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# Path Configuration
from tools.preprocess import *
# Processing context
trait = "Bladder_Cancer"
cohort = "GSE185264"
# Input paths
in_trait_dir = "../DATA/GEO/Bladder_Cancer"
in_cohort_dir = "../DATA/GEO/Bladder_Cancer/GSE185264"
# Output paths
out_data_file = "./output/preprocess/3/Bladder_Cancer/GSE185264.csv"
out_gene_data_file = "./output/preprocess/3/Bladder_Cancer/gene_data/GSE185264.csv"
out_clinical_data_file = "./output/preprocess/3/Bladder_Cancer/clinical_data/GSE185264.csv"
json_path = "./output/preprocess/3/Bladder_Cancer/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")
# 1. Gene Expression Data Availability
# Yes - RNA quantification data from NanoString nCounter platform
is_gene_available = True
# 2. Variable Availability and Row Numbers
trait_row = 12 # recurrence data available
age_row = None # age not available
gender_row = 7 # gender data available
# 2.2 Conversion Functions
def convert_trait(value: str) -> Optional[int]:
"""Convert recurrence status to binary (0: no recurrence, 1: recurrence)"""
if pd.isna(value) or value == "NA":
return None
value = value.split(": ")[-1]
if value == "No.Recurrence":
return 0
elif value == "Recurrence":
return 1
return None
def convert_age(value: str) -> Optional[float]:
"""Convert age to float - not used since age data unavailable"""
return None
def convert_gender(value: str) -> Optional[int]:
"""Convert gender to binary (0: female, 1: male)"""
if pd.isna(value):
return None
value = value.split(": ")[-1]
if value == "F":
return 0
elif value == "M":
return 1
return 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. Extract Clinical Features
selected_clinical_df = 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 selected features
print(preview_df(selected_clinical_df))
# Save clinical data
selected_clinical_df.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)
requires_gene_mapping = False
# 1. Normalize gene symbols and save normalized gene data
gene_data.index = gene_data.index.str.replace('-mRNA', '')
gene_data = normalize_gene_symbols_in_index(gene_data)
os.makedirs(os.path.dirname(out_gene_data_file), exist_ok=True)
gene_data.to_csv(out_gene_data_file)
# 2. Link clinical and genetic data
linked_data = geo_link_clinical_genetic_data(selected_clinical_df, gene_data)
# 3. Handle missing values
linked_data = handle_missing_values(linked_data, trait)
# 4. Check for biased features and remove them if needed
is_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_biased,
df=linked_data,
note="NanoString nCounter RNA profiling data for bladder cancer recurrence study"
)
# 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) |