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ENSCORESW-2792: one UCSC parser per species

Marek Szuba requested to merge feature/ucsc_parser into master

Created by: magaliruffier

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

Using one or more sentences, describe in detail the proposed changes. Human has a dedicated UCSC parser rather than using the generic one.

Use case

Describe the problem. Please provide an example representing the motivation behind the need for having these changes in place. Mouse has a separate UCSC parser to avoid cross contamination between species. To be consistent, human now also has a separate parser and the generic one is only inherited from. Also updated the naming to remove the camel casing

Benefits

If applicable, describe the advantages the changes will have. It is clearer that every species has a dedicated parser rather than mouse being the exception. It will also make it easier to add more species if we so desired.

Possible Drawbacks

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

Testing

Have you added/modified unit tests to test the changes? Pipeline has been run on mouse and human, all UCSC xrefs were correctly updated.

If so, do the tests pass/fail?

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

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