From 638c9babc66aa084e81a44ae57708995657b3d17 Mon Sep 17 00:00:00 2001 From: Eric Marinier Date: Mon, 10 Jul 2023 15:29:24 -0500 Subject: [PATCH 1/3] Updating enterobacteriaceae to enterobacteriales. --- staramr/blast/plasmidfinder/PlasmidfinderBlastDatabase.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/staramr/blast/plasmidfinder/PlasmidfinderBlastDatabase.py b/staramr/blast/plasmidfinder/PlasmidfinderBlastDatabase.py index d32137b..38297fe 100644 --- 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', 'enterobacteriales'] @classmethod def get_config_table(cls, database_dir: str) -> pd.DataFrame: From 0cdb20fd481478ea19bc71026d80b0f95b0914d0 Mon Sep 17 00:00:00 2001 From: Eric Marinier Date: Mon, 17 Jul 2023 11:18:14 -0500 Subject: [PATCH 2/3] Removing duplicate. --- staramr/blast/plasmidfinder/PlasmidfinderBlastDatabase.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/staramr/blast/plasmidfinder/PlasmidfinderBlastDatabase.py b/staramr/blast/plasmidfinder/PlasmidfinderBlastDatabase.py index 38297fe..f9a2708 100644 --- 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', 'enterobacteriales', 'enterobacteriales'] + return ['gram_positive', 'enterobacteriales'] @classmethod def get_config_table(cls, database_dir: str) -> pd.DataFrame: From c8b7a86c207b01f28827fcf1748dd73b599a3406 Mon Sep 17 00:00:00 2001 From: Eric Marinier Date: Mon, 17 Jul 2023 11:20:33 -0500 Subject: [PATCH 3/3] Updating changelog. --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index ddc7dcf..894a306 100644 --- 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. # Version 0.9.1