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)