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 betas_clock_linreg(data, annotations, attributes, method_params=None):
config_root = Config(data=copy.deepcopy(data),
experiment=Experiment(
data=DataType.betas,
task=Task.clock,
method=Method.linreg,
method_params=copy.deepcopy(method_params)),
annotations=copy.deepcopy(annotations),
attributes=copy.deepcopy(attributes),
is_run=True,
is_root=True)
root = Node(name=str(config_root), config=config_root)
config_child = Config(data=copy.deepcopy(data),
experiment=Experiment(data=DataType.betas,
task=Task.table,
method=Method.linreg),
annotations=copy.deepcopy(annotations),
attributes=copy.deepcopy(attributes),
is_run=True,
is_root=False)
Node(name=str(config_child), config=config_child, parent=root)
build_tree(root)
calc_tree(root)
def cpg_proc_clock_linreg_dev(data,
annotations,
attributes,
child_method=Method.linreg,
params=None):
config_root = Config(data=copy.deepcopy(data),
experiment=Experiment(type=DataType.cpg,
task=Task.clock,
method=Method.linreg,
params=copy.deepcopy(params)),
annotations=copy.deepcopy(annotations),
attributes=copy.deepcopy(attributes),
is_run=True,
is_root=True)
root = Node(name=str(config_root), config=config_root)
config_child = Config(data=copy.deepcopy(data),
experiment=Experiment(
type=DataType.cpg,
task=Task.table,
method=copy.deepcopy(child_method),
params={}),
annotations=copy.deepcopy(annotations),
attributes=copy.deepcopy(attributes),
is_run=True,
is_root=False)
Node(name=str(config_child), config=config_child, parent=root)
build_tree(root)
calc_tree(root)
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 betas_adj_table_approach_3(data, annotations, attributes, target_list,
data_params_list):
config_root = Config(data=copy.deepcopy(data),
experiment=Experiment(data=DataType.betas_adj,
task=Task.table,
method=Method.aggregator,
data_params=copy.deepcopy(
data_params_list[0])),
annotations=copy.deepcopy(annotations),
attributes=copy.deepcopy(attributes),
is_run=True,
is_root=True)
root = Node(name=str(config_root), config=config_root)
for id, target in enumerate(target_list):
attributes_common = copy.deepcopy(attributes)
attributes_common.target = target
config_common = Config(data=copy.deepcopy(data),
experiment=Experiment(
data=DataType.betas_adj,
task=Task.table,
method=Method.oma,
data_params=copy.deepcopy(
data_params_list[id])),
annotations=copy.deepcopy(annotations),
attributes=attributes_common,
is_run=True,
is_root=False)
Node(name=str(config_common), config=config_common, parent=root)
build_tree(root)
calc_tree(root)
def cpg_proc_clock_linreg(
data,
annotations,
attributes,
child_method = Method.linreg
):
config_root = Config(
data=data,
experiment=Experiment(
type=DataType.cpg,
task=Task.clock,
method=Method.linreg,
params={}
),
annotations=annotations,
attributes=attributes
)
root = Node(name=str(config_root), config=config_root)
config_child = Config(
data=data,
experiment=Experiment(
type=DataType.cpg,
task=Task.table,
method=child_method,
params={}
),
annotations=annotations,
attributes=attributes
)
Node(name=str(config_child), config=config_child, parent=root)
calc_tree(root)
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))
def table_aggregator_approach_4(
data_type,
data,
annotations,
attributes,
observables_list,
data_params,
):
config_root = Config(
data=copy.deepcopy(data),
experiment=Experiment(
data=data_type,
task=Task.table,
method=Method.aggregator,
data_params=copy.deepcopy(data_params),
),
annotations=copy.deepcopy(annotations),
attributes=copy.deepcopy(attributes),
is_run=True,
is_root=True
)
root = Node(name=str(config_root), config=config_root)
for d in observables_list:
observables_lvl_1 = Observables(
name=copy.deepcopy(attributes.observables.name),
types=d
)
cells_lvl_1 = Cells(
name=copy.deepcopy(attributes.cells.name),
types=copy.deepcopy(attributes.cells.types)
)
attributes_lvl_1 = Attributes(
target=copy.deepcopy(attributes.target),
observables=observables_lvl_1,
cells=cells_lvl_1,
)
config_lvl_1 = Config(
data=copy.deepcopy(data),
experiment=Experiment(
data=data_type,
task=Task.table,
method=Method.heteroskedasticity,
data_params=copy.deepcopy(data_params)
),
annotations=copy.deepcopy(annotations),
attributes=attributes_lvl_1,
is_run=True,
is_root=False
)
Node(name=str(config_lvl_1), config=config_lvl_1, parent=root)
build_tree(root)
calc_tree(root)
def cpg_plot_methylation_scatter(
data,
annotations,
attributes,
cpg_list,
observables_list,
child_method=Method.linreg,
):
for cpg in cpg_list:
config_root = Config(
data=data,
experiment=Experiment(
type=DataType.cpg,
task=Task.methylation,
method=Method.scatter,
params={}
),
annotations=annotations,
attributes=attributes
)
config_root.experiment.params['item'] = cpg
root = Node(name=str(config_root), config=config_root)
for d in observables_list:
observables_child = Observables(
name=attributes.observables.name,
types=d
)
cells_child = Cells(
name=attributes.cells.name,
types=attributes.cells.types
)
attributes_child = Attributes(
target=attributes.target,
observables=observables_child,
cells=cells_child,
)
config_child = Config(
data=data,
experiment=Experiment(
type=DataType.cpg,
task=Task.table,
method=child_method,
params={}
),
annotations=annotations,
attributes=attributes_child,
is_run=False
)
Node(name=str(config_child), config=config_child, parent=root)
calc_tree(root)
def betas_plot_variance_histogram_dev(data,
annotations,
attributes,
cpg_list,
observables_list,
child_method=Method.linreg,
method_params=None):
for cpg in cpg_list:
config_root = Config(data=copy.deepcopy(data),
experiment=Experiment(
data=DataType.betas,
task=Task.methylation,
method=Method.variance_histogram,
method_params=copy.deepcopy(method_params)),
annotations=copy.deepcopy(annotations),
attributes=copy.deepcopy(attributes),
is_run=True,
is_root=True,
is_load_child=False)
if config_root.experiment.method_params is None:
config_root.experiment.method_params = dict()
config_root.experiment.method_params['item'] = cpg
root = Node(name=str(config_root), config=config_root)
for d in observables_list:
observables_child = Observables(name=copy.deepcopy(
attributes.observables.name),
types=d)
cells_child = Cells(name=copy.deepcopy(attributes.cells.name),
types=copy.deepcopy(attributes.cells.types))
attributes_child = Attributes(
target=copy.deepcopy(attributes.target),
observables=observables_child,
cells=cells_child,
)
config_child = Config(data=copy.deepcopy(data),
experiment=Experiment(
data=DataType.betas,
task=Task.table,
method=copy.deepcopy(child_method)),
annotations=copy.deepcopy(annotations),
attributes=attributes_child,
is_run=False,
is_root=False,
is_load_child=False)
Node(name=str(config_child), config=config_child, parent=root)
build_tree(root)
calc_tree(root)
def plot_scatter(data_type,
data,
annotations,
attributes,
observables_list,
child_method=Method.linreg,
data_params=None,
method_params=None):
task_params = {'type': 'run'}
config_root = Config(data=copy.deepcopy(data),
experiment=Experiment(
data=data_type,
task=Task.plot,
method=Method.scatter,
data_params=copy.deepcopy(data_params),
method_params=copy.deepcopy(method_params),
task_params=task_params),
annotations=copy.deepcopy(annotations),
attributes=copy.deepcopy(attributes),
is_run=True,
is_root=True,
is_load_child=False)
root = Node(name=str(config_root), config=config_root)
for d in observables_list:
observables_child = Observables(name=copy.deepcopy(
attributes.observables.name),
types=d)
cells_child = Cells(name=copy.deepcopy(attributes.cells.name),
types=copy.deepcopy(attributes.cells.types))
attributes_child = Attributes(
target=copy.deepcopy(attributes.target),
observables=observables_child,
cells=cells_child,
)
config_child = Config(data=copy.deepcopy(data),
experiment=Experiment(
data=data_type,
task=Task.table,
method=copy.deepcopy(child_method),
data_params=copy.deepcopy(data_params),
),
annotations=copy.deepcopy(annotations),
attributes=attributes_child,
is_run=False,
is_root=False,
is_load_child=False)
Node(name=str(config_child), config=config_child, parent=root)
build_tree(root)
calc_tree(root)
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))
def cpg_proc_table_polygon(
data,
annotations,
attributes,
observables_list,
child_method = Method.linreg
):
config_root = Config(
data=data,
experiment=Experiment(
type=DataType.cpg,
task=Task.table,
method=Method.polygon,
params={}
),
annotations=annotations,
attributes=attributes
)
root = Node(name=str(config_root), config=config_root)
for d in observables_list:
observables_child = Observables(
name=attributes.observables.name,
types=d
)
cells_child = Cells(
name=attributes.cells.name,
types=attributes.cells.types
)
attributes_child = Attributes(
target=attributes.target,
observables=observables_child,
cells=cells_child,
)
config_child = Config(
data=data,
experiment=Experiment(
type=DataType.cpg,
task=Task.table,
method=child_method,
params={}
),
annotations=annotations,
attributes=attributes_child
)
Node(name=str(config_child), config=config_child, parent=root)
calc_tree(root)
def entropy_plot(data,
annotations,
attributes,
observables_list,
method,
data_params=None,
method_params=None):
config_root = Config(data=copy.deepcopy(data),
experiment=Experiment(
data=DataType.entropy,
task=Task.plot,
method=method,
data_params=copy.deepcopy(data_params),
method_params=copy.deepcopy(method_params)),
annotations=copy.deepcopy(annotations),
attributes=copy.deepcopy(attributes),
is_run=True,
is_root=True)
root = Node(name=str(config_root), config=config_root)
for types in observables_list:
observables_child = Observables(name=copy.deepcopy(
attributes.observables.name),
types=types)
cells_child = Cells(name=copy.deepcopy(attributes.cells.name),
types=copy.deepcopy(attributes.cells.types))
attributes_child = Attributes(
target=copy.deepcopy(attributes.target),
observables=observables_child,
cells=cells_child,
)
config_child = Config(data=copy.deepcopy(data),
experiment=Experiment(
data=DataType.entropy,
task=Task.table,
method=Method.mock,
data_params=copy.deepcopy(data_params)),
annotations=copy.deepcopy(annotations),
attributes=attributes_child,
is_run=False,
is_root=False)
Node(name=str(config_child), config=config_child, parent=root)
build_tree(root)
calc_tree(root)
def cpg_proc_special_clock_linreg_dev(
data,
annotations,
attributes,
file,
params=None,
):
if os.path.isfile(file):
head, tail = os.path.split(file)
fn = os.path.splitext(tail)[0]
ext = os.path.splitext(tail)[1]
config_root = Config(data=copy.deepcopy(data),
experiment=Experiment(
type=DataType.cpg,
task=Task.clock,
method=Method.linreg,
params=copy.deepcopy(params)),
annotations=copy.deepcopy(annotations),
attributes=copy.deepcopy(attributes),
is_run=True,
is_root=True)
root = Node(name=str(config_root), config=config_root)
config_child = Config(data=copy.deepcopy(data),
experiment=Experiment(type=DataType.cpg,
task=Task.table,
method=Method.special,
params={'file_name': fn}),
annotations=copy.deepcopy(annotations),
attributes=copy.deepcopy(attributes),
is_run=False,
is_root=False)
Node(name=str(config_child), config=config_child, parent=root)
build_tree(root)
new_file = get_save_path(config_child) + '/' + \
get_file_name(config_child) + ext
copyfile(file, new_file)
calc_tree(root)
else:
raise FileNotFoundError(f'File {file} not found.')
def residuals_table_approach_3(data, annotations, attributes,
target_sex_specific, target_age_related,
data_params_sex_specific,
data_params_age_related):
config_root = Config(
data=copy.deepcopy(data),
experiment=Experiment(
data=DataType.residuals,
task=Task.table,
method=Method.aggregator,
data_params=copy.deepcopy(data_params_sex_specific)),
annotations=copy.deepcopy(annotations),
attributes=copy.deepcopy(attributes),
is_run=True,
is_root=True)
root = Node(name=str(config_root), config=config_root)
attributes_ss = copy.deepcopy(attributes)
attributes_ss.target = target_sex_specific
config_ss = Config(
data=copy.deepcopy(data),
experiment=Experiment(
data=DataType.residuals,
task=Task.table,
method=Method.pbc,
data_params=copy.deepcopy(data_params_sex_specific)),
annotations=copy.deepcopy(annotations),
attributes=attributes_ss,
is_run=True,
is_root=False)
Node(name=str(config_ss), config=config_ss, parent=root)
attributes_ar = copy.deepcopy(attributes)
attributes_ar.target = target_age_related
config_ar = Config(data=copy.deepcopy(data),
experiment=Experiment(
data=DataType.residuals,
task=Task.table,
method=Method.oma,
data_params=copy.deepcopy(data_params_age_related)),
annotations=copy.deepcopy(annotations),
attributes=attributes_ar,
is_run=True,
is_root=False)
Node(name=str(config_ar), config=config_ar, parent=root)
build_tree(root)
calc_tree(root)
def table(
data,
annotations,
attributes,
data_type,
method,
data_params=None,
task_params=None,
method_params=None
):
config_root = Config(
data=copy.deepcopy(data),
experiment=Experiment(
data=data_type,
task=Task.table,
method=method,
data_params=copy.deepcopy(data_params),
task_params=copy.deepcopy(task_params),
method_params=copy.deepcopy(method_params)
),
annotations=copy.deepcopy(annotations),
attributes=copy.deepcopy(attributes),
is_run=True,
is_root=True
)
root = Node(name=str(config_root), config=config_root)
build_tree(root)
calc_tree(root)
def epimutations_load(data):
config = Config(
data=copy.deepcopy(data),
experiment=Experiment(
data=DataType.epimutations,
task=None,
method=None
),
annotations=Annotations(
name='annotations',
exclude='bad_cpgs',
cross_reactive='any',
snp='any',
chr='NS',
gene_region='any',
geo='any',
probe_class='any'
),
attributes=Attributes(
target=None,
observables=None,
cells=None
),
is_run=True,
is_root=True
)
load_epimutations(config)
def betas_horvath_calculator_create_regular(
chip_type,
observables_fn,
data,
data_params,
):
annotations = Annotations(name='annotations',
type=chip_type,
exclude='none',
select_dict={})
cells = Cells(name='cell_counts_part(wo_noIntensity_detP)', types='any')
observables = Observables(name=observables_fn, types={})
attributes = Attributes(target='Age', observables=observables, cells=cells)
config_root = Config(data=copy.deepcopy(data),
experiment=Experiment(
data=DataType.betas_horvath_calculator,
task=Task.create,
method=Method.regular,
data_params=copy.deepcopy(data_params)),
annotations=copy.deepcopy(annotations),
attributes=copy.deepcopy(attributes),
is_run=True,
is_root=True)
root = Node(name=str(config_root), config=config_root)
build_tree(root)
calc_tree(root)
def setUp(self):
data = Data(name='cpg_beta', path=ROOT_DIR, base='fixtures')
experiment = Experiment(type=DataType.cpg,
task='',
method='',
params={})
annotations = Annotations(name='annotations',
exclude=CommonTypes.none.value,
cross_reactive=CrossReactive.exclude.value,
snp=SNP.exclude.value,
chr=Chromosome.non_sex.value,
gene_region=GeneRegion.yes.value,
geo=CommonTypes.any.value,
probe_class=CommonTypes.any.value)
observables = Observables(name='observables', types={})
cells = Cells(name='cells', types=CommonTypes.any.value)
attributes = Attributes(target='age',
observables=observables,
cells=cells)
self.config = Config(
data=data,
experiment=experiment,
annotations=annotations,
attributes=attributes,
)
def attributes_plot_observables_histogram(
data,
annotations,
attributes,
observables_list,
):
config_root = Config(
data=data,
experiment=Experiment(
type=DataType.attributes,
task=Task.observables,
method=Method.histogram,
params={}
),
annotations=annotations,
attributes=attributes
)
root = Node(name=str(config_root), config=config_root)
for d in observables_list:
observables_child = Observables(
name=attributes.observables.name,
types=d
)
cells_child = Cells(
name=attributes.cells.name,
types=attributes.cells.types
)
attributes_child = Attributes(
target=attributes.target,
observables=observables_child,
cells=cells_child,
)
config_child = Config(
data=data,
experiment=config_root.experiment,
annotations=annotations,
attributes=attributes_child,
is_run=False
)
Node(name=str(config_child), config=config_child, parent=root)
calc_tree(root)
def cpg_proc_table_z_test_linreg_dev(data,
annotations,
attributes,
observables_list,
child_method=Method.linreg,
params=None):
config_root = Config(data=copy.deepcopy(data),
experiment=Experiment(type=DataType.cpg,
task=Task.table,
method=Method.z_test_linreg,
params=copy.deepcopy(params)),
annotations=copy.deepcopy(annotations),
attributes=copy.deepcopy(attributes),
is_run=True,
is_root=True)
root = Node(name=str(config_root), config=config_root)
for d in observables_list:
observables_child = Observables(name=copy.deepcopy(
attributes.observables.name),
types=d)
cells_child = Cells(name=copy.deepcopy(attributes.cells.name),
types=copy.deepcopy(attributes.cells.types))
attributes_child = Attributes(
target=copy.deepcopy(attributes.target),
observables=observables_child,
cells=cells_child,
)
config_child = Config(data=copy.deepcopy(data),
experiment=Experiment(
type=DataType.cpg,
task=Task.table,
method=copy.deepcopy(child_method),
params={}),
annotations=copy.deepcopy(annotations),
attributes=attributes_child,
is_run=True,
is_root=False)
Node(name=str(config_child), config=config_child, parent=root)
build_tree(root)
calc_tree(root)
def attributes_plot_observables_histogram_dev(data,
annotations,
attributes,
observables_list,
params=None):
config_root = Config(data=copy.deepcopy(data),
experiment=Experiment(type=DataType.attributes,
task=Task.observables,
method=Method.histogram,
params=copy.deepcopy(params)),
annotations=copy.deepcopy(annotations),
attributes=copy.deepcopy(attributes),
is_run=True,
is_root=True)
root = Node(name=str(config_root), config=config_root)
for d in observables_list:
observables_child = Observables(name=copy.deepcopy(
attributes.observables.name),
types=d)
cells_child = Cells(name=copy.deepcopy(attributes.cells.name),
types=copy.deepcopy(attributes.cells.types))
attributes_child = Attributes(
target=copy.deepcopy(attributes.target),
observables=observables_child,
cells=cells_child,
)
config_child = Config(data=copy.deepcopy(data),
experiment=config_root.experiment,
annotations=copy.deepcopy(annotations),
attributes=attributes_child,
is_run=False,
is_root=True)
Node(name=str(config_child), config=config_child, parent=root)
build_tree(root)
calc_tree(root)
def load_beta_config(data, annotations, attributes, data_params=None):
config = Config(data=copy.deepcopy(data),
experiment=Experiment(
data=DataType.betas,
task=Task.load,
method=Method.mock,
data_params=copy.deepcopy(data_params)),
annotations=copy.deepcopy(annotations),
attributes=copy.deepcopy(attributes),
is_run=True,
is_root=True)
context = Context(config)
context.load(config)
return config
def epimutations_load(data):
config = Config(data=copy.deepcopy(data),
experiment=Experiment(data=DataType.epimutations,
task=None,
method=None),
annotations=Annotations(name='annotations',
type='450k',
exclude='bad_cpgs',
select_dict={'CHR': ['-X', '-Y']}),
attributes=Attributes(target=None,
observables=None,
cells=None),
is_run=True,
is_root=True)
load_epimutations(config)
def cpg_proc_table_variance_linreg_dev(data,
annotations,
attributes,
params=None):
config_root = Config(data=copy.deepcopy(data),
experiment=Experiment(type=DataType.cpg,
task=Task.table,
method=Method.variance_linreg,
params=copy.deepcopy(params)),
annotations=copy.deepcopy(annotations),
attributes=copy.deepcopy(attributes),
is_run=True,
is_root=True)
root = Node(name=str(config_root), config=config_root)
build_tree(root)
calc_tree(root)
def cpg_proc_table_variance_linreg(
data,
annotations,
attributes
):
config_root = Config(
data=data,
experiment=Experiment(
type=DataType.cpg,
task=Task.table,
method=Method.variance_linreg,
params={}
),
annotations=annotations,
attributes=attributes
)
root = Node(name=str(config_root), config=config_root)
calc_tree(root)
def betas_spec_create_regular(
data,
data_params,
observables
):
annotations = Annotations(
name='annotations',
type='450k',
exclude='none',
select_dict={
'CHR': ['-X', '-Y']
}
)
cells = Cells(
name='cells',
types='any'
)
attributes = Attributes(
target='age',
observables=observables,
cells=cells
)
config_root = Config(
data=copy.deepcopy(data),
experiment=Experiment(
data=DataType.betas_spec,
task=Task.create,
method=Method.regular,
data_params=data_params
),
annotations=copy.deepcopy(annotations),
attributes=copy.deepcopy(attributes),
is_run=True,
is_root=True
)
root = Node(name=str(config_root), config=config_root)
build_tree(root)
calc_tree(root)
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))