def testPointfinderSingleMultipleGeneSame(self):
df = pd.DataFrame([
[
'file1', 'gyrA', 'codon', 67, 'GCC -> CCC (A -> P)', 99.96,
100.0, '2637/2637'
],
[
'file1', 'gyrA', 'codon', 67, 'GCC -> CCC (A -> P)', 99.96,
100.0, '2637/2637'
],
],
columns=self.columns_pointfinder)
files = ['file1']
amr_detection_summary = AMRDetectionSummary(
files, self.resfinder_table_empty,
self.quality_module_table_single_file, df,
self.plasmidfinder_table_empty)
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, gyrA', summary['Genotype'].iloc[0],
'Genes not equal')
def testResfinderSingleGene(self):
amr_detection_summary = AMRDetectionSummary(self.resfinder_table1_files, self.resfinder_table1)
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', summary['Genotype'].iloc[0], 'Genes not equal')
def testPointfinderSingleMultipleGene(self):
amr_detection_summary = AMRDetectionSummary(self.pointfinder_table_multiple_gene_files,
self.resfinder_table_empty, self.pointfinder_table_multiple_gene)
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, gyrAB', summary['Genotype'].iloc[0], 'Genes not equal')
def testResfinderMultipleSameGeneSameResistance(self):
amr_detection_summary = AMRDetectionSummary(self.resfinder_table_mult_same_gene_same_resistance_files,
self.resfinder_table_mult_same_gene_same_resistance)
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, blaIMP-42', summary['Genotype'].iloc[0], 'Genes not equal')
def testResfinderSingleGeneWithNegativesIncluded(self):
files = ['file1', 'file2']
amr_detection_summary = AMRDetectionSummary(files, self.resfinder_table1)
summary = amr_detection_summary.create_summary(True)
self.assertEqual(2, len(summary.index), 'Invalid number of rows in results')
self.assertEqual('file1', summary.index[0], 'File name not equal')
self.assertEqual('blaIMP-42', summary['Genotype'].iloc[0], 'Genes not equal')
self.assertEqual('file2', summary.index[1], 'Negative file not included')
self.assertEqual('None', summary['Genotype'].iloc[1], 'Negative gene not valid')
def testResfinderMultipleFile(self):
amr_detection_summary = AMRDetectionSummary(self.resfinder_table_mult_file_files,
self.resfinder_table_mult_file)
summary = amr_detection_summary.create_summary()
self.assertEqual(2, len(summary.index), 'Invalid number of rows in results')
self.assertEqual('file1', summary.index[0], 'File name not equal')
self.assertEqual('blaIMP-42, newGene', summary['Genotype'].iloc[0], 'Genes not equal')
self.assertEqual('file2', summary.index[1], 'File name not equal')
self.assertEqual('blaIMP-42', summary['Genotype'].iloc[1], 'Genes not equal')
def testPlasmidfinderSingleGene(self):
amr_detection_summary = AMRDetectionSummary(
self.plasmidfinder_table1_files, self.resfinder_table_empty,
self.quality_module_table_file_4, self.plasmidfinder_table1)
summary = amr_detection_summary.create_summary()
self.assertEqual(1, len(summary.index),
'Invalid number of rows in results')
self.assertEqual('file4', summary.index[0], 'File name not equal')
self.assertEqual('IncFIB(S)', summary['Genotype'].iloc[0],
'Genes not equal')
def testPlasmidfinderMultipleSameGeneSameResistance(self):
amr_detection_summary = AMRDetectionSummary(
self.plasmidfinder_table_mult_same_gene_same_resistance_files,
self.resfinder_table_empty, self.quality_module_table_file_4,
self.plasmidfinder_table_mult_same_gene_same_resistance)
summary = amr_detection_summary.create_summary()
self.assertEqual(1, len(summary.index),
'Invalid number of rows in results')
self.assertEqual('file4', summary.index[0], 'File name not equal')
self.assertEqual('IncFIB(S), IncFII(S)', summary['Genotype'].iloc[0],
'Genes not equal')
def testPointfinderResfinderSingleGene(self):
files = ['file1']
amr_detection_summary = AMRDetectionSummary(
files, self.resfinder_table1,
self.quality_module_table_single_file, self.pointfinder_table,
self.plasmidfinder_table_empty)
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')
def testResfinderMultipleGeneResistance(self):
amr_detection_summary = AMRDetectionSummary(
self.resfinder_table_mult_resistance_files,
self.resfinder_table_mult_resistance,
self.quality_module_table_single_file,
self.plasmidfinder_table_empty)
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, newGene', summary['Genotype'].iloc[0],
'Genes not equal')
def testPlasmidfinderSingleGeneWithNegativesIncluded(self):
files = ['file4', 'file5']
amr_detection_summary = AMRDetectionSummary(
files, self.resfinder_table_empty,
self.quality_module_table_file_4_and_5, self.plasmidfinder_table1)
summary = amr_detection_summary.create_summary(True)
self.assertEqual(2, len(summary.index),
'Invalid number of rows in results')
self.assertEqual('file4', summary.index[0], 'File name not equal')
self.assertEqual('IncFIB(S)', summary['Genotype'].iloc[0],
'Genes not equal')
self.assertEqual('file5', summary.index[1],
'Negative file not included')
self.assertEqual('None', summary['Genotype'].iloc[1],
'Negative gene not valid')
def testResfinderSingleGeneWithTwoNegativesIncludedDifferentOrder(self):
files = ['file2', 'file1', 'file3']
amr_detection_summary = AMRDetectionSummary(
files, self.resfinder_table1,
self.quality_module_table_three_files,
self.plasmidfinder_table_empty)
summary = amr_detection_summary.create_summary(True)
self.assertEqual(3, len(summary.index),
'Invalid number of rows in results')
self.assertEqual('file1', summary.index[0], 'File name not equal')
self.assertEqual('blaIMP-42', summary['Genotype'].iloc[0],
'Genes not equal')
self.assertEqual('file2', summary.index[1],
'Negative file not included')
self.assertEqual('None', summary['Genotype'].iloc[1],
'Negative gene not valid')
self.assertEqual('file3', summary.index[2],
'Negative file not included')
self.assertEqual('None', summary['Genotype'].iloc[2],
'Negative gene not valid')
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) -> DataFrame:
amr_detection_summary = AMRDetectionSummary(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, pointfinder_dataframe):
amr_detection_summary = AMRDetectionSummary(files, resfinder_dataframe,
pointfinder_dataframe)
return amr_detection_summary.create_summary(self._include_negative_results)