Closed apetkau closed 5 years ago
It looks like the command-line option --exclude-resistance-phenotypes is not quite working out. This should have the behaviour of excluding the Predicted Phenotype columns, but they are still present for the Summary and Detailed_Summary results.
--exclude-resistance-phenotypes
This command-line option works by selecting whether or not we are using the AMRDetectionSummary.py or AMRDetectionSummaryResistance.py classes (in https://github.com/phac-nml/staramr/blob/befb44bda34e6691c0df744547146604971b3efb/staramr/detection/AMRDetectionFactory.py#L31).
AMRDetectionSummary.py
AMRDetectionSummaryResistance.py
To fix, you may need to shift some of the code in the AMRDetectionSummary.py class which adds the Predicted Phenotype column down to the subclass AMRDetectionSummaryResistance.py.
Fixed in #67
apetkau
commented
5 years ago
It looks like the command-line option
--exclude-resistance-phenotypesis not quite working out. This should have the behaviour of excluding the Predicted Phenotype columns, but they are still present for the Summary and Detailed_Summary results.This command-line option works by selecting whether or not we are using the
AMRDetectionSummary.pyorAMRDetectionSummaryResistance.pyclasses (in https://github.com/phac-nml/staramr/blob/befb44bda34e6691c0df744547146604971b3efb/staramr/detection/AMRDetectionFactory.py#L31).To fix, you may need to shift some of the code in the AMRDetectionSummary.py class which adds the Predicted Phenotype column down to the subclass AMRDetectionSummaryResistance.py.