p3/preprocess/Rectal_Cancer/code/GSE119409.py

# Path Configuration
from tools.preprocess import *

# Processing context
trait = "Rectal_Cancer"
cohort = "GSE119409"

# Input paths
in_trait_dir = "../DATA/GEO/Rectal_Cancer"
in_cohort_dir = "../DATA/GEO/Rectal_Cancer/GSE119409"

# Output paths
out_data_file = "./output/preprocess/3/Rectal_Cancer/GSE119409.csv"
out_gene_data_file = "./output/preprocess/3/Rectal_Cancer/gene_data/GSE119409.csv"
out_clinical_data_file = "./output/preprocess/3/Rectal_Cancer/clinical_data/GSE119409.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
# From series title and summary, this dataset contains gene expression data
is_gene_available = True

# 2.1 Data Availability
# Trait (sensitivity to therapy) is in row 2
trait_row = 2

# Age is in row 3
age_row = 3 

# Gender is not available
gender_row = None

# 2.2 Data Type Conversion Functions
def convert_trait(x):
    if not isinstance(x, str):
        return None
    x = x.split(': ')[1].lower()
    if x == 'sensitive':
        return 1
    elif x == 'resistant':
        return 0
    return None

def convert_age(x):
    if not isinstance(x, str):
        return None
    try:
        age = int(x.split(': ')[1])
        return age
    except:
        return None

def convert_gender(x):
    return None

# 3. Save Metadata
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
# Extract features since trait data is available
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)

# Preview the extracted features
print("Preview of clinical features:")
print(preview_df(clinical_df))

# Save to CSV
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 gene identifiers in the data appear to be Affymetrix probe IDs (e.g. "1007_s_at", "1053_at")
# These are not standard gene symbols and need to be mapped to HGNC gene symbols
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))
# From the preview, we can see 'ID' contains probe IDs matching gene expression data
# and 'Gene Symbol' contains corresponding gene symbols

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

# Convert probe data to gene expression data 
gene_data = apply_gene_mapping(genetic_data, gene_mapping)

# Normalize the gene symbols in the data
gene_data = normalize_gene_symbols_in_index(gene_data)

# Print shape of final gene data
print("Gene expression data shape:", gene_data.shape)
print("\nPreview of gene data:")
print(preview_df(gene_data))
# Reload clinical data that was processed earlier
selected_clinical_df = pd.read_csv(out_clinical_data_file, index_col=0)

# 1. Normalize gene symbols 
gene_data = normalize_gene_symbols_in_index(gene_data)
gene_data.to_csv(out_gene_data_file)

# 2. Link clinical and genetic data
linked_data = geo_link_clinical_genetic_data(selected_clinical_df, gene_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 rectal cancer patients examining chemoradiotherapy response."
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)