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<p class="MsoNormal"><span style="color:#1F497D">Heres my query:<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">select <o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">vf.variation_name, vf.seq_region_id, vf.seq_region_start, vf.source_id,
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">s.name, vf.minor_allele_freq, tv.feature_stable_id, tv.allele_string, tv.consequence_types
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">from <o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">variation_feature vf, <o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">transcript_variation tv, <o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">source s<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">WHERE <o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">s.source_id=vf.source_id and<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">vf.variation_feature_id=tv.variation_feature_id and
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">--tv.feature_stable_id ='ENST00000544455'
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">tv.feature_stable_id in<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">('ENST00000380152','ENST00000530893','ENST00000528762','ENST00000470094','ENST00000533776','ENST00000544455')<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">and<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">vf.variation_id not in<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">(<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">select <o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">vf.variation_id<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">from <o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">variation_feature vf,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">transcript_variation tv, <o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">failed_variation fv<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">where <o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">fv.variation_id=vf.variation_id <o:p>
</o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">and <o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">vf.variation_feature_id=tv.variation_feature_id<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">and <o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">--tv.feature_stable_id ='ENST00000544455'<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">tv.feature_stable_id in<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">('ENST00000380152','ENST00000530893','ENST00000528762','ENST00000470094','ENST00000533776','ENST00000544455')<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">When I try this on my local copy.. it runs for 5 mins with no result!<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> dev-bounces@ensembl.org [mailto:dev-bounces@ensembl.org]
<b>On Behalf Of </b>Jayaraman, Pushkala<br>
<b>Sent:</b> Thursday, September 05, 2013 2:25 PM<br>
<b>To:</b> dev@ensembl.org<br>
<b>Subject:</b> [ensembl-dev] querying a copy of the ensembl human variation 72_37<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Hello, <o:p></o:p></p>
<p class="MsoNormal">I seem to be having trouble querying the failed_variation table
<o:p></o:p></p>
<p class="MsoNormal">I cannot even seem to get count of the rows.. <o:p></o:p></p>
<p class="MsoNormal">Is there any additional indexes you guys apply to the failed_variation table?<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><span style="font-size:16.0pt;font-family:"Arabic Typesetting"">Pushkala Jayaraman<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:16.0pt;font-family:"Arabic Typesetting"">Programmer/Analyst - Rat Genome Database<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:16.0pt;font-family:"Arabic Typesetting"">Human and Molecular Genetics Center<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:16.0pt;font-family:"Arabic Typesetting"">Medical College of Wisconsin<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:16.0pt;font-family:"Arabic Typesetting"">414-955-2229<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:16.0pt;font-family:"Arabic Typesetting""><a href="http://rgd.mcw.edu">http://rgd.mcw.edu</a><o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
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