|
|
|
from tools.preprocess import * |
|
|
|
|
|
trait = "COVID-19" |
|
|
|
|
|
tcga_root_dir = "../DATA/TCGA" |
|
|
|
|
|
out_data_file = "./output/preprocess/3/COVID-19/TCGA.csv" |
|
out_gene_data_file = "./output/preprocess/3/COVID-19/gene_data/TCGA.csv" |
|
out_clinical_data_file = "./output/preprocess/3/COVID-19/clinical_data/TCGA.csv" |
|
json_path = "./output/preprocess/3/COVID-19/cohort_info.json" |
|
|
|
|
|
lung_dirs = [d for d in os.listdir(tcga_root_dir) if 'LUNG' in d] |
|
|
|
if not lung_dirs: |
|
is_usable = validate_and_save_cohort_info(is_final=False, |
|
cohort="TCGA", |
|
info_path=json_path, |
|
is_gene_available=False, |
|
is_trait_available=False) |
|
raise ValueError("No suitable TCGA cohort found for COVID-19") |
|
|
|
|
|
cohort_dir = os.path.join(tcga_root_dir, "TCGA_Lung_Cancer_(LUNG)") |
|
|
|
|
|
clinical_file_path, genetic_file_path = tcga_get_relevant_filepaths(cohort_dir) |
|
|
|
|
|
clinical_df = pd.read_csv(clinical_file_path, index_col=0, sep='\t') |
|
|
|
|
|
genetic_df = pd.read_csv(genetic_file_path, index_col=0, sep='\t') |
|
|
|
|
|
print("Clinical data columns:") |
|
print(clinical_df.columns.tolist()) |
|
|
|
candidate_age_cols = ['age_at_initial_pathologic_diagnosis', 'days_to_birth'] |
|
candidate_gender_cols = ['gender'] |
|
|
|
|
|
clinical_file_path = None |
|
for subdir in os.listdir(tcga_root_dir): |
|
subdir_path = os.path.join(tcga_root_dir, subdir) |
|
if os.path.isdir(subdir_path): |
|
try: |
|
clinical_file_path, _ = tcga_get_relevant_filepaths(subdir_path) |
|
if clinical_file_path: |
|
break |
|
except: |
|
continue |
|
|
|
if clinical_file_path: |
|
clinical_data = pd.read_csv(clinical_file_path, index_col=0, delimiter='\t') |
|
|
|
|
|
age_preview = {} |
|
for col in candidate_age_cols: |
|
if col in clinical_data.columns: |
|
age_preview[col] = clinical_data[col].head(5).tolist() |
|
print("Age columns preview:") |
|
print(age_preview) |
|
|
|
|
|
gender_preview = {} |
|
for col in candidate_gender_cols: |
|
if col in clinical_data.columns: |
|
gender_preview[col] = clinical_data[col].head(5).tolist() |
|
print("\nGender columns preview:") |
|
print(gender_preview) |
|
else: |
|
print("No clinical data file found") |
|
|
|
age_col = 'age_at_initial_pathologic_diagnosis' |
|
gender_col = 'gender' |
|
|
|
|
|
print(f"Selected age column: {age_col}") |
|
print(f"Selected gender column: {gender_col}") |
|
|
|
is_usable = validate_and_save_cohort_info( |
|
is_final=False, |
|
cohort="TCGA", |
|
info_path=json_path, |
|
is_gene_available=True, |
|
is_trait_available=False, |
|
note="TCGA cancer data cannot be repurposed for COVID-19 analysis" |
|
) |
|
|
|
|
|
raise ValueError("TCGA data is not suitable for COVID-19 analysis. This trait will be skipped.") |