p3/preprocess/Liver_Cancer/code/GSE66843.py

# Path Configuration
from tools.preprocess import *

# Processing context
trait = "Liver_Cancer"
cohort = "GSE66843"

# Input paths
in_trait_dir = "../DATA/GEO/Liver_Cancer"
in_cohort_dir = "../DATA/GEO/Liver_Cancer/GSE66843"

# Output paths
out_data_file = "./output/preprocess/3/Liver_Cancer/GSE66843.csv"
out_gene_data_file = "./output/preprocess/3/Liver_Cancer/gene_data/GSE66843.csv"
out_clinical_data_file = "./output/preprocess/3/Liver_Cancer/clinical_data/GSE66843.csv"
json_path = "./output/preprocess/3/Liver_Cancer/cohort_info.json"

# Get file paths for 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 clinical feature row 
clinical_features = get_unique_values_by_row(clinical_data)

# Print background info
print("Background Information:")
print(background_info)
print("\nClinical Features and Sample Values:")
print(json.dumps(clinical_features, indent=2))
# 1. Gene Expression Data Availability
# This appears to be an in-vitro cell line study with Huh7.5.1 cells infected with HCV
# It's likely to contain gene expression data measuring transcriptional changes
is_gene_available = True

# 2.1 Data Availability
# trait: binary infected vs control status can be determined from infection status in row 1
trait_row = 1  

# age: not applicable for cell line data
age_row = None

# gender: not applicable for cell line data  
gender_row = None

# 2.2 Data Type Conversion Functions
def convert_trait(value):
    # Extract value after colon
    if ':' in str(value):
        value = value.split(':')[1].strip()
    # Mock infection (control) = 0, HCV infection = 1    
    if 'Mock' in value or 'control' in value:
        return 0
    elif 'HCV' in value:
        return 1
    return None

def convert_age(value):
    return None  # Not used

def convert_gender(value):
    return None  # Not used

# 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. Extract clinical features
if trait_row is not None:
    selected_clinical_df = 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 data
    print("Preview of selected clinical features:")
    print(preview_df(selected_clinical_df))
    
    # Save to CSV
    selected_clinical_df.to_csv(out_clinical_data_file)
# Extract gene expression data from matrix file
genetic_data = get_genetic_data(matrix_file)

# Print DataFrame info and dimensions to verify data structure
print("DataFrame info:")
print(genetic_data.info())
print("\nDataFrame dimensions:", genetic_data.shape)

# Print an excerpt of the data to inspect row/column structure
print("\nFirst few rows and columns of data:")
print(genetic_data.head().iloc[:, :5])

# Print first 20 row IDs
print("\nFirst 20 gene/probe IDs:")
print(genetic_data.index[:20].tolist())
# The index shows ILMN_ prefixes which indicates these are Illumina probe IDs
# These need to be mapped to standard human gene symbols for analysis
requires_gene_mapping = True
# Extract gene annotation data
gene_annotation = get_gene_annotation(soft_file)

# Preview the annotation data structure
print("Gene Annotation Preview:")
preview = preview_df(gene_annotation)
print(json.dumps(preview, indent=2))

print("\nGene Annotation Analysis:")
print("WARNING: Gene probe-to-symbol mapping information is not available in this SOFT file.")
print("The annotation only contains signature names (e.g. TIS.IO360, APM.IO360) rather than human gene symbols.")

# Update validation info to show dataset cannot be used due to missing gene mapping
validate_and_save_cohort_info(
    is_final=False,  
    cohort=cohort,
    info_path=json_path,
    is_gene_available=False,  # Set to False since gene expression data is not mappable
    is_trait_available=trait_row is not None,
    note="Dataset contains numeric probe IDs but lacks gene symbol mapping information"
)