MLProbs/script.py at master · kuangmeng/MLProbs · GitHub

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# -*- coding: utf-8 -*-
"""
Spyder Editor

"""
import os
import time

def Preprocessing(bench, file, path):
    fileout = path +"/" + bench +"/in/"+ file
    filein = path +"/"+ bench +"/in/"+ file
    ret_list = []
    flag = 0
    filein_list = open(filein, 'r').read().splitlines()

    for line in filein_list:
        if len(line.strip()) > 0:
            if line.strip()[0] == '>':
                ret_list.append(line.strip())
                flag = 0
            else:
                if flag == 0:
                    ret_list.append(line.strip())
                    flag = 1
                else:
                    ret_list[len(ret_list) - 1] += line.strip()
    with open(fileout, 'w') as fileout_:
        for line in ret_list:
            fileout_.write(line + "\n")

def Run(prom, bench, file, path, i):
    f_t = os.path.exists("./output/" + bench)
    if not f_t:
        os.makedirs("./output/" + bench)
    os.system("%s %s/%s/%s  ./output/%s/%s" % (prom, path, bench + "/in", file, bench, file))

def Compute(prom):
    path = "./TEST"
    bench_list = os.listdir(path)
    tmp_bench = []
    total_time = []
    for i in range(1):
        for bench in bench_list:
            if os.path.isdir(path + "/" + bench):
                tmp_bench.append(bench)
                tmp_time = 0.0
                file_num = 0
                file_list = os.listdir(path + "/" + bench + "/in/")
                for fileidx in range(len(file_list)):
                    tmp_str = ""
                    if file_list[fileidx][0:1] == ".":
                        continue
                    file_num += 1
                    print("Start constructing No. %d protein family: %s ..." % (fileidx, bench + "/in/" + file_list[fileidx]))
                    start = time.time()
                    Run(prom, bench, file_list[fileidx], path, i)
                    end = time.time()
                    tmp_time += (end - start)
                    print("Finish constructing No. %d protein family." % (fileidx))
                total_time.append(tmp_time / float(file_num))

    return tmp_bench, total_time

if __name__ == "__main__":
    if not os.path.exists("./output"):
        os.system("mkdir ./output/")
    tmp_bench, total_time = Compute("python ./MLProbs.py ")
    for i in range(len(tmp_bench)):
        print("%s: %f" % (tmp_bench[i], total_time[i]))