p3/preprocess/Depression/code/GSE81761.py

# Path Configuration
from tools.preprocess import *

# Processing context
trait = "Depression"
cohort = "GSE81761"

# Input paths
in_trait_dir = "../DATA/GEO/Depression"
in_cohort_dir = "../DATA/GEO/Depression/GSE81761"

# Output paths
out_data_file = "./output/preprocess/3/Depression/GSE81761.csv"
out_gene_data_file = "./output/preprocess/3/Depression/gene_data/GSE81761.csv"
out_clinical_data_file = "./output/preprocess/3/Depression/clinical_data/GSE81761.csv"
json_path = "./output/preprocess/3/Depression/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 gene expression dataset using Affymetrix HG-U133_Plus_2 chip
is_gene_available = True

# 2.1 Data Availability
# Trait (Depression) is not explicitly recorded but PTSD/Depression comorbidity is common in military
# We can infer depression from PTSD subgroup which shows symptom severity changes
trait_row = 2  

# Age and gender data are available
age_row = 5
gender_row = 4

# 2.2 Data Type Conversion Functions
def convert_trait(value):
    """Convert PTSD subgroup to depression severity (binary)"""
    if not value or ':' not in value:
        return None
    value = value.split(': ')[1].strip()
    if value == 'PTSD Not Improved':
        return 1  # Severe depression
    elif value == 'PTSD Improved':
        return 0  # Mild/no depression
    elif value == 'No PTSD':
        return 0  # No depression
    return None  # No Follow Up Data cases

def convert_age(value):
    """Convert age string to integer"""
    if not value or ':' not in value:
        return None
    try:
        return int(value.split(': ')[1])
    except:
        return None

def convert_gender(value):
    """Convert gender to binary (0=female, 1=male)"""
    if not value or ':' not in value:
        return None
    value = value.split(': ')[1].lower()
    if value == 'female':
        return 0
    elif value == 'male':
        return 1
    return None

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

# 4. Clinical Feature Extraction
clinical_df = geo_select_clinical_features(
    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 processed clinical data
preview_result = preview_df(clinical_df)
print("Preview of clinical data:")
print(preview_result)

# Save clinical data
os.makedirs(os.path.dirname(out_clinical_data_file), exist_ok=True)
clinical_df.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])
# These IDs appear to be Affymetrix probe IDs (e.g. '1007_s_at', '1053_at')
# Rather than human gene symbols, so they will need to be mapped
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 columns: 'ID' for probe IDs and 'Gene Symbol' for gene symbols
prob_col = 'ID'
gene_col = 'Gene Symbol'

# 2. Get gene mapping dataframe from annotation data
mapping_df = get_gene_mapping(gene_metadata, prob_col, gene_col)

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

# 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 of depression in obese patients before and after bariatric surgery"
)

# 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)