extract_network_module_genes.py

import pandas as pd
import argparse

parser = argparse.ArgumentParser(prog='extract_network_module_genes.py')
parser.add_argument('-r', '--result_path', type=str, default='survival_network/', help='path to the NetCore network propagation result directory')
parser.add_argument('-o', '--output_file', type=str, default='survival_network/network_module_genes.txt', help='file name where the network module genes are written to')

args = parser.parse_args()

result_path = args.result_path
output_file = args.output_file


module_df = pd.read_csv("%s/core_norm_subnetworks.txt" % result_path)

module_df['nodes'] = module_df['nodes'].str.split('\t')

module_genes = module_df.explode('nodes')['nodes']

module_genes.to_csv(output_file, header=False, index=False)