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Feature/biotype update to keep legacy biotype()

Marek Szuba requested to merge github/fork/tgrego/feature/biotype into master

Created by: tgrego


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    • do not modify code without testing for regression
    • provide simple unit tests to test the changes
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One or more sentences describing in detail the proposed changes.

Recent addition of Biotype objects used the old biotype method in gene and transcript. This proven not to be 100% backwards compatible, so this is to include legacy biotype() dealing with the biotype name string, together with new get_Biotype and set_Biotype methods that deal with biotype objects.

Use case

Describe the problem. Please provide an example representing the motivation behind the need for having these changes in place.

to_json($gene->biotype) would refuse to do it's job because $gene->biotype was returning an object, even though that object would behave as a string if to_json would make the effort to try it... Now we bring $gene->biotype back to being a real string, and provide new methods to deal with objects.


Backwards compatibility

Possible Drawbacks

If applicable, describe any possible undesirable consequence of the changes.

Might have missed something


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


If so, do the tests pass/fail?

Pass, of course.

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


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