p3/preprocess/Huntingtons_Disease/code/GSE26927.py

# Path Configuration
from tools.preprocess import *

# Processing context
trait = "Huntingtons_Disease"
cohort = "GSE26927"

# Input paths
in_trait_dir = "../DATA/GEO/Huntingtons_Disease"
in_cohort_dir = "../DATA/GEO/Huntingtons_Disease/GSE26927"

# Output paths
out_data_file = "./output/preprocess/3/Huntingtons_Disease/GSE26927.csv"
out_gene_data_file = "./output/preprocess/3/Huntingtons_Disease/gene_data/GSE26927.csv"
out_clinical_data_file = "./output/preprocess/3/Huntingtons_Disease/clinical_data/GSE26927.csv"
json_path = "./output/preprocess/3/Huntingtons_Disease/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)

# Get unique values for each clinical feature 
unique_values_dict = get_unique_values_by_row(clinical_data)

# Print background information
print("Background Information:")
print(background_info)
print("\nSample Characteristics:")
print(json.dumps(unique_values_dict, indent=2))
# 1. Gene Expression Data Availability
# Yes, this is gene expression data from Illumina HumanRef8 v2 BeadChip
is_gene_available = True

# 2. Variable Availability and Data Type Conversion
# 2.1 Data Availability
trait_row = 0  # disease information in row 0
age_row = 2    # age information in row 2 
gender_row = 1 # gender information in row 1

# 2.2 Data Type Conversion Functions
def convert_trait(value):
    if not isinstance(value, str):
        return None
    if ":" not in value:
        return None
    disease = value.split(":")[1].strip().lower()
    # Convert to binary based on whether it's Huntington's disease
    if "huntington" in disease:
        return 1
    return 0

def convert_age(value):
    if not isinstance(value, str):
        return None
    try:
        # Extract age value after colon and convert to float
        age = float(value.split(":")[1].strip().split()[0])
        return age
    except:
        return None

def convert_gender(value):
    if not isinstance(value, str):
        return None
    gender = value.split(":")[1].strip()
    if gender == "F":
        return 0
    elif gender == "M":
        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=trait_row is not None
)

# 4. Clinical Feature Extraction
if trait_row is not None:
    clinical_features = 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
    preview = preview_df(clinical_features)
    print("Preview of clinical features:", preview)
    
    # Save to CSV
    clinical_features.to_csv(out_clinical_data_file)
# Extract gene expression data from the matrix file
genetic_data = get_genetic_data(matrix_file_path)

# Print first 20 row IDs
print("First 20 row IDs:")
print(genetic_data.index[:20].tolist())
requires_gene_mapping = True
# Extract gene annotation data from SOFT file
gene_metadata = get_gene_annotation(soft_file_path)

# Display information about the annotation data
print("Column names:")
print(gene_metadata.columns.tolist())
print("\nPreview of first few rows:")
print(json.dumps(preview_df(gene_metadata), indent=2))
# 1. Identify mapping columns
# The probe identifiers in gene expression data start with "ILMN_", matching the "ID" column in annotations
# Gene symbols are in the "SYMBOL" column
prob_col = "ID"
gene_col = "SYMBOL"

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

# 3. Convert probe measurements to gene expression data
gene_data = apply_gene_mapping(genetic_data, mapping_df)
# 1. Normalize gene symbols
gene_data = normalize_gene_symbols_in_index(gene_data)
gene_data.to_csv(out_gene_data_file)

# Get clinical features 
clinical_features = geo_select_clinical_features(
    clinical_data,
    trait=trait,
    trait_row=trait_row,
    convert_trait=convert_trait,
    gender_row=gender_row,
    convert_gender=convert_gender
)

# 2. Link clinical and genetic data
linked_data = geo_link_clinical_genetic_data(clinical_features, gene_data)

# 3. Handle missing values
linked_data = handle_missing_values(linked_data, trait)

# 4. Judge whether features are biased and remove biased demographic features
is_biased, linked_data = judge_and_remove_biased_features(linked_data, trait)

# 5. Final validation and save metadata
note = "Dataset contains gene expression data from human embryonic stem cells and their neural stem cell progeny, comparing HD mutation carriers with wild type controls"
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=is_biased,
    df=linked_data,
    note=note
)

# 6. Save the linked data only if it's usable
if is_usable:
    os.makedirs(os.path.dirname(out_data_file), exist_ok=True)
    linked_data.to_csv(out_data_file)