def DisSim_by_mpDisNet(): input_file1 = "./Dataset/mpDisNet/omim_dm.txt" input_file2 = "./Dataset/mpDisNet/omim_mg.txt" input_file3 = "./Dataset/mpDisNet/PPI.txt" disease_miRNA = FileUtil.readFile2List(input_file1) miRNA_gene = FileUtil.readFile2List(input_file2) gene_gene = FileUtil.readFile2List(input_file3) output_file = "./Result/mpDisNet_sim.txt" mpDisNet.calculateDisSim(disease_miRNA, miRNA_gene, gene_gene, output_file, path_type=2) # ------------------------ evaluation --------------------------------------- file_path1 = "./Evaluation/benchmark_MeSH_RADAR.txt" BenChmark_MeSH1 = FileUtil.readFile2List(file_path1) simi_Result = FileUtil.readFile2List(output_file) benchmark_evaluation.evaluate_by_benchmark(BenChmark_MeSH1, simi_Result, times=10)
def DisSim_by_CosineDFV(): input_file1 = "./Dataset/disease-symptom.txt" output_file = "./Result/CosineDFV_sim.txt" disease_symptom = FileUtil.readFile2List(input_file1, header=True) CosineDFV.calculateDisSim(disease_symptom, output_file)
def DisSim_by_IDN(): input_file = "./Dataset/disease-gene.txt" output_file = "./Result/IDN_gene.txt" lines = FileUtil.readFile2List(input_file) dis_sim = IDN.calculateDisSim(lines) FileUtil.writeDic2File(dis_sim, output_file)
def DisSim_by_MicrobeSim(): input_file1 = "./Dataset/disease-microbe.txt" output_file = "./Result/MicrobeSim_sim.txt" disease_microbe = FileUtil.readFile2List(input_file1, header=True) MicrobeSim.calculateDisSim(disease_microbe, output_file)
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_Resink(): input_file1 = "./Dataset/DO_DAG.txt" input_file3 = "./Dataset/disease-gene_SIDD.txt" output_file = "./Result/Resink_sim.txt" DO_DAG = FileUtil.readFile2List(input_file1, header=True) disease_genes = FileUtil.readFile2List(input_file3) ResinkSim.calculateDisSim(DO_DAG, output_file) # ------------------------------------------------------------------- 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_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)
def line2upper(input_file, output_file): lines = FileUtil.readFile2List(input_file) new_lines = [line.upper() for line in lines] FileUtil.writeList2File(new_lines, output_file)
else: for i in range(0, top_number): simi_line = disease_pairs2[i] # print(simi_line) for j in range(0, len(disease_pairs1)): if simi_line[0] in disease_pairs1[j] and simi_line[ 1] in disease_pairs1[j]: top_match_number += 1 break if i % 10000 == 0: print("top {} match {}.".format(i, top_match_number)) if __name__ == "__main__": file_path1 = "./benchmark_MeSH_RADAR.txt" file_path3 = "./benchmark_DOID.txt" file_path2 = "../Result/ModuleSim_sim.txt" file_path4 = "../Result/standard_Resnik_result.txt" file_path5 = "../Result/mpDisNet_sim.txt" file_path6 = "../Result/FunSim_sim.txt" # # get_basic_info( file_path1, file_path3) # get_top_number_match(file_path1, file_path2, top_number= 110000) # --------------------------------------读取以MeSH id为标签的标准集--------------------------------------- BenChmark_MeSH1 = FileUtil.readFile2List(file_path3) simi_Result = FileUtil.readFile2List(file_path4) evaluate_by_benchmark(BenChmark_MeSH1, simi_Result, times=10)