[ensembl-dev] Bug in VEP

[Will McLaren]

I'm surprised you're seeing this error using --cache, since it
shouldn't be fetching data from the DB adaptor unless it is outside
the chromosome/position range covered by the cache.

Do you have some weirdly named chromosomes in your input file, or
perhaps some coordinates that may fall outside of the GRCh37 normal
coordinates?

In any case, I've committed a fix that should bypass this problem. Let
me know if it doesn't work, and preferably in this case if you could
give me a line of input that recreates the problem (as I've said
before, this is always extremely useful when debugging) that would be
great.

Thanks

Will

On 14 September 2012 12:55, Nathan Johnson <njohnson at ebi.ac.uk> wrote:
> Hi Duarte
>
> That is caused by a bad logical test which I have corrected in the patch
> below(updated on the head). However, this is indicative of another problem
> as the reason it is dying is due to the Slice argument being passed to the
> method in question, being undefined.
>
> ...over to Will
>
> Thanks
>
> Nath
>
>
> Index: BaseFeatureAdaptor.pm
> ===================================================================
> RCS file:
> /nfs/ensembl/cvsroot/ensembl-functgenomics/modules/Bio/EnsEMBL/Funcgen/DBSQL/BaseFeatureAdaptor.pm,v
> retrieving revision 1.65
> diff -u -r1.65 BaseFeatureAdaptor.pm
> --- BaseFeatureAdaptor.pm       16 Jul 2012 12:10:40 -0000      1.65
> +++ BaseFeatureAdaptor.pm       14 Sep 2012 11:52:48 -0000
> @@ -5,7 +5,7 @@
>
>  =head1 LICENSE
>
> -  Copyright (c) 1999-2011 The European Bioinformatics Institute and
> +  Copyright (c) 1999-2012 The European Bioinformatics Institute and
>    Genome Research Limited.  All rights reserved.
>
>    This software is distributed under a modified Apache license.
> @@ -132,8 +132,8 @@
>
>    my @result;
>
> -  if(!ref($slice) || !$slice->isa("Bio::EnsEMBL::Slice")) {
> -    throw("Bio::EnsEMBL::Slice argument expected.");
> +  if(! (ref($slice) && $slice->isa('Bio::EnsEMBL::Slice')) {
> +    throw('Bio::EnsEMBL::Slice argument expected.');
>    }
>
>    $constraint ||= '';
>
>
>
>
>
> On 14 Sep 2012, at 12:44, Duarte Molha wrote:
>
> Dear developers,
>
> I am sorry to bother you again (especially Will J ) but in testing the
> VEP26, I got a crash using the command:
>
> perl variant_effect_predictor.pl -i input_variants.vcf.gz -o output.ann
> --config vep.ini
>
> Here is the error output:
>
> 2012-09-14 12:29:30 - Reading regulatory data from cache and/or database
> [==================================>
> ]   [ 22% ]
> Can't call method "isa" on unblessed reference at
> /NGS_Tools/bin/VEP_26_testing/Bio/EnsEMBL/Funcgen/DBSQL/BaseFeatureAdaptor.pm
> line 135, <GEN0> line 28406.
>
> In attachment is the config file I use.
>
> Best regards,
>
> Duarte Molha
>
> <vep.ini>_______________________________________________
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> Nathan Johnson
> Senior Scientific Programmer
> Ensembl Regulation
> European Bioinformatics Institute
> Wellcome Trust Genome Campus
> Hinxton
> Cambridge CB10 1SD
>
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