p3/preprocess/Cystic_Fibrosis/code/GSE100521.py

# Path Configuration
from tools.preprocess import *

# Processing context
trait = "Cystic_Fibrosis"
cohort = "GSE100521"

# Input paths
in_trait_dir = "../DATA/GEO/Cystic_Fibrosis"
in_cohort_dir = "../DATA/GEO/Cystic_Fibrosis/GSE100521"

# Output paths
out_data_file = "./output/preprocess/3/Cystic_Fibrosis/GSE100521.csv"
out_gene_data_file = "./output/preprocess/3/Cystic_Fibrosis/gene_data/GSE100521.csv"
out_clinical_data_file = "./output/preprocess/3/Cystic_Fibrosis/clinical_data/GSE100521.csv"
json_path = "./output/preprocess/3/Cystic_Fibrosis/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
is_gene_available = True  # Illumina HumanHT-12 v4 BeadChip indicates gene expression data

# 2.1 Variable Row Keys
trait_row = 0  # Patient ID contains CF status
age_row = 1
gender_row = 2

# 2.2 Conversion Functions
def convert_trait(x: str) -> int:
    """Convert CF status to binary: 0 for non-CF, 1 for CF"""
    if not isinstance(x, str):
        return None
    value = x.split(": ")[1] if ": " in x else x
    if "CF patient" in value:
        return 1
    elif "Non CF subject" in value:
        return 0
    return None

def convert_age(x: str) -> float:
    """Convert age to continuous value"""
    if not isinstance(x, str):
        return None
    value = x.split(": ")[1] if ": " in x else x
    try:
        return float(value)
    except:
        return None

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

# 3. Save Initial 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. Extract Clinical Features
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 clinical features
    clinical_features.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 ID format starting with 'ILMN_' indicates these are Illumina BeadArray
# probe identifiers, which need to be mapped to standard human gene symbols
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))
# Get gene mapping dataframe
mapping_df = get_gene_mapping(gene_metadata, prob_col='ID', gene_col='Symbol')

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

# Preview results
print("Gene mapping shape:", mapping_df.shape)
print("\nGene expression data shape:", gene_data.shape)
print("\nFirst few rows and columns of gene 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(clinical_features, 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="Cell line study comparing deltaF508 CFTR mutant with wildtype CFTR in cystic fibrosis bronchial epithelial cells"
)

# 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)