p3/preprocess/Epilepsy/code/GSE65106.py

# Path Configuration
from tools.preprocess import *

# Processing context
trait = "Epilepsy"
cohort = "GSE65106"

# Input paths
in_trait_dir = "../DATA/GEO/Epilepsy"
in_cohort_dir = "../DATA/GEO/Epilepsy/GSE65106"

# Output paths
out_data_file = "./output/preprocess/3/Epilepsy/GSE65106.csv"
out_gene_data_file = "./output/preprocess/3/Epilepsy/gene_data/GSE65106.csv"
out_clinical_data_file = "./output/preprocess/3/Epilepsy/clinical_data/GSE65106.csv"
json_path = "./output/preprocess/3/Epilepsy/cohort_info.json"

# Get paths to the SOFT and matrix files
soft_file, matrix_file = geo_get_relevant_filepaths(in_cohort_dir)

# Get background info and clinical data from matrix file
background_info, clinical_data = get_background_and_clinical_data(matrix_file)

# Get unique values for each feature (row) in clinical data 
unique_values_dict = get_unique_values_by_row(clinical_data)

# Print background info
print("=== Dataset Background Information ===")
print(background_info)
print("\n=== Sample Characteristics ===")
print(json.dumps(unique_values_dict, indent=2))
# 1. Gene Expression Data Availability
# Yes, this is a microarray gene expression dataset studying gene expression profiles in ASD
is_gene_available = True

# 2. Variable Availability and Row Numbers
# 2.1 Data Availability
trait_row = 1  # Disease type indicates ASD vs Normal
age_row = 3    # Donor age is available 
gender_row = 4 # Donor sex is available

# 2.2 Data Type Conversion Functions
def convert_trait(value: str) -> Optional[int]:
    """Convert disease type to binary (0: Normal/WT, 1: ASD)"""
    if not isinstance(value, str):
        return None
    value = value.split(": ")[-1].strip().upper()
    if value == "ASD":
        return 1
    elif value in ["NORMAL", "WT"]:
        return 0
    return None

def convert_age(value: str) -> Optional[float]:
    """Convert age to continuous numeric value"""
    if not isinstance(value, str):
        return None
    value = value.split(": ")[-1].strip().lower()
    if value == "embryonic":
        return None
    try:
        return float(value)
    except:
        return None

def convert_gender(value: str) -> Optional[int]:
    """Convert gender to binary (0: Female, 1: Male)"""
    if not isinstance(value, str):
        return None
    value = value.split(": ")[-1].strip().upper()
    if value == "FEMALE":
        return 0
    elif value == "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 
# Since trait_row is not None, we need to extract clinical features
selected_clinical = 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 the extracted clinical features
print(preview_df(selected_clinical))

# Save clinical data
selected_clinical.to_csv(out_clinical_data_file)
# Extract gene expression data from matrix file
genetic_df = get_genetic_data(matrix_file)

# Print DataFrame shape and first 20 row IDs
print("DataFrame shape:", genetic_df.shape)
print("\nFirst 20 row IDs:")
print(genetic_df.index[:20])

print("\nPreview of first few rows and columns:")
print(genetic_df.head().iloc[:, :5])
# Analyzing gene identifiers - these appear to be probe IDs from Illumina arrays 
# (numeric format starting with 7892xxx) rather than standard human gene symbols
# Therefore, they need to be mapped to their corresponding gene symbols
requires_gene_mapping = True
# Extract gene annotation data, excluding control probe lines
gene_metadata = get_gene_annotation(soft_file) 

# Preview filtered annotation data
print("Column names:")
print(gene_metadata.columns)
print("\nPreview of gene annotation data:")
print(preview_df(gene_metadata))
# 1. Identify relevant columns
# From preview: 'ID' column contains probe IDs matching gene expression data
# 'gene_assignment' column contains gene symbol information

# 2. Extract mapping between probe IDs and gene symbols
mapping = get_gene_mapping(gene_metadata, prob_col='ID', gene_col='gene_assignment')

# 3. Apply mapping to convert probe data to gene expression data
gene_data = apply_gene_mapping(genetic_df, mapping)

# Preview results
print("Gene expression data shape:", gene_data.shape)
print("\nFirst few rows and columns:")
print(gene_data.head().iloc[:, :5])
# 1. Normalize gene symbols and save
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)

# 2. Link clinical and genetic data
clinical_df = pd.read_csv(out_clinical_data_file, index_col=0)
linked_data = geo_link_clinical_genetic_data(clinical_df, gene_data)

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

# 4. Check for biased features
trait_biased, linked_data = judge_and_remove_biased_features(linked_data, trait)

# 5. Final validation and metadata saving
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="Study comparing ERα-chromatin interactions in endometrial tumors from patients with/without tamoxifen treatment history"
)

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