p3/preprocess/Schizophrenia/code/GSE285666.py

# Path Configuration
from tools.preprocess import *

# Processing context
trait = "Schizophrenia"
cohort = "GSE285666"

# Input paths
in_trait_dir = "../DATA/GEO/Schizophrenia"
in_cohort_dir = "../DATA/GEO/Schizophrenia/GSE285666"

# Output paths
out_data_file = "./output/preprocess/3/Schizophrenia/GSE285666.csv"
out_gene_data_file = "./output/preprocess/3/Schizophrenia/gene_data/GSE285666.csv"
out_clinical_data_file = "./output/preprocess/3/Schizophrenia/clinical_data/GSE285666.csv"
json_path = "./output/preprocess/3/Schizophrenia/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("Background Information:")
print(background_info)
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)
# Gene Expression Data Availability
# Yes, according to background info "Exon- and gene-Level transcriptional profiling" and "Expression analysis using Affymetrix Human Exon arrays"
is_gene_available = True

# Clinical Data Availability and Conversion
trait_row = 0  # Found trait info in row 0 "disease state"
age_row = None # Age not available
gender_row = None # Gender not available

def convert_trait(value: str) -> int:
    """Convert disease state to binary - controls:0, patients:1"""
    if pd.isna(value) or not isinstance(value, str):
        return None
    value = value.split(": ")[-1].lower()
    if "unaffected" in value or "control" in value:
        return 0
    elif "patient" in value or "williams syndrome" in value:
        return 1
    return None

# 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)

# Extract clinical features since trait data is available
clinical_df = geo_select_clinical_features(clinical_data,
                                         trait=trait,
                                         trait_row=trait_row,
                                         convert_trait=convert_trait)

# Preview the processed clinical data
print("Preview of clinical data:")
print(preview_df(clinical_df))

# Save clinical data
os.makedirs(os.path.dirname(out_clinical_data_file), exist_ok=True)
clinical_df.to_csv(out_clinical_data_file)
# Get gene expression data from matrix file
genetic_data = get_genetic_data(matrix_file_path)

# Examine data structure
print("Data structure and head:")
print(genetic_data.head())

print("\nShape:", genetic_data.shape)

print("\nFirst 20 row IDs (gene/probe identifiers):")
print(list(genetic_data.index)[:20])

# Get a few column names to verify sample IDs
print("\nFirst 5 column names:")
print(list(genetic_data.columns)[:5])
# These appear to be numerical probe IDs, not human gene symbols
# They will need to be mapped to gene symbols before analysis
requires_gene_mapping = True
# Extract gene annotation data
gene_annotation = get_gene_annotation(soft_file_path)

# Preview column names and values from annotation dataframe
print("Gene annotation DataFrame preview:")
print(preview_df(gene_annotation))
# From observation: 'ID' in gene annotation matches gene identifiers in expression data
# 'gene_assignment' contains gene symbols in the format "RefSeq // GeneSymbol // Description"

# Get mapping between probes and genes 
mapping_df = get_gene_mapping(gene_annotation, prob_col='ID', gene_col='gene_assignment')

# Convert probe-level data to gene-level data
gene_data = apply_gene_mapping(genetic_data, mapping_df)

# Preview the mapped gene data
print("Gene expression data preview after mapping:")
print(gene_data.head())
print("\nShape:", gene_data.shape)

# Save gene data
os.makedirs(os.path.dirname(out_gene_data_file), exist_ok=True)
gene_data.to_csv(out_gene_data_file)
# 1. Normalize gene symbols
gene_data = normalize_gene_symbols_in_index(gene_data)
print("Gene data shape after normalization:", gene_data.shape)
os.makedirs(os.path.dirname(out_gene_data_file), exist_ok=True) 
gene_data.to_csv(out_gene_data_file)

# Load clinical data previously processed
selected_clinical_df = pd.read_csv(out_clinical_data_file, index_col=0)
print("\nClinical data shape:", selected_clinical_df.shape)

# 2. Link clinical and genetic data
linked_data = geo_link_clinical_genetic_data(selected_clinical_df, gene_data)
print("\nLinked data shape:", linked_data.shape)

# 3. Handle missing values systematically  
if trait in linked_data.columns:
    linked_data = handle_missing_values(linked_data, trait)

    # 4. Check for bias in trait and demographic features
    trait_biased, linked_data = judge_and_remove_biased_features(linked_data, trait)

    # 5. Final validation and information saving
    note = "This dataset contains gene expression data from myxoid liposarcoma samples, with metastasis status as the trait."
    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=trait_biased,
        df=linked_data,
        note=note
    )

    # 6. Save linked data only if usable and not biased
    if is_usable and not trait_biased:
        os.makedirs(os.path.dirname(out_data_file), exist_ok=True)
        linked_data.to_csv(out_data_file)
else:
    # Handle case where clinical features were not properly extracted
    note = "Failed to extract clinical trait information from sample characteristics."
    validate_and_save_cohort_info(
        is_final=True,
        cohort=cohort,
        info_path=json_path, 
        is_gene_available=True,
        is_trait_available=False,
        is_biased=None,
        df=None,
        note=note
    )