[ensembl-dev] N in motif issue

[Daniel Zerbino]

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):
>
> 292326168.GT
>
> http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&highlight=hg19.chr2%3A92326168-92326168&position=chr2%3A92326123-92326212 
> <http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&highlight=hg19.chr2:92326168-92326168&position=chr2:92326123-92326212> 
>
>
> 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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