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# Path Configuration
from tools.preprocess import *
# Processing context
trait = "Head_and_Neck_Cancer"
cohort = "GSE218109"
# Input paths
in_trait_dir = "../DATA/GEO/Head_and_Neck_Cancer"
in_cohort_dir = "../DATA/GEO/Head_and_Neck_Cancer/GSE218109"
# Output paths
out_data_file = "./output/preprocess/3/Head_and_Neck_Cancer/GSE218109.csv"
out_gene_data_file = "./output/preprocess/3/Head_and_Neck_Cancer/gene_data/GSE218109.csv"
out_clinical_data_file = "./output/preprocess/3/Head_and_Neck_Cancer/clinical_data/GSE218109.csv"
json_path = "./output/preprocess/3/Head_and_Neck_Cancer/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()
# Gene expression data availability check
# This dataset is about transcriptional profiling of ESCC tumors,
# indicating it contains gene expression data
is_gene_available = True
# Define trait row and converter function
# p53 status (row 5) can be converted to binary with NS+ as 1 and NS- as 0
trait_row = 5
def convert_trait(value):
if not value or 'NA' in value:
return None
value = value.split(': ')[1]
if 'NS+' in value:
return 1
elif 'NS-' in value:
return 0
return None
# Define age row and converter function
age_row = 1
def convert_age(value):
if not value or 'NA' in value:
return None
try:
return float(value.split(': ')[1])
except:
return None
# Define gender row and converter function
gender_row = 0
def convert_gender(value):
if not value or 'NA' in value:
return None
value = value.split(': ')[1]
if value.upper() == 'F':
return 0
elif value.upper() == 'M':
return 1
return None
# Validate dataset availability
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))
# Extract clinical features
clinical_features = geo_select_clinical_features(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
preview_df(clinical_features)
clinical_features.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 identifiers appear to be numeric probe IDs rather than human gene symbols
# These need to be mapped to gene symbols for proper biological interpretation
requires_gene_mapping = True
# Extract gene annotation from SOFT file
gene_annotation = get_gene_annotation(soft_file_path)
# Filter out control probes
gene_annotation = gene_annotation[gene_annotation['CONTROL_TYPE'] != 'pos']
# Preview column names and first 20 values
preview_dict = preview_df(gene_annotation, n=20)
print("Column names and preview values:")
for col, values in preview_dict.items():
print(f"\n{col}:")
print(values)
# Extract gene mapping from annotation
# 'ID' column in gene_annotation matches probe IDs in genetic_data
# 'GENE_SYMBOL' column contains human gene symbols
mapping_data = get_gene_mapping(gene_annotation, prob_col='ID', gene_col='GENE_SYMBOL')
# Convert probe-level measurements to gene expression data
gene_data = apply_gene_mapping(genetic_data, mapping_data)
# Preview first few rows of gene data
print("\nFirst few rows of gene expression data:")
print(gene_data.head())
# 1. Normalize gene symbols and save normalized gene data
normalized_gene_data = normalize_gene_symbols_in_index(gene_data)
os.makedirs(os.path.dirname(out_gene_data_file), exist_ok=True)
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 = "Gene expression data from glucocorticoid sensitivity study."
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:
os.makedirs(os.path.dirname(out_data_file), exist_ok=True)
linked_data.to_csv(out_data_file)
else:
print(f"Dataset {cohort} did not pass quality validation and will not be saved.") |