p3/preprocess/Kidney_Chromophobe/code/GSE19949.py

# Path Configuration
from tools.preprocess import *

# Processing context
trait = "Kidney_Chromophobe"
cohort = "GSE19949"

# Input paths
in_trait_dir = "../DATA/GEO/Kidney_Chromophobe"
in_cohort_dir = "../DATA/GEO/Kidney_Chromophobe/GSE19949"

# Output paths
out_data_file = "./output/preprocess/3/Kidney_Chromophobe/GSE19949.csv"
out_gene_data_file = "./output/preprocess/3/Kidney_Chromophobe/gene_data/GSE19949.csv"
out_clinical_data_file = "./output/preprocess/3/Kidney_Chromophobe/clinical_data/GSE19949.csv"
json_path = "./output/preprocess/3/Kidney_Chromophobe/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)

# Get unique values for each clinical feature 
unique_values_dict = get_unique_values_by_row(clinical_data)

# Print background information
print("Background Information:")
print(background_info)
print("\nSample Characteristics:")
print(json.dumps(unique_values_dict, indent=2))
# 1. Gene Expression Data Availability
is_gene_available = True  # Based on background info mentioning "genome-wide expression profiling"

# 2.1 Variable Key Identification
trait_row = 4  # icd-o 3 diagnosis text
gender_row = 6  # gender
age_row = None  # age not provided

# 2.2 Data Type Conversion Functions
def convert_trait(x):
    if pd.isna(x):
        return None
    val = x.split(': ')[-1].lower()
    if 'chromophobe' in val:
        return 1
    elif 'renal cell carcinoma' in val or 'adenocarcinoma' in val:
        return 0
    return None

def convert_gender(x):
    if pd.isna(x):
        return None
    val = x.split(': ')[-1].lower()
    if 'female' in val:
        return 0
    elif 'male' in val:
        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. Clinical Feature Extraction
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,
        gender_row=gender_row,
        convert_gender=convert_gender
    )
    
    print("Preview of extracted clinical features:")
    print(preview_df(selected_clinical_df))
    
    # Save clinical data
    selected_clinical_df.to_csv(out_clinical_data_file)
# Extract gene expression data from the matrix file
genetic_data = get_genetic_data(matrix_file_path)

# Print first 20 row IDs
print("First 20 row IDs:")
print(genetic_data.index[:20].tolist())
# The identifiers appear to be Affymetrix probe IDs (e.g. "1007_s_at") rather than standard human gene symbols
# Affymetrix IDs need to be mapped to gene symbols for biological interpretation
requires_gene_mapping = True
# Extract gene annotation data from SOFT file
gene_metadata = get_gene_annotation(soft_file_path)

# Display information about the annotation data
print("Column names:")
print(gene_metadata.columns.tolist())

# Look at general data statistics 
print("\nData shape:", gene_metadata.shape)

# Preview the first few rows
print("\nPreview of the annotation data:")
print(json.dumps(preview_df(gene_metadata), indent=2))
# 1 & 2. Extract gene mapping information
# From previewing data, 'ID' column matches probe IDs in expression data, 'Gene Symbol' contains target symbols
mapping_data = get_gene_mapping(gene_metadata, prob_col='ID', gene_col='Gene Symbol')

# 3. Apply gene mapping to convert probe-level data to gene-level data
gene_data = apply_gene_mapping(genetic_data, mapping_data)

# Print info about the result
print("Gene expression data shape after mapping:", gene_data.shape)
print("\nFirst 10 gene symbols:")
print(gene_data.index[:10].tolist())
# 1. Normalize gene symbols
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(selected_clinical_df, gene_data)

# 3. Handle missing values
linked_data = handle_missing_values(linked_data, trait)

# Early exit if trait values are all NaN
if linked_data[trait].isna().all():
    is_biased = True
    linked_data = None
else:
    # 4. Judge whether features are biased and remove biased demographic features
    is_biased, linked_data = judge_and_remove_biased_features(linked_data, trait)

# 5. Final validation and save metadata
note = "Dataset from a cancer gene expression study using oligonucleotide microarrays, containing samples of kidney chromophobe tumors and normal tissues."
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=is_biased,
    df=linked_data,
    note=note
)

# 6. Save the linked data only if it's usable
if is_usable:
    os.makedirs(os.path.dirname(out_data_file), exist_ok=True)
    linked_data.to_csv(out_data_file)