p3/preprocess/Celiac_Disease/code/GSE112102.py

# Path Configuration
from tools.preprocess import *

# Processing context
trait = "Celiac_Disease"
cohort = "GSE112102"

# Input paths
in_trait_dir = "../DATA/GEO/Celiac_Disease"
in_cohort_dir = "../DATA/GEO/Celiac_Disease/GSE112102"

# Output paths
out_data_file = "./output/preprocess/3/Celiac_Disease/GSE112102.csv"
out_gene_data_file = "./output/preprocess/3/Celiac_Disease/gene_data/GSE112102.csv"
out_clinical_data_file = "./output/preprocess/3/Celiac_Disease/clinical_data/GSE112102.csv"
json_path = "./output/preprocess/3/Celiac_Disease/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
is_gene_available = True  # Based on series design mentioning gene expression analysis

# 2. Variable Availability and Data Type Conversion
# 2.1 Identify rows containing data
trait_row = 1  # "group" contains disease status
age_row = 2   # "age" is available 
gender_row = 4  # "gender" is available

# 2.2 Conversion functions
def convert_trait(value: str) -> int:
    """Convert disease status to binary: CeD=1, others=0"""
    if not value or ':' not in value:
        return None
    val = value.split(':')[1].strip().lower()
    if 'ced' in val:
        return 1
    elif 'control' in val or 'fdr' in val:
        return 0
    return None

def convert_age(value: str) -> float:
    """Convert age to float"""
    if not value or ':' not in value:
        return None
    try:
        return float(value.split(':')[1].strip())
    except:
        return None

def convert_gender(value: str) -> int:
    """Convert gender to binary: Female=0, Male=1"""
    if not value or ':' not in value:
        return None
    val = value.split(':')[1].strip().lower()
    if 'female' in val:
        return 0
    elif 'male' in val:
        return 1
    return None

# 3. Save metadata
is_filtered = 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. 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 features
print("Preview of extracted clinical features:")
print(preview_df(selected_clinical))

# Save clinical features
os.makedirs(os.path.dirname(out_clinical_data_file), exist_ok=True)
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])
# The gene IDs start with "ILMN", indicating they are Illumina probe IDs
# These need to be mapped to standard human gene symbols for analysis
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))
# Extract probe-to-gene mapping columns
# 'ID' column contains probe IDs matching gene expression data
# 'Symbol' column contains gene symbols to map to
mapping_df = get_gene_mapping(gene_metadata, prob_col='ID', gene_col='Symbol')

# Map probe IDs to gene symbols and aggregate expression values
gene_data = apply_gene_mapping(genetic_df, mapping_df)

# Print shape and preview mapped gene data
print("Mapped gene expression data shape:", gene_data.shape)
print("\nPreview of mapped gene expression data:")  
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  
linked_data = geo_link_clinical_genetic_data(selected_clinical, 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=is_gene_available,
    is_trait_available=True,
    is_biased=trait_biased,
    df=linked_data,
    note="Dataset contains gene expression data from intestinal mucus of celiac patients and controls"
)

# 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)