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# Path Configuration
from tools.preprocess import *
# Processing context
trait = "Mesothelioma"
cohort = "GSE163721"
# Input paths
in_trait_dir = "../DATA/GEO/Mesothelioma"
in_cohort_dir = "../DATA/GEO/Mesothelioma/GSE163721"
# Output paths
out_data_file = "./output/preprocess/3/Mesothelioma/GSE163721.csv"
out_gene_data_file = "./output/preprocess/3/Mesothelioma/gene_data/GSE163721.csv"
out_clinical_data_file = "./output/preprocess/3/Mesothelioma/clinical_data/GSE163721.csv"
json_path = "./output/preprocess/3/Mesothelioma/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)
# 1. Gene Expression Analysis
is_gene_available = True # Background info indicates microarray data analysis
# 2. Variable Analysis
trait_row = 0 # All samples are tumor, indicating mesothelioma
age_row = None # Age data not available
gender_row = None # Gender data not available
# 2.2 Conversion Functions
def convert_trait(x):
if not isinstance(x, str):
return None
if "tumor" in x.lower():
return 1
return None
convert_age = None
convert_gender = 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. Extract Clinical Features
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 and save clinical data
print("Preview of clinical features:")
print(preview_df(clinical_features))
clinical_features.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])
# Examining the row IDs which are just numeric strings without any gene/probe identifiers
# This indicates the need for mapping from probe IDs to gene symbols
requires_gene_mapping = True
# Extract gene annotation data
gene_annotation = get_gene_annotation(soft_file_path)
# Display column names and preview data
print("Column names:")
print(gene_annotation.columns)
print("\nPreview of gene annotation data:")
print(preview_df(gene_annotation))
# Extract gene mapping from annotation
# 'ID' column in gene_annotation matches numeric 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')
# Apply gene mapping to convert probe-level data to gene expression data
gene_data = apply_gene_mapping(genetic_data, mapping_data)
# Preview the mapped gene data
print("\nMapped gene expression data shape:", gene_data.shape)
print("\nFirst few rows of mapped gene expression data:")
print(gene_data.head())
# 1. Normalize gene symbols
genetic_data = normalize_gene_symbols_in_index(gene_data)
genetic_data.to_csv(out_gene_data_file)
# 2. Link clinical and genetic data
linked_data = geo_link_clinical_genetic_data(clinical_features, genetic_data)
# 3. Handle missing values systematically
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 = "Dataset contains only tumor samples without a control group, making it unsuitable for associational studies."
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, # Force biased=True since all samples are tumor samples
df=linked_data,
note=note
)
# 6. Save linked data only if usable (which won't happen since is_biased=True)
if is_usable:
os.makedirs(os.path.dirname(out_data_file), exist_ok=True)
linked_data.to_csv(out_data_file) |