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# Path Configuration
from tools.preprocess import *
# Processing context
trait = "Kidney_Chromophobe"
cohort = "GSE19949"
# Input paths
in_trait_dir = "../DATA/GEO/Kidney_Chromophobe"
in_cohort_dir = "../DATA/GEO/Kidney_Chromophobe/GSE19949"
# Output paths
out_data_file = "./output/preprocess/3/Kidney_Chromophobe/GSE19949.csv"
out_gene_data_file = "./output/preprocess/3/Kidney_Chromophobe/gene_data/GSE19949.csv"
out_clinical_data_file = "./output/preprocess/3/Kidney_Chromophobe/clinical_data/GSE19949.csv"
json_path = "./output/preprocess/3/Kidney_Chromophobe/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)
# Get unique values for each clinical feature
unique_values_dict = get_unique_values_by_row(clinical_data)
# Print background information
print("Background Information:")
print(background_info)
print("\nSample Characteristics:")
print(json.dumps(unique_values_dict, indent=2))
# 1. Gene Expression Data Availability
is_gene_available = True # Based on background info mentioning "genome-wide expression profiling"
# 2.1 Variable Key Identification
trait_row = 4 # icd-o 3 diagnosis text
gender_row = 6 # gender
age_row = None # age not provided
# 2.2 Data Type Conversion Functions
def convert_trait(x):
if pd.isna(x):
return None
val = x.split(': ')[-1].lower()
if 'chromophobe' in val:
return 1
elif 'renal cell carcinoma' in val or 'adenocarcinoma' in val:
return 0
return None
def convert_gender(x):
if pd.isna(x):
return None
val = x.split(': ')[-1].lower()
if 'female' in val:
return 0
elif 'male' in val:
return 1
return None
# 3. Save Initial 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:
selected_clinical_df = geo_select_clinical_features(
clinical_df=clinical_data,
trait=trait,
trait_row=trait_row,
convert_trait=convert_trait,
gender_row=gender_row,
convert_gender=convert_gender
)
print("Preview of extracted clinical features:")
print(preview_df(selected_clinical_df))
# Save clinical data
selected_clinical_df.to_csv(out_clinical_data_file)
# Extract gene expression data from the matrix file
genetic_data = get_genetic_data(matrix_file_path)
# Print first 20 row IDs
print("First 20 row IDs:")
print(genetic_data.index[:20].tolist())
# The identifiers appear to be Affymetrix probe IDs (e.g. "1007_s_at") rather than standard human gene symbols
# Affymetrix IDs need to be mapped to gene symbols for biological interpretation
requires_gene_mapping = True
# Extract gene annotation data from SOFT file
gene_metadata = get_gene_annotation(soft_file_path)
# Display information about the annotation data
print("Column names:")
print(gene_metadata.columns.tolist())
# Look at general data statistics
print("\nData shape:", gene_metadata.shape)
# Preview the first few rows
print("\nPreview of the annotation data:")
print(json.dumps(preview_df(gene_metadata), indent=2))
# 1 & 2. Extract gene mapping information
# From previewing data, 'ID' column matches probe IDs in expression data, 'Gene Symbol' contains target symbols
mapping_data = get_gene_mapping(gene_metadata, prob_col='ID', gene_col='Gene Symbol')
# 3. Apply gene mapping to convert probe-level data to gene-level data
gene_data = apply_gene_mapping(genetic_data, mapping_data)
# Print info about the result
print("Gene expression data shape after mapping:", gene_data.shape)
print("\nFirst 10 gene symbols:")
print(gene_data.index[:10].tolist())
# 1. Normalize gene symbols
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)
# Early exit if trait values are all NaN
if linked_data[trait].isna().all():
is_biased = True
linked_data = None
else:
# 4. Judge whether features are biased and remove biased demographic features
is_biased, linked_data = judge_and_remove_biased_features(linked_data, trait)
# 5. Final validation and save metadata
note = "Dataset from a cancer gene expression study using oligonucleotide microarrays, containing samples of kidney chromophobe tumors and normal tissues."
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
)
# 6. Save the linked data only if it's usable
if is_usable:
os.makedirs(os.path.dirname(out_data_file), exist_ok=True)
linked_data.to_csv(out_data_file) |