class TestLoadCpG(unittest.TestCase):
def setUp(self):
data = Data(path=ROOT_DIR, base='fixtures')
experiment = Experiment(
data=None,
task=None,
method=None,
)
annotations = Annotations(name='annotations',
exclude='none',
cross_reactive='ex',
snp='ex',
chr='NS',
gene_region='yes',
geo='any',
probe_class='any')
observables = Observables(name='observables', types={})
cells = Cells(name='cells', types='any')
attributes = Attributes(target='age',
observables=observables,
cells=cells)
self.config = Config(data=data,
experiment=experiment,
annotations=annotations,
attributes=attributes,
is_run=True,
is_root=True)
self.config.initialize()
def tearDown(self):
clear_cache(self.config)
def test_load_excluded_check_none_excluded(self):
self.assertEqual([], load_excluded(self.config))
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 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))
class TestLoadCpG(unittest.TestCase):
def setUp(self):
data = Data(path=ROOT_DIR, base='fixtures')
experiment = Experiment(
data=None,
task=None,
method=None,
)
annotations = Annotations(name='annotations',
exclude='none',
cross_reactive='ex',
snp='ex',
chr='NS',
gene_region='yes',
geo='any',
probe_class='any')
observables = Observables(name='observables', types={})
cells = Cells(name='cells', types='any')
attributes = Attributes(target='age',
observables=observables,
cells=cells)
self.config = Config(data=data,
experiment=experiment,
annotations=annotations,
attributes=attributes,
is_run=True,
is_root=True)
self.config.initialize()
def tearDown(self):
clear_cache(self.config)
def test_load_cpg_check_files_creation(self):
fn_dict = get_data_base_path(self.config) + '/' + 'betas_dict.pkl'
fn_data = get_data_base_path(self.config) + '/' + 'betas'
fn_npz = fn_data + '.npz'
load_betas(self.config)
self.assertEqual(True,
os.path.isfile(fn_dict) and os.path.isfile(fn_npz))
def test_load_cpg_check_len_cpg_dict(self):
load_betas(self.config)
self.assertEqual(300, len(list(self.config.betas_dict)))
def test_load_cpg_check_shape_cpg_data(self):
load_betas(self.config)
self.assertEqual((300, 729), self.config.betas_data.shape)
class TestLoadCpG(unittest.TestCase):
def setUp(self):
data = Data(path=ROOT_DIR, base='fixtures')
experiment = Experiment(
data=None,
task=None,
method=None,
)
annotations = Annotations(name='annotations',
type='450k',
exclude='excluded',
select_dict={
'CROSS_R': ['0'],
'Probe_SNPs': ['empty'],
'Probe_SNPs_10': ['empty'],
'CHR': ['-X', '-Y'],
'UCSC_REFGENE_NAME': ['non-empty'],
})
observables = Observables(name='observables', types={})
cells = Cells(name='cells', types='any')
attributes = Attributes(target='age',
observables=observables,
cells=cells)
self.config = Config(data=data,
experiment=experiment,
annotations=annotations,
attributes=attributes,
is_run=True,
is_root=True)
self.config.initialize()
def tearDown(self):
clear_cache(self.config)
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 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))
class TestLoadAnnotations(unittest.TestCase):
def setUp(self):
data = Data(path=ROOT_DIR, base='fixtures')
experiment = Experiment(data=None, task=None, method=None)
annotations = Annotations(name='annotations',
type='450k',
exclude='excluded',
select_dict={
'CROSS_R': ['0'],
'Probe_SNPs': ['empty'],
'Probe_SNPs_10': ['empty'],
'CHR': ['-X', '-Y'],
'UCSC_REFGENE_NAME': ['non-empty'],
})
observables = Observables(name='observables', types={})
cells = Cells(name='cells', types='any')
attributes = Attributes(target='age',
observables=observables,
cells=cells)
self.config = Config(data=data,
experiment=experiment,
annotations=annotations,
attributes=attributes,
is_run=True,
is_root=True)
self.config.initialize()
def tearDown(self):
clear_cache(self.config)
def test_load_observables_dict_num_elems(self):
observables_dict = load_observables_dict(self.config)
self.assertEqual(len(observables_dict['age']), 729)
def test_load_observables_dict_age_range(self):
observables_dict = load_observables_dict(self.config)
self.assertEqual(
max(observables_dict['age']) - min(observables_dict['age']), 80)
def test_load_observables_dict_check_pkl_file_creation(self):
load_observables_dict(self.config)
create = os.path.isfile(
get_data_base_path(self.config) + '/' +
self.config.attributes.observables.name + '.pkl')
self.assertEqual(True, create)
def test_load_observables_dict_check_sum_smoke(self):
observables_dict = load_observables_dict(self.config)
sum_smoke = sum(list(map(int, observables_dict['smoke'])))
self.assertEqual(188, sum_smoke)
def test_load_observables_dict_num_Male(self):
observables_dict = load_observables_dict(self.config)
indexes = [
ind for ind, val in enumerate(observables_dict['gender'])
if val == 'M'
]
self.assertEqual(341, len(indexes))
def test_load_observables_dict_num_Female(self):
observables_dict = load_observables_dict(self.config)
indexes = [
ind for ind, val in enumerate(observables_dict['gender'])
if val == 'F'
]
self.assertEqual(388, len(indexes))
class TestLoadResidualsCommon(unittest.TestCase):
def setUp(self):
data = Data(path=ROOT_DIR, base='fixtures')
data_params = {'cells': ['B', 'CD4T', 'NK', 'CD8T', 'Gran']}
experiment = Experiment(data=None,
task=None,
method=None,
data_params=data_params)
annotations = Annotations(name='annotations',
type='450k',
exclude='excluded',
select_dict={
'CROSS_R': ['0'],
'Probe_SNPs': ['empty'],
'Probe_SNPs_10': ['empty'],
'CHR': ['-X', '-Y'],
'UCSC_REFGENE_NAME': ['non-empty'],
})
observables = Observables(name='observables', types={})
cells = Cells(name='cells', types='any')
attributes = Attributes(target='age',
observables=observables,
cells=cells)
self.config = Config(data=data,
experiment=experiment,
annotations=annotations,
attributes=attributes,
is_run=True,
is_root=True)
self.config.initialize()
def test_load_residuals_check_files_creation(self):
suffix = '_' + self.config.experiment.get_data_params_str()
fn_dict = get_data_base_path(
self.config) + '/' + 'residuals_dict' + suffix + '.pkl'
fn_data = get_data_base_path(
self.config) + '/' + 'residuals' + suffix + '.npz'
load_residuals(self.config)
self.assertEqual(True,
os.path.isfile(fn_dict) and os.path.isfile(fn_data))
def tearDown(self):
clear_cache(self.config)
def test_load_residuals_check_len_cpg_dict(self):
load_residuals(self.config)
self.assertEqual(300, len(list(self.config.residuals_dict)))
def test_load_residuals_check_shape_cpg_data(self):
load_residuals(self.config)
self.assertEqual((300, 729), self.config.residuals_data.shape)
class TestLoadResidualsCommon(unittest.TestCase):
def setUp(self):
data = Data(
path=ROOT_DIR,
base='fixtures'
)
data_params = {'cells': ['B', 'CD4T', 'NK', 'CD8T', 'Gran']}
experiment = Experiment(
data=None,
task=None,
method=None,
data_params=data_params
)
annotations = Annotations(
name='annotations',
exclude='none',
cross_reactive='ex',
snp='ex',
chr='NS',
gene_region='yes',
geo='any',
probe_class='any'
)
observables = Observables(
name='observables',
types={}
)
cells = Cells(
name='cells',
types='any'
)
attributes = Attributes(
target='age',
observables=observables,
cells=cells
)
self.config = Config(
data=data,
experiment=experiment,
annotations=annotations,
attributes=attributes,
is_run=True,
is_root=True
)
self.config.initialize()
def test_load_residuals_check_files_creation(self):
suffix = '_' + self.config.experiment.get_data_params_str()
fn_dict = get_data_base_path(self.config) + '/' + 'residuals_common_dict.pkl'
fn_data = get_data_base_path(self.config) + '/' + 'residuals_common' + suffix + '.npz'
load_residuals_common(self.config)
self.assertEqual(True, os.path.isfile(fn_dict) and os.path.isfile(fn_data))
def tearDown(self):
clear_cache(self.config)
def test_load_residuals_check_len_cpg_dict(self):
load_residuals_common(self.config)
self.assertEqual(300, len(list(self.config.residuals_dict)))
def test_load_residuals_check_shape_cpg_data(self):
load_residuals_common(self.config)
self.assertEqual((300, 729), self.config.residuals_data.shape)
class TestLoadAnnotations(unittest.TestCase):
def setUp(self):
data = Data(path=ROOT_DIR, base='fixtures')
experiment = Experiment(data=None, task=None, method=None)
annotations = Annotations(name='annotations',
exclude='none',
cross_reactive='ex',
snp='ex',
chr='NS',
gene_region='yes',
geo='any',
probe_class='any')
observables = Observables(name='observables', types={})
cells = Cells(name='cells', types='any')
attributes = Attributes(target='age',
observables=observables,
cells=cells)
self.config = Config(data=data,
experiment=experiment,
annotations=annotations,
attributes=attributes,
is_run=True,
is_root=True)
self.config.initialize()
def tearDown(self):
clear_cache(self.config)
def test_load_attributes_dict_num_elems(self):
attributes_dict = load_observables_dict(self.config)
self.assertEqual(len(attributes_dict['age']), 729)
def test_load_attributes_dict_age_range(self):
attributes_dict = load_observables_dict(self.config)
self.assertEqual(
max(attributes_dict['age']) - min(attributes_dict['age']), 80)
def test_load_attributes_dict_check_pkl_file_creation(self):
load_observables_dict(self.config)
create = os.path.isfile(
get_data_base_path(self.config) + '/' +
self.config.attributes.observables.name + '.pkl')
self.assertEqual(True, create)
def test_load_attributes_dict_check_sum_smoke(self):
attributes_dict = load_observables_dict(self.config)
sum_smoke = sum(list(map(int, attributes_dict['smoke'])))
self.assertEqual(188, sum_smoke)
def test_load_attributes_dict_num_Male(self):
attributes_dict = load_observables_dict(self.config)
indexes = [
ind for ind, val in enumerate(attributes_dict['gender'])
if val == 'M'
]
self.assertEqual(341, len(indexes))
def test_load_attributes_dict_num_Female(self):
attributes_dict = load_observables_dict(self.config)
indexes = [
ind for ind, val in enumerate(attributes_dict['gender'])
if val == 'F'
]
self.assertEqual(388, len(indexes))
class TestLoadAnnotations(unittest.TestCase):
def setUp(self):
data = Data(path=ROOT_DIR, base='fixtures')
experiment = Experiment(
data=None,
task=None,
method=None,
)
annotations = Annotations(name='annotations',
exclude='none',
cross_reactive='ex',
snp='ex',
chr='NS',
gene_region='yes',
geo='any',
probe_class='any')
observables = Observables(name='observables', types={})
cells = Cells(name='cells', types='any')
attributes = Attributes(target='age',
observables=observables,
cells=cells)
self.config = Config(data=data,
experiment=experiment,
annotations=annotations,
attributes=attributes,
is_run=True,
is_root=True)
self.config.initialize()
def tearDown(self):
clear_cache(self.config)
def compare_cross_r_cpg(self, cpg_list, ann_dict):
compare = True
for cpg in cpg_list:
index = ann_dict[AnnotationKey.cpg.value].index(cpg)
if not ann_dict[AnnotationKey.cross_reactive.value][index]:
compare = False
break
return compare
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_keys(self):
annotations_dict = load_annotations_dict(self.config)
self.assertEqual(len(list(annotations_dict.keys())), 10)
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_bops(self):
annotations_dict = load_annotations_dict(self.config)
self.assertEqual(len(set(annotations_dict['BOP'])), 82)
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_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_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_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_class(self):
annotations_dict = load_annotations_dict(self.config)
self.assertEqual(
len(set(annotations_dict[AnnotationKey.probe_class.value])), 4)