If a user tries to request a cds or protein type in the sequence endp…

Created by: lairdm

…oint using an exon id, that should be an error. We don't know what transcript to associate with that exon.

We don't need to create an entire top level elsif for Bio::EnsEMBL::Exon, that would cause duplication of the default behaviour code for all other 'type' arguments. If in the future the logic becomes more complex, then yes Exons can get their on entry in the Gene, Transcript, etc top level if/else statements. But this is a very specific corner case.

Requirements

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• 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
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Description

If a user tries to request a cds or protein type in the sequence endpoint using an exon id, that should be an error. We don't know what transcript to associate with that exon. So... throw an error.

Use case

A user does type=protein or type=cds on the sequence endpoint with an exon id, that's lunacy. Lunacy, I tell you!

Benefits

Users won't think they're getting exons with the UTR trimmed, when they're not.

Possible Drawbacks

Break legacy code that doesn't take it in to account.

Testing

Added tests for this situation, plus a successful exon retrieval test which never existed.

If so, do the tests pass/fail?

Pass

Changelog

[/sequence/id] Retrieving sequence using an exon id and types protein or cds now return an error, this combination of parameters is not valid.