p3/preprocess/Kidney_Chromophobe/code/GSE40911.py

# Path Configuration
from tools.preprocess import *

# Processing context
trait = "Kidney_Chromophobe"
cohort = "GSE40911"

# Input paths
in_trait_dir = "../DATA/GEO/Kidney_Chromophobe"
in_cohort_dir = "../DATA/GEO/Kidney_Chromophobe/GSE40911"

# Output paths
out_data_file = "./output/preprocess/3/Kidney_Chromophobe/GSE40911.csv"
out_gene_data_file = "./output/preprocess/3/Kidney_Chromophobe/gene_data/GSE40911.csv"
out_clinical_data_file = "./output/preprocess/3/Kidney_Chromophobe/clinical_data/GSE40911.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
# The series title and summary indicate this dataset contains expression analysis data
# It uses cDNA microarray platform enriched in gene fragments, so gene data is available
is_gene_available = True

# 2.1 Data Availability
# Trait: tissue type indicates tumor vs non-tumor status (row 2)
trait_row = 2
# Age: age at surgery available (row 4) 
age_row = 4
# Gender: gender data available (row 3)
gender_row = 3

# 2.2 Data Type Conversion Functions
def convert_trait(value: str) -> int:
    """Convert tissue type to binary: 1 for tumor, 0 for non-tumor"""
    if not isinstance(value, str):
        return None
    value = value.lower().split(": ")[-1]
    if "tumor" in value and "non" not in value and "adjacent" not in value:
        return 1
    elif "adjacent" in value or "non" in value:
        return 0
    return None

def convert_age(value: str) -> float:
    """Convert age string to float value"""
    if not isinstance(value, str):
        return None
    try:
        age = float(value.split(": ")[-1])
        return age
    except:
        return None

def convert_gender(value: str) -> int:
    """Convert gender to binary: 1 for male, 0 for female"""
    if not isinstance(value, str):
        return None
    value = value.lower().split(": ")[-1]
    if value == "male":
        return 1
    elif value == "female":
        return 0
    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
selected_clinical = 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
print("Preview of extracted clinical features:")
print(preview_df(selected_clinical))

# Save clinical data
os.makedirs(os.path.dirname(out_clinical_data_file), exist_ok=True)
selected_clinical.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 row IDs look like ID numbers, not gene symbols
# These need to be mapped to gene symbols for downstream analysis 
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. ID is storing same type of identifiers as in gene expression data
# GENE_SYMBOL is storing gene symbols
prob_col = 'ID'
gene_col = 'GENE_SYMBOL'

# 2. Extract mapping between probe IDs and gene symbols
mapping_data = get_gene_mapping(gene_metadata, prob_col, gene_col)

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

# Preview the mapped gene data
print("Preview of gene expression data after mapping:")
print("Shape:", gene_data.shape)
print("\nFirst 5 gene symbols:")
print(gene_data.index[:5].tolist())
# 1. Normalize gene symbols
gene_data = normalize_gene_symbols_in_index(gene_data)
gene_data.to_csv(out_gene_data_file)

# Get clinical features 
clinical_features = 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
)

# 2. Link clinical and genetic data
linked_data = geo_link_clinical_genetic_data(clinical_features, 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 from various tissue types including kidney, lung, stomach and other organs, with both tumor 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)