Merge pull request #182 from phac-nml/fix/enterobacteriales

Updating Plasmidfinder Blast Database "enterobacteriaceae" to "enterobacteriales"
phac-nml · Jul 21, 2023 · 9861f84 · 9861f84
2 parents 41b9f67 + 4a616b8
commit 9861f84
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -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

diff --git a/staramr/blast/plasmidfinder/PlasmidfinderBlastDatabase.py b/staramr/blast/plasmidfinder/PlasmidfinderBlastDatabase.py
@@ -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: