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Merge the output of the 2018 xref sprint

Marek Szuba requested to merge feature/xref_sprint into master

Created by: mkszuba


Merge the output of the 2018 xref sprint into Ensembl mainline.

Important notes:

  • this is a really, really big branch but we have had a review process for merging changes into feature/xref_sprint both during the sprint itself and during the recent merge push. Therefore, there should be no need to review the code too carefully;
  • that said, the current plan is to perform integration testing (i.e. run the whole xref pipeline for a chosen set of species) on feature/xref_sprint and only conduct the merge into master afterwards.

Use case



Cleaner code in quite a few xref parsers, unit tests for same, Mim2Gene and UCSC parsing will not actually work (the relevant parsers on master use long-outdated file formats for same)

Possible Drawbacks

Slight increase in run time for some of the parser.


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

Yes, all the refactored parsers have now got unit tests. Mind you, these are located in misc-scripts/xref_mapping/t rather than modules/t so they a) require their own MultiTestDB.conf and b) may have to be run separately (but at least on my system, running ensembl - i.e. on the whole repo rather than specifically on the test directory - does pick up tests from misc-scripts/xref_mapping).

If so, do the tests pass/fail?

They pass.

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

Yes, no regression.

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