appris method on Transcript

[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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Description

See ENSCORESW-2915

There are 3 main available Transcript tags (TSL, GENCODE Basic and APPRIS)
https://www.ensembl.org/info/genome/genebuild/transcript_quality_tags.html
On a Transcript object, the first 2 can be fetched with the tsl() and gencode_basic() methods, but there is no equivalent method to retrieve the appris tags.

This adds the missing appris() to Transcript. It returns the tag string (if available) or undef. This is the same behaviour as in tsl().

Use case

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

Benefits

Easy access to appris tags.

Possible Drawbacks

none I can see

Testing

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

If so, do the tests pass/fail?
pass

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

[coveralls]

Coverage increased (+0.003%) to 81.464% when pulling b0b32e7 on appris into 6699433 on master.

[mkszuba]

Note for future readers: accepting this occurrence of postfix notation for consistency with gencode_basic() and tsl().