<div dir="ltr">Thanks Will. I suppose <font face="arial, sans-serif">UpDownDistance.pm considers upstream and downstream distances </font><span style="font-family:arial,sans-serif">respectively</span><font face="arial, sans-serif"> from the start and the end of the SV. Is that right?</font><div>
<span style="font-family:arial,sans-serif;font-size:13px"><br></span></div><div><span style="font-family:arial,sans-serif;font-size:13px">Cheers,</span></div><div><span style="font-family:arial,sans-serif;font-size:13px"><br>
</span></div><div><span style="font-family:arial,sans-serif;font-size:13px">Mike</span></div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On 23 June 2014 13:50, Will McLaren <span dir="ltr"><<a href="mailto:wm2@ebi.ac.uk" target="_blank">wm2@ebi.ac.uk</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hi guys,<div><br></div><div>Thanks for finding this issue. I've had to patch a fix to the ensembl-variation API module as it wasn't executing plugins correctly for SVs.</div>
<div><br></div><div>A couple of further points:</div>
<div><br></div><div>The variant_feature_types() sub must get the name of the feature type e.g. VariationFeature (not Variation). I have updated the TSSDistance plugin to use the common base class BaseVariationFeature (both VariationFeature and StructuralVariationFeature are child classes of this).</div>
<div><br></div><div>The plugin will not work for the variant you cite, since as explained in the blurb at the top the plugin is for upstream variants only (though it does work if you extend using UpDownDistance as I suspect you have been). To modify it to work for downstream variants too you could remove the if{} clause around the return statement and return the abs() value of $dist</div>
<div><br></div><div>Regards</div><div><br></div><div>Will McLaren</div><div>Ensembl Variation</div><div><br></div><div><br></div></div><div class="gmail_extra"><br><br><div class="gmail_quote"><div><div class="h5">On 23 June 2014 10:54, Mike Pierce <span dir="ltr"><<a href="mailto:mikepierce2000@gmail.com" target="_blank">mikepierce2000@gmail.com</a>></span> wrote:<br>
</div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div class="h5"><div dir="ltr">Hi,<div><br></div><div>Thanks Genomeo for bringing this up seems like an important issue. Ensembl folks, could you please clarify whether Structural variants are processed by the plugin by default or whether the variant_feature_types is required?</div>
<div><br></div><div>Cheers,</div><div><br></div><div>Mike<div><div><br><div class="gmail_extra"><br><br><div class="gmail_quote">On 20 June 2014 18:25, Genomeo Dev <span dir="ltr"><<a href="mailto:genomeodev@gmail.com" target="_blank">genomeodev@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div dir="ltr">Hi Will/others,<div><br></div><div>TSSDistance.pm currently does not seem to consider structural variants. Based on this doxygen documentation:</div>
<div><br></div><div><div style="font-size:11.818181991577148px;font-family:'Lucida Grande',Verdana,Geneva,Arial,sans-serif;color:rgb(37,53,85);border-top-width:1px;border-top-style:solid;border-top-color:rgb(168,184,217);border-left-width:1px;border-left-style:solid;border-left-color:rgb(168,184,217);border-right-width:1px;border-right-style:solid;border-right-color:rgb(168,184,217);padding:6px 0px;font-weight:bold;border-top-right-radius:8px;border-top-left-radius:8px;background-image:url(http://static.ensembl.org/info/docs/Doxygen/compara-api/nav_f.png);background-color:rgb(226,232,242);background-repeat:repeat-x">
<table style="color:black;white-space:nowrap;margin-left:6px"><tbody><tr style="vertical-align:top"><td style="font-size:1em;border:0px;color:rgb(51,51,51);margin-left:6px">public Listref Bio::EnsEMBL::Variation::Utils::BaseVepPlugin::variant_feature_types</td>
<td style="font-size:1em;border:0px;color:rgb(51,51,51)">(</td><td style="font-size:1em;border:0px;color:rgb(96,32,32)"></td><td style="font-size:1em;border:0px;color:rgb(51,51,51)">)</td><td style="font-size:1em;border:0px;color:rgb(51,51,51)">
</td></tr></tbody></table></div><div style="font-size:11.818181991577148px;font-family:'Lucida Grande',Verdana,Geneva,Arial,sans-serif;color:rgb(0,0,0);border-width:0px 1px 1px;border-bottom-style:solid;border-bottom-color:rgb(168,184,217);border-left-style:solid;border-left-color:rgb(168,184,217);border-right-style:solid;border-right-color:rgb(168,184,217);padding:2px 5px;border-bottom-left-radius:8px;border-bottom-right-radius:8px;background-color:rgb(251,252,253)">
<pre style="font-family:'Courier New',Courier,monospace;font-size:1em;margin-top:0px;margin-bottom:16px;line-height:16px"> Description: To indicate which types of variation features a plugin is interested
in, plugins should return a listref of the types of variation feature
they can deal with. Currently this list should include one or more of:
'VariationFeature' or 'StructuralVariationFeature'
Returntype : listref
Status : Experimental</pre></div><div><br></div><div>I tried adding the following code at the top of the plugin:</div><div><br></div><div><div>sub variant_feature_types {</div><div> return [<span style="color:rgb(0,0,0);font-family:'Courier New',Courier,monospace;font-size:1em;line-height:16px">'Variation','</span>StructuralVariation'];</div>
<div>}</div></div><div><br></div><div>but it does not work. This is the input in VCF:</div><div>5<span style="white-space:pre-wrap"> </span>104269332<span style="white-space:pre-wrap"> </span>CNV7<span style="white-space:pre-wrap"> </span>G<span style="white-space:pre-wrap"> </span><DEL><span style="white-space:pre-wrap"> </span>.<span style="white-space:pre-wrap"> </span>PASS<span style="white-space:pre-wrap"> </span>SVTYPE=DEL;END=104278677<br>
</div><div><br></div><div>Any thoughts on that?</div><div><br></div><div>Thanks,</div><span><font color="#888888"><div><br></div>-- <br><div dir="ltr">G.</div>
</font></span></div></div></blockquote></div></div></div></div></div></div>
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