[ensembl-dev] Bio/EnsEMBL/Funcgen/DBSQL/SegmentationFeatureAdaptor.pm not included in API 88?

andrew126 at mac.com andrew126 at mac.com
Tue Apr 25 18:08:59 BST 2017


Hi,

I am using API version 88.

Compared to version 86, ensembl-funcgen/modules/Bio/EnsEMBL/Funcgen/DBSQL/ no longer contains SegmentationFeatureAdaptor.pm.

This is causing the API to complain/fail when I perform

	my $annotated_features = $current_annotated_feature_set->get_Features_by_Slice($slice);

	(as described on http://www.ensembl.org/info/docs/api/funcgen/regulation_tutorial.html <http://www.ensembl.org/info/docs/api/funcgen/regulation_tutorial.html>)

The error is shown below.

Is there a revised call that should be used for version 88?  Is there something else I’m doing wrong?

Thanks for any help.

Best regards,

Andrew	



-------------------- WARNING ----------------------
MSG: 'Bio::EnsEMBL::Funcgen::DBSQL::SegmentationFeatureAdaptor' cannot be found.
Exception Can't locate Bio/EnsEMBL/Funcgen/DBSQL/SegmentationFeatureAdaptor.pm in @INC (you may need to install the Bio::EnsEMBL::Funcgen::DBSQL::SegmentationFeatureAdaptor module) (@INC contains: /home/andrew/gte/src_88/bioperl-live /home/andrew/gte/src_88/ensembl/modules /home/andrew/gte/src_88/ensembl-io/modules /home/andrew/gte/src_88/ensembl-compara/modules /home/andrew/gte/src_88/ensembl-variation/modules /home/andrew/gte/src_88/ensembl-funcgen/modules /home/andrew/gte/src_88/lib/perl/5.18.2/ /home/andrew/gte/src_88/share/perl/5.18.2/ /home/andrew/gte/src_88/lib/perl5/x86_64-linux-gnu-thread-multi/ /etc/perl /usr/local/lib/perl/5.18.2 /usr/local/share/perl/5.18.2 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.18 /usr/share/perl/5.18 /usr/local/lib/site_perl .) at (eval 493) line 2.


FILE: Bio/EnsEMBL/Registry.pm LINE: 1174
CALLED BY: EnsEMBL/DBSQL/DBAdaptor.pm  LINE: 989
Date (localtime)    = Tue Apr 25 12:45:25 2017
Ensembl API version = 88
---------------------------------------------------

-------------------- WARNING ----------------------
MSG: Could not find SegmentationFeature adaptor in the registry for homo_sapiens funcgen

FILE: EnsEMBL/DBSQL/DBAdaptor.pm LINE: 992
CALLED BY: EnsEMBL/Funcgen/FeatureSet.pm  LINE: 256
Date (localtime)    = Tue Apr 25 12:45:25 2017
Ensembl API version = 88
---------------------------------------------------

-------------------- EXCEPTION --------------------
MSG: Could not get adaptor SegmentationFeature for homo_sapiens funcgen

STACK Bio::EnsEMBL::DBSQL::DBAdaptor::AUTOLOAD /home/andrew/gte/src_88/ensembl/modules/Bio/EnsEMBL/DBSQL/DBAdaptor.pm:996
STACK Bio::EnsEMBL::Funcgen::FeatureSet::get_FeatureAdaptor /home/andrew/gte/src_88/ensembl-funcgen/modules/Bio/EnsEMBL/Funcgen/FeatureSet.pm:256
STACK Bio::EnsEMBL::Funcgen::FeatureSet::get_Features_by_Slice /home/andrew/gte/src_88/ensembl-funcgen/modules/Bio/EnsEMBL/Funcgen/FeatureSet.pm:280
Etc.


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