def do_analysis(self):
"""
Generator that performs the analysis. Uses data from the files within the folder that was given at runtime.
Currently, only GWAS is supported.
:return: loads all files from the folder given at runtime, parses data with the load_data function, returns the
results of the analysis with this data
"""
app_output_list = sorted(checkList(getList(self.args_dict['folder'])))
for each in app_output_list:
if self.args_dict['beta'] is not None:
if self.args_dict['covar'] is not None:
score_column, beta_column, covar_column = self.load_data(each)
else:
score_column, beta_column = self.load_data(each)
covar_column = None
else:
if self.args_dict['covar'] is not None:
score_column, covar_column = self.load_data(each)
beta_column = None
else:
score_column = self.load_data(each)
beta_column = None
covar_column = None
if self.args_dict['analysis'] == 'GWAS':
yield self.do_gwas(score_column, beta_column, covar_column)
else:
# Add other analysis methods here
print 'Currently, only GWAS is supported.'
def do_analysis(self):
"""
Generator that performs the analysis. Uses data from the files within the folder that was given at runtime.
Currently, only GWAS is supported.
:return: loads all files from the folder given at runtime, parses data with the load_data function, returns the
results of the analysis with this data
"""
app_output_list = sorted(checkList(getList(self.args_dict['folder'])))
for each in app_output_list:
if self.args_dict['beta'] is not None:
if self.args_dict['covar'] is not None:
score_column, beta_column, covar_column = self.load_data(
each)
else:
score_column, beta_column = self.load_data(each)
covar_column = None
else:
if self.args_dict['covar'] is not None:
score_column, covar_column = self.load_data(each)
beta_column = None
else:
score_column = self.load_data(each)
beta_column = None
covar_column = None
if self.args_dict['analysis'] == 'GWAS':
yield self.do_gwas(each, score_column, beta_column,
covar_column)
else:
# Add other analysis methods here
print 'Currently, only GWAS is supported.'
def load_ote(self):
"""
Loads only truth and effect type known truth file.
:return: sets the instance list variables snp_true_false and beta_true_false with data from the known truth file
given at runtime, separated by the given delimiter
"""
app_output_list = checkList(getList(self.args_dict['folder']))
kt_file = loadKT(self.args_dict['truth'], self.args_dict['kt_type_separ'])
acquired_data = loadFile(self.args_dict['folder'], app_output_list[0], self.args_dict['separ'])
snp_column = data_to_list(acquired_data, 1, acquired_data.header.index(self.args_dict['snp']))
kt_snps = data_to_list(kt_file, 1, 0)
kt_betas = data_to_list(kt_file, 1, 1)
for each in snp_column:
self.snp_true_false.append(trueFalse(each, kt_snps))
self.load_ote_betas(snp_column, kt_snps, kt_betas)
def load_ote(self):
"""
Loads only truth and effect type known truth file.
:return: sets the instance list variables snp_true_false and beta_true_false with data from the known truth file
given at runtime, separated by the given delimiter
"""
app_output_list = sorted(checkList(getList(self.args_dict['folder'])))
acquired_data = loadFile(self.args_dict['folder'], app_output_list[0],
self.args_dict['separ'])
kt_file = loadKT(self.args_dict['truth'],
self.args_dict['kt_type_separ'])
snp_column = data_to_list(
acquired_data, 1,
acquired_data.header.index(self.args_dict['snp']))
kt_snps = data_to_list(kt_file, 1, 0)
kt_betas = data_to_list(kt_file, 1, 1)
for each in snp_column:
self.snp_true_false.append(trueFalse(each, kt_snps))
self.load_ote_betas(snp_column, kt_snps, kt_betas)
