def test_count_gene_region_condition(self):
self.config.excluded = load_excluded(self.config)
self.config.annotations_dict = load_annotations_dict(self.config)
count = self.get_count(gene_region_condition)
self.assertEqual(count, 292)
def test_exclude_condition(self):
self.config.excluded = load_excluded(self.config)
self.config.annotations_dict = {
self.config.annotations.id_name: [['cg00000165']]
}
condition = exclude_condition(self.config, 0)
self.assertEqual(False, condition)
def test_load_excluded_check_pkl_creation(self):
self.config.annotations.exclude = 'excluded'
fn = get_data_base_path(
self.config) + '/' + self.config.annotations.exclude + '.pkl'
self.config.excluded = load_excluded(self.config)
self.assertEqual(True, os.path.isfile(fn))
def initialize(self):
self.excluded = load_excluded(self)
self.annotations_dict = load_annotations_dict(self)
subset_annotations(self)
self.attributes_dict = load_attributes_dict(self)
self.attributes_indexes = get_indexes(self)
subset_attributes(self)
self.cells_dict = load_cells_dict(self)
subset_cells(self)
def test_check_conditions(self):
self.config.excluded = load_excluded(self.config)
self.config.annotations_dict = {
self.config.annotations.id_name: [['cg00001249']],
'CROSS_R': [['0']],
'Probe_SNPs': [[]],
'Probe_SNPs_10': [[]],
'CHR': [['14']],
'UCSC_REFGENE_NAME': [['PRR4', 'TAS2R20']],
'RELATION_TO_UCSC_CPG_ISLAND': [['S_Shelf']],
'Class': [['ClassA']]
}
condition = global_check(self.config, 0)
self.assertEqual(True, condition)
self.config.annotations_dict['CHR'] = [['X']]
condition = global_check(self.config, 0)
self.assertEqual(False, condition)
def test_count_check_conditions(self):
self.config.excluded = load_excluded(self.config)
tmp_dict = load_annotations_dict(self.config)
for i, value in enumerate(tmp_dict['Class']):
if value == 'ClassA':
tmp_dict['Class'][i] = 'A'
elif value == 'ClassB':
tmp_dict['Class'][i] = 'B'
elif value == 'ClassC':
tmp_dict['Class'][i] = 'C'
elif value == 'ClassD':
tmp_dict['Class'][i] = 'D'
self.config.annotations_dict = tmp_dict
count = self.get_count(check_conditions)
self.assertEqual(count, 151)
def test_check_conditions(self):
self.config.excluded = load_excluded(self.config)
annotations_dict = {
AnnotationKey.cpg.value: 'cg00001249',
AnnotationKey.cross_reactive.value: '0',
AnnotationKey.Probe_SNPs.value: '',
AnnotationKey.Probe_SNPs_10.value: '',
AnnotationKey.chr.value: '14',
AnnotationKey.gene.value: ['PRR4', 'TAS2R20'],
AnnotationKey.geo.value: 'S_Shelf',
AnnotationKey.probe_class.value: 'A'
}
condition1 = check_conditions(self.config, annotations_dict)
annotations_dict[AnnotationKey.chr.value] = 'X'
condition2 = check_conditions(self.config, annotations_dict)
self.assertEqual((True, False), (condition1, condition2))
def initialize(self):
if self.is_init:
if self.annotations is not None:
self.excluded = load_excluded(self)
self.annotations_dict = load_annotations_dict(self)
subset_annotations(self)
self.observables_dict = load_observables_dict(self)
self.observables_categorical_dict = load_observables_categorical_dict(
self)
self.is_observables_categorical = get_is_observables_categorical(
self)
self.attributes_indexes = get_indexes(self)
subset_observables(self)
if self.attributes.cells is not None:
self.cells_dict = load_cells_dict(self)
subset_cells(self)
def test_load_excluded_check_len_excluded(self):
self.config.annotations.exclude = 'excluded'
self.config.excluded = load_excluded(self.config)
self.assertEqual(3, len(self.config.excluded))
def test_load_excluded_check_none_excluded(self):
self.assertEqual([], load_excluded(self.config))
def test_count_check_conditions(self):
self.config.excluded = load_excluded(self.config)
self.config.annotations_dict = load_annotations_dict(self.config)
count = self.get_count(global_check)
self.assertEqual(count, 151)
def test_exclude_condition(self):
self.config.excluded = load_excluded(self.config)
ex_cpg = {AnnotationKey.cpg.value: 'cg00000165'}
is_not_excluded = exclude_condition(self.config, ex_cpg)
self.assertEqual(False, is_not_excluded)
