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phac-nml / staramr

Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.
Apache License 2.0
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Adding Notes to the Resfinder and Pointfinder Outputs #185

Closed emarinier closed 11 months ago

emarinier commented 11 months ago

resfinder.tsv and pointfinder.tsv outputs now have a Notes column that are derived from the CGE drug key database and phenotypes.txt databases (respectively) for each mutation identified.

emarinier commented 11 months ago

Thanks so much @emarinier . This looks great 😄. I still have to test out by running staramr on real data.

1. In addition to adding the unit test cases, could you also add an integration test case. Specifically, adding an `assertEquals` statement to at least one of the lookups of mutations for our test data in our integration test cases?

I believe I've added a couple tests to check this now.

apetkau commented 11 months ago

I ran the test suite on my machine and it is passing. Something is wrong with the GitHub actions tests that we can revisit later.

Two additional comments:

  1. Can you change the column name Notes to CGE Notes? I noticed in the notes there's references to phenotypes and I want to make sure it's more clear that these are referring to the CGE phenotypes.
  2. Can you add the Notes column to the detailed_summary.tsv output?
apetkau commented 11 months ago

Actually, re-thinking this, let's leave Notes out of detailed_summary.tsv. Sorry about that.

emarinier commented 11 months ago

Changed Notes to CGE Notes