p3/preprocess/Amyotrophic_Lateral_Sclerosis/code/GSE139384.py

# Path Configuration
from tools.preprocess import *

# Processing context
trait = "Amyotrophic_Lateral_Sclerosis"
cohort = "GSE139384"

# Input paths
in_trait_dir = "../DATA/GEO/Amyotrophic_Lateral_Sclerosis"
in_cohort_dir = "../DATA/GEO/Amyotrophic_Lateral_Sclerosis/GSE139384"

# Output paths
out_data_file = "./output/preprocess/3/Amyotrophic_Lateral_Sclerosis/GSE139384.csv"
out_gene_data_file = "./output/preprocess/3/Amyotrophic_Lateral_Sclerosis/gene_data/GSE139384.csv"
out_clinical_data_file = "./output/preprocess/3/Amyotrophic_Lateral_Sclerosis/clinical_data/GSE139384.csv"
json_path = "./output/preprocess/3/Amyotrophic_Lateral_Sclerosis/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")
# Gene expression data availability check - Yes, it uses Illumina HumanHT-12 v4 Expression BeadChip
is_gene_available = True

# Variable Data Mapping and Conversion Functions

# Trait data is in Feature 0 and 1, need to map clinical phenotypes
trait_row = 0  # Using Feature 0 as primary source

def convert_trait(value):
    if 'clinical phenotypes:' not in str(value):
        return None
    value = str(value).split('clinical phenotypes:')[1].strip().lower()
    # ALS vs non-ALS binary classification
    if 'als' in value or 'als+d' in value or 'pdc+a' in value:
        return 1  # ALS or ALS-related
    elif value in ['healthy control', 'alzheimer`s disease', 'pdc']:
        return 0  # Non-ALS
    return None

# Age data is in Feature 2 and 3
age_row = 2  # Using Feature 2 as primary source

def convert_age(value):
    if 'age:' not in str(value):
        return None
    try:
        return float(str(value).split('age:')[1].strip())
    except:
        return None

# Gender data is in Feature 1 and 2
gender_row = 1  # Using Feature 1 as primary source

def convert_gender(value):
    if 'gender:' not in str(value):
        return None
    value = str(value).split('gender:')[1].strip().lower()
    if value == 'female':
        return 0
    elif value == 'male':
        return 1
    return None

# Initial filtering and metadata saving
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
)

# Clinical feature extraction since trait_row is not None
if trait_row is not None:
    clinical_features = 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 processed clinical features
    preview = preview_df(clinical_features)
    print("Preview of clinical features:")
    print(preview)
    
    # Save clinical features to CSV
    clinical_features.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)
# The gene identifiers start with "ILMN_", which stands for Illumina array probe IDs
# These are not human gene symbols and need to be mapped to official gene symbols
requires_gene_mapping = True
# Extract gene annotation from SOFT file and get meaningful data 
gene_annotation = get_gene_annotation(soft_file)

# Preview gene annotation data
print("Gene annotation shape:", gene_annotation.shape)
print("\nGene annotation preview:")
print(preview_df(gene_annotation))

print("\nNumber of non-null values in each column:")
print(gene_annotation.count())

print("\nNote: Gene mapping will use:")
print("'ID' column: Probe identifiers")
print("'Symbol' column: Contains gene symbols")
print("\nExample Symbol value:")
print(gene_annotation['Symbol'].iloc[0])
# Get gene mapping dataframe from annotation
mapping_df = get_gene_mapping(gene_annotation, 'ID', 'Symbol')

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

# Print output to verify results
print("Shape of gene-level data:", gene_data.shape)
print("\nFirst few rows of mapped gene data:")
print(gene_data.head())
print("\nFirst 20 gene symbols:")
print(gene_data.index[:20])
# 1. Normalize gene symbols
gene_data = normalize_gene_symbols_in_index(gene_data)

# Save normalized gene data
gene_data.to_csv(out_gene_data_file)

# 2. Link clinical and genetic data
try:
    clinical_data = pd.read_csv(out_clinical_data_file, index_col=0)
    linked_data = geo_link_clinical_genetic_data(clinical_data, gene_data)

    # 3. Handle missing values
    linked_data = handle_missing_values(linked_data, trait)

    # 4. Determine if features are biased
    is_trait_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_trait_biased,
        df=linked_data,
        note="Gene expression data successfully mapped and linked with clinical features"
    )

    # 6. Save linked data only if usable AND trait is not biased
    if is_usable and not is_trait_biased:
        linked_data.to_csv(out_data_file)

except Exception as e:
    print(f"Error in data linking and processing: {str(e)}")
    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=True,
        df=pd.DataFrame(),
        note=f"Data processing failed: {str(e)}"
    )