def DisSim_by_NetSim():
input_file1 = "./Dataset/disease-gene_SIDD.txt"
input_file2 = "./Dataset/HumanNet_symbol.txt"
output_file = "./Result/NetSim_sim_DO.txt"
disease2gene = FileUtil.readFile2DictSet(input_file1, header=True)
gene_gene = FileUtil.readFile2List(input_file2)
NetSim.calculateDisSim(disease2gene, gene_gene, output_file)
def DisSim_by_ModuleSim():
input_file1 = "./Dataset/disease-gene.txt"
input_file2 = "./Dataset/PPI.txt"
output_file = "./Result/ModuleSim_sim.txt"
dis2gene = FileUtil.readFile2DictSet(input_file1)
gene_net = ModuleSim.read_interactome(input_file2, False, False)
print("number of vertices: {}, number of edges: {}".format(
gene_net.vcount(), gene_net.ecount()))
sims = ModuleSim.similarity_cal_spavgn(dis2gene, gene_net)
FileUtil.write_sims(sims, output_file)
def DisSim_by_FunSim():
input_file1 = "./Dataset/disease-gene_SIDD.txt"
input_file2 = "./Dataset/HumanNet_symbol_weighted.txt"
output_file = "./Result/FunSim_sim.txt"
disease2genes = FileUtil.readFile2DictSet(input_file1)
weighted_PPI = FileUtil.readFile2List(input_file2)
FunSim.calculateDisSim(disease2genes, weighted_PPI, output_file)
# ------------------------ evaluation ---------------------------------------
file_path1 = "./Evaluation/benchmark_DOID.txt"
BenChmark_DO = FileUtil.readFile2List(file_path1)
simi_Result = FileUtil.readFile2List(output_file)
benchmark_evaluation.evaluate_by_benchmark(BenChmark_DO,
simi_Result,
times=10)
def DisSim_by_XuanSim():
input_file1 = "./Dataset/DO_DAG.txt"
input_file2 = "./Dataset/disease-gene_SIDD.txt"
output_file = "./Result/XuanSim_sim.txt"
DO_DAG = FileUtil.readFile2List(input_file1, header=True)
diseases2genes = FileUtil.readFile2DictSet(input_file2)
XuanSim.calculateDisSim(DO_DAG,
output_file,
selected_diseases=set(diseases2genes.keys()))
file_path1 = "./Evaluation/benchmark_DOID.txt"
BenChmark_DO = FileUtil.readFile2List(file_path1)
simi_Result = FileUtil.readFile2List(output_file)
benchmark_evaluation.evaluate_by_benchmark(BenChmark_DO,
simi_Result,
times=10)