[ensembl-dev] question on variation API

[Laurent Gil]

Hi Nathalie,

Concerning the first question, this was a bug and I committed a fix on 
the branch 73 of the ensembl-variation CVS.
You can find the list of phenotype on the Ensembl website, e.g. for 
human: www.ensembl.org/Homo_sapiens/Phenotype/All

Best regards,

Laurent
Ensembl Variation

On 03/10/2013 13:57, Nathalie Conte wrote:
> hi, I am trying ot use this method in order to get only the variation 
> I am interested in using phenotype as a filter:
> public Reference 
> Bio::EnsEMBL::Variation::DBSQL::VariationFeatureAdaptor::fetch_all_with_phenotype_by_Slice 
> 	( 	
> 	) 	
>
>    Arg [1]    : Bio::EnsEMBL:Variation::Slice  <http://www.ensembl.org/info/docs/Doxygen/core-api/classBio_1_1EnsEMBL_1_1Slice.html>  $slice
>    Arg [2]    : $variation_feature_source [optional]
>    Arg [3]    : $phenotype_source [optional]
>    Arg [4]    : $phenotype_name [optional]
>    Example    :
>   my @vfs = @{$vfa->fetch_all_with_phenotype_by_Slice($slice)};
>    Description: Retrieves all germline variation features associated with phenotypes for
>                 a given slice.
>                 The optional $variation_feature_source argument can be used to
>                 retrieve only variation features from a paricular source.
>                 The optional $phenotype source argument can be used to
>                 retrieve only variation features with phenotypes provided by
>                 a particular source.
>                 The optional $phenotype_name argument can
>                 be used to retrieve only variation features associated with
>                 that phenotype - this can also be a phenotype's dbID.
>    Returntype : reference to listBio::EnsEMBL::Variation::VariationFeature  <http://www.ensembl.org/info/docs/Doxygen/variation-api/classBio_1_1EnsEMBL_1_1Variation_1_1VariationFeature.html>
>    Exceptions : throw on bad argument
>    Caller     : general
>    Status     : Stable
> I have 2 questions
> 1-I first tried to use this without any option
> my $vf_adaptor = Bio::EnsEMBL::Registry->get_adaptor('human', 
> 'variation', 'variationfeature');
>  my @vfs = 
> @{$vf_adaptor->fetch_all_with_phenotype_by_Slice($human_slice)};
> this is the output I get, any idea?
> DBD::mysql::st execute failed: Unknown column 'pf.seq_region_id' in 
> 'where clause' at 
> /src/ensembl-variation/modules/Bio/EnsEMBL/Variation/DBSQL/VariationFeatureAdaptor.pm 
> line 446, <> line 2.
> DBD::mysql::st execute failed: Unknown column 'pf.seq_region_id' in 
> 'where clause' at 
> /src/ensembl-variation/modules/Bio/EnsEMBL/Variation/DBSQL/VariationFeatureAdaptor.pm 
> line 446, <> line 2.
>
> 2-the optional $phenotype_name argument can be used, where can I find 
> a lit of all phenotype name please?
>
> Many thanks
> Nathalie
>
> -- 
>
>
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