[ensembl-dev] DNAMethylationFeature

njohnson njohnson at ebi.ac.uk
Thu Nov 27 14:25:19 GMT 2014


Hi

The DNAMethylationFeatureAdaptor uses the BigBedAdaptor which is now located in the ensembl-webcode repository. So you will need to check that out and add it to your PERL5LIB.


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 27 Nov 2014, at 11:02, Sungsam Gong <gong.sungsam at gmail.com> wrote:

> Hi,
> 
> While trying to load 'DNAMethylationFeatureAdaptor', it failed with
> following error message:
> 
> -------------------- WARNING ----------------------
> MSG: 'Bio::EnsEMBL::Funcgen::DBSQL::DNAMethylationFeatureAdaptor'
> cannot be found.
> Exception Can't locate
> Bio/EnsEMBL/ExternalData/BigFile/BigBedAdaptor.pm in @INC (@INC
> contains: /data/Install/Perl/ensembl-compara/modules
> /data/Install/Perl/ensembl-funcgen/modules
> /data/Install/Perl/ensembl-variation/modules
> /data/Install/Perl/ensembl/modules /data/Install/Perl/bioperl-live
> /data/Develop/Gloria /data/Install/Perl/ensembl-compara/modules
> /data/Install/Perl/ensembl-variation/modules
> /data/Install/Perl/ensembl/modules /data/Install/Perl/bioperl-live
> /data/Develop/Gloria
> /home/MINTS/ssg29/perl5/lib/perl5/x86_64-linux-gnu-thread-multi
> /home/MINTS/ssg29/perl5/lib/perl5
> /data/Install/Perl/ensembl-compara/modules
> /data/Install/Perl/ensembl-variation/modules
> /data/Install/Perl/ensembl/modules /data/Install/Perl/bioperl-live
> /data/Develop/Gloria /etc/perl /usr/local/lib/perl/5.14.2
> /usr/local/share/perl/5.14.2 /usr/lib/perl5 /usr/share/perl5
> /usr/lib/perl/5.14 /usr/share/perl/5.14 /usr/local/lib/site_perl .) at
> /data/Install/Perl/ensembl-funcgen/modules/Bio/EnsEMBL/Funcgen/DBSQL/DNAMethylationFeatureAdaptor.pm
> line 97.
> BEGIN failed--compilation aborted at
> /data/Install/Perl/ensembl-funcgen/modules/Bio/EnsEMBL/Funcgen/DBSQL/DNAMethylationFeatureAdaptor.pm
> line 97.
> Compilation failed in require at (eval 72) line 2.
> 
> 
> FILE: Bio/EnsEMBL/Registry.pm LINE: 1040
> CALLED BY: Placentome/bin/get_encode_methylome.pl  LINE: 65
> Date (localtime)    = Thu Nov 27 10:49:20 2014
> Ensembl API version = 75
> ---------------------------------------------------
> 
> Below shows line 65 where the error was caught:
> my $met_adaptor = $reg->get_adaptor('human','funcgen','DNAMethylationFeature');
> 
> Actually, as shown in the warning message,
> 'Bio/EnsEMBL/ExternalData/BigFile/BigBedAdaptor.pm' is not in @INC,
> which seems required from DNAMethylationFeatureAdaptor.pm:
> use Bio::EnsEMBL::ExternalData::BigFile::BigBedAdaptor;
> 
> It seems only BlastAdaptor.pm and ExternalFeatureAdaptor.pm are
> available from Bio/EnsEMBL/External chain. Where can I find/install
> use Bio::EnsEMBL::ExternalData::BigFile::BigBedAdaptor? Is there
> external dependency to retreive Encode methylation data via
> Bio::EnsEMBL::Funcgen?
> 
> Regards,
> Sung
> 
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