[ensembl-dev] VEP HGVS issue

[Stuart Watt]

Hi folks

I'm using VEP and I might have I just found and fixed a small issue, so I thought I'd pass it on.

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.

The error reported is:

2012-11-07 10:46:05 - Checking/creating FASTA index
…
2012-11-07 10:46:35 - Analyzing chromosome 9
2012-11-07 10:46:35 - Analyzing variants
2012-11-07 10:47:06 - Calculating consequences
Quantifier follows nothing in regex; marked by <-- HERE in m/* <-- HERE / at /Users/swatt/variant_effect_predictor/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 877.

Note the * is a valid HGVS reference and a regex metacharacter. This is a fatal error, so the process stops.

The lines at issue are:

      }
      elsif( (length($hgvs_notation->{alt}) >  length($hgvs_notation->{ref}) ) &&
           $hgvs_notation->{alt} =~ /$hgvs_notation->{ref}/ ) {
          ### capture duplication event described as TTT/TTTTT
          $hgvs_notation->{type} = "dup";
      }

My quick fix was as follows - the run then completes. There are probably better fixes conceptually, but this worked for me.

-           $hgvs_notation->{alt} =~ /$hgvs_notation->{ref}/ ) {
+           $hgvs_notation->{alt} =~ /\Q$hgvs_notation->{ref}\E/ ) {

I hope I'm doing this right for you. VEP is a great tool, and it's already delivering excellent results for us.

All the best
Stuart

--

Stuart Watt, PhD

Senior Software Developer

Ontario Institute for Cancer Research

MaRS Centre, South Tower
101 College Street, Suite 800
Toronto, Ontario, Canada M5G 0A3

Toll-free: 1-866-678-6427
www.oicr.on.ca<http://www.oicr.on.ca>


This message and any attachments may contain confidential and/or privileged information for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this message in error, please contact the sender and delete all copies. Opinions, conclusions or other information contained in this message may not be that of the organization.

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20121107/0c708cb5/attachment.html>