| # Path Configuration | |
| from tools.preprocess import * | |
| # Processing context | |
| trait = "Kidney_Clear_Cell_Carcinoma" | |
| cohort = "GSE102807" | |
| # Input paths | |
| in_trait_dir = "../DATA/GEO/Kidney_Clear_Cell_Carcinoma" | |
| in_cohort_dir = "../DATA/GEO/Kidney_Clear_Cell_Carcinoma/GSE102807" | |
| # Output paths | |
| out_data_file = "./output/preprocess/3/Kidney_Clear_Cell_Carcinoma/GSE102807.csv" | |
| out_gene_data_file = "./output/preprocess/3/Kidney_Clear_Cell_Carcinoma/gene_data/GSE102807.csv" | |
| out_clinical_data_file = "./output/preprocess/3/Kidney_Clear_Cell_Carcinoma/clinical_data/GSE102807.csv" | |
| json_path = "./output/preprocess/3/Kidney_Clear_Cell_Carcinoma/cohort_info.json" | |
| # Get file paths | |
| soft_file_path, matrix_file_path = geo_get_relevant_filepaths(in_cohort_dir) | |
| # Get background info and clinical data from SOFT file instead of matrix file | |
| background_info, clinical_data = get_background_and_clinical_data(soft_file_path) | |
| # Get unique values for each clinical feature | |
| unique_values_dict = get_unique_values_by_row(clinical_data) | |
| # Print background information | |
| print("Background Information:") | |
| print(background_info) | |
| print("\nSample Characteristics:") | |
| print(json.dumps(unique_values_dict, indent=2)) | |
| # Gene expression data availability | |
| is_gene_available = False # Based on metadata, this appears to be ChIP-seq data, not gene expression | |
| # Define variable rows and conversion functions | |
| trait_row = None # No clinical trait info available | |
| age_row = None # No age info available | |
| gender_row = None # No gender info available | |
| def convert_trait(x): | |
| return None | |
| def convert_age(x): | |
| return None | |
| def convert_gender(x): | |
| return None | |
| # Save metadata | |
| validate_and_save_cohort_info( | |
| is_final=False, | |
| cohort=cohort, | |
| info_path=json_path, | |
| is_gene_available=is_gene_available, | |
| is_trait_available=(trait_row is not None) | |
| ) |