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)