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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 $var (
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<span style="color: rgb(0, 0, 0); font-family: 'Lucida Grande',
Verdana, Geneva, Arial, sans-serif; font-size: 18px; font-style:
normal; font-variant: normal; font-weight: bold; letter-spacing:
normal; line-height: normal; orphans: auto; text-align: start;
text-indent: 0px; text-transform: none; white-space: normal;
widows: 1; word-spacing: 0px; -webkit-text-stroke-width: 0px;
display: inline !important; float: none; background-color:
rgb(249, 250, 252);">Variation::Variation</span>) from inside VEP
plugin.<br>
I'm trying with
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$self->{variant} but I'm getting always an "undef" value.<br>
<br>
Regards,<br>
Guillermo.<br>
<br>
<div class="moz-cite-prefix">On 04/04/16 14:50, Will McLaren wrote:<br>
</div>
<blockquote
cite="mid:CAMVEDX04zX2Ar6ZUbuZcPejtitU5jihVyt-3PrNbRNfP20x=yg@mail.gmail.com"
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The data you refer to has been retracted from the Ensembl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 moz-do-not-send="true"
href="http://www.ensembl.org/info/docs/api/variation/variation_tutorial.html#phenotype">http://www.ensembl.org/info/docs/api/variation/variation_tutorial.html#phenotype</a></div>
<div>[2] <a moz-do-not-send="true"
href="http://www.ensembl.org/info/docs/Doxygen/variation-api/classBio_1_1EnsEMBL_1_1Variation_1_1DBSQL_1_1PhenotypeFeatureAdaptor.html#aee2a195b2f6f19952f562511d3ce1a72">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 moz-do-not-send="true"
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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