[ensembl-dev] Retrieving a gene name without isoform information

[Gautier Koscielny]

Dear Guiseppe,

First of all, there is an error with the external name in Drosophila 
melanogaster.
It really should be the FlyBase gene name and this will be sorted in the 
forthcoming Ensembl Genomes 7.

Secondly, I've attached a script that should return the information you 
require without using regular expressions.

Best regards,

-Gautier-


On 07/11/2010 12:34, Giuseppe Gallone wrote:
> Hi,
>
> just in case somebody else is interested. My question was the following:
>
> When I query ensembl core with a stable gene id, and I try to retrieve 
> that gene's name, I'll get a transcript name instead
>
> my $gene = $gene_adaptor->fetch_by_stable_id('FBgn0013812');
> my $name = $gene->external_name;
>
> $name will be Dhc93AB-RB. As I'm not interested in the transcript 
> info, can I get the gene name as it appears in flybase? (Dhc93AB).
>
> One solution is getting the flybase_name DB link and getting the name 
> from there works (unless you want to use local regexes of course).
>
> my @dblinks = @{ $gene->get_all_DBLinks("FlyBaseName_Gene%") };
> my $flybasenamelink = $dblinks[0];
> my $name = $flybasenamelink->display_id;
>
> Unfortunately I had to find that "FlyBaseName_Gene" string by 
> debugging and looking at all the db links. This means it's a problem 
> when I want to query ids from several other organisms. In such case, 
> is my only option to trim with a regex?
>
> Regards,
> G
>
> On 05/11/10 20:52, Giuseppe Gallone wrote:
>> Hi,
>>
>> is there a method to get the gene name from a gene object without the
>> isoform info (like it used to be before)?
>>
>> Cheers,
>> G
>


-- 
Best Regards/Cordialement/Mit freundlichen Grüßen
Gautier Koscielny, Ph.D.
phone: +44 (0)1223 494 650
EMBL Outstation - The European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton CB10 1SD
UK

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