SequenceOntologyMapper deprecation

Created by: tgrego

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• Review the contributing guidelines for this repository; remember in particular:
  • do not modify code without testing for regression
  • provide simple unit tests to test the changes
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Description

This PR deprecates the SequenceOntologyMapper, providing the missing alternative ways to have all the functionality it provides. To get the SO acc of a feature: $feature->feature_so_acc To get the SO acc of a gene/transcript biotype: $feature->get_Biotype->so_acc To get the SO name of a SO acc: $oa = Bio::EnsEMBL::Registry->get_adaptor('multi','ontology','OntologyTerm'); $so_name = $oa->fetch_by_accession($so_acc)->name;

If you want biotype SOs and fallback to feature SOs, implement that logic in your code.

Use case

SequenceOntologyMapper provides a way to access SO terms for biotypes and feature types, through a series of lookup tables. The Gene and Transcript biotype SO terms could already be accessed alternatively using the Biotype object that can be accessed by the get_Biotype method on gene and transcript objects. Feature type SO terms were missing and are now implemented, through the new method feature_so_acc that is inherited and can be overridden by features.

Benefits

Removing the SequenceOntologyMapper

Possible Drawbacks

Although a 'feature' thing, Slice implements feature_so_acc. Slice is however not a feature, but will return either the SO of its coordinate system if available or of a generic region.

Bio::EnsEMBL::Compara::ConstrainedElement was included in the SequenceOntologyMapper. It is however not a feature, and thus will need implementation of feature_so_acc. Attention, this is in ensembl-compara.

GFFSerializer in this repo used the SequenceOntologyMapper and was updated to use the alternative ways, removing the SequenceOntologyMapper requirement. Other modules in ensembl-production and ensembl-io (and maybe more?) make use of SequenceOntologyMapper and require similar updates.

Testing

Have you added/modified unit tests to test the changes?

Yes.

If so, do the tests pass/fail?

Pass, of course.

Have you run the entire test suite and no regression was detected?

Yes.