p3/preprocess/Mesothelioma/code/GSE248514.py

# Path Configuration
from tools.preprocess import *

# Processing context
trait = "Mesothelioma"
cohort = "GSE248514"

# Input paths
in_trait_dir = "../DATA/GEO/Mesothelioma"
in_cohort_dir = "../DATA/GEO/Mesothelioma/GSE248514"

# Output paths
out_data_file = "./output/preprocess/3/Mesothelioma/GSE248514.csv"
out_gene_data_file = "./output/preprocess/3/Mesothelioma/gene_data/GSE248514.csv"
out_clinical_data_file = "./output/preprocess/3/Mesothelioma/clinical_data/GSE248514.csv"
json_path = "./output/preprocess/3/Mesothelioma/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
background_info, clinical_data = get_background_and_clinical_data(matrix_file_path)
print("Background Information:")
print(background_info)
print("\nSample Characteristics:")

# Get dictionary of unique values per row 
unique_values_dict = get_unique_values_by_row(clinical_data)
for row, values in unique_values_dict.items():
    print(f"\n{row}:")
    print(values)
# 1. Gene Expression Data Availability
# Yes - background info shows nanoString nCounter platform was used for gene expression analysis
is_gene_available = True

# 2. Variable Availability and Data Type Conversion
# 2.1 Data Availability 
trait_row = 5  # progression-free at 6 months row
age_row = None  # age not available 
gender_row = 3  # gender row

# 2.2 Data Type Conversion Functions
def convert_trait(x):
    if pd.isna(x):
        return None
    val = str(x).split(': ')[-1].strip()
    if val == 'Yes':
        return 1
    elif val == 'No':
        return 0
    return None

def convert_gender(x):
    if pd.isna(x):
        return None
    val = str(x).split(': ')[-1].strip()
    if val == 'Female':
        return 0
    elif val == 'Male':
        return 1
    return None

# 3. 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
)

# 4. Clinical Feature Extraction 
if trait_row is not None:
    clinical_features = geo_select_clinical_features(
        clinical_df=clinical_data,
        trait=trait,
        trait_row=trait_row,
        convert_trait=convert_trait,
        age_row=age_row,
        convert_age=None,
        gender_row=gender_row,
        convert_gender=convert_gender
    )
    
    # Preview the extracted features
    print("Preview of clinical features:")
    print(preview_df(clinical_features))
    
    # Save clinical features
    clinical_features.to_csv(out_clinical_data_file)
# Get gene expression data from matrix file
genetic_data = get_genetic_data(matrix_file_path)

# Examine data structure
print("Data structure and head:")
print(genetic_data.head())

print("\nShape:", genetic_data.shape)

print("\nFirst 20 row IDs (gene/probe identifiers):")
print(list(genetic_data.index)[:20])

# Get a few column names to verify sample IDs
print("\nFirst 5 column names:")
print(list(genetic_data.columns)[:5])
# The gene identifiers shown in the first 20 rows are already in standard human gene symbol format 
# (e.g., A2M, ABCF1, ACVR1C, etc). These are official HGNC gene symbols.
# No mapping is required.

requires_gene_mapping = False
# 1. Normalize gene symbols
genetic_data = normalize_gene_symbols_in_index(genetic_data)
genetic_data.to_csv(out_gene_data_file)

# 2. Link clinical and genetic data
linked_data = geo_link_clinical_genetic_data(clinical_features, genetic_data)

# 3. Handle missing values systematically  
linked_data = handle_missing_values(linked_data, trait)

# 4. Check for bias in trait and demographic features
trait_biased, linked_data = judge_and_remove_biased_features(linked_data, trait)

# 5. Final validation and information saving
note = "Dataset contains gene expression data from mesothelioma samples, but case/control ratio is heavily imbalanced."
is_usable = validate_and_save_cohort_info(
    is_final=True,
    cohort=cohort, 
    info_path=json_path,
    is_gene_available=True,
    is_trait_available=True,
    is_biased=trait_biased,
    df=linked_data,
    note=note
)

# 6. Save linked data only if usable
if is_usable:
    os.makedirs(os.path.dirname(out_data_file), exist_ok=True)
    linked_data.to_csv(out_data_file)