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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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Include CGE-Predicted Phenotypes for PointFinder results #170

Closed apetkau closed 10 months ago

apetkau commented 1 year ago

As a complement to https://github.com/phac-nml/staramr/pull/167 (which included CGE-Predicted Phenotypes for ResFinder results) it would be nice to do the same thing for the PointFinder results. For example, as shown in the Phenotype column here https://bitbucket.org/genomicepidemiology/pointfinder_db/src/master/salmonella/phenotypes.txt

emarinier commented 1 year ago

As discussed, as far as I can tell, the phenotypes.txt files only exist in newer versions of the database (June 2022 onwards).

Since we don't use this version of the database, I will close this, as instructed. If we update our version of the database used and want to implement this later, the WIP branch is here:

emarinier commented 11 months ago

https://bitbucket.org/genomicepidemiology/pointfinder_db/src/master/salmonella/resistens-overview.txt

The resistens-overview.txt files have a Resistance column that can be used for Pointfinder.

apetkau commented 10 months ago

Fixed in #190