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Hi folks
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<div>I'm using VEP and I might have I just found and fixed a small issue, so I thought I'd pass it on. </div>
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<div>We're using VEP (offline) to do a fairly large set of HGVS nomenclatures, and it's working great except for a Perl error in a few cases.</div>
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<div>The error reported is:</div>
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<div>2012-11-07 10:46:05 - Checking/creating FASTA index<br>
…</div>
<div>2012-11-07 10:46:35 - Analyzing chromosome 9<br>
2012-11-07 10:46:35 - Analyzing variants<br>
2012-11-07 10:47:06 - Calculating consequences<br>
Quantifier follows nothing in regex; marked by <-- HERE in m/* <-- HERE / at /Users/swatt/variant_effect_predictor/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 877.</div>
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<div>Note the * is a valid HGVS reference and a regex metacharacter. This is a fatal error, so the process stops. </div>
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<div>The lines at issue are:</div>
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<div> }<br>
elsif( (length($hgvs_notation->{alt}) > length($hgvs_notation->{ref}) ) &&<br>
$hgvs_notation->{alt} =~ /$hgvs_notation->{ref}/ ) {<br>
### capture duplication event described as TTT/TTTTT<br>
$hgvs_notation->{type} = "dup";<br>
}<br>
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My quick fix was as follows - the run then completes. There are probably better fixes conceptually, but this worked for me. </div>
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<div>- $hgvs_notation->{alt} =~ /$hgvs_notation->{ref}/ ) {<br>
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<div>+ $hgvs_notation->{alt} =~ /\Q$hgvs_notation->{ref}\E/ ) {<br>
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<div>I hope I'm doing this right for you. VEP is a great tool, and it's already delivering excellent results for us. </div>
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<div>All the best</div>
<div>Stuart</div>
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<b>Stuart Watt, PhD</b></div>
<p style="font-family: Verdana, sans-serif; font-size: 8pt; margin-top: 0px; ">Senior Software Developer</p>
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<b>Ontario Institute for Cancer Research</b></p>
<p style="font-family: Verdana, sans-serif; font-size: 8pt; margin-top: 0px; ">MaRS Centre, South Tower<br>
101 College Street, Suite 800<br>
Toronto, Ontario, Canada M5G 0A3</p>
<p style="font-family: Verdana, sans-serif; font-size: 8pt; ">Toll-free: 1-866-678-6427<br>
<a href="http://www.oicr.on.ca">www.oicr.on.ca</a></p>
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