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

Michael Nuhn mnuhn at ebi.ac.uk
Tue May 2 17:09:56 BST 2017


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.
>
>
>
>
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