# Path Configuration from tools.preprocess import * # Processing context trait = "Epilepsy" # Input paths tcga_root_dir = "../DATA/TCGA" # Output paths out_data_file = "./output/preprocess/3/Epilepsy/TCGA.csv" out_gene_data_file = "./output/preprocess/3/Epilepsy/gene_data/TCGA.csv" out_clinical_data_file = "./output/preprocess/3/Epilepsy/clinical_data/TCGA.csv" json_path = "./output/preprocess/3/Epilepsy/cohort_info.json" # List available cohorts first cohorts = os.listdir(tcga_root_dir) # Try each cohort until we find one with the data files we need clinical_df = None for cohort in cohorts: try: cohort_dir = os.path.join(tcga_root_dir, cohort) clinical_file_path, _ = tcga_get_relevant_filepaths(cohort_dir) clinical_df = pd.read_csv(clinical_file_path, sep='\t', index_col=0) break except: continue if clinical_df is not None: columns = clinical_df.columns.tolist() candidate_age_cols = [col for col in columns if 'age' in col.lower() or 'years' in col.lower()] candidate_gender_cols = [col for col in columns if 'gender' in col.lower() or 'sex' in col.lower()] else: candidate_age_cols = [] candidate_gender_cols = [] print(f"candidate_age_cols = {candidate_age_cols}") print(f"candidate_gender_cols = {candidate_gender_cols}") # Set age_col using the most suitable column from the candidate_age_cols age_col = 'age_at_initial_pathologic_diagnosis' # This is the standard age column in TCGA data # Set gender_col based on candidate column(s) gender_col = 'gender' if candidate_gender_cols else None # Print chosen columns print(f'Selected age column: {age_col}') print(f'Selected gender column: {gender_col}') # 1. Extract and standardize clinical features clinical_df = tcga_select_clinical_features(clinical_df, trait, age_col, gender_col) # 2. Normalize gene expression data gene_expression_dir = os.path.join(tcga_root_dir, cohort) _, gene_file_path = tcga_get_relevant_filepaths(gene_expression_dir) genetic_df = pd.read_csv(gene_file_path, sep='\t', index_col=0) normalized_genetic_df = normalize_gene_symbols_in_index(genetic_df) os.makedirs(os.path.dirname(out_gene_data_file), exist_ok=True) normalized_genetic_df.to_csv(out_gene_data_file) # 3. Link clinical and genetic data linked_data = pd.merge(normalized_genetic_df.T, clinical_df, left_index=True, right_index=True) # Add trait labels based on sample IDs linked_data[trait] = linked_data.index.map(tcga_convert_trait) # 4. Handle missing values linked_data = handle_missing_values(linked_data, trait) # 5. Check for bias in features is_biased, linked_data = judge_and_remove_biased_features(linked_data, trait) # 6. Validate and save cohort info is_usable = validate_and_save_cohort_info( is_final=True, cohort=cohort, info_path=json_path, is_gene_available=len(normalized_genetic_df.columns) > 0, is_trait_available=trait in linked_data.columns, is_biased=is_biased, df=linked_data, note=f"Data from {cohort} cohort" ) # 7. Save linked data if usable if is_usable: os.makedirs(os.path.dirname(out_data_file), exist_ok=True) linked_data.to_csv(out_data_file)