[ensembl-dev] WARNNING FunMotifs Plugin
Souhila Amanzougarene
souhila.amanzougarene at cnrs.fr
Mon Apr 6 18:40:34 BST 2020
Hello,
I'm Souhila AMANZOUGARENE, a bioinformatician in the UMR 8199 from CNRS
(France).
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
by:
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
Bio-Informaticienne
UMR CNRS 1283
(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
59045 LILLE CEDEX
FRANCE
souhila.amanzougarene at cnrs.fr
03 74 00 81 05
http://www.good.cnrs.fr/ - http://www.egid.fr/
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