def test_validate_input_values(self): # should not raise error _validate_input_columns(md, "ind", "Group", "Time", None) _validate_input_columns(md, "ind", None, None, None) _validate_input_values(md, "Value", "ind", "Group", "Time", None, None) with self.assertRaisesRegex(ValueError, "state_1 and state_2"): _validate_input_values(md, "Value", "ind", "Group", "Time", 1, 1) with self.assertRaisesRegex(ValueError, "not present"): _validate_input_values(md, "Value", "ind", "Group", "Time", 1, 3) with self.assertRaisesRegex(ValueError, "not a column"): _validate_input_values(md, "Value", "ind", "Group", "Days", 1, 2) with self.assertRaisesRegex(ValueError, "not a column"): _validate_input_columns(md, "ind", ["Group", "More stuff"], "Time", "Value") with self.assertRaisesRegex(ValueError, "unique values"): _validate_input_columns(md, "ind", "Time", "Time", "Value") with self.assertRaisesRegex(ValueError, "state_column must contain"): _validate_input_columns( md[md['Time'] == 1], "ind", "Group", "Time", "Value") dropped = md.drop(['9', '10', '11']) with self.assertRaisesRegex(ValueError, "not represented"): _validate_input_values( dropped, "Value", "ind", "Group", "Time", 1, 2) with self.assertRaisesRegex(ValueError, "state_1 and state_2"): pairwise_differences( output_dir=self.temp_dir.name, table=None, metadata=self.md_ecam_fp, group_column='delivery', state_column='month', state_1=0, state_2=0, individual_id_column='studyid', metric='observed_otus', replicate_handling='drop') with self.assertRaisesRegex(ValueError, "Detected replicate samples"): _get_group_pairs( md_dup, 'a', individual_id_column='ind', group_column='Group', state_column='Time', state_values=[1, 2], replicate_handling='error')
def test_pairwise_differences(self): pairwise_differences( output_dir=self.temp_dir.name, table=None, metadata=self.md_ecam_fp, group_column='delivery', state_column='month', state_1=0, state_2=3, individual_id_column='studyid', metric='observed_otus', replicate_handling='drop')
def test_pairwise_differences_taxa(self): pairwise_differences( output_dir=self.temp_dir.name, table=self.table_ecam_fp, metadata=self.md_ecam_fp, group_column='delivery', state_column='month', state_1=0, state_2=3, individual_id_column='studyid', metric='e2c3ff4f647112723741aa72087f1bfa', replicate_handling='drop')
def test_validate_input_values(self): with self.assertRaisesRegex(ValueError, "state_1 and state_2"): _validate_input_values(md, "ind", "Group", "Time", 1, 1) with self.assertRaisesRegex(ValueError, "not present"): _validate_input_values(md, "ind", "Group", "Time", 1, 3) with self.assertRaisesRegex(ValueError, "not a column"): _validate_input_values(md, "ind", "Group", "Days", 1, 2) with self.assertRaisesRegex(ValueError, "not a column"): _validate_input_columns(md, "ind", ["Group", "More stuff"], "Time") dropped = md.drop(['9', '10', '11']) with self.assertRaisesRegex(ValueError, "not represented"): _validate_input_values(dropped, "ind", "Group", "Time", 1, 2) with self.assertRaisesRegex(ValueError, "state_1 and state_2"): pairwise_differences( output_dir=self.temp_dir.name, table=None, metadata=self.md_ecam_fp, group_column='delivery', state_column='month', state_1=0, state_2=0, individual_id_column='studyid', metric='observed_otus', replicate_handling='drop')