[ensembl-dev] DNAMethylationFeature

[njohnson]

I should also say that these data are contained in flat files, and normally only used by the webcode to draw the methylation tracks. Hence to access them via the API you will need to have access to a copy of those files from our ftp site and add the following entry to the meta_table:

	insert into meta values(NULL, 1, 'dbfile.data_root', '/path/to/your/assembly/specific/data/dir/');  

This is absent from the DB as it is normally over-ridden by the webcode, and would only contain something specific to our internal infrastructure which would be useless to other users.

In that directory you should have the dna_methylation_feature directory from our ftp site:

	ftp://ftp.ensembl.org/pub/release-77/data_files/homo_sapiens/GRCh38/

I hope this helps.

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/
http://twitter.com/#!/ensembl
https://www.facebook.com/Ensembl.org

On 27 Nov 2014, at 14:25, njohnson <njohnson at ebi.ac.uk> wrote:

> 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/
> http://twitter.com/#!/ensembl
> https://www.facebook.com/Ensembl.org
> 
> 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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>