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# Path Configuration
from tools.preprocess import *
# Processing context
trait = "Thyroid_Cancer"
cohort = "GSE107754"
# Input paths
in_trait_dir = "../DATA/GEO/Thyroid_Cancer"
in_cohort_dir = "../DATA/GEO/Thyroid_Cancer/GSE107754"
# Output paths
out_data_file = "./output/preprocess/3/Thyroid_Cancer/GSE107754.csv"
out_gene_data_file = "./output/preprocess/3/Thyroid_Cancer/gene_data/GSE107754.csv"
out_clinical_data_file = "./output/preprocess/3/Thyroid_Cancer/clinical_data/GSE107754.csv"
json_path = "./output/preprocess/3/Thyroid_Cancer/cohort_info.json"
# Get file paths for SOFT and matrix files
soft_file_path, matrix_file_path = geo_get_relevant_filepaths(in_cohort_dir)
# Get background info and clinical data from the matrix file
background_info, clinical_data = get_background_and_clinical_data(matrix_file_path)
# Create dictionary of unique values for each feature
unique_values_dict = get_unique_values_by_row(clinical_data)
# Print the information
print("Dataset Background Information:")
print(background_info)
print("\nSample Characteristics:")
for feature, values in unique_values_dict.items():
print(f"\n{feature}:")
print(values)
# 1. Gene Expression Data Availability
# The background shows this is human genome gene expression microarray data
is_gene_available = True
# 2.1 Data Availability
# Trait (thyroid cancer vs other cancers) from tissue field
trait_row = 2
# Age not available
age_row = None
# Gender available
gender_row = 0
# 2.2 Data Type Conversion Functions
def convert_trait(value):
if not value:
return None
value = value.lower()
if 'tissue:' in value:
value = value.split('tissue:')[1].strip()
elif ':' in value:
value = value.split(':')[1].strip()
return 1 if value == 'thyroid cancer' else 0
def convert_gender(value):
if not value or ':' not in value:
return None
value = value.split(': ')[1].lower()
return 1 if value == 'male' else 0
convert_age = None
# 3. 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)
# 4. Clinical Feature Extraction
if trait_row is not None:
clinical_df = geo_select_clinical_features(clinical_data, trait, trait_row, convert_trait,
age_row=age_row, convert_age=convert_age,
gender_row=gender_row, convert_gender=convert_gender)
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)
# Extract genetic data matrix
genetic_data = get_genetic_data(matrix_file_path)
# Print first few rows with column names to examine data structure
print("Data preview:")
print("\nColumn names:")
print(list(genetic_data.columns)[:5])
print("\nFirst 5 rows:")
print(genetic_data.head())
print("\nShape:", genetic_data.shape)
# Verify this is gene expression data and check identifiers
is_gene_available = True
# Save updated 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)
)
# Save gene expression data
genetic_data.to_csv(out_gene_data_file)
# Observing the gene identifiers starting with "A_23_P" which are Agilent probe IDs
# These are not human gene symbols and need to be mapped
requires_gene_mapping = True
# Extract gene annotation data
gene_metadata = get_gene_annotation(soft_file_path)
# Preview column names and first few values
preview = preview_df(gene_metadata)
print("\nGene annotation columns and sample values:")
print(preview)
# Based on previous output, 'ID' in gene annotation matches probe IDs in expression data
# and 'GENE_SYMBOL' contains the corresponding gene symbols
mapping_df = get_gene_mapping(gene_metadata, prob_col='ID', gene_col='GENE_SYMBOL')
# Map probe IDs to gene symbols and aggregate the expression data
gene_data = apply_gene_mapping(genetic_data, mapping_df)
# 1. Normalize gene symbols and save 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)
# 2. Link clinical and genetic data
clinical_features = pd.read_csv(out_clinical_data_file, index_col=0)
linked_data = geo_link_clinical_genetic_data(clinical_features, normalized_gene_data)
# 3. Handle missing values
linked_data = handle_missing_values(linked_data, trait)
# 4. Judge bias in features and remove biased ones
trait_biased, linked_data = judge_and_remove_biased_features(linked_data, trait)
# 5. Final validation and save metadata
is_usable = validate_and_save_cohort_info(
is_final=True,
cohort=cohort,
info_path=json_path,
is_gene_available=is_gene_available,
is_trait_available=True,
is_biased=trait_biased,
df=linked_data,
note="Dataset contains gene expression data comparing 27 follicular thyroid cancers with 25 follicular thyroid adenomas."
)
# 6. 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) |