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# Path Configuration
from tools.preprocess import *
# Processing context
trait = "Osteoarthritis"
cohort = "GSE141934"
# Input paths
in_trait_dir = "../DATA/GEO/Osteoarthritis"
in_cohort_dir = "../DATA/GEO/Osteoarthritis/GSE141934"
# Output paths
out_data_file = "./output/preprocess/3/Osteoarthritis/GSE141934.csv"
out_gene_data_file = "./output/preprocess/3/Osteoarthritis/gene_data/GSE141934.csv"
out_clinical_data_file = "./output/preprocess/3/Osteoarthritis/clinical_data/GSE141934.csv"
json_path = "./output/preprocess/3/Osteoarthritis/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 Data Availability
# This is a transcriptional data study of CD4+ T cells, so gene expression data should be available
is_gene_available = True
# 2. Variable Availability and Data Type Conversion
# Trait: Found in working_diagnosis, row 6
trait_row = 6
def convert_trait(value):
if not isinstance(value, str):
return None
value = value.split(': ')[1] if ': ' in value else value
# Convert to binary - 1 for Osteoarthritis, 0 for others
if value == 'Osteoarthritis':
return 1
elif value in ['Rheumatoid Arthritis', 'Psoriatic Arthritis', 'Reactive Arthritis',
'Crystal Arthritis', 'Non-Inflammatory', 'Undifferentiated Inflammatory Arthritis',
'Other Inflammatory Arthritis', 'Enteropathic Arthritis',
'Undifferentiated Spondylo-Arthropathy', 'Unknown']:
return 0
return None
# Age: Found in row 2
age_row = 2
def convert_age(value):
if not isinstance(value, str):
return None
try:
age = int(value.split(': ')[1]) if ': ' in value else int(value)
return age
except:
return None
# Gender: Found in row 1
gender_row = 1
def convert_gender(value):
if not isinstance(value, str):
return None
value = value.split(': ')[1] if ': ' in value else value
if value.upper() == 'F':
return 0
elif value.upper() == 'M':
return 1
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
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 extracted features
print("Preview of clinical features:")
print(preview_df(clinical_features))
# Save to CSV
os.makedirs(os.path.dirname(out_clinical_data_file), exist_ok=True)
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])
# These are Illumina probe IDs (starting with "ILMN_"), they need to be mapped 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))
# Get mapping dataframe from gene annotation data
mapping_data = get_gene_mapping(gene_annotation, prob_col='ID', gene_col='Symbol')
# Apply gene mapping to convert probe measurements to gene expression data
gene_data = apply_gene_mapping(genetic_data, mapping_data)
print("\nShape of gene expression data after mapping:", gene_data.shape)
print("\nPreview of first 5 mapped genes and their values:")
print(gene_data.head())
# Reload clinical data that was processed earlier
selected_clinical_df = pd.read_csv(out_clinical_data_file, index_col=0)
# 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(selected_clinical_df, 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 = "Contains gene expression data with metabolic rate (inferred from multicentric occurrence-free survival days) measurements"
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
if is_usable:
os.makedirs(os.path.dirname(out_data_file), exist_ok=True)
linked_data.to_csv(out_data_file) |