p3/preprocess/Essential_Thrombocythemia/code/GSE159514.py

# Path Configuration
from tools.preprocess import *

# Processing context
trait = "Essential_Thrombocythemia"
cohort = "GSE159514"

# Input paths
in_trait_dir = "../DATA/GEO/Essential_Thrombocythemia"
in_cohort_dir = "../DATA/GEO/Essential_Thrombocythemia/GSE159514"

# Output paths
out_data_file = "./output/preprocess/3/Essential_Thrombocythemia/GSE159514.csv"
out_gene_data_file = "./output/preprocess/3/Essential_Thrombocythemia/gene_data/GSE159514.csv"
out_clinical_data_file = "./output/preprocess/3/Essential_Thrombocythemia/clinical_data/GSE159514.csv"
json_path = "./output/preprocess/3/Essential_Thrombocythemia/cohort_info.json"

# Get relevant file paths
soft_file_path, matrix_file_path = geo_get_relevant_filepaths(in_cohort_dir)

# Extract background info and clinical data from the matrix file
background_info, clinical_data = get_background_and_clinical_data(matrix_file_path)

# Get dictionary of unique values per row in clinical data
unique_values_dict = get_unique_values_by_row(clinical_data)

# Print background info
print("Background Information:")
print("-" * 50)
print(background_info)
print("\n")

# Print clinical data unique values
print("Sample Characteristics:")
print("-" * 50)
for row, values in unique_values_dict.items():
    print(f"{row}:")
    print(f"  {values}")
    print()
# 1. Gene Expression Data Availability
is_gene_available = True  # This is microarray gene expression data based on background info

# 2.1 Data Availability 
# The disease field (row 0) contains disease status that indicates whether a patient has MF condition
trait_row = 0 
# Age and gender not available in the characteristics data
age_row = None
gender_row = None

# 2.2 Data Type Conversion Functions
def convert_trait(value: str) -> int:
    """Convert disease status to binary - 1 for Pre-PMF and Overt-PMF (primary MF), 
    0 for PPV and PET (secondary MF)"""
    if not isinstance(value, str):
        return None
    value = value.split(': ')[-1].strip()
    if value in ['Pre-PMF', 'Overt-PMF']:
        return 1  # Primary MF
    elif value in ['PPV', 'PET']:
        return 0  # Secondary MF
    return None

def convert_age(value: str) -> float:
    return None  # Not used since age data unavailable

def convert_gender(value: str) -> int:
    return None  # Not used since gender data unavailable

# 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
if trait_row is not None:
    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
    )
    
    print("Preview of selected clinical features:")
    print(preview_df(selected_clinical))
    
    # Save clinical data
    selected_clinical.to_csv(out_clinical_data_file)
# Extract gene expression data
genetic_data = get_genetic_data(matrix_file_path)

# Print first 20 probe IDs
print("First 20 probe IDs:")
print(genetic_data.index[:20])
# The gene identifiers appear to be probe IDs from a microarray platform
# These are not standard human gene symbols and need to be mapped
requires_gene_mapping = True
# Extract gene annotation from SOFT file
gene_annotation = get_gene_annotation(soft_file_path)

# Preview column names and first few values
preview_dict = preview_df(gene_annotation)
print("Column names and preview values:")
for col, values in preview_dict.items():
    print(f"\n{col}:")
    print(values)
# 1. & 2. Get gene mapping dataframe
# 'ID' column in gene annotation matches probe IDs in gene expression data
# 'Gene Symbol' column contains the target gene symbols
mapping_data = get_gene_mapping(gene_annotation, prob_col='ID', gene_col='Gene Symbol')

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

# Preview the result
print("\nFirst few rows and columns of gene expression data:")
print(preview_df(gene_data))
# 1. Normalize gene symbols and save normalized gene data
normalized_gene_data = normalize_gene_symbols_in_index(gene_data) 
normalized_gene_data.to_csv(out_gene_data_file)

# Read the processed clinical data file
clinical_df = pd.read_csv(out_clinical_data_file, index_col=0)

# Link clinical and genetic data using the normalized gene data
linked_data = geo_link_clinical_genetic_data(clinical_df, normalized_gene_data)

# Handle missing values systematically 
linked_data = handle_missing_values(linked_data, trait)

# Detect bias in trait and demographic features, remove biased demographic features
is_biased, linked_data = judge_and_remove_biased_features(linked_data, trait)

# Validate data quality and save cohort info
note = "Expression data comparing patients with Essential Thrombocythemia to controls with other myeloproliferative disorders (PMF, PV). No age or gender data available."
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
)

# Save linked data if usable
if is_usable:
    linked_data.to_csv(out_data_file)
else:
    print(f"Dataset {cohort} did not pass quality validation and will not be saved.")