def test_load_annotations_check_pkl_file_creation(self):
load_annotations_dict(self.config)
create = os.path.isfile(
get_data_base_path(self.config) + '/' +
self.config.annotations.name + '.pkl')
self.assertEqual(True, create)
def test_get_num_X_chr(self):
self.config.annotations_dict = load_annotations_dict(self.config)
self.config.annotations.chr = 'X'
count = self.get_count(chromosome_condition)
self.assertEqual(count, 24)
def test_cross_reactive_condition(self):
self.config.annotations_dict = load_annotations_dict(self.config)
self.config.annotations.cross_reactive = 'ex'
count = self.get_count(cross_reactive_condition)
self.assertEqual(count, 278)
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_get_num_s_shore_geo(self):
self.config.annotations_dict = load_annotations_dict(self.config)
self.config.annotations.geo = 'shores_s'
count = self.get_count(geo_condition)
self.assertEqual(count, 40)
def test_get_num_island_geo(self):
self.config.annotations_dict = load_annotations_dict(self.config)
self.config.annotations.geo = 'islands'
count = self.get_count(geo_condition)
self.assertEqual(count, 92)
def test_comb_conditions_X_Island(self):
self.config.annotations_dict = load_annotations_dict(self.config)
self.config.annotations.chr = 'X'
self.config.annotations.geo = 'islands'
count = self.modified_get_count(geo_condition, chromosome_condition)
self.assertEqual(count, 5)
def test_comb_conditions_S_Shore_ClassA(self):
self.config.annotations_dict = load_annotations_dict(self.config)
self.config.annotations.probe_class = 'ClassA'
self.config.annotations.geo = 'shores_s'
count = self.modified_get_count(probe_class_condition, geo_condition)
self.assertEqual(count, 39)
def test_load_annotations_num_cross_r_cpgs(self):
annotations_dict = load_annotations_dict(self.config)
num_of_cross_r_cpg = sum(
list(map(int,
annotations_dict[AnnotationKey.cross_reactive.value])))
self.assertEqual(num_of_cross_r_cpg, 22)
def test_cross_reactive_condition(self):
self.config.annotations_dict = load_annotations_dict(self.config)
target_keys = [self.config.annotations.id_name, 'CROSS_R']
new_dict = {}
for key in target_keys:
new_dict[key] = self.config.annotations_dict[key]
self.config.annotations_dict = new_dict
count = self.get_count(check_condition)
self.assertEqual(count, 278)
def test_get_num_NS_chr(self):
self.config.annotations_dict = load_annotations_dict(self.config)
target_keys = [self.config.annotations.id_name, 'CHR']
new_dict = {}
for key in target_keys:
new_dict[key] = self.config.annotations_dict[key]
self.config.annotations_dict = new_dict
count = self.get_count(check_condition)
self.assertEqual(count, 276)
def test_count_probe_class_condition(self):
self.config.annotations_dict = load_annotations_dict(self.config)
target_keys = [self.config.annotations.id_name, 'Class']
new_dict = {}
for key in target_keys:
new_dict[key] = self.config.annotations_dict[key]
self.config.annotations_dict = new_dict
count = self.get_count(check_condition)
self.assertEqual(count, 202)
def test_comb_conditions_N_Shore_cross_react(self):
self.config.annotations_dict = load_annotations_dict(self.config)
self.config.annotations.geo = 'shores_n'
self.config.annotations.cross_reactive = 'ex'
count = self.modified_get_count(cross_reactive_condition,
geo_condition)
self.assertEqual(count, 40)
def test_count_gene_region_condition(self):
self.config.annotations_dict = load_annotations_dict(self.config)
target_keys = [self.config.annotations.id_name, 'UCSC_REFGENE_NAME']
new_dict = {}
for key in target_keys:
new_dict[key] = self.config.annotations_dict[key]
self.config.annotations_dict = new_dict
count = self.get_count(check_condition)
self.assertEqual(count, 292)
def test_count_snp_condition(self):
self.config.annotations_dict = load_annotations_dict(self.config)
target_keys = [
self.config.annotations.id_name, 'Probe_SNPs', 'Probe_SNPs_10'
]
new_dict = {}
for key in target_keys:
new_dict[key] = self.config.annotations_dict[key]
self.config.annotations_dict = new_dict
count = self.get_count(check_condition)
self.assertEqual(count, 250)
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_load_annotations_dict_compare_cross_r_cpg(self):
cross_r_cpg = [
'cg03242964', 'cg06142509', 'cg06352932', 'cg07110474',
'cg07208077', 'cg07818063', 'cg08555389', 'cg08683088',
'cg09720033', 'cg11032157', 'cg14502651', 'cg14829303',
'cg14894369', 'cg18241189', 'cg20188490', 'cg20418818',
'cg21752292', 'cg22505295', 'cg22805813', 'cg23146713',
'cg24653967', 'cg25677688'
]
annotations_dict = load_annotations_dict(self.config)
compare = self.compare_cross_r_cpg(cross_r_cpg, annotations_dict)
self.assertEqual(True, compare)
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 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_annotations_dict_num_bops(self):
annotations_dict = load_annotations_dict(self.config)
self.assertEqual(len(set(annotations_dict['BOP'])), 82)
def test_load_annotations_dict_num_geo(self):
annotations_dict = load_annotations_dict(self.config)
num_geo = len(set(annotations_dict[AnnotationKey.geo.value]))
self.assertEqual(6, num_geo)
def test_load_annotations_dict_num_chrs(self):
annotations_dict = load_annotations_dict(self.config)
self.assertEqual(len(set(annotations_dict['CHR'])), 11)
def test_load_annotations_dict_num_keys(self):
annotations_dict = load_annotations_dict(self.config)
self.assertEqual(len(list(annotations_dict.keys())), 10)
def test_load_annotations_dict_num_elems(self):
annotations_dict = load_annotations_dict(self.config)
self.assertEqual(len(annotations_dict['ID_REF']), 300)
def test_load_annotations_dict_num_class(self):
annotations_dict = load_annotations_dict(self.config)
self.assertEqual(
len(set(annotations_dict[AnnotationKey.probe_class.value])), 4)
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)
