def testDetailedSummary_noFinders(self):
amr_detection_summary = AMRDetectionSummaryResistance(
self.resfinder_table1_files,
self.resfinder_table_empty.set_index('Isolate ID'),
self.quality_module_table_file_1,
self.pointfinder_table_empty.set_index('Isolate ID'),
self.plasmidfinder_table_empty.set_index('Isolate ID'))
detailed_summary = amr_detection_summary.create_detailed_summary()
self.assertEqual(2, len(detailed_summary.index),
'Invalid number of rows, expected 2')
self.assertEqual('file1', detailed_summary.index[0],
'File name not equal')
self.assertEqual('file1', detailed_summary.index[1],
'File name not equal')
self.assertEqual('Plasmid', detailed_summary['Data Type'].iloc[0],
'Incorrect Data Type')
self.assertEqual('Resistance', detailed_summary['Data Type'].iloc[1],
'Incorrect Data Type')
self.assertEqual('None', detailed_summary['Gene'].iloc[0],
'Genes not equal')
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')
def testDetailedSummary_noPoint(self):
plasmid_table = self.plasmidfinder_table1
plasmid_table['Isolate ID'] = 'file1'
plasmid_table = plasmid_table.set_index('Isolate ID')
amr_detection_summary = AMRDetectionSummaryResistance(
self.resfinder_table1_files,
self.resfinder_table1.set_index('Isolate ID'),
self.quality_module_table_file_1,
plasmidfinder_dataframe=plasmid_table)
detailed_summary = amr_detection_summary.create_detailed_summary()
self.assertEqual(2, len(detailed_summary.index),
'Invalid number of rows, expected 2')
self.assertEqual('file1', detailed_summary.index[0],
'File name not equal')
self.assertEqual('file1', detailed_summary.index[1],
'File name not equal')
self.assertEqual('Plasmid', detailed_summary['Data Type'].iloc[0],
'Incorrect Data Type')
self.assertEqual('Resistance', detailed_summary['Data Type'].iloc[1],
'Incorrect Data Type')
self.assertEqual('IncFIB(S)', detailed_summary['Gene'].iloc[0],
'Genes not equal')
self.assertEqual('blaIMP-42', detailed_summary['Gene'].iloc[1],
'Genes not equal')
self.assertEqual('', detailed_summary['Predicted Phenotype'].iloc[0],
'Predicted Phenotype not equal')
self.assertEqual('', detailed_summary['Predicted Phenotype'].iloc[1],
'Predicted Phenotype not equal')
def testPointfinderResfinder(self):
amr_detection_summary = AMRDetectionSummaryResistance(self.files, self.resfinder_table, self.pointfinder_table)
summary = amr_detection_summary.create_summary()
self.assertEqual(1, len(summary.index), 'Invalid number of rows in results')
self.assertEqual('file1', summary.index[0], 'File name not equal')
self.assertEqual('blaIMP-42, gyrA', summary['Genotype'].iloc[0], 'Genes not equal')
self.assertEqual('ampicillin, amoxi/clav, cefoxitin, ceftriaxone, meropenem, ciprofloxacin I/R, nalidixic acid',
summary['Predicted Phenotype'].iloc[0], 'Phenotypes not equal')
def testResfinderDuplicateResistances(self):
amr_detection_summary = AMRDetectionSummaryResistance(self.files, self.resfinder_table_duplicate_resistances)
summary = amr_detection_summary.create_summary()
self.assertEqual(1, len(summary.index), 'Invalid number of rows in results')
self.assertEqual('file1', summary.index[0], 'File name not equal')
self.assertEqual('blaCTX-M-55, blaIMP-42', summary['Genotype'].iloc[0], 'Genes not equal')
self.assertEqual('ampicillin, ceftriaxone',
summary['Predicted Phenotype'].iloc[0], 'Phenotypes not equal')
def testPointfinder(self):
amr_detection_summary = AMRDetectionSummaryResistance(self.files, self.resfinder_table_empty,
self.pointfinder_table)
summary = amr_detection_summary.create_summary()
self.assertEqual(1, len(summary.index), 'Invalid number of rows in results')
self.assertEqual('file1', summary.index[0], 'File name not equal')
self.assertEqual('gyrA', summary['Genotype'].iloc[0], 'Genes not equal')
self.assertEqual('ciprofloxacin I/R, nalidixic acid',
summary['Predicted Phenotype'].iloc[0], 'Phenotypes not equal')
def _create_detailed_amr_summary(self, files: List[str], resfinder_dataframe: DataFrame, quality_module_dataframe: DataFrame,
pointfinder_dataframe: Optional[BlastResultsParserPointfinder],
plasmidfinder_dataframe: DataFrame, mlst_dataframe) -> DataFrame:
amr_detection_summary = AMRDetectionSummaryResistance(files, resfinder_dataframe,quality_module_dataframe,
pointfinder_dataframe, plasmidfinder_dataframe, mlst_dataframe)
return amr_detection_summary.create_detailed_summary(self._include_negative_results)
def _create_amr_summary(self, files, resfinder_dataframe, quality_module_dataframe,pointfinder_dataframe, plasmidfinder_dataframe, mlst_dataframe):
amr_detection_summary = AMRDetectionSummaryResistance(files, resfinder_dataframe,quality_module_dataframe,pointfinder_dataframe,
plasmidfinder_dataframe, mlst_dataframe)
return amr_detection_summary.create_summary(self._include_negative_results)
def testDetailedSummary_multiFiles(self):
amr_detection_summary = AMRDetectionSummaryResistance(
self.detailed_summary_multi_files,
self.resfinder_table_mult_file.set_index('Isolate ID'),
self.quality_module_table_file_1_and_2_and_4_and_5,
self.pointfinder_table_multiple_gene.set_index('Isolate ID'),
self.plasmidfinder_table_mult_file.set_index('Isolate ID'))
detailed_summary = amr_detection_summary.create_detailed_summary()
self.assertEqual(12, len(detailed_summary.index),
'Invalid number of rows, expected 12')
self.assertEqual('file1', detailed_summary.index[0],
'File name not equal')
self.assertEqual('file1', detailed_summary.index[4],
'File name not equal')
self.assertEqual('file2', detailed_summary.index[5],
'File name not equal')
self.assertEqual('file2', detailed_summary.index[6],
'File name not equal')
self.assertEqual('file4', detailed_summary.index[7],
'File name not equal')
self.assertEqual('file4', detailed_summary.index[9],
'File name not equal')
self.assertEqual('file5', detailed_summary.index[10],
'File name not equal')
self.assertEqual('file5', detailed_summary.index[11],
'File name not equal')
self.assertEqual('Plasmid', detailed_summary['Data Type'].iloc[0],
'Incorrect Data Type')
self.assertEqual('Resistance', detailed_summary['Data Type'].iloc[1],
'Incorrect Data Type')
self.assertEqual('Plasmid', detailed_summary['Data Type'].iloc[5],
'Incorrect Data Type')
self.assertEqual('Resistance', detailed_summary['Data Type'].iloc[6],
'Incorrect Data Type')
self.assertEqual('Plasmid', detailed_summary['Data Type'].iloc[8],
'Incorrect Data Type')
self.assertEqual('Resistance', detailed_summary['Data Type'].iloc[9],
'Incorrect Data Type')
self.assertEqual('Plasmid', detailed_summary['Data Type'].iloc[10],
'Incorrect Data Type')
self.assertEqual('Resistance', detailed_summary['Data Type'].iloc[11],
'Incorrect Data Type')
self.assertEqual('None', detailed_summary['Gene'].iloc[0],
'Genes not equal')
self.assertEqual('blaIMP-42', detailed_summary['Gene'].iloc[1],
'Genes not equal')
self.assertEqual('None', detailed_summary['Gene'].iloc[5],
'Genes not equal')
self.assertEqual('blaIMP-42', detailed_summary['Gene'].iloc[6],
'Genes not equal')
self.assertEqual('IncFIB(S)', detailed_summary['Gene'].iloc[7],
'Genes not equal')
self.assertEqual('None', detailed_summary['Gene'].iloc[9],
'Genes not equal')
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')