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)
