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# Path Configuration
from tools.preprocess import *
# Processing context
trait = "Endometrioid_Cancer"
cohort = "GSE40785"
# Input paths
in_trait_dir = "../DATA/GEO/Endometrioid_Cancer"
in_cohort_dir = "../DATA/GEO/Endometrioid_Cancer/GSE40785"
# Output paths
out_data_file = "./output/preprocess/3/Endometrioid_Cancer/GSE40785.csv"
out_gene_data_file = "./output/preprocess/3/Endometrioid_Cancer/gene_data/GSE40785.csv"
out_clinical_data_file = "./output/preprocess/3/Endometrioid_Cancer/clinical_data/GSE40785.csv"
json_path = "./output/preprocess/3/Endometrioid_Cancer/cohort_info.json"
# Get paths to the SOFT and matrix files
soft_file, matrix_file = geo_get_relevant_filepaths(in_cohort_dir)
# Get background info and clinical data from matrix file
background_info, clinical_data = get_background_and_clinical_data(matrix_file)
# Get unique values for each feature (row) in clinical data
unique_values_dict = get_unique_values_by_row(clinical_data)
# Print background info
print("=== Dataset Background Information ===")
print(background_info)
print("\n=== Sample Characteristics ===")
print(json.dumps(unique_values_dict, indent=2))
# 1. Gene Expression Data Availability
# Based on background info, this is gene expression data on cancer cell lines
is_gene_available = True
# 2. Variable Availability and Data Type Conversion
# 2.1 Data Availability
# Trait (Endometrioid Cancer) can be inferred from histology field (row 1)
trait_row = 1
# Age and gender not available
age_row = None
gender_row = None
# 2.2 Data Type Conversion Functions
def convert_trait(value):
# Extract value after colon if present
if ':' in str(value):
value = value.split(':')[1].strip()
# Look for endometrioid in histology
if 'Endometrioid' in str(value):
return 1
elif pd.isna(value):
return None
else:
return 0
def convert_age(value):
return None # Not used since age not available
def convert_gender(value):
return None # Not used since gender not available
# 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_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
)
print("Preview of clinical features:")
print(preview_df(clinical_df))
# Save clinical data
clinical_df.to_csv(out_clinical_data_file)
# Extract gene expression data from matrix file
genetic_df = get_genetic_data(matrix_file)
# Print DataFrame shape and first 20 row IDs
print("DataFrame shape:", genetic_df.shape)
print("\nFirst 20 row IDs:")
print(genetic_df.index[:20])
print("\nPreview of first few rows and columns:")
print(genetic_df.head().iloc[:, :5])
# The IDs starting with "ILMN_" are Illumina probe IDs, not gene symbols.
# These need to be mapped to HUGO gene symbols for standardization.
requires_gene_mapping = True
# Extract gene annotation data, excluding control probe lines
gene_metadata = get_gene_annotation(soft_file)
# Preview filtered annotation data
print("Column names:")
print(gene_metadata.columns)
print("\nPreview of gene annotation data:")
print(preview_df(gene_metadata))
# 1. Identify mapping columns
# 'ID' column in annotation contains Illumina probe IDs (ILMN_*) matching gene expression data
# 'Symbol' column contains gene symbols
# 2. Get gene mapping dataframe
mapping_df = get_gene_mapping(gene_metadata, prob_col='ID', gene_col='Symbol')
# 3. Apply gene mapping to convert probe data to gene expression data
gene_data = apply_gene_mapping(genetic_df, mapping_df)
# 1. Normalize gene symbols and save
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
clinical_df = pd.read_csv(out_clinical_data_file, index_col=0)
linked_data = geo_link_clinical_genetic_data(clinical_df, gene_data)
# 3. Handle missing values
linked_data = handle_missing_values(linked_data, trait)
# 4. Check for biased features
trait_biased, linked_data = judge_and_remove_biased_features(linked_data, trait)
# 5. Final validation and metadata saving
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="Study comparing ERα-chromatin interactions in endometrial tumors from patients with/without tamoxifen treatment history"
)
# 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) |