[ensembl-dev] N in motif issue

[Konrad Karczewski]

Ah, great thanks!



-Konrad

On Fri, May 29, 2015 at 4:19 AM, njohnson <njohnson at ebi.ac.uk> wrote:

> 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
> http://www.ensembl.info/
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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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