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# Path Configuration
from tools.preprocess import *
# Processing context
trait = "Bipolar_disorder"
cohort = "GSE120340"
# Input paths
in_trait_dir = "../DATA/GEO/Bipolar_disorder"
in_cohort_dir = "../DATA/GEO/Bipolar_disorder/GSE120340"
# Output paths
out_data_file = "./output/preprocess/1/Bipolar_disorder/GSE120340.csv"
out_gene_data_file = "./output/preprocess/1/Bipolar_disorder/gene_data/GSE120340.csv"
out_clinical_data_file = "./output/preprocess/1/Bipolar_disorder/clinical_data/GSE120340.csv"
json_path = "./output/preprocess/1/Bipolar_disorder/cohort_info.json"
# STEP1
from tools.preprocess import *
# 1. Identify the paths to the SOFT file and the matrix file
soft_file, matrix_file = geo_get_relevant_filepaths(in_cohort_dir)
# 2. Read the matrix file to obtain background information and sample characteristics data
background_prefixes = ['!Series_title', '!Series_summary', '!Series_overall_design']
clinical_prefixes = ['!Sample_geo_accession', '!Sample_characteristics_ch1']
background_info, clinical_data = get_background_and_clinical_data(matrix_file, background_prefixes, clinical_prefixes)
# 3. Obtain the sample characteristics dictionary from the clinical dataframe
sample_characteristics_dict = get_unique_values_by_row(clinical_data)
# 4. Explicitly print out all the background information and the sample characteristics dictionary
print("Background Information:")
print(background_info)
print("Sample Characteristics Dictionary:")
print(sample_characteristics_dict)
# 1. Decide if gene expression data is available
# From the background info, this is an Affymetrix gene expression dataset.
is_gene_available = True
# 2. Identify data availability and create row references
# Row 0 has multiple disease states (control, SCZ, BD(-), BD(+)), use it as the trait data.
trait_row = 0
age_row = None
gender_row = None
# 2.2 Define data conversion functions
def convert_trait(x: str):
"""
Convert disease state to a binary indicator for Bipolar_disorder:
1 if BD(-) or BD(+), 0 for controls/SCZ, None otherwise.
"""
# Parse the part after the colon
parts = x.split(":")
val = parts[-1].strip().lower() if len(parts) > 1 else x.strip().lower()
if "bd" in val:
return 1
elif "control" in val or "scz" in val:
return 0
else:
return None
def convert_age(x: str):
return None # No age data available
def convert_gender(x: str):
return None # No gender data available
# 3. Save metadata (initial filtering)
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
# Only proceed if trait_row is not None (i.e., trait data is available).
if trait_row is not None:
selected_clinical_df = geo_select_clinical_features(
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_df(selected_clinical_df, n=5))
selected_clinical_df.to_csv(out_clinical_data_file, index=False)
# STEP3
# 1. Use the get_genetic_data function from the library to get the gene_data from the matrix_file previously defined.
gene_data = get_genetic_data(matrix_file)
# 2. Print the first 20 row IDs (gene or probe identifiers) for future observation.
print(gene_data.index[:20])
# Observing the gene identifiers, they appear to be Affymetrix microarray probe IDs (e.g., '10000_at', '10009_at'),
# not standard gene symbols. Therefore, gene mapping is required.
print("requires_gene_mapping = True")
# STEP5
# 1. Use the 'get_gene_annotation' function from the library to get gene annotation data from the SOFT file.
gene_annotation = get_gene_annotation(soft_file)
# 2. Use the 'preview_df' function from the library to preview the data and print out the results.
print("Gene annotation preview:")
print(preview_df(gene_annotation))
# STEP: Gene Identifier Mapping
# 1 & 2. Identify the columns in 'gene_annotation' that correspond to the probe IDs and gene symbols.
# From our observation, 'ID' matches the probe IDs in the gene data,
# and 'Description' contains the gene symbol or gene name information.
mapping_df = get_gene_mapping(
annotation=gene_annotation,
prob_col='ID', # Column storing probe IDs
gene_col='Description' # Column storing gene symbol (or gene name) information
)
# 3. Apply the mapping to convert probe-level measurements to gene-level expression data.
gene_data = apply_gene_mapping(
expression_df=gene_data,
mapping_df=mapping_df
)
# (The resulting 'gene_data' now contains the aggregated gene expression values, indexed by gene symbol.)
# STEP7
# 1. Normalize the obtained gene data using the NCBI Gene synonym database
normalized_gene_data = normalize_gene_symbols_in_index(gene_data)
normalized_gene_data.to_csv(out_gene_data_file)
# 2. Link the clinical and genetic data
# Replace df_clinical with the actual clinical dataframe from previous steps, i.e., selected_clinical_df
linked_data = geo_link_clinical_genetic_data(selected_clinical_df, normalized_gene_data)
# 3. Handle missing values systematically using the actual column name (stored in variable trait)
linked_data_processed = handle_missing_values(linked_data, trait_col=trait)
# 4. Check for biased trait and remove any biased demographic features
trait_biased, linked_data_final = judge_and_remove_biased_features(linked_data_processed, trait)
# 5. Final quality 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_final,
note="Dataset processed with GEO pipeline. Checked for missing values and bias."
)
# 6. If dataset is usable, save the final linked data
if is_usable:
linked_data_final.to_csv(out_data_file)