diff --git a/CHANGELOG.md b/CHANGELOG.md index ddc7dcf..5ca9519 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. +* Changed the word sensitive to susceptible in outputs. # Version 0.9.1 diff --git a/staramr/results/AMRDetectionSummary.py b/staramr/results/AMRDetectionSummary.py index 296920f..92e1036 100644 --- a/staramr/results/AMRDetectionSummary.py +++ b/staramr/results/AMRDetectionSummary.py @@ -78,7 +78,7 @@ def _get_negative_resistance_entries(self, names_set: Set, resistance_frame: Dat if self._include_phenotype(): negative_resistance_entries = pd.DataFrame( - [[x, 'None', 'Sensitive', '', ''] for x in negative_res_names_set], + [[x, 'None', 'Susceptible', '', ''] for x in negative_res_names_set], columns=negative_columns).set_index('Isolate ID') else: negative_resistance_entries = pd.DataFrame([[x, 'None', '', ''] for x in negative_res_names_set], diff --git a/staramr/results/AMRDetectionSummaryResistance.py b/staramr/results/AMRDetectionSummaryResistance.py index 0ba4c2d..673e4d3 100644 --- a/staramr/results/AMRDetectionSummaryResistance.py +++ b/staramr/results/AMRDetectionSummaryResistance.py @@ -61,7 +61,7 @@ def _get_detailed_negative_columns(self): return ['Isolate ID', 'Gene', 'Predicted Phenotype', 'Start', 'End'] def _get_summary_empty_values(self): - return {'Genotype': 'None', 'Predicted Phenotype': 'Sensitive'} + return {'Genotype': 'None', 'Predicted Phenotype': 'Susceptible'} def _get_summary_resistance_columns(self): return ['Genotype', 'Predicted Phenotype', 'CGE Predicted Phenotype', 'Plasmid'] diff --git a/staramr/subcommand/Search.py b/staramr/subcommand/Search.py index 7d9ccc7..490a48e 100644 --- a/staramr/subcommand/Search.py +++ b/staramr/subcommand/Search.py @@ -124,7 +124,7 @@ def _setup_args(self, arg_parser): default=ExcludeGenesList.get_default_exclude_file(), required=False) report_group.add_argument('--exclude-negatives', action='store_true', dest='exclude_negatives', - help='Exclude negative results (those sensitive to antimicrobials) [False].', + help='Exclude negative results (those susceptible to antimicrobials) [False].', required=False) report_group.add_argument('--exclude-resistance-phenotypes', action='store_true', dest='exclude_resistance_phenotypes', diff --git a/staramr/tests/integration/detection/test_AMRDetectionPlasmid.py b/staramr/tests/integration/detection/test_AMRDetectionPlasmid.py index 992a084..c5310b9 100644 --- a/staramr/tests/integration/detection/test_AMRDetectionPlasmid.py +++ b/staramr/tests/integration/detection/test_AMRDetectionPlasmid.py @@ -199,7 +199,7 @@ def testIndexRangePlasmids(self): self.assertEqual(len(summary_results.index), 1, 'Wrong number of rows') self.assertEqual(summary_results['Genotype'].iloc[0], 'None', msg='Wrong Genotype value') - self.assertEqual(summary_results['Predicted Phenotype'].iloc[0], 'Sensitive', + self.assertEqual(summary_results['Predicted Phenotype'].iloc[0], 'Susceptible', msg='Wrong Predicted Phenotype value') self.assertEqual(summary_results['Plasmid'].iloc[0], 'IncFII(pKPX1)', msg='Wrong Plasmid Type') @@ -217,7 +217,7 @@ def testParseUnderscoresBracketsInFASTA(self): self.assertEqual(len(summary_results.index), 1, 'Wrong number of rows') self.assertEqual(summary_results['Genotype'].iloc[0], 'None', msg='Wrong Genotype value') - self.assertEqual(summary_results['Predicted Phenotype'].iloc[0], 'Sensitive', + self.assertEqual(summary_results['Predicted Phenotype'].iloc[0], 'Susceptible', msg='Wrong Predicted Phenotype value') self.assertEqual(summary_results['Plasmid'].iloc[0], 'rep21', msg='Wrong Plasmid Type') diff --git a/staramr/tests/unit/results/test_AMRDetectionSummary.py b/staramr/tests/unit/results/test_AMRDetectionSummary.py index 89967bd..1a1110b 100644 --- a/staramr/tests/unit/results/test_AMRDetectionSummary.py +++ b/staramr/tests/unit/results/test_AMRDetectionSummary.py @@ -597,7 +597,7 @@ def testDetailedSummary_noRes_noPoint(self): self.assertEqual('None', detailed_summary['Gene'].iloc[1], 'Genes not equal') self.assertEqual('', detailed_summary['Predicted Phenotype'].iloc[0], 'Predicted Phenotype not equal') - self.assertEqual('Sensitive', detailed_summary['Predicted Phenotype'].iloc[1], 'Predicted Phenotype not equal') + self.assertEqual('Susceptible', detailed_summary['Predicted Phenotype'].iloc[1], 'Predicted Phenotype not equal') def testDetailedSummary_noRes_noPlasmid(self): point_table = self.pointfinder_table @@ -676,7 +676,7 @@ def testDetailedSummary_noFinders(self): self.assertEqual('None', detailed_summary['Gene'].iloc[1], 'Genes not equal') self.assertEqual('', detailed_summary['Predicted Phenotype'].iloc[0], 'Predicted Phenotype not equal') - self.assertEqual('Sensitive', detailed_summary['Predicted Phenotype'].iloc[1], 'Predicted Phenotype not equal') + self.assertEqual('Susceptible', detailed_summary['Predicted Phenotype'].iloc[1], 'Predicted Phenotype not equal') def testDetailedSummary_multiFiles(self): amr_detection_summary = AMRDetectionSummaryResistance(self.detailed_summary_multi_files, @@ -726,8 +726,8 @@ def testDetailedSummary_multiFiles(self): self.assertEqual('IncFIB(K)', detailed_summary['Gene'].iloc[10], 'Genes not equal') self.assertEqual('None', detailed_summary['Gene'].iloc[11], 'Genes not equal') - self.assertEqual('Sensitive', detailed_summary['Predicted Phenotype'].iloc[9], 'Predicted Phenotype not equal') - self.assertEqual('Sensitive', detailed_summary['Predicted Phenotype'].iloc[11], 'Predicted Phenotype not equal') + self.assertEqual('Susceptible', detailed_summary['Predicted Phenotype'].iloc[9], 'Predicted Phenotype not equal') + self.assertEqual('Susceptible', detailed_summary['Predicted Phenotype'].iloc[11], 'Predicted Phenotype not equal') def testSimplifyingPointfinderMutations(self): df = pd.DataFrame([