p3/preprocess/X-Linked_Lymphoproliferative_Syndrome/code/GSE222124.py

# Path Configuration
from tools.preprocess import *

# Processing context
trait = "X-Linked_Lymphoproliferative_Syndrome"
cohort = "GSE222124"

# Input paths
in_trait_dir = "../DATA/GEO/X-Linked_Lymphoproliferative_Syndrome"
in_cohort_dir = "../DATA/GEO/X-Linked_Lymphoproliferative_Syndrome/GSE222124"

# Output paths
out_data_file = "./output/preprocess/3/X-Linked_Lymphoproliferative_Syndrome/GSE222124.csv"
out_gene_data_file = "./output/preprocess/3/X-Linked_Lymphoproliferative_Syndrome/gene_data/GSE222124.csv"
out_clinical_data_file = "./output/preprocess/3/X-Linked_Lymphoproliferative_Syndrome/clinical_data/GSE222124.csv"
json_path = "./output/preprocess/3/X-Linked_Lymphoproliferative_Syndrome/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 shape and first few rows to verify data
print("Background Information:")
print(background_info)
print("\nClinical Data Shape:", clinical_data.shape)
print("\nFirst few rows of Clinical Data:")
print(clinical_data.head())

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
is_gene_available = True  # based on title and summary, this is a gene expression study

# 2.1 Data Availability
# Not suitable for X-Linked Lymphoproliferative Syndrome studies:
# - All samples are cell lines (Jurkat, THP1, KHYG-1)
# - The leukemia types shown are not X-Linked Lymphoproliferative Syndrome
# - No appropriate control samples
trait_row = None
age_row = None  # age data not available
gender_row = None  # gender data not available 

# 2.2 Data Type Conversion Functions 
def convert_trait(value: str) -> int:
    """Not used as trait data is not appropriately available"""
    return None

def convert_age(value: str) -> float:
    """Not used as age data is not available"""
    return None

def convert_gender(value: str) -> int:
    """Not used as gender data is not available"""
    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 is skipped since trait_row is None
# Extract gene expression data from matrix file
genetic_data = get_genetic_data(matrix_file_path)

# Print first 20 row IDs and shape of data
print("Shape of genetic data:", genetic_data.shape)
print("\nFirst 5 rows with sample columns:")
print(genetic_data.head())
print("\nFirst 20 gene/probe IDs:")
print(list(genetic_data.index[:20]))

# Print first few lines of raw matrix file to inspect format
print("\nFirst few lines of raw matrix file:")
with gzip.open(matrix_file_path, 'rt') as f:
    for i, line in enumerate(f):
        if i < 10:  # Print first 10 lines
            print(line.strip())
        elif "!series_matrix_table_begin" in line:
            print("\nFound table marker at line", i)
            # Print next 3 lines after marker
            for _ in range(3):
                print(next(f).strip())
            break
# Looking at the gene IDs which are in the format like '1007_s_at', '1053_at', etc.
# These are Affymetrix probe IDs which need to be mapped to gene symbols
requires_gene_mapping = True
# Extract gene annotation from SOFT file
gene_annotation = get_gene_annotation(soft_file_path)

# Preview annotation structure 
preview = preview_df(gene_annotation)
print("Gene annotation preview:")
print(preview)
# Get gene mapping DataFrame
mapping_data = get_gene_mapping(gene_annotation, prob_col='ID', gene_col='Gene Symbol')

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

# Save gene expression data
gene_data.to_csv(out_gene_data_file)

# Print shape of generated data
print("\nGene expression data shape:", gene_data.shape)
print("\nFirst few genes and their expression values:")
print(gene_data.head())
# 1. Normalize gene symbols in gene expression data
genetic_data = normalize_gene_symbols_in_index(gene_data)
os.makedirs(os.path.dirname(out_gene_data_file), exist_ok=True)
genetic_data.to_csv(out_gene_data_file)
print("\nGene data shape (normalized gene-level):", genetic_data.shape)

# Create empty DataFrame to satisfy function requirements
empty_df = pd.DataFrame()

# Since we determined in step 2 that trait data is not available (trait_row is None),
# we cannot proceed with data linking and subsequent steps.
# Instead, we validate and save the metadata indicating this dataset is not usable.

note = "Dataset contains gene expression data but lacks appropriate clinical data for X-Linked Lymphoproliferative Syndrome analysis (all samples are cancer cell lines)."
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=True,  # Set to True since data is unsuitable
    df=empty_df,     # Provide empty DataFrame
    note=note
)