p3/preprocess/Schizophrenia/code/GSE120340.py

# Path Configuration
from tools.preprocess import *

# Processing context
trait = "Schizophrenia"
cohort = "GSE120340"

# Input paths
in_trait_dir = "../DATA/GEO/Schizophrenia"
in_cohort_dir = "../DATA/GEO/Schizophrenia/GSE120340"

# Output paths
out_data_file = "./output/preprocess/3/Schizophrenia/GSE120340.csv"
out_gene_data_file = "./output/preprocess/3/Schizophrenia/gene_data/GSE120340.csv"
out_clinical_data_file = "./output/preprocess/3/Schizophrenia/clinical_data/GSE120340.csv"
json_path = "./output/preprocess/3/Schizophrenia/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
# Since the title mentions "Affymetrix" and there's gene expression profiling mentioned in series design
is_gene_available = True

# 2. Variable Availability and Data Type Conversion
# Trait (SCZ vs Control) is in index 0
trait_row = 0
def convert_trait(value: str) -> Optional[int]:
    if not isinstance(value, str):
        return None
    value = value.split(": ")[-1].strip().lower()
    if value == "control":
        return 0
    elif value == "scz":
        return 1
    return None

# Age and gender not available in sample characteristics
age_row = None
gender_row = None
convert_age = None
convert_gender = None

# 3. Save Metadata
# Initial filtering - only checking data availability at this stage
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
# Since trait_row exists, we need to extract clinical features
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
)
print("Preview of clinical data:")
print(preview_df(clinical_df))

# Save clinical data
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])
# The '_at' suffix in gene identifiers indicates these are probe IDs from an Affymetrix microarray
# These need to be mapped to standard human gene symbols for downstream analysis
requires_gene_mapping = True
# Extract gene annotation data
gene_annotation = get_gene_annotation(soft_file_path)

# Preview column names and values from annotation dataframe
print("Gene annotation DataFrame preview:")
print(preview_df(gene_annotation))
# Get gene mapping by extracting ID and Description columns
mapping_data = get_gene_mapping(gene_annotation, prob_col='ID', gene_col='Description')

# Apply gene mapping to convert probe-level data to gene expression data
gene_data = apply_gene_mapping(genetic_data, mapping_data)

# Preview the mapped gene data
print("Preview of mapped gene expression data:")
print(preview_df(gene_data))

# Save gene data
gene_data.to_csv(out_gene_data_file)
# 1. Normalize gene symbols
print("\nSample gene symbols before normalization:", list(gene_data.index)[:5])

try:
    # Verify synonym dictionary
    with open("./metadata/gene_synonym.json", "r") as f:
        synonym_dict = json.load(f)
    print("\nNumber of entries in synonym dictionary:", len(synonym_dict))
    print("Sample entries from synonym dict:", list(synonym_dict.items())[:2])
    
    genetic_data = normalize_gene_symbols_in_index(gene_data)
    print("\nGene data shape after normalization:", genetic_data.shape)
    
    if genetic_data.shape[0] == 0:
        raise ValueError("Gene symbol normalization resulted in empty dataset")
        
    os.makedirs(os.path.dirname(out_gene_data_file), exist_ok=True) 
    genetic_data.to_csv(out_gene_data_file)
    
    # Load clinical data previously processed
    selected_clinical_df = pd.read_csv(out_clinical_data_file, index_col=0)
    print("\nClinical data shape:", selected_clinical_df.shape)

    # 2. Link clinical and genetic data
    linked_data = geo_link_clinical_genetic_data(selected_clinical_df, genetic_data)
    print("\nLinked data shape:", linked_data.shape)

    # 3. Handle missing values systematically  
    if trait in linked_data.columns:
        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 = "This dataset studies alcohol dependence in brain tissue samples, containing gene expression data from the prefrontal cortex."
        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 and not biased
        if is_usable and not trait_biased:
            os.makedirs(os.path.dirname(out_data_file), exist_ok=True)
            linked_data.to_csv(out_data_file)
            
except Exception as e:
    print(f"\nError during preprocessing: {str(e)}")
    # Record failure
    note = f"Failed during gene symbol normalization: {str(e)}"
    validate_and_save_cohort_info(
        is_final=True,
        cohort=cohort,
        info_path=json_path,
        is_gene_available=True,  
        is_trait_available=True,
        is_biased=None,
        df=None,
        note=note
    )