p3/preprocess/Lung_Cancer/code/GSE222124.py

# Path Configuration
from tools.preprocess import *

# Processing context
trait = "Lung_Cancer"
cohort = "GSE222124"

# Input paths
in_trait_dir = "../DATA/GEO/Lung_Cancer"
in_cohort_dir = "../DATA/GEO/Lung_Cancer/GSE222124"

# Output paths
out_data_file = "./output/preprocess/3/Lung_Cancer/GSE222124.csv"
out_gene_data_file = "./output/preprocess/3/Lung_Cancer/gene_data/GSE222124.csv"
out_clinical_data_file = "./output/preprocess/3/Lung_Cancer/clinical_data/GSE222124.csv"
json_path = "./output/preprocess/3/Lung_Cancer/cohort_info.json"

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

# Extract background info and clinical data using specified prefixes
background_info, clinical_data = get_background_and_clinical_data(
    matrix_file,
    prefixes_a=['!Series_title', '!Series_summary', '!Series_overall_design'],
    prefixes_b=['!Sample_geo_accession', '!Sample_characteristics_ch1']
)

# 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
is_gene_available = True # Series title mentions gene expression alterations

# 2.1 Data Availability
trait_row = None # No patient trait data - these are cell lines
age_row = None # No age data
gender_row = None # No gender data

# 2.2 Data Type Conversion Functions
def convert_trait(x):
    return None

def convert_age(x):
    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. Skip clinical feature extraction since trait_row is None
# Get file paths
soft_file, matrix_file = geo_get_relevant_filepaths(in_cohort_dir)

# 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)
# Based on the identifier format (e.g. "1007_s_at"), these are Affymetrix probe IDs
# from microarray data that need to be mapped to human gene symbols
requires_gene_mapping = True
# Extract gene annotation data
gene_metadata = get_gene_annotation(soft_file)

# Try searching for ID patterns in all columns
print("All column names:", gene_metadata.columns.tolist())
print("\nPreview first few rows of each column to locate numeric IDs:")
for col in gene_metadata.columns:
    sample_values = gene_metadata[col].dropna().head().tolist()
    print(f"\n{col}:")
    print(sample_values)

# Inspect raw file to see unfiltered annotation format
import gzip
print("\nRaw SOFT file preview:")
with gzip.open(soft_file, 'rt', encoding='utf-8') as f:
    header = []
    for i, line in enumerate(f):
        header.append(line.strip())
        if i >= 10:  # Preview first 10 lines
            break
print('\n'.join(header))
# Get mapping between probe IDs and gene symbols
mapping_data = get_gene_mapping(gene_metadata, prob_col='ID', gene_col='Gene Symbol')

# Apply gene mapping to convert probe-level data to gene-level data 
gene_data = apply_gene_mapping(gene_data, mapping_data)
# 1. Normalize gene symbols in gene expression data
gene_data = normalize_gene_symbols_in_index(gene_data)
gene_data.to_csv(out_gene_data_file)

# 2. Create a DataFrame for validation even though it's not suitable for trait analysis
df = gene_data.copy()
is_biased = True # Mark as biased since it's cell line data

# 3. Save info about dataset usability
is_usable = validate_and_save_cohort_info(
    is_final=True,
    cohort=cohort,
    info_path=json_path,
    is_gene_available=True,
    is_trait_available=False,
    is_biased=is_biased,
    df=df,
    note="Dataset contains gene expression data from cell lines, not suitable for associational studies requiring human trait data."
)

# Skip saving linked data since not usable for trait analysis