<div dir="ltr">Hi Guillermo,<div><br></div><div>It may be that what you are trying to do is already encapsulated in our (new to release 84) Phenotypes plugin:</div><div><br></div><div><a href="https://github.com/Ensembl/VEP_plugins/blob/release/84/Phenotypes.pm">https://github.com/Ensembl/VEP_plugins/blob/release/84/Phenotypes.pm</a><br></div><div><br></div><div>It has the benefit of reducing DB lookups to a single download the first time you run it. It's fully configurable to retrieve phenotypes associated with whatever feature types (variants, genes etc) you like, as well as limiting by source. One caveat is that to get rich data from it you must currently use JSON output.</div><div><br></div><div>If you wish to continue looking up by variant in your own plugin, you should enable co-located variant lookup with --check_existing (add --check_alleles to match alleles to your input variants), then you can use fetch_all_by_object_id() [1] using the rsIDs in $tva->variation_feature->{existing}, something like:</div><div><br></div><div>sub run {</div><div> my ($self, $tva) = @_;</div><div> </div><div> ### get phenotype feature adaptor $pfa somehow</div><div> </div><div> foreach my $id(map {$_->{variation_name}} @{$tva->variation_feature->{existing} || []}) {</div><div> my $pfs = $pfa->fetch_all_by_object_id($id);</div><div><br></div><div> ### do something with the phenotype features returned</div><div> }</div><div>}</div><div><br></div><div>Cheers</div><div><br></div><div>Will</div><div><br></div><div>[1] <a href="http://www.ensembl.org/info/docs/Doxygen/variation-api/classBio_1_1EnsEMBL_1_1Variation_1_1DBSQL_1_1PhenotypeFeatureAdaptor.html#a93fcd05eafcf9bae4f9b9a5754904e4c">http://www.ensembl.org/info/docs/Doxygen/variation-api/classBio_1_1EnsEMBL_1_1Variation_1_1DBSQL_1_1PhenotypeFeatureAdaptor.html#a93fcd05eafcf9bae4f9b9a5754904e4c</a></div></div><div class="gmail_extra"><br><div class="gmail_quote">On 4 April 2016 at 16:12, Guillermo Marco Puche <span dir="ltr"><<a href="mailto:guillermo.marco@sistemasgenomicos.com" target="_blank">guillermo.marco@sistemasgenomicos.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div text="#000066" bgcolor="#FFFFFF">
Hello Will,<br>
<br>
Code in example [1] is working perfectly for me since I would like
to get the phenotype features related to the variant and not to the
gene. However I don't how to get $var (
<span style="color:rgb(0,0,0);font-family:'Lucida Grande',Verdana,Geneva,Arial,sans-serif;font-size:18px;font-style:normal;font-variant:normal;font-weight:bold;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;display:inline!important;float:none;background-color:rgb(249,250,252)">Variation::Variation</span>) from inside VEP
plugin.<br>
I'm trying with
$self->{variant} but I'm getting always an "undef" value.<br>
<br>
Regards,<br>
Guillermo.<div><div class="h5"><br>
<br>
<div>On 04/04/16 14:50, Will McLaren wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">Hi Guillermo,
<div><br>
</div>
<div>The data you refer to has been retracted from the Ensembl
core database while we resolve some issues with external
reference mapping between Ensembl and MIM.</div>
<div><br>
</div>
<div>You should be able to access the same annotations via the
variation API, using phenotype features. [1] shows an example
fetching via a variation object, but you can also query by
gene [2].</div>
<div><br>
</div>
<div>Hope that helps</div>
<div><br>
</div>
<div>Will McLaren</div>
<div>Ensembl Variation</div>
<div><br>
</div>
<div>[1] <a href="http://www.ensembl.org/info/docs/api/variation/variation_tutorial.html#phenotype" target="_blank">http://www.ensembl.org/info/docs/api/variation/variation_tutorial.html#phenotype</a></div>
<div>[2] <a href="http://www.ensembl.org/info/docs/Doxygen/variation-api/classBio_1_1EnsEMBL_1_1Variation_1_1DBSQL_1_1PhenotypeFeatureAdaptor.html#aee2a195b2f6f19952f562511d3ce1a72" target="_blank">http://www.ensembl.org/info/docs/Doxygen/variation-api/classBio_1_1EnsEMBL_1_1Variation_1_1DBSQL_1_1PhenotypeFeatureAdaptor.html#aee2a195b2f6f19952f562511d3ce1a72</a></div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On 4 April 2016 at 11:46, Guillermo
Marco Puche <span dir="ltr"><<a href="mailto:guillermo.marco@sistemasgenomicos.com" target="_blank">guillermo.marco@sistemasgenomicos.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div text="#000066" bgcolor="#FFFFFF"> Dear devs,<br>
<br>
Up to VEP version 83 I was using the following code in a
plugin to retrieve gene OMIM related information.<br>
<br>
my @db_entries = @{$gene->get_all_DBEntries()};<br>
foreach my $db_entry(@db_entries){<br>
if ($db_entry->dbname eq "MIM_GENE"){<br>
$mim_id = $db_entry->primary_id;<br>
}<br>
if ($db_entry->dbname eq "MIM_MORBID"){<br>
push(@mim_morbid_ids,
$db_entry->primary_id);<br>
}<br>
}<br>
<br>
However since I've updated to VEP 84 I don't get any
MIM_MORBID db_entry associated to any gene. Has this been
removed or changed location?<br>
<br>
Best regards,<br>
Guillermo.<br>
<br>
</div>
<br>
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