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Bugfix/pf multispecies db

Marek Szuba requested to merge bugfix/pf_multispecies_db into release/93

Created by: premanand17

Requirements

  • Filling out the template is required. Any pull request that does not include enough information to be reviewed in a timely manner may be closed at the maintainers' discretion;
  • 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
    • if you change the schema you must patch the test databases as well, see Updating the schema
    • the PR must not fail unit testing

Description

In e!92 ProteinFeatureAdaptor.pm was updated to be a BaseAlignFeatureAdaptor rather than a BaseAdaptor to support GIFTS import, with a side effect of failing for collection databases. There is already a hack in place for feature types that needs to be restricted to species_id (in coord_system table), which helps the UnmappedObjectAdaptor to get around it. Similar workaround is implemented for BaseAlignFeatureAdaptor.

Use case

The production pipeline (VEP cache creation pipeline on EG collection databases) and the transcript pages for species that are in collection db failed with similar error messages ( 'Unknown column 'pf.seq_region_id' in 'where clause' at BaseAdaptor.pm).

Benefits

Both the above use cases works with the changes in place.

Possible Drawbacks

None.

Testing

Yes

If so, do the tests pass/fail?

Pass

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