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

[andrew126 at mac.com]

Hi Michael,

Thanks for the fix.  Seems to work ok now .. smile.

Best,

Andrew

> On May 2, 2017, at 9:09 AM, Michael Nuhn <mnuhn at ebi.ac.uk> wrote:
> 
> Hello Andrew,
> 
> sorry for the late reply.
> 
> This is a bug in our api. I have just pushed a fix to our release/88 branch.
> 
> Can you please do a
> 
> ```
> git pull
> ```
> 
> of the ensembl-funcgen repository?
> 
> The script should work after that.
> 
> Sorry again for the long wait!
> 
> Michael.
> 
> 
> On 25/04/17 18:08, andrew126 at mac.com wrote:
>> 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)
>> 
>> 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.
>> 
>> 
>> 
>> 
>> _______________________________________________
>> Dev mailing list    Dev at ensembl.org
>> Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev
>> Ensembl Blog: http://www.ensembl.info/
>> 
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/