Skip to content

ENSCORESW-2553: retrieve correct accession for peptides

Marek Szuba requested to merge bugfix/refseq_coordinate 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. Retrieve RefSeq accessions for peptide when it is not stored as a stable ID

Use case

Describe the problem. Please provide an example representing the motivation behind the need for having these changes in place. For some species, the refseq_import format changes. The stable id is a randomly generated unique ID and the refseq accession is stored as an xref. The code was updated to deal with this change but only transcript accessions were correctly retrieved. This change deals with the peptide accessions.

Benefits

If applicable, describe the advantages the changes will have. We have RefSeq accessions for peptides.

Possible Drawbacks

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

Testing

Have you added/modified unit tests to test the changes? This was tested on the latest human refseq import in the new format and correctly stores the accessions and versions.

If so, do the tests pass/fail? The results are now as expected

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

Merge request reports