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appris method on Transcript

Marek Szuba requested to merge appris into master

Created by: tgrego

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

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

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