p3/preprocess/Bladder_Cancer/code/GSE185264.py

# Path Configuration
from tools.preprocess import *

# Processing context
trait = "Bladder_Cancer"
cohort = "GSE185264"

# Input paths
in_trait_dir = "../DATA/GEO/Bladder_Cancer"
in_cohort_dir = "../DATA/GEO/Bladder_Cancer/GSE185264"

# Output paths
out_data_file = "./output/preprocess/3/Bladder_Cancer/GSE185264.csv"
out_gene_data_file = "./output/preprocess/3/Bladder_Cancer/gene_data/GSE185264.csv"
out_clinical_data_file = "./output/preprocess/3/Bladder_Cancer/clinical_data/GSE185264.csv"
json_path = "./output/preprocess/3/Bladder_Cancer/cohort_info.json"

# Get file paths
soft_file, matrix_file = geo_get_relevant_filepaths(in_cohort_dir)

# Extract background info and clinical data 
background_info, clinical_data = get_background_and_clinical_data(matrix_file)

# Get unique values per clinical feature
sample_characteristics = get_unique_values_by_row(clinical_data)

# Print background info
print("Dataset Background Information:")
print(f"{background_info}\n")

# Print sample characteristics
print("Sample Characteristics:")
for feature, values in sample_characteristics.items():
    print(f"Feature: {feature}")
    print(f"Values: {values}\n")
# 1. Gene Expression Data Availability
# Yes - RNA quantification data from NanoString nCounter platform
is_gene_available = True

# 2. Variable Availability and Row Numbers
trait_row = 12  # recurrence data available
age_row = None  # age not available 
gender_row = 7  # gender data available

# 2.2 Conversion Functions
def convert_trait(value: str) -> Optional[int]:
    """Convert recurrence status to binary (0: no recurrence, 1: recurrence)"""
    if pd.isna(value) or value == "NA":
        return None
    value = value.split(": ")[-1]
    if value == "No.Recurrence":
        return 0
    elif value == "Recurrence":
        return 1
    return None

def convert_age(value: str) -> Optional[float]:
    """Convert age to float - not used since age data unavailable"""
    return None

def convert_gender(value: str) -> Optional[int]:
    """Convert gender to binary (0: female, 1: male)"""
    if pd.isna(value):
        return None
    value = value.split(": ")[-1]
    if value == "F":
        return 0
    elif value == "M":
        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. Extract Clinical Features
selected_clinical_df = 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 selected features
print(preview_df(selected_clinical_df))

# Save clinical data
selected_clinical_df.to_csv(out_clinical_data_file)
# Extract gene expression data from matrix file
gene_data = get_genetic_data(matrix_file)

# Print first 20 row IDs and shape of data to help debug
print("Shape of gene expression data:", gene_data.shape)
print("\nFirst few rows of data:")
print(gene_data.head())
print("\nFirst 20 gene/probe identifiers:")
print(gene_data.index[:20])

# Inspect a snippet of raw file to verify identifier format
import gzip
with gzip.open(matrix_file, 'rt', encoding='utf-8') as f:
    lines = []
    for i, line in enumerate(f):
        if "!series_matrix_table_begin" in line:
            # Get the next 5 lines after the marker
            for _ in range(5):
                lines.append(next(f).strip())
            break
print("\nFirst few lines after matrix marker in raw file:")
for line in lines:
    print(line)
requires_gene_mapping = False
# 1. Normalize gene symbols and save normalized gene data
gene_data.index = gene_data.index.str.replace('-mRNA', '')
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)

# 4. Check for biased features and remove them if needed
is_biased, linked_data = judge_and_remove_biased_features(linked_data, trait)

# 5. Validate and save cohort info
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="NanoString nCounter RNA profiling data for bladder cancer recurrence study"
)

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