[ensembl-dev] WARNNING FunMotifs Plugin

Souhila Amanzougarene souhila.amanzougarene at cnrs.fr
Mon Apr 6 18:40:34 BST 2020


I'm Souhila AMANZOUGARENE, a bioinformatician in the UMR 8199 from CNRS 
I'm using VEP to annotate SNPs in human data and I use many plugins to 
do this. I have tried FunMotifs plugin, but it doesn't seem to work.

Here is the error warning:

WARNING: Failed to compile plugin FunMotifs: Experimental shift on 
scalar is now forbidden at 
/media/Data/Ensembl_hg19/EnsemblVepCache/Plugins/FunMotifs.pm line 106, 
near "$params if"

Compilation failed in require at (eval 79) line 2.

BEGIN failed--compilation aborted at (eval 79) line 2.

I have modified the line 106 code:

shift $params if ($params->[0] =~ /.gz/i); #Removes filename


shift @{$params} if ($params->[0] =~ /.gz/i); #Removes filename

After this change, I do not get a warning but it doesn't annotate with 
the file funmotifs_sorted.bed.gz, and I have blank column for all SNPs.

Could you help me please to find a solution to this problem?

Best regards

Souhila Amanzougarene


(Epi)génomique Fonctionnelle et Physiologie Moléculaire Du Diabète et Maladies Associées

FR3508 European Genomic Institute for Diabetes (E.G.I.D.)
Faculté de médecine - Pôle Recherche

sous sol, Aile Ouest
1 place de Verdun
souhila.amanzougarene at cnrs.fr
03 74 00 81 05

http://www.good.cnrs.fr/ - http://www.egid.fr/

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