods that need complex return types, such as the list of lists required
> for your usecase. More often than not, users require other attributes of
> the objects too, so you would still end up with a list of exons. I hope
> that helps.
>
> Regards,
>
> Kieron
>
>
> Kieron Taylor PhD.
> Ensembl Core senior software developer
>
> EMBL, European Bioinformatics Institute
>
>
>
>
>
> > On 16 Apr 2015, at 09:15, Duarte Molha <duartemolha at gmail.com> wrote:
> >
> > Anyone able to provide me some help on this?
> >
> > I have now found away around this issue by finding the exonic regions
> within the reported URT, but would very much like to understand the
> thinking behind this.
> >
> > Best regards
> >
> > Duarte
> >
> >
> > =========================
> >      Duarte Miguel Paulo Molha
> >          http://about.me/duarte
> > =========================
> >
> > On 14 April 2015 at 13:40, Duarte Molha <duartemolha at gmail.com> wrote:
> > Dear Developers
> >
> > Please consider the transcript :
> >
> > ENST00000470357
> >
> > I am trying to retrieve the coordinates of UTR regions of this transcript
> > To this end I have a script that basicaly starts with the transcript
> feature object $transcript
> >
> > my $five_prime  = $transcript->five_prime_utr_Feature;
> >
> > $feature_params->{start} = $five_prime->start;
> > $feature_params->{end}  = $five_prime->end;
> >
> > However, in this case the script will output the coordinates from the
> start of the 1st non_coding exon to the end of the non-coding portion of
> the 3rd exon (chr1     7772707 7777171).
> > How can I change this so that the script will only output the
> coordinates of the non-coding exon portions?
> >
> > In this case I would like to output:
> >
> > chr1  7772707 7773198
> > chr1  7773442 7773511
> > chr1  7777160 7777171
> >
> > This there a simple way of achieving this?
> >
> > Many thanks
> >
> > Duarte
> >
> >
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