def testgene(org, arraylist, env):
#Creates organism.cpp file and compiles it
writec("./habitat/" +org.folder, org)
call('g++ ./habitat/' + org.folder + '*.cpp ./habitat/biosort.o -o ./habitat/' + org.folder + 'organism.out -g', shell = True)
total_opcount = 0 #Sum of all individual opcounts
#Runs an organism x times where x is the number of runs per generation
for i in range(env.runs):
array = ' '.join(str(x) for x in arraylist[i]) #Pulls array to sort from the given arraylist.
command = './habitat/' + org.folder + 'organism.out '+str(env.pressure)+' '+array #Command to run organism on array from the command line
fileout = Popen(command, stdin = PIPE, stdout = PIPE, stderr = PIPE, bufsize = 1, shell = True) #Retrieves the operations performed by the C++ before it ended
# Gets opcount and adds to total_opcount
ops = fileout.stdout.readline()
org.ops.append(int(ops))
if org.ops[i] >= env.pressure:
org.ops[i] += env.penalty
total_opcount += org.ops[i]
# Calculates mean number of ops
org.avgops = total_opcount / env.runs
return
def make_random_kid(env, folder, num, parent_num):
org = makegene(random.randint(1, env.maxgenes+1)) # make a random gene
org.folder = folder.path # set org folder (created in init of bfolder)
org.logloc = "P_"+str(num+1)+"_B_"+str(parent_num+1) # set log output for location
org.is_primeval = True # came from random, so its primeval
folder.org = org # add the org to the folder
writec(folder.path, folder.org) # write out the file
if env.debug == True:
call('g++ '+ folder.path + '*.cpp ./habitat/biosort.o -o ' + folder.path + 'organism.out -g -O0', shell = True)
else:
call('g++ '+ folder.path + '*.cpp ./habitat/biosort.o -o ' + folder.path + 'organism.out -O0', shell = True)
def make_random(env, folder, num):
org = makegene(random.randint(1, env.maxgenes+1))
org.folder = folder.path
org.logloc = "R_"+str(num)
org.is_primeval = True
folder.org = org
writec(folder.path, folder.org)
if env.debug == True:
call('g++ '+folder.path+'*.cpp ./habitat/biosort.o -o '+folder.path+'organism.out -g -O0', shell = True)
else:
call('g++ '+ folder.path + '*.cpp ./habitat/biosort.o -o ' + folder.path + 'organism.out -O0', shell = True)
def make_random_breeder(env, folder, num):
org = makegene(random.randint(1, env.maxgenes+1)) # Make a random gene
org.is_primeval = True # Came from random, so its primeval
org.folder = folder.path # set org folder (needed for mutate)
org.logloc = "B_"+str(num) # set log output for location
folder.org = org
writec(folder.path, folder.org) # write out the file
if env.debug == True:
call('g++ '+ folder.path + '*.cpp ./habitat/biosort.o -o ' + folder.path + 'organism.out -g -O0', shell = True)
else:
call('g++ '+ folder.path + '*.cpp ./habitat/biosort.o -o ' + folder.path + 'organism.out -O0', shell = True)
copy('./habitat/biosort.h', './habitat/breeder'+str(num))
def make_kid(env, folder, orgfrom, kidnum, breedernum):
org = Organism(orgfrom.genesequence) # create a new organism based off parent
org.folder = folder.path # set organism folder
org.logloc = "P_"+str(kidnum+1)+"_B_"+str(breedernum+1) # set log file representation of folder
org.lineage_id = orgfrom.lineage_id
org.is_primeval = False # Did not come from random, not primeval
folder.org = org # place org in folder
mutate(folder.org, env.mutations+env.adds*kidnum, env.weight, env.maxgenes) # mutate the gene and write mutation to file
writec(folder.path, folder.org)
if env.debug == True:
call('g++ '+ folder.path + '*.cpp ./habitat/biosort.o -o ' + folder.path + 'organism.out -g -O0', shell = True)
else:
call('g++ '+ folder.path + '*.cpp ./habitat/biosort.o -o ' + folder.path + 'organism.out -O0', shell = True)