p3/preprocess/Rectal_Cancer/code/GSE94104.py

# Path Configuration
from tools.preprocess import *

# Processing context
trait = "Rectal_Cancer"
cohort = "GSE94104"

# Input paths
in_trait_dir = "../DATA/GEO/Rectal_Cancer"
in_cohort_dir = "../DATA/GEO/Rectal_Cancer/GSE94104"

# Output paths
out_data_file = "./output/preprocess/3/Rectal_Cancer/GSE94104.csv"
out_gene_data_file = "./output/preprocess/3/Rectal_Cancer/gene_data/GSE94104.csv"
out_clinical_data_file = "./output/preprocess/3/Rectal_Cancer/clinical_data/GSE94104.csv"
json_path = "./output/preprocess/3/Rectal_Cancer/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
# The background info mentions RNA and expression beadchip, so gene expression data is likely available
is_gene_available = True

# 2. Variable Availability and Data Type Conversion
# 2.1 Data Availability
trait_row = 2  # Tumour regression grade is available and varies
age_row = None  # Age not provided
gender_row = None  # Gender not provided

# 2.2 Data Type Conversion Functions
def convert_trait(value):
    if not isinstance(value, str):
        return None
    # Extract numeric grade after colon
    try:
        grade = int(value.split(': ')[1])
        # Convert to binary: grade 1-2 (good response) vs grade 3 (poor response)
        return 0 if grade <= 2 else 1
    except:
        return None

# No age or gender conversion functions needed since data not available
convert_age = None
convert_gender = 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:
    # Extract available features
    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:")
    print(preview)
    
    # Save to CSV
    clinical_features.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 gene identifiers start with "ILMN_" which indicates these are Illumina probe IDs
# They 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)

# 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. Identify relevant columns
# The gene expression data uses "ILMN_" IDs which match the 'ID' column in annotation
# The 'Symbol' column contains gene symbols

# 2. Get mapping between probe IDs and gene symbols
mapping_df = get_gene_mapping(gene_annotation, prob_col='ID', gene_col='Symbol')

# 3. Apply mapping to convert probe data to gene expression data
gene_data = apply_gene_mapping(genetic_data, mapping_df)
# 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 = "Dataset contains gene expression data from CD14+ cells of Psoriatic Arthritis patients and healthy 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=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)