p3/preprocess/Thymoma/code/GSE131027.py

# Path Configuration
from tools.preprocess import *

# Processing context
trait = "Thymoma"
cohort = "GSE131027"

# Input paths
in_trait_dir = "../DATA/GEO/Thymoma"
in_cohort_dir = "../DATA/GEO/Thymoma/GSE131027"

# Output paths
out_data_file = "./output/preprocess/3/Thymoma/GSE131027.csv"
out_gene_data_file = "./output/preprocess/3/Thymoma/gene_data/GSE131027.csv"
out_clinical_data_file = "./output/preprocess/3/Thymoma/clinical_data/GSE131027.csv"
json_path = "./output/preprocess/3/Thymoma/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 shape and first few rows to verify data
print("Background Information:")
print(background_info)
print("\nClinical Data Shape:", clinical_data.shape)
print("\nFirst few rows of Clinical Data:")
print(clinical_data.head())

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)
# Gene expression data availability
is_gene_available = True  # Based on series summary mentioning expression features

# Clinical data availability and conversion functions
def convert_trait(value):
    if value is None:
        return None
    value = value.split(': ')[-1].strip()
    return 1 if value == 'Thymoma' else 0

def convert_age(value):
    # Age data not available in sample characteristics
    return None  

def convert_gender(value):
    # Gender data not available in sample characteristics
    return None

# Find row index for trait data
trait_row = 1  # Cancer type is in row 1
age_row = None  # Age not available 
gender_row = None  # Gender not available

# Save initial 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)

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

# Print first 20 row IDs 
print("First 20 gene/probe IDs:")
print(list(genetic_data.index[:20]))
# These appear to be Affymetrix probe IDs rather than human gene symbols
# Affymetrix probes need to be mapped to official gene symbols
requires_gene_mapping = True
# Extract gene annotation from SOFT file 
gene_annotation = get_gene_annotation(soft_file_path)

# Preview annotation structure
preview = preview_df(gene_annotation)
print("Gene annotation preview:")
print(preview)
# Get mapping between probe IDs and gene symbols 
mapping_data = get_gene_mapping(gene_annotation, prob_col='ID', gene_col='Gene Symbol')

# Apply mapping to convert probe data to gene expression data
gene_data = apply_gene_mapping(genetic_data, mapping_data)

# Print shape and preview first few gene symbols
print("\nGene expression data shape after mapping:", gene_data.shape)
print("\nFirst 10 gene symbols:")
print(list(gene_data.index[:10]))
# 1. Normalize gene symbols in gene expression data
gene_data = normalize_gene_symbols_in_index(gene_data)
os.makedirs(os.path.dirname(out_gene_data_file), exist_ok=True)
gene_data.to_csv(out_gene_data_file)
print("\nGene data shape (normalized gene-level):", gene_data.shape) 

# Load clinical data previously processed
selected_clinical_df = pd.read_csv(out_clinical_data_file, index_col=0)
print("\nClinical data shape:", selected_clinical_df.shape)

# 2. Link clinical and genetic data using normalized gene-level data
linked_data = geo_link_clinical_genetic_data(selected_clinical_df, gene_data)
print("\nLinked data shape:", linked_data.shape)

# 3. Handle missing values systematically  
if trait in linked_data.columns:
    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 = "Data was successfully preprocessed from probe-level to gene-level expression using gene symbol normalization with NCBI Gene database."
    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 and not biased
    if is_usable and not trait_biased:
        os.makedirs(os.path.dirname(out_data_file), exist_ok=True)
        linked_data.to_csv(out_data_file)