[ensembl-dev] Question regarding UTR retrieval from database

[Duarte Molha]

Many thanks Magali

It is certainly very useful

Cheers

Duarte
On 17 Jul 2015 07:55, "mag" <mr6 at ebi.ac.uk> wrote:

>  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> 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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