[ensembl-dev] question on variation API

[nconte at ebi.ac.uk]

HI Laurent, Thanks for fixing the bug,
concerning the list, does it work like an ontology or you have to select
all terms corresponding to a condition?
example if you want all SNP concerning ADDISON disease you have to select
all 4 phenotypes below?
ADDISON DISEASE

Addison disease, susceptibility to

Addison's disease

Addisons disease

thanks
Nat
> 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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