[ensembl-dev] VEP HGVS issue

Sarah Hunt seh at ebi.ac.uk
Wed Nov 7 16:39:38 GMT 2012


Hi Stuart,

Thanks for reporting this bug.  It looks like a problem we fixed in
the e!69 branch after the main release but I realise it's not always
convenient to monitor for and pick up post release updates, so it's
good you found a fix.

It's great to hear you are finding VEP useful.

Best wishes,

Sarah

On Wed, Nov 7, 2012 at 4:12 PM, Stuart Watt <Stuart.Watt at oicr.on.ca> wrote:
> 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
>
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