#!/usr/bin/python import string import re import sys import os def createTrack (profilFileName): with open(profilFileName, 'a') as profilFile: profilFile.write(raw_input("Track name : ")+'\n') profilFile.write(raw_input("Inactive inputs (ex : O_stress,AA_starvation,TLR4) : ")+'\n') profilFile.write(raw_input("Active inputs (ex : Inflamation,DAN_damage) : ")+'\n') profilFile.write(raw_input("Custom rate nodes (ex : u:node1:0.15,u:node2:0.1,d:node2:0.1) : ")+'\n') profilFile.write(raw_input("Custom state nodes ( ex : node1:0.1,node2:0.4) : ") +'\n') profilFile.write(raw_input("Outputs (ex : BECN1,Ulk_C,PIK3C3) : ")+'\n') ###################################################################### def createProfil (configFileName): choice = raw_input("No profil file was given. Do you wish to create a new profil file ? (y/n)") if choice == "n": print("Quitting...") exit(-3) else : name = raw_input("Base name of the profil file (no path) : ") dirName = os.path.dirname(configFileName) if dirName != "" : profileFileName = os.path.dirname(configFileName)+name else : profileFileName = name createTrack(profileFileName) return profileFileName ###################################################################### def displayTracks (profilFileName): with open(profilFileName, 'r') as profilFile: profilFileLines = profilFile.readlines() print("Existing tracks :") i = 0 while i < len(profilFileLines): print(str((i/6)+1) + ")" + profilFileLines[i].rstrip()) i = i+6 ###################################################################### def deleteTrack(profilFileName): displayTracks(profilFileName) trackNumbers = raw_input("Select single (ex : 1) or multiple tracks to be deleted (ex : 1,2,3) :").split(',') with open(profilFileName, 'r') as profilFile: profilFileLines = profilFile.readlines() trackNumbers = [ (int(trackNumber)-1)*5 for trackNumber in trackNumbers ] trackNumbers = [ (x,x+1,x+2,x+3, x+4) for x in trackNumbers ] trackNumbers = [ x for sublist in trackNumbers for x in sublist ] with open(profilFileName, 'w') as profilFile: i = 0 while i < len(profilFileLines): if i not in trackNumbers: profilFile.write(profilFileLines[i]) i = i+1 print(sum(1 for line in open(profilFileName))) if sum(1 for line in open(profilFileName)) < 2: print("All tracks have been erased. Consider creating new tracks to start simulations.") commandLine = "rm "+profilFileName os.system(commandLine) ####################################################################### def createConfigFiles(configFileName, profilFileName, mutationFileName): displayTracks(profilFileName) with open(profilFileName, 'r') as profilFile: profilFileLines = profilFile.readlines() with open(configFileName, 'r') as cfgFile: cfgFileLines = cfgFile.readlines() selectedTracks = raw_input("Select tracks to use(ex : 1,3,5,6) : ").split(',') selectedTracks = [(int(number)-1)*6 for number in selectedTracks] configFileList = [] if mutationFileName != "": with open(mutationFileName, 'r') as mutationFile: mutationFileLines = mutationFile.readlines() mutationTable = [mutationFileLine.rstrip().split(',') for mutationFileLine in mutationFileLines] #print(mutationTable) mutationTable = [ [mutation.split(':') for mutation in mutationGroup] for mutationGroup in mutationTable] #print(mutationTable) for track in selectedTracks: trackName = profilFileLines[track].rstrip() inactiveInputs = profilFileLines[track+1].rstrip().split(',') activeInputs = profilFileLines[track+2].rstrip().split(',') customRates = profilFileLines[track+3].rstrip().split(',') customRates = [ customRate.split(':') for customRate in customRates ] customStates = profilFileLines[track+4].rstrip().split(',') customStates = [ customState.split(':') for customState in customStates ] outputs = profilFileLines[track+5].rstrip().split(',') ratesTable = [] internalTable = [] parametersTable = [] for cfgFileLine in cfgFileLines: if cfgFileLine[0] == '$': ratesTable.append(cfgFileLine) elif re.search('istate=0', cfgFileLine): internalTable.append(re.sub('istate=0', 'is_internal=1', cfgFileLine)) else: parametersTable.append(cfgFileLine) #####Parsing bien degueu pour creer les fichiers de config j=0 while j < len(parametersTable): if re.search('sample_count', parametersTable[j]): parametersTable[j] = re.sub('500000', '50000', parametersTable[j]) elif re.search('max_time', parametersTable[j]): parametersTable[j] = re.sub('5', '100', parametersTable[j]) elif re.search('time_tick', parametersTable[j]): parametersTable[j] = re.sub('0[.]01', '0.1', parametersTable[j]) elif re.search('thread_count', parametersTable[j]): parametersTable[j] = re.sub('4', '8', parametersTable[j]) elif re.search('statdist_traj_count', parametersTable[j]): parametersTable[j] = re.sub('100', '0', parametersTable[j]) j = j+1 j=0 while j < len(internalTable): for output in outputs: pattern = "^"+output+"[.]" if re.search(pattern, internalTable[j]): internalTable[j] = re.sub('=1', '=0', internalTable[j]) j = j+1 j = 0 if customRates != [['']]: while j < len(ratesTable): for customRate in customRates: if re.match("[$]"+customRate[0]+"_"+customRate[1], ratesTable[j]): ratesTable[j] = re.sub("=1", "="+customRate[2], ratesTable[j]) j = j+1 if mutationFileName == "" : newCfgFileName = re.sub("[.]cfg", "", configFileName) + "_" + trackName + ".cfg" configFileList.append(newCfgFileName) with open(newCfgFileName, 'w') as newCfgFile: for rate in ratesTable: newCfgFile.write(rate) newCfgFile.write('\n') for inputNode in activeInputs: if inputNode != "": newCfgFile.write(inputNode+".istate=1;\n") for inputNode in inactiveInputs: if inputNode != "": newCfgFile.write(inputNode+".istate=0;\n") for customState in customStates: if customState != ['']: newCfgFile.write("["+customState[0]+"]"+".istate="+str(1-float(customState[1]))+"[0],"+customState[1]+"[1];\n") newCfgFile.write('\n') for internal in internalTable: newCfgFile.write(internal) for parameter in parametersTable: newCfgFile.write(parameter) else : for mutationGroup in mutationTable: tempRatesTable = list(ratesTable) tempActiveInputs = list(activeInputs) tempInactiveInputs = list(inactiveInputs) for mutation in mutationGroup : if mutation[0] == 'u' : tempActiveInputs.append(mutation[1]) i = 0 while i < len(tempRatesTable) : if re.match("[$]d_"+mutation[1], tempRatesTable[i]): tempRatesTable[i] = re.sub("=.+", "=0;", tempRatesTable[i]) i = i+1 else : tempInactiveInputs.append(mutation[1]) i = 0 while i < len(tempRatesTable) : if re.match("[$]u"+"_"+mutation[1], tempRatesTable[i]): tempRatesTable[i] = re.sub("=.+", "=0;", tempRatesTable[i]) i = i+1 newCfgFileName = re.sub("[.]cfg", "", configFileName) + "_" + trackName + "_" + '_'.join([ '_'.join(mutation) for mutation in mutationGroup]) + ".cfg" configFileList.append(newCfgFileName) with open(newCfgFileName, 'w') as newCfgFile: for rate in tempRatesTable: newCfgFile.write(rate) newCfgFile.write('\n') for inputNode in tempActiveInputs: if inputNode != "": newCfgFile.write(inputNode+".istate=1;\n") for inputNode in tempInactiveInputs: if inputNode != "": newCfgFile.write(inputNode+".istate=0;\n") for customState in customStates: if customState != [''] and customState[0] not in tempInactiveInputs and customState[0] not in tempActiveInputs : print(customState[0]) newCfgFile.write("["+customState[0]+"]"+".istate="+str(1-float(customState[1]))+"[0],"+customState[1]+"[1];\n") newCfgFile.write('\n') for internal in internalTable: newCfgFile.write(internal) for parameter in parametersTable: newCfgFile.write(parameter) return configFileList ############################################################# def PBSProcedure(configFileList): i=1 for configFile in configFileList: if os.path.dirname(configFile) != '' : os.chdir(os.path.dirname(configFile)) scriptName = "MaBoSS_simulation_"+str(i)+".sh" with open(scriptName, 'w') as scriptFile: scriptFile.write("#!/bin/bash\n## Torque Configuration\n# resources \n#PBS -l walltime=06:00:00\n#PBS -l mem=24gb\n#PBS -l nodes=1:ppn=8\n#PBS -q batch\n## Command section\ncd $PBS_O_WORKDIR\n \necho Running on host `hostname`\necho Time is `date`\necho Directory is `pwd`\n\n./FormatMaBoSS.pl "+" "+os.path.basename(re.sub("[.]cfg", ".bnd", sys.argv[1]))+" "+os.path.basename(configFile)+" 0.1") commandLine = "qsub "+scriptName os.system(commandLine) i = i+1 ############################################################ def internalLaunchProcedure(configFileList): for configFile in configFileList: if os.path.dirname(configFile) != '' : os.chdir(os.path.dirname(configFile)) commandLine = "./FormatMaBoSS.pl "+" "+os.path.basename(re.sub("[.]cfg", ".bnd", sys.argv[1]))+" "+os.path.basename(configFile)+" 0.1" os.system(commandLine) ###############################################################" if len(sys.argv) != 2 and len(sys.argv) != 3 and len(sys.argv) != 4: print("Requires at least one argument (a config file)") exit(-2) configFileName = sys.argv[1] if len(sys.argv) == 2: profilFileName = createProfil(configFileName) else : profilFileName = sys.argv[2] if len(sys.argv) == 4: mutationFileName = sys.argv[3] else : mutationFileName = "" choice = "1" while (choice != "0" ): choice = raw_input("generate config files using exiting tracks (0), create a new track (1) or delete a track (2): ") if choice == "0" or choice == "1" or choice == "2": if choice == "1": createTrack(profilFileName) if choice == "2": deleteTrack(profilFileName) if choice == "0": if os.path.isfile(profilFileName) : configFileList = createConfigFiles(configFileName, profilFileName, mutationFileName) else : choice = "1" print("The profil file doesn't exist. Creating new track... Please folow instructions") createTrack(profilFileName) while (choice != "y" and choice != "n"): choice = raw_input("Launch simulation on cluster ? (y/n)") if choice == "y": PBSProcedure(configFileList) else : internalLaunchProcedure(configFileList)