[ensembl-dev] N in motif issue

[njohnson]

Hi Konrad

I am assuming you are still using v79? In version 80 we put in a stop gap solution to ignore these motifs, so the VEP should not longer die in these cases.  We hope to put in a more robust solution once we have decided on the best approach.

Thanks

Nathan Johnson

Ensembl Regulation
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom

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> On 29 May 2015, at 09:08, Daniel Zerbino <zerbino at ebi.ac.uk> wrote:
> 
> Hello Konrad,
> 
> Thanks, we're working on it now.
> 
> Cheers,
> 
> Daniel
> 
> On 5/29/15 5:36 AM, Konrad Karczewski wrote:
>> Hi Ensembl/VEP team,
>> 
>> Another corner case variant (yay!), though this one doesn't look as bad (or at least is obvious what's going on). Found the following variant (don't ask how):
>> 
>> 2 92326168 . G T
>> 
>> http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&highlight=hg19.chr2%3A92326168-92326168&position=chr2%3A92326123-92326212
>> 
>> that happens to sit near a bunch of N's in the reference genome, which is throwing an error (I'm guessing in looking for motifs) as shown below.
>> 
>> -Konrad
>> 
>> -------------------- EXCEPTION --------------------
>> MSG: Sequence GCTTNNNNNNNNNNNNN contains invalid characters: Only Aa Cc Gg Tt accepted
>> STACK Bio::EnsEMBL::Funcgen::BindingMatrix::relative_affinity /humgen/atgu1/fs03/konradk/vep/ensembl-tools-release-79/scripts/variant_effect_predictor/Bio/EnsEMBL/Funcgen/BindingMatrix.pm:301
>> STACK Bio::EnsEMBL::Variation::MotifFeatureVariationAllele::motif_score_delta /humgen/atgu1/fs03/konradk/vep/ensembl-tools-release-79/scripts/variant_effect_predictor/Bio/EnsEMBL/Variation/MotifFeatureVariationAllele.pm:226
>> STACK Bio::EnsEMBL::Variation::Utils::VEP::mfva_to_line /humgen/atgu1/fs03/konradk/vep/ensembl-tools-release-79/scripts/variant_effect_predictor/Bio/EnsEMBL/Variation/Utils/VEP.pm:2371
>> STACK Bio::EnsEMBL::Variation::Utils::VEP::vfoa_to_line /humgen/atgu1/fs03/konradk/vep/ensembl-tools-release-79/scripts/variant_effect_predictor/Bio/EnsEMBL/Variation/Utils/VEP.pm:2130
>> STACK Bio::EnsEMBL::Variation::Utils::VEP::vf_to_consequences /humgen/atgu1/fs03/konradk/vep/ensembl-tools-release-79/scripts/variant_effect_predictor/Bio/EnsEMBL/Variation/Utils/VEP.pm:1844
>> STACK Bio::EnsEMBL::Variation::Utils::VEP::vf_list_to_cons /humgen/atgu1/fs03/konradk/vep/ensembl-tools-release-79/scripts/variant_effect_predictor/Bio/EnsEMBL/Variation/Utils/VEP.pm:1373
>> STACK Bio::EnsEMBL::Variation::Utils::VEP::get_all_consequences /humgen/atgu1/fs03/konradk/vep/ensembl-tools-release-79/scripts/variant_effect_predictor/Bio/EnsEMBL/Variation/Utils/VEP.pm:1202
>> STACK main::main /humgen/atgu1/fs03/konradk/vep/ensembl-tools-release-79/scripts/variant_effect_predictor/variant_effect_predictor.pl:313
>> STACK toplevel /humgen/atgu1/fs03/konradk/vep/ensembl-tools-release-79/scripts/variant_effect_predictor/variant_effect_predictor.pl:144
>> Date (localtime)    = Wed May 27 18:28:55 2015
>> Ensembl API version = 79
>> 
>> 
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