def do_tissue_correlation_for_all_traits(this_trait,
trait_symbol_dict,
corr_params,
tissue_dataset_id=1):
#Gets tissue expression values for the primary trait
primary_trait_tissue_vals_dict = correlation_functions.get_trait_symbol_and_tissue_values(
symbol_list=[this_trait.symbol])
if this_trait.symbol.lower() in primary_trait_tissue_vals_dict:
primary_trait_tissue_values = primary_trait_tissue_vals_dict[
this_trait.symbol.lower()]
corr_result_tissue_vals_dict = correlation_functions.get_trait_symbol_and_tissue_values(
symbol_list=trait_symbol_dict.values())
tissue_corr_data = {}
for trait, symbol in trait_symbol_dict.iteritems():
if symbol and symbol.lower() in corr_result_tissue_vals_dict:
this_trait_tissue_values = corr_result_tissue_vals_dict[
symbol.lower()]
result = correlation_functions.cal_zero_order_corr_for_tiss(
primary_trait_tissue_values, this_trait_tissue_values,
corr_params['method'])
tissue_corr_data[trait] = [
result[0], result[1], result[2], symbol
]
return tissue_corr_data
def do_tissue_correlation_for_all_traits(self, tissue_dataset_id=1):
#Gets tissue expression values for the primary trait
primary_trait_tissue_vals_dict = correlation_functions.get_trait_symbol_and_tissue_values(
symbol_list = [self.this_trait.symbol])
if self.this_trait.symbol.lower() in primary_trait_tissue_vals_dict:
primary_trait_tissue_values = primary_trait_tissue_vals_dict[self.this_trait.symbol.lower()]
#print("trait_gene_symbols: ", pf(trait_gene_symbols.values()))
corr_result_tissue_vals_dict= correlation_functions.get_trait_symbol_and_tissue_values(
symbol_list=list(self.trait_symbol_dict.values()))
#print("corr_result_tissue_vals: ", pf(corr_result_tissue_vals_dict))
#print("trait_gene_symbols: ", pf(trait_gene_symbols))
tissue_corr_data = {}
for trait, symbol in list(self.trait_symbol_dict.items()):
if symbol and symbol.lower() in corr_result_tissue_vals_dict:
this_trait_tissue_values = corr_result_tissue_vals_dict[symbol.lower()]
result = correlation_functions.cal_zero_order_corr_for_tiss(primary_trait_tissue_values,
this_trait_tissue_values,
self.corr_method)
tissue_corr_data[trait] = [symbol, result[0], result[2]]
tissue_corr_data = collections.OrderedDict(sorted(list(tissue_corr_data.items()),
key=lambda t: -abs(t[1][1])))
return tissue_corr_data
def do_tissue_correlation_for_trait_list(self, tissue_dataset_id=1):
"""Given a list of correlation results (self.correlation_results), gets the tissue correlation value for each"""
#Gets tissue expression values for the primary trait
primary_trait_tissue_vals_dict = correlation_functions.get_trait_symbol_and_tissue_values(
symbol_list=[self.this_trait.symbol])
if self.this_trait.symbol.lower() in primary_trait_tissue_vals_dict:
primary_trait_tissue_values = primary_trait_tissue_vals_dict[
self.this_trait.symbol.lower()]
gene_symbol_list = [
trait.symbol for trait in self.correlation_results
if trait.symbol
]
corr_result_tissue_vals_dict = correlation_functions.get_trait_symbol_and_tissue_values(
symbol_list=gene_symbol_list)
for trait in self.correlation_results:
if trait.symbol and trait.symbol.lower(
) in corr_result_tissue_vals_dict:
this_trait_tissue_values = corr_result_tissue_vals_dict[
trait.symbol.lower()]
result = correlation_functions.cal_zero_order_corr_for_tiss(
primary_trait_tissue_values, this_trait_tissue_values,
self.corr_method)
trait.tissue_corr = result[0]
trait.tissue_pvalue = result[2]
def do_tissue_correlation_for_all_traits(self, tissue_dataset_id=1):
#Gets tissue expression values for the primary trait
primary_trait_tissue_vals_dict = correlation_functions.get_trait_symbol_and_tissue_values(
symbol_list = [self.this_trait.symbol])
if self.this_trait.symbol.lower() in primary_trait_tissue_vals_dict:
primary_trait_tissue_values = primary_trait_tissue_vals_dict[self.this_trait.symbol.lower()]
#print("trait_gene_symbols: ", pf(trait_gene_symbols.values()))
corr_result_tissue_vals_dict= correlation_functions.get_trait_symbol_and_tissue_values(
symbol_list=self.trait_symbol_dict.values())
#print("corr_result_tissue_vals: ", pf(corr_result_tissue_vals_dict))
#print("trait_gene_symbols: ", pf(trait_gene_symbols))
tissue_corr_data = {}
for trait, symbol in self.trait_symbol_dict.iteritems():
if symbol and symbol.lower() in corr_result_tissue_vals_dict:
this_trait_tissue_values = corr_result_tissue_vals_dict[symbol.lower()]
result = correlation_functions.cal_zero_order_corr_for_tiss(primary_trait_tissue_values,
this_trait_tissue_values,
self.corr_method)
tissue_corr_data[trait] = [symbol, result[0], result[2]]
tissue_corr_data = collections.OrderedDict(sorted(tissue_corr_data.items(),
key=lambda t: -abs(t[1][1])))
return tissue_corr_data
def get_tissue_correlation_input(this_trait, trait_symbol_dict):
"""Gets tissue expression values for the primary trait and target tissues values"""
primary_trait_tissue_vals_dict = correlation_functions.get_trait_symbol_and_tissue_values(
symbol_list=[this_trait.symbol])
if this_trait.symbol.lower() in primary_trait_tissue_vals_dict:
primary_trait_tissue_values = primary_trait_tissue_vals_dict[
this_trait.symbol.lower()]
corr_result_tissue_vals_dict = correlation_functions.get_trait_symbol_and_tissue_values(
symbol_list=list(trait_symbol_dict.values()))
primary_tissue_data = {
"this_id": this_trait.name,
"tissue_values": primary_trait_tissue_values
}
target_tissue_data = {
"trait_symbol_dict": trait_symbol_dict,
"symbol_tissue_vals_dict": corr_result_tissue_vals_dict
}
return (primary_tissue_data, target_tissue_data)
def do_tissue_correlation_for_trait_list(self, tissue_dataset_id=1):
"""Given a list of correlation results (self.correlation_results), gets the tissue correlation value for each"""
#Gets tissue expression values for the primary trait
primary_trait_tissue_vals_dict = correlation_functions.get_trait_symbol_and_tissue_values(
symbol_list = [self.this_trait.symbol])
if self.this_trait.symbol.lower() in primary_trait_tissue_vals_dict:
primary_trait_tissue_values = primary_trait_tissue_vals_dict[self.this_trait.symbol.lower()]
gene_symbol_list = [trait.symbol for trait in self.correlation_results if trait.symbol]
corr_result_tissue_vals_dict= correlation_functions.get_trait_symbol_and_tissue_values(
symbol_list=gene_symbol_list)
for trait in self.correlation_results:
if trait.symbol and trait.symbol.lower() in corr_result_tissue_vals_dict:
this_trait_tissue_values = corr_result_tissue_vals_dict[trait.symbol.lower()]
result = correlation_functions.cal_zero_order_corr_for_tiss(primary_trait_tissue_values,
this_trait_tissue_values,
self.corr_method)
trait.tissue_corr = result[0]
trait.tissue_pvalue = result[2]
def test_get_trait_symbol_and_tissue_values(self, mock_class):
"""test for getting trait symbol and tissue_values"""
mock_class_instance = mock_class.return_value
mock_class_instance.gene_symbols = ["k1", "k2", "k3"]
mock_class_instance.get_symbol_values_pairs.return_value = {
"k1": ["v1", "v2", "v3"],
"k2": ["v2", "v3"],
"k3": ["k3"]
}
results = get_trait_symbol_and_tissue_values(
symbol_list=["k1", "k2", "k3"])
mock_class.assert_called_with(gene_symbols=['k1', 'k2', 'k3'])
self.assertEqual(
{
"k1": ["v1", "v2", "v3"],
"k2": ["v2", "v3"],
"k3": ["k3"]
}, results)