[ensembl-dev] retrieving appris tag from API

[Tiago Grego]

Dear Duarte,

GRCh37 is data freeze since March 2014, and at the time APPRIS data was 
not available.
We keep an archive of GRCh37 data, but since then new data releases 
happen on the newer GRCh38 assembly.

Please email your user support queries to helpdesk at ensembl.org or 
dev at ensembl.org

Best regards,
Tiago



On 21/11/2018 16:31, Duarte Molha wrote:
> 
> Just an additional question
> 
> I see that only GRCH38 has the APPRIS tags, however on the APPRIS 
> website they also include the GRCh37
> 
> http://appris.bioinfo.cnio.es/#/downloads
> 
> Any change this could be also included on the GRCh37 dataset ?
> 
> Thanks
> 
> Duarte
> 
> 
> 
> 
> On Wed, 21 Nov 2018 at 12:54, Duarte Molha <duartemolha at gmail.com 
> <mailto:duartemolha at gmail.com>> wrote:
> 
>     perfect... thanks
> 
>     May I humbly suggest you add a note to that link explaining this ?
> 
>     I think it would be helpful for more people.
> 
> 
> 
> 
>     On Wed, 21 Nov 2018 at 12:50, Tiago Grego <tgrego at ebi.ac.uk
>     <mailto:tgrego at ebi.ac.uk>> wrote:
> 
>         Dear Duarte,
> 
>         On a transcript you may indeed call is_canonical() and
>         genecode_basic().
>         You can also call the method tsl() on a transcript object to get
>         the
>         corresponding transcript support level.
> 
>         You are correct that at this time there is no equivalent method to
>         directly access the appris tag. I will propose to create that
>         method for
>         a future Ensembl release.
> 
>         In the mean time, you may access the appris tag of a $transcript
>         object
>         in the following way:
> 
>             my $appris_attr = shift(
>         $transcript->get_all_Attributes('appris') );
>             my $appris_tag = $appris_attr->value if $appris_attr;
> 
>         $appris_tag will contain the corresponding value for the transcript
>         object, or be null if it does not exist.
> 
>         Hope it helps.
> 
>         Best regards,
>         Tiago
> 
> 
> 
>         On 21/11/2018 11:57, Duarte Molha wrote:
>          > Hi
>          >
>          > I read here:
>          >
>         https://www.ensembl.org/info/genome/genebuild/transcript_quality_tags.html
>          >
>          > That I can use appris tags to select principal transcripts
>         from my genes
>          > of interest, but I have been looking at the documentation and
>         can only find
>          > is_canonical method and genecode_basic() method
>          >
>          > How do I access the appris tag for my transcripts?
>          >
>          > Many thanks
>          >
>          > Duarte
>          >
>          >
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