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<div class="moz-cite-prefix">Hi Nathalie,<br>
<br>
Concerning the first question, this was a bug and I committed a
fix on the branch 73 of the ensembl-variation CVS.<br>
You can find the list of phenotype on the Ensembl website, e.g.
for human: <a href="www.ensembl.org/Homo_sapiens/Phenotype/All">www.ensembl.org/Homo_sapiens/Phenotype/All<br>
</a><br>
Best regards,<br>
<pre class="moz-signature" cols="72">Laurent
Ensembl Variation
</pre>
On 03/10/2013 13:57, Nathalie Conte wrote:<br>
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hi, I am trying ot use this method in order to get only the
variation I am interested in using phenotype as a filter:<br>
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<td class="memname">public Reference
Bio::EnsEMBL::Variation::DBSQL::VariationFeatureAdaptor::fetch_all_with_phenotype_by_Slice
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<td>(</td>
<td class="paramname"><br>
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<pre> Arg [1] : Bio::EnsEMBL:Variation::<a moz-do-not-send="true" class="elRef" doxygen="ensembl.tag:../core-api//" href="http://www.ensembl.org/info/docs/Doxygen/core-api/classBio_1_1EnsEMBL_1_1Slice.html">Slice</a> $slice
Arg [2] : $variation_feature_source [optional]
Arg [3] : $phenotype_source [optional]
Arg [4] : $phenotype_name [optional]
Example :</pre>
<div class="fragment">
<pre class="fragment"> my @vfs = @{$vfa->fetch_all_with_phenotype_by_Slice($slice)};
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<pre> 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 list <a moz-do-not-send="true" class="el" href="http://www.ensembl.org/info/docs/Doxygen/variation-api/classBio_1_1EnsEMBL_1_1Variation_1_1VariationFeature.html">Bio::EnsEMBL::Variation::VariationFeature</a>
Exceptions : throw on bad argument
Caller : general
Status : Stable</pre>
I have 2 questions<br>
1-I first tried to use this without any option<br>
my $vf_adaptor = Bio::EnsEMBL::Registry->get_adaptor('human',
'variation', 'variationfeature'); <br>
my @vfs =
@{$vf_adaptor->fetch_all_with_phenotype_by_Slice($human_slice)};<br>
this is the output I get, any idea?<br>
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.<br>
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.<br>
<br>
2-the optional $phenotype_name argument can be used, where can I
find a lit of all phenotype name please?<br>
<br>
Many thanks<br>
Nathalie<br>
<br>
<pre class="moz-signature" cols="72">--
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