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# Path Configuration
from tools.preprocess import *
# Processing context
trait = "Cystic_Fibrosis"
cohort = "GSE71799"
# Input paths
in_trait_dir = "../DATA/GEO/Cystic_Fibrosis"
in_cohort_dir = "../DATA/GEO/Cystic_Fibrosis/GSE71799"
# Output paths
out_data_file = "./output/preprocess/3/Cystic_Fibrosis/GSE71799.csv"
out_gene_data_file = "./output/preprocess/3/Cystic_Fibrosis/gene_data/GSE71799.csv"
out_clinical_data_file = "./output/preprocess/3/Cystic_Fibrosis/clinical_data/GSE71799.csv"
json_path = "./output/preprocess/3/Cystic_Fibrosis/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,
prefixes_a=['!Series_title', '!Series_summary', '!Series_overall_design'],
prefixes_b=['!Sample_geo_accession', '!Sample_characteristics_ch1', '!Sample_source_name_ch1', '!Sample_description', '!Sample_title']
)
# Get unique values for each feature (row) in clinical data
unique_values_dict = get_unique_values_by_row(clinical_data, max_len=10)
# 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 study measures gene expression in PBMC cells
is_gene_available = True
# 2.1 Data Availability
# Trait can be derived from Sample_description (row 3)
trait_row = 3
# No age data available
age_row = None
# No gender data available
gender_row = None
# 2.2 Data Type Conversion Functions
def convert_trait(value):
# Extract substring after colon if present
if ':' in str(value):
value = value.split(':', 1)[1].strip()
# Convert based on description field
if "unrelated healthy control" in value.lower():
return 0
elif "cystic fibrosis" in value.lower():
return 1
return None
def convert_age(value):
return None
def convert_gender(value):
return None
# 3. Save initial 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. Extract clinical features
if trait_row is not None:
clinical_features = 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 extracted features
preview = preview_df(clinical_features)
print("Preview of clinical features:")
print(preview)
# Save to CSV
clinical_features.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])
# These identifiers are from Affymetrix microarray probes and need to be mapped to gene symbols
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))
# From the preview we can see that 'ID' in gene_metadata matches probe IDs in expression data
# and 'Gene Symbol' contains the target gene symbols
# Get mapping between probe IDs and gene symbols
mapping_df = get_gene_mapping(gene_metadata, prob_col='ID', gene_col='Gene Symbol')
# Apply mapping to convert probe-level data to gene-level data
gene_data = apply_gene_mapping(genetic_df, mapping_df)
# Preview the mapped gene expression data
print("Gene expression data shape:", gene_data.shape)
print("\nFirst few rows and columns:")
print(gene_data.head().iloc[:, :5])
# 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_features = clinical_features.T
linked_data = geo_link_clinical_genetic_data(clinical_features, 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="Gene expression analysis comparing cystic fibrosis patients with healthy controls using PBMC samples"
)
# 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) |