[ensembl-dev] Wrongly documented gene_adaptor method ?

[Monika Komorowska]

Hi Trevor

Apologies, but we seem to have the wrong method called in the example for fetch_all_by_display_label
It should state: 

Example    : my @genes = @{$geneAdaptor->fetch_all_by_display_label("PPP1R2P1")};

I committed the change to the GeneAdaptor 'fetch_all_by_display_label' method documentation head code, which will be released in a month with release 68.

fetch_all_by_display_label (as Bert mentioned) will return an arrayref of genes.
Sorry about the confusion which the wrong example has caused.

Thanks
Monika

On 25 Jun 2012, at 13:50, PATERSON Trevor wrote:

>  
> According to the Perl documentation, you should be able to get a list of genes for a given display label, using:
>  
> public    Listref    Bio::EnsEMBL::DBSQL::GeneAdaptor::fetch_all_by_display_label ( )
>  
> However,  this method is wrongly documented in the online perl docs, and does not return an array – but a single gene object
>  
> my @genes = @{$geneAdaptor->fetch_by_display_label("TBC1D3B")};
> DEBUGGER ERROR MESSAGE : Not an ARRAY reference
>  
> When you look at the real code in Release 67 API, rather than the www perldocs, the method actually returns a single gene, preferring one that is on a reference slice.
>  
> I am looking for a way of getting alternative gene models on Patch exceptions: and this method would have been promising. e.g for the gene ENSG00000224226 Location Chromosome 17: 34,493,061-34,503,984 how do I get its equivalent on the patch-fix ENSG00000260069 Location Chromosome HG75_PATCH: 34,493,132-34,503,984.
>  
>  
> obviously I can dig into the API and call the appropriate sql code myself:
>  
> my $constraint = "x.display_label = '". $gene->display_xref()->display_id()."' AND g.is_current = 1";
> my @same_labelled_genes = @{ $gene_adaptor->generic_fetch($constraint) };
>  
>  
> but is there an alternative (simple) method to get either ‘same_labelled’ genes  or ideally ‘equivalent-exception’ genes for a given gene?
>  
> the method
> public    Listref    Bio::EnsEMBL::Gene::get_all_alt_alleles ( )
>  
> of course does something similar using the alt_alleles table , but only for alternative haplotypes not patches.
>  
> Thanks
>  
> Trevor
>  
>  
> Trevor Paterson PhD
> trevor.paterson at roslin.ed.ac.uk
> Bioinformatics 
> The Roslin Institute
> Royal (Dick) School of Veterinary Studies
> University of Edinburgh
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> 
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> 
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Monika Komorowska
EnsEMBL Software Developer

European Bioinformatics Institute (EMBL-EBI)
tel: +44(0) 1233 494 409

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