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Use seq_region_start and seq_region_end when updating gene coordinate…

Marek Szuba requested to merge github/fork/thibauthourlier/hotfix/gene_update_coords into master

Created by: thibauthourlier

…oordinates in the database

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. Use seq_region_start and seq_region_end when updating the coordinates of a gene in a database.

Use case

Describe the problem. Please provide an example representing the motivation behind the need for having these changes in place. If the gene is on a sub Slice and start and end are called, they return the start and end relative to the slice. When start and end are used in update_coords, it will then insert the wrong coordinates of the gene in the database.

Benefits

If applicable, describe the advantages the changes will have. It will store the correct coordinates of a gene when updating the coordinates in the database.

Possible Drawbacks

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

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?

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