[ensembl-dev] Question regarding UTR retrieval from database

[Duarte Molha]

Yes... I knew of that method... had just forgot it. I still think the
reverse of it would be useful on it own. get_all_untranslateable_Exons.


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

On 16 April 2015 at 21:29, <mr6 at ebi.ac.uk> wrote:

> Hi Duarte,
>
> You might find the get_all_translateable_Exons method useful.
>
> http://www.ensembl.org/info/docs/Doxygen/core-api/classBio_1_1EnsEMBL_1_1Transcript.html#a17e718ddd3d054de7b358029e6d48d20
>
> This would correspond to the get_coding_regions you are looking for, as
> the exons returned are truncated to their coding region.
> For the get_noncoding_regions however, you would need to look at all the
> features from get_all_Exons that are not in get_all_translateable_Exons.
>
>
> Hope that helps,
> Magali
>
> > 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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> >>
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>
>
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