p3/preprocess/Obstructive_sleep_apnea/code/GSE135917.py

# Path Configuration
from tools.preprocess import *

# Processing context
trait = "Obstructive_sleep_apnea"
cohort = "GSE135917"

# Input paths
in_trait_dir = "../DATA/GEO/Obstructive_sleep_apnea"
in_cohort_dir = "../DATA/GEO/Obstructive_sleep_apnea/GSE135917"

# Output paths
out_data_file = "./output/preprocess/3/Obstructive_sleep_apnea/GSE135917.csv"
out_gene_data_file = "./output/preprocess/3/Obstructive_sleep_apnea/gene_data/GSE135917.csv"
out_clinical_data_file = "./output/preprocess/3/Obstructive_sleep_apnea/clinical_data/GSE135917.csv"
json_path = "./output/preprocess/3/Obstructive_sleep_apnea/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 mentions gene expression microarray data
is_gene_available = True

# 2.1 Data Row Identification
# Group 2 baseline vs after design - use same data structure
# Note: OSA state distinguishes cases/controls
trait_row = None  # No direct OSA status labeling in characteristics
age_row = 0  # Age information in row 0
gender_row = 1  # Sex information in row 1 

# 2.2 Data Type Conversion Functions
def convert_trait(x):
    # Not implemented since trait_row is None
    return None

def convert_age(x):
    # Extract numeric value after colon
    try:
        age = float(x.split(': ')[1])
        return age
    except:
        return None

def convert_gender(x):
    # Convert F->0, M->1 after colon
    try:
        gender = x.split(': ')[1]
        if gender == 'F':
            return 0
        elif gender == 'M':
            return 1
        return None
    except:
        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. Skip clinical feature extraction since trait_row is None
# 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])
# Review gene identifiers
# The row IDs appear to be numeric probe identifiers (e.g. 7892501) rather than human gene symbols
# Therefore, we need to map these probe IDs to actual gene symbols
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))
# Identify probe ID and gene symbol columns
# 'ID' matches probe IDs in expression data
# 'gene_assignment' contains gene symbol info
mapping_df = get_gene_mapping(gene_annotation, prob_col='ID', gene_col='gene_assignment')

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

# Print first few rows of resulting gene data to verify
print("\nFirst few rows of mapped gene expression data:")
print(gene_data.head())
print("\nShape of gene data:", gene_data.shape)
# Early validation of data availability
is_usable = validate_and_save_cohort_info(
    is_final=False,
    cohort=cohort,
    info_path=json_path,
    is_gene_available=True,
    is_trait_available=False  # No trait data available
)