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Updating Plasmidfinder Blast Database "enterobacteriaceae" to "enterobacteriales" #182

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merged 4 commits into from
Jul 21, 2023
Merged

Updating Plasmidfinder Blast Database "enterobacteriaceae" to "enterobacteriales" #182

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638c9ba
Updating enterobacteriaceae to enterobacteriales.
emarinier Jul 10, 2023
0cdb20f
Removing duplicate.
emarinier Jul 17, 2023
c8b7a86
Updating changelog.
emarinier Jul 17, 2023
4a616b8
Merge branch 'development' into fix/enterobacteriales
apetkau Jul 21, 2023
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -4,6 +4,7 @@
* Adds the ability to handle "complex" pbp5 mutations. When appriopriate many pbp5 point mutations will be reported as a single mutation.
* Resfinder CGE-predicted phenotypes are now reported in the summary and detailed summary alongside existing predictions.
* Corrected a typo in the position for acrB in the PointFinder drug key table.
* Removed "enterobacteriaceae" from the list of supported PlasmindFinder databases.
* Changed the word sensitive to susceptible in outputs.

# Version 0.9.1
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2 changes: 1 addition & 1 deletion staramr/blast/plasmidfinder/PlasmidfinderBlastDatabase.py
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Expand Up @@ -67,7 +67,7 @@ def get_available_databases(cls) -> list:
A Class Method to get a list of plasmidfinder databases that are currently supported by staramr.
:return: The list of database_type currently supported by staramr.
"""
return ['gram_positive', 'enterobacteriaceae', 'enterobacteriales']
return ['gram_positive', 'enterobacteriales']

@classmethod
def get_config_table(cls, database_dir: str) -> pd.DataFrame:
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