p3/preprocess/Sarcoma/code/GSE142162.py

# Path Configuration
from tools.preprocess import *

# Processing context
trait = "Sarcoma"
cohort = "GSE142162"

# Input paths
in_trait_dir = "../DATA/GEO/Sarcoma"
in_cohort_dir = "../DATA/GEO/Sarcoma/GSE142162"

# Output paths
out_data_file = "./output/preprocess/3/Sarcoma/GSE142162.csv"
out_gene_data_file = "./output/preprocess/3/Sarcoma/gene_data/GSE142162.csv"
out_clinical_data_file = "./output/preprocess/3/Sarcoma/clinical_data/GSE142162.csv"
json_path = "./output/preprocess/3/Sarcoma/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
# Based on background info, this is an affymetrix hgu133Plus2 array expression profiling study
is_gene_available = True

# 2.1 Data Availability and 2.2 Data Type Conversion
# Trait data: Can be inferred from tumor type in row 2
trait_row = 2
def convert_trait(x: str) -> int:
    # Binary: 1 for primary tumor
    if not isinstance(x, str):
        return None
    value = x.split(': ')[1].lower() if ': ' in x else x.lower()
    if 'primary tumor' in value:
        return 1
    return None

# Age data is in row 1
age_row = 1
def convert_age(x: str) -> float:
    if not isinstance(x, str):
        return None
    try:
        return float(x.split(': ')[1])
    except:
        return None

# Gender data is in row 0
gender_row = 0
def convert_gender(x: str) -> int:
    if not isinstance(x, str):
        return None
    value = x.split(': ')[1].lower() if ': ' in x else x.lower()
    if 'female' in value:
        return 0
    elif 'male' in value:
        return 1
    return None

# 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. Clinical Feature Extraction
if trait_row is not None:
    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
    preview = preview_df(clinical_df)
    print("Clinical data preview:", preview)
    
    # Save clinical features
    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 identifiers end with "_at" which indicates these are Affymetrix probe IDs
# They need to be mapped to gene symbols for downstream analysis
requires_gene_mapping = True
# Extract gene annotation data
gene_annotation = get_gene_annotation(soft_file_path)

# Preview column names and values from annotation dataframe
print("Gene annotation DataFrame preview:")
print(preview_df(gene_annotation))
# 1. ID column contains affymetrix probe IDs ending with "_at" matching gene expression data
# Description column contains gene symbols though descriptive
mapping_df = get_gene_mapping(gene_annotation, prob_col='ID', gene_col='Description')

# 3. Convert probe data to gene expression using the mapping
gene_data = apply_gene_mapping(genetic_data, mapping_df)

# Preview the mapped gene data 
print("\nGene expression data preview:")
print(gene_data.head())
print("\nShape after mapping:", gene_data.shape)
# 1. Normalize gene symbols
gene_data = normalize_gene_symbols_in_index(gene_data)
print("Gene data shape after normalization:", gene_data.shape)
os.makedirs(os.path.dirname(out_gene_data_file), exist_ok=True) 
gene_data.to_csv(out_gene_data_file)

# Load clinical data previously processed
selected_clinical_df = pd.read_csv(out_clinical_data_file, index_col=0)
print("\nClinical data shape:", selected_clinical_df.shape)

# 2. Link clinical and genetic data
linked_data = geo_link_clinical_genetic_data(selected_clinical_df, gene_data)
print("\nLinked data shape:", linked_data.shape)

# 3. Handle missing values systematically  
if trait in linked_data.columns:
    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 = "This dataset contains gene expression data from myxoid liposarcoma samples, with metastasis status as the trait."
    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)
else:
    # Handle case where clinical features were not properly extracted
    note = "Failed to extract clinical trait information from sample characteristics."
    validate_and_save_cohort_info(
        is_final=True,
        cohort=cohort,
        info_path=json_path, 
        is_gene_available=True,
        is_trait_available=False,
        is_biased=None,
        df=None,
        note=note
    )