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RFAMParser: relax selection criteria on analysis.logic_name

Marek Szuba requested to merge bugfix/rfamparser_analysis_logic_name into master

Created by: mkszuba


Update analysis.logic_name selection criteria in RFAMParser to account for ncRNA-related changes made during release 98.

Issue: ENSINT-402

Use case

Due to changes in the structure of the production database, since release 98 the value of analysis.logic_name corresponding to non-coding RNA can be either 'ncrna' (which is what we used before) or 'ncrna_species_name'. Change the SQL query used to map RFAM IDs to Ensembl stable IDs so that it can correctly handle species using the latter syntax, i.e. human, mouse and zebrafish.


Will be able to load RFAM xrefs for human, mouse and zebrafish again.

Possible Drawbacks

None I can think of, we should probably rebase feature/xref_sprint against master before merging it in anyway.


Have you added/modified unit tests to test the changes?


If so, do the tests pass/fail?


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

No, there are no unit tests for RFAMParser. I have, however, tested the updated SQL query against homo_sapiens_core_97_38, homo_sapiens_core_98_38 and homo_sapiens_core_99_38 (the first two on the public MySQL server, the last one on staging); returns a non-empty set on all three.

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