[ensembl-dev] Question regarding UTR retrieval from database

[mag]

Hi Duarte,

As of this release (81), new methods are available from the transcript 
object:
- get_all_five_prime_UTR
- get_all_three_prime_UTR
- get_all_CDS

These methods return a list of regions representing the coding/noncoding 
regions of the transcript's exons.


Hope that helps,
Magali

On 16/04/2015 20:12, Duarte Molha wrote:
> 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 
> <mailto: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
>     <mailto: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
>     <mailto: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
>     >
>     >
>     > _______________________________________________
>     > Dev mailing list Dev at ensembl.org <mailto:Dev at ensembl.org>
>     > Posting guidelines and subscribe/unsubscribe info:
>     http://lists.ensembl.org/mailman/listinfo/dev
>     > Ensembl Blog: http://www.ensembl.info/
>
>
>     _______________________________________________
>     Dev mailing list Dev at ensembl.org <mailto:Dev at ensembl.org>
>     Posting guidelines and subscribe/unsubscribe info:
>     http://lists.ensembl.org/mailman/listinfo/dev
>     Ensembl Blog: http://www.ensembl.info/
>
>
>
>
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20150717/f58310b5/attachment.html>