p3/preprocess/Osteoarthritis/code/GSE236924.py

# Path Configuration
from tools.preprocess import *

# Processing context
trait = "Osteoarthritis"
cohort = "GSE236924"

# Input paths
in_trait_dir = "../DATA/GEO/Osteoarthritis"
in_cohort_dir = "../DATA/GEO/Osteoarthritis/GSE236924"

# Output paths
out_data_file = "./output/preprocess/3/Osteoarthritis/GSE236924.csv"
out_gene_data_file = "./output/preprocess/3/Osteoarthritis/gene_data/GSE236924.csv"
out_clinical_data_file = "./output/preprocess/3/Osteoarthritis/clinical_data/GSE236924.csv"
json_path = "./output/preprocess/3/Osteoarthritis/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. Assess gene expression data availability
# Based on series title containing "array" and series design mentioning joint tissue comparison, 
# this likely contains gene expression data
is_gene_available = True

# 2.1 Identify data rows
# From Sample Characteristics, disease status is in row 0
trait_row = 0
# Age and gender not available in sample characteristics
age_row = None
gender_row = None

# 2.2 Define conversion functions
def convert_trait(value: str) -> Optional[int]:
    """Convert OA status to binary (0: no OA, 1: has OA)"""
    if not value or ':' not in value:
        return None
    value = value.split(':')[1].strip().upper()
    if value == 'OA':
        return 1
    elif value == 'CONTROL':
        return 0
    return None

def convert_age(value: str) -> Optional[float]:
    """Convert age to float"""
    return None  # Not used since age data unavailable

def convert_gender(value: str) -> Optional[int]:
    """Convert gender to binary (0: female, 1: male)"""
    return None  # Not used since gender data unavailable

# 3. Save metadata
is_trait_available = trait_row is not None
validate_and_save_cohort_info(is_final=False, 
                            cohort=cohort,
                            info_path=json_path,
                            is_gene_available=is_gene_available,
                            is_trait_available=is_trait_available)

# 4. Extract clinical features since trait data is available
clinical_df = geo_select_clinical_features(clinical_data, 
                                         trait=trait,
                                         trait_row=trait_row,
                                         convert_trait=convert_trait)

# Preview and save clinical data
print(preview_df(clinical_df))
clinical_df.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])
# Based on the gene identifier format (e.g. '1007_s_at', '1053_at'), these appear to be probe IDs 
# from an Affymetrix microarray platform rather than human gene symbols.
# They will need to be mapped to gene symbols for analysis.
requires_gene_mapping = True
# Extract gene annotation data
gene_annotation = get_gene_annotation(soft_file_path)

# Display column names and preview data
print("Column names:")
print(gene_annotation.columns)

print("\nPreview of gene annotation data:")
print(preview_df(gene_annotation))
# Extract mapping between probe IDs and gene symbols
# From previewing data, the 'ID' column contains probe IDs matching genetic data index
# and 'Gene Symbol' contains corresponding gene symbols
mapping_data = get_gene_mapping(gene_annotation, prob_col='ID', gene_col='Gene Symbol')

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

# Preview the result
print("Mapped gene expression data:")
print(gene_data.head())
print("\nShape:", gene_data.shape)
# Reload clinical data that was processed earlier
selected_clinical_df = pd.read_csv(out_clinical_data_file, index_col=0)

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

# 2. Link clinical and genetic data
linked_data = geo_link_clinical_genetic_data(selected_clinical_df, 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 = "Contains gene expression data with metabolic rate (inferred from multicentric occurrence-free survival days) measurements"
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)