<html>
<head>
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
</head>
<body text="#000000" bgcolor="#FFFFFF">
<div class="moz-cite-prefix">
<meta http-equiv="content-type" content="text/html;
charset=ISO-8859-1">
<br>
Crisp and clear - Thanks a lot !<br>
<br>
<pre class="moz-signature" cols="72">Jérôme Dauvillier
SIB | Swiss Institute of Bioinformatics
</pre>
Le 02/05/14 16:07, Will McLaren a écrit :<br>
</div>
<blockquote
cite="mid:CAMVEDX0wO-nHqNwVRHG12D26JoBUigVkbvLPSF9=6U1Ju=GJ1g@mail.gmail.com"
type="cite">
<div dir="ltr">Hello,
<div><br>
</div>
<div>We keep a record of merged rsIDs in the variation_synonym
table of our database.</div>
<div><br>
</div>
<div>When you do a look-up by rsID, e.g.</div>
<div><br>
</div>
<div>my $variation =
$variation_adaptor->fetch_by_name('rs7335199');</div>
<div><br>
</div>
<div>the API checks both the variation (for the primary ID) and
variation_synonym (for the archived IDs). </div>
<div><br>
</div>
<div>In the above example this will actually return the
variation object corresponding to rs3, to which it has been
merged.</div>
<div><br>
</div>
<div>Once you have the variation object you can ask for synonyms
(i.e. all of the archived IDs) with the following call:</div>
<div><br>
</div>
<div>my @synonyms = @{$variation->get_all_synonyms()};</div>
<div>
<br>
</div>
<div>To limit this to just rsIDs, for example, add the source
'dbSNP' as an argument:</div>
<div><br>
</div>
<div>my @rs_synonyms =
@{$variation->get_all_synonyms('dbSNP')};<br>
</div>
<div><br>
</div>
<div>In the example, both of these lists will then contain the
archived rsID that you initially searched for.</div>
<div><br>
</div>
<div>We do not retain variation_feature records corresponding to
archived rsIDs, since they are considered to be merged with
the primary rsID's variation_feature(s).</div>
<div><br>
</div>
<div>Hope that helps</div>
<div><br>
</div>
<div>Will McLaren</div>
<div>Ensembl Variation</div>
</div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">On 2 May 2014 14:56, Jerome Dauvillier
<span dir="ltr"><<a moz-do-not-send="true"
href="mailto:jerome.dauvillier@isb-sib.ch" target="_blank">jerome.dauvillier@isb-sib.ch</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Ensembl
dev,<br>
<br>
Is there some support in the API for<br>
- Detecting a rs-ID refers to a synonymous variation ?<br>
- Given the rs-ID of a synonymous variation, getting the
variation it was merged into, and the corresponding
variation feature object ?<br>
<br>
Many thanks in advance !<br>
<br>
Best,<span class="HOEnZb"><font color="#888888"><br>
<br>
-- <br>
Jérôme Dauvillier<br>
SIB | Swiss Institute of Bioinformatics<br>
<br>
<br>
_______________________________________________<br>
Dev mailing list <a moz-do-not-send="true"
href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a><br>
Posting guidelines and subscribe/unsubscribe info: <a
moz-do-not-send="true"
href="http://lists.ensembl.org/mailman/listinfo/dev"
target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</a><br>
Ensembl Blog: <a moz-do-not-send="true"
href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info/</a><br>
</font></span></blockquote>
</div>
<br>
</div>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
<pre wrap="">_______________________________________________
Dev mailing list <a class="moz-txt-link-abbreviated" href="mailto:Dev@ensembl.org">Dev@ensembl.org</a>
Posting guidelines and subscribe/unsubscribe info: <a class="moz-txt-link-freetext" href="http://lists.ensembl.org/mailman/listinfo/dev">http://lists.ensembl.org/mailman/listinfo/dev</a>
Ensembl Blog: <a class="moz-txt-link-freetext" href="http://www.ensembl.info/">http://www.ensembl.info/</a>
</pre>
</blockquote>
<br>
</body>
</html>