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Backport JGI_ProteinParser (and JGI_Parser) from ensembl-xref

Marek Szuba requested to merge backport/ENSCORESW-3214 into feature/xref_sprint

Created by: mkszuba

Description

Port changes made to JGI_Parser (base package) and JGI_ProteinParser (the actual parser) in ensembl-xref, including unit tests, back to ensembl:feature/xref_sprint. Merge the latter into the former.

Use case

See ENSCORESW-3214. Originally worked on by Alessandro.

Benefits

Salvage more work from the 2018 xref sprint.

Possible Drawbacks

Increased test-suite run time (note: Travis does not automatically execute tests from misc-scripts/xref_mapping yet).

Testing

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

Yes.

If so, do the tests pass/fail?

They pass.

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

Yes (including tests from misc-scripts/xref_mapping), no regression detected.

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