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

[Giuseppe Gallone]

Hi Gautier,

thanks for explaining the fact that it's a temporary error only 
affecting fly. As for your proposed temporary hack, It looks to me like 
it's basically what I had been doing already but, again, thank you for 
taking the time to post that.

Best,
G

On 08/11/10 10:48, Gautier Koscielny wrote:
> 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
>>
>
>

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