p3/preprocess/Obsessive-Compulsive_Disorder/code/GSE78104.py

# Path Configuration
from tools.preprocess import *

# Processing context
trait = "Obsessive-Compulsive_Disorder"
cohort = "GSE78104"

# Input paths
in_trait_dir = "../DATA/GEO/Obsessive-Compulsive_Disorder"
in_cohort_dir = "../DATA/GEO/Obsessive-Compulsive_Disorder/GSE78104"

# Output paths
out_data_file = "./output/preprocess/3/Obsessive-Compulsive_Disorder/GSE78104.csv"
out_gene_data_file = "./output/preprocess/3/Obsessive-Compulsive_Disorder/gene_data/GSE78104.csv"
out_clinical_data_file = "./output/preprocess/3/Obsessive-Compulsive_Disorder/clinical_data/GSE78104.csv"
json_path = "./output/preprocess/3/Obsessive-Compulsive_Disorder/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, based on the Series title and design, this dataset contains mRNA expression data
is_gene_available = True

# 2. Variable Availability and Data Type Conversion
# 2.1 Data Availability
trait_row = 1  # disease state row contains trait info
age_row = 3    # age information available 
gender_row = 2 # gender information available

# 2.2 Data Type Conversion Functions
def convert_trait(x):
    # Binary: Convert OCD vs control
    if not isinstance(x, str):
        return None
    value = x.split(': ')[-1].lower()
    if 'obsessive-compulsive disorder' in value:
        return 1
    elif 'normal control' in value:
        return 0
    return None

def convert_age(x):
    # Continuous: Extract age number
    if not isinstance(x, str):
        return None
    value = x.split(': ')[-1].lower()
    if 'y' in value:
        try:
            return int(value.replace('y',''))
        except:
            return None
    return None

def convert_gender(x):
    # Binary: Female=0, Male=1
    if not isinstance(x, str):
        return None
    value = x.split(': ')[-1].lower()
    if 'female' in value:
        return 0
    elif 'male' in value:
        return 1
    return None

# 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. Clinical Feature Extraction
if trait_row is not None:
    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 selected clinical features:")
    print(preview_df(selected_clinical))
    
    # Save clinical data
    selected_clinical.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])
# Looking at the identifiers in the gene expression data, they appear to be Agilent probe IDs 
# (starting with "A_19_") and control probes, not standard human gene symbols.
# Therefore we need to map them to 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))
# 1. From observation:
# gene expression data uses probe IDs like "A_19_P00315459"
# gene annotation data has these IDs in the "ID" column
# gene symbols are in "GeneSymbol" column

# 2. Get gene mapping from annotation data
prob_col = 'ID'
gene_col = 'GeneSymbol' 
mapping_df = get_gene_mapping(gene_annotation, prob_col, gene_col)

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

# Preview the result
print("Gene expression data shape:", gene_data.shape)
print("\nFirst few genes and their expression values:")
print(gene_data.head())
# 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)