[ensembl-dev] Wrongly documented gene_adaptor method ?

[PATERSON Trevor]

Cheers andy

using the gene->get_all_alt_alleles(),  then getting their slice and querying the exception type seems to do everything I need...

trevor



Trevor Paterson PhD
trevor.paterson at roslin.ed.ac.uk
Bioinformatics 
The Roslin Institute
Royal (Dick) School of Veterinary Studies
University of Edinburgh
Easter Bush
Midlothian
EH25 9RG
Scotland UK

phone +44 (0)131 651 9157

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-----Original Message-----
From: dev-bounces at ensembl.org [mailto:dev-bounces at ensembl.org] On Behalf Of Andy Yates
Sent: 25 June 2012 14:40
To: Ensembl developers list
Subject: Re: [ensembl-dev] Wrongly documented gene_adaptor method ?

Hi Trevor,

Alt allele does cover patches as well as haplotype regions. For example if we take the patch fix region GL383517.1 (which is HG999_2_PATCH in Ensembl) and run the following query:

select aa.alt_allele_id
from seq_region sr
join gene g using (seq_region_id)
join alt_allele aa on (g.gene_id = aa.gene_id) where sr.name = 'HG999_2_PATCH';

That gives us an alt_allele_id of 1579. We then try to find the stable IDs linked to this ID & if it's the reference gene or not:

select stable_id, is_ref
from gene
join alt_allele using (gene_id)
where alt_allele_id = 1579;

stable_id	is_ref
ENSG00000229663	1
ENSG00000260191	0

This same logic is available from the $gene->get_all_alt_alleles() method. Once you have the other genes you can decipher the type of assembly exception we have performed using the $slice->assembly_exception_type() method which will report REF, PATCH_FIX, PATCH_NOVEL or HAP.

Regards,

Andy


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 geneENSG00000224226 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 
> Easter Bush Midlothian
> EH25 9RG
> Scotland UK
> 
> phone +44 (0)131 651 9157
> 
> http://bioinformatics.roslin.ed.ac.uk/
> 
> Please consider the environment before printing this e-mail The 
> University of Edinburgh is a charitable body, registered in Scotland 
> with registration number SC005336 Disclaimer:This e-mail and any attachments are confidential and intended solely for the use of the recipient(s) to whom they are addressed. If you have received it in error, please destroy all copies and inform the sender.
>  
> The University of Edinburgh is a charitable body, registered in 
> Scotland, with registration number SC005336.
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