[ensembl-dev] method to fetch 5' and /or 3' from a feature- ensembl variation

[Nathalie Conte]

HI Kieron,
Thanks -
At the moment I am using the  get_nearest_Gene() from core-
http://www.ensembl.org/info/docs/Doxygen/core-api/classBio_1_1EnsEMBL_1_1Feature.html#a8a7c8af129910c4daa088b87171b86a6
I receive a warning that this method is deprecated:
------------------ DEPRECATED ---------------------
Deprecated method call in file /net/isilon5/ma/home/nconte/src/ensembl/modules/Bio/EnsEMBL/Feature.pm line 1434.
Method Bio::EnsEMBL::DBSQL::GeneAdaptor::fetch_nearest_Gene_by_Feature is deprecated.
fetch_nearest_Gene_by_Feature() is a deprecated method. Strand and stream implementations are unreliable. Please use with c
aution
Ensembl API version = 75

I have several questions please  -
When the next method you mentioned : feature/getnearestgene will be available? and will it fetch nearest 3' and 5' at the same time?
Will we be able to narrow the search to only protein coding genes rather than all genes? 

Thanks
Nathalie


On 21 Jul 2014, at 14:07, Kieron Taylor <ktaylor at ebi.ac.uk> wrote:

> Hi Nathalie,
> 
> We are working on a method to support this kind of enquiry, but it turns out to be quite finely nuanced to find the nearest feature when it overlaps others. I hope to get it included in release 77.
> 
> If you're curious, take a look at the feature/getnearestgene branch on Github. This code is functional but I don't recommend using it until we release it properly, as it will continue to evolve.
> 
> 
> Regards,
> 
> Kieron Taylor
> Ensembl Core
> 
> 
> On 18/07/2014 16:27, Nathalie Conte wrote:
>> Hi Dev team,
>> Any method in ensembl perl API to fetch nearest gene in 5' and 3' from a feature (ie variation object?)?
>> thanks
>> Nathalie
> 
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