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Hello Will,<br>
<br>
Thank you for your quick response. That was my guess.<br>
<br>
Regards,<br>
Guillermo.<br>
<br>
<div class="moz-cite-prefix">On 20/06/16 15:28, Will McLaren wrote:<br>
</div>
<blockquote
cite="mid:CAMVEDX0ZzdHn0kF09QiqurRNfNmCQjO4je0SE1K3O1rv_wYyUg@mail.gmail.com"
type="cite">
<div dir="ltr">Hi Guillermo,<br>
<br>
<div>For the ClinVar data Ensembl doesn't import the RefSeq
reported, only the associated gene symbol. This along with
other data are available in the attributes of the phenotype
feature object ($pf->get_all_attributes).</div>
<div><br>
</div>
<div>Regards</div>
<div><br>
</div>
<div>Will McLaren</div>
<div>Ensembl Variation<br>
<div><br>
</div>
<div><br>
<div class="gmail_extra">
<div class="gmail_quote">On 17 June 2016 at 12:29,
Guillermo Marco Puche <span dir="ltr"><<a
moz-do-not-send="true"
href="mailto:guillermo.marco@sistemasgenomicos.com"
target="_blank"><a class="moz-txt-link-abbreviated" href="mailto:guillermo.marco@sistemasgenomicos.com">guillermo.marco@sistemasgenomicos.com</a></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>
I've been using this plugin I made with the help of
Will McLaren: <a moz-do-not-send="true"
href="https://gist.github.com/guillermomarco/be0751f77b798d37ded14e5a884e4ff0"
target="_blank">https://gist.github.com/guillermomarco/be0751f77b798d37ded14e5a884e4ff0</a><br>
I'm pretty happy with the results however I would
like to improve it. At this moment plugin outputs
the selected phenotypes for all the consequences per
transcript. However this is not right.<br>
<br>
If I annotate the following record:<br>
<ul>
<li>chr11 128911444 . T C</li>
</ul>
<p>I get ClinVar information for all the transcripts
consequences of the variant. However If I'm not
wrong I should only output ClinVar for those
consequences with same RefSeq as described by
ClinVar, in this case "NM_000890.3" associated to
RCV000126421.3.<br>
</p>
<p>I don't understand exactly how does Ensembl
handles Phenotype information and if this kind of
check is possible. The point should be only output
phentoypes not only based on variation but check
that transcript between phentoype and variation is
the same.<br>
</p>
<p>Regards,<br>
Guillermo.<br>
</p>
</div>
<br>
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<pre wrap="">_______________________________________________
Dev mailing list <a class="moz-txt-link-abbreviated" href="mailto:Dev@ensembl.org">Dev@ensembl.org</a>
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