[ensembl-dev] DNAMethylationFeature

[Sungsam Gong]

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