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from tools.preprocess import * |
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trait = "Endometrioid_Cancer" |
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tcga_root_dir = "../DATA/TCGA" |
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out_data_file = "./output/preprocess/3/Endometrioid_Cancer/TCGA.csv" |
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out_gene_data_file = "./output/preprocess/3/Endometrioid_Cancer/gene_data/TCGA.csv" |
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out_clinical_data_file = "./output/preprocess/3/Endometrioid_Cancer/clinical_data/TCGA.csv" |
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json_path = "./output/preprocess/3/Endometrioid_Cancer/cohort_info.json" |
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print("Available directories in TCGA root:") |
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tcga_dirs = os.listdir(tcga_root_dir) |
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print(tcga_dirs) |
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cohort_name = "TCGA.UCEC.sampleMap" |
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cohort_dir = os.path.join(tcga_root_dir, cohort_name) |
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clinical_file, genetic_file = tcga_get_relevant_filepaths(cohort_dir) |
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clinical_df = pd.read_csv(clinical_file, sep='\t', index_col=0) |
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genetic_df = pd.read_csv(genetic_file, sep='\t', index_col=0) |
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print("\nClinical data columns:") |
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print(clinical_df.columns.tolist()) |
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validate_and_save_cohort_info( |
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is_final=False, |
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cohort="TCGA", |
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info_path=json_path, |
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is_gene_available=len(genetic_df.columns) > 0, |
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is_trait_available=True |
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) |
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print(f"TCGA root directory path: {tcga_root_dir}") |
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if os.path.exists(tcga_root_dir): |
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print("Directory exists. Contents:", os.listdir(tcga_root_dir)) |
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cohort_dir = os.path.join(tcga_root_dir, "TCGA_Endometrioid_Cancer_(UCEC)") |
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clinical_file, genetic_file = tcga_get_relevant_filepaths(cohort_dir) |
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clinical_df = pd.read_csv(clinical_file, sep='\t', index_col=0) |
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genetic_df = pd.read_csv(genetic_file, sep='\t', index_col=0) |
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print("\nClinical data columns:") |
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print(clinical_df.columns.tolist()) |
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validate_and_save_cohort_info( |
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is_final=False, |
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cohort="TCGA", |
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info_path=json_path, |
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is_gene_available=len(genetic_df.columns) > 0, |
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is_trait_available=True |
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) |
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else: |
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print("Directory does not exist") |
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validate_and_save_cohort_info( |
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is_final=False, |
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cohort="TCGA", |
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info_path=json_path, |
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is_gene_available=False, |
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is_trait_available=False |
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) |