def createTreeFile(logFilname,quick,nRobots,gTime,cutDeadLeaf):
print "############################"
print "## Parsing of the logFile ##"
fileContentArray = open(options.logFile,'r').readlines()
currentTimeStamp = -1 # Detection of changement in the timestamps
precTimeStamp = -1 # Detection of changement in the timestamps
removeDone = False
beg= int(options.begin)
nGen = int(options.end)
step = int(options.step)
if(quick):table=[[-1 for i in range(nRobots)] for i in range(nGen + 1)]
allPhy = []
newAllPhy=allPhy
print "G",
for line in fileContentArray:
# A line is valid only if it starts by an interation number
#timeStampDescription = 'Info\(([0-9]+)\) : robot nb.([0-9]+) take the genome from the robot nb.([0-9]+)'
timeStampDescription = '([0-9]+) : ([0-9]+) take ([0-9]+)'
timeStampEvaluation = re.compile(timeStampDescription)
match = timeStampEvaluation.search(line)
if ( match ):
#Mechanism to detect a changement in the timestamps ( There might be many lines with the same timeStamp)
timeStamp = (int(match.group(1))+1)#/gTime
if (timeStamp > int(options.end)):
break
if ( currentTimeStamp == -1):
precTimeStamp = timeStamp
else:
precTimeStamp = currentTimeStamp
currentTimeStamp = timeStamp
newGeneration = not (precTimeStamp == currentTimeStamp)
#We continue to parse the file while we have not reached the first generation wanted
if (timeStamp >= beg) :
if(timeStamp == beg and allPhy == []) : allPhy = initAllPhy(beg-1,nRobots)
if ( newGeneration ):
print "-"+str(timeStamp),
stdout.flush()
allRoot=[]
allPhy=newAllPhy
newAllPhy = []
father = int(match.group(3))
son = int(match.group(2))
################## tree dendropy creation
sonId = str(timeStamp) + ' ' + str(son)
fatherId = str(timeStamp - 1) + ' ' + str(father)
for tree in allPhy :
if(cutDeadLeaf):
if(newGeneration):
leaves= tree.leaf_nodes()
for l in leaves:
if ( (l.level() < (timeStamp-1)) and (l.level() > 1)):
p= l.parent_node
p.remove_child(l)
while(p.is_leaf() and p.level() > 1) :
f= p.parent_node
f.remove_child(p)
p=f
n = None
ancestor = None #ancestor at the level N-S
allNodes = tree.nodes()
#Why look all node and not leaves only? Not sure but the dendropy function which gives us all leaves is faster than looking for leaves manually. And if you choose to look leaves only, be sure to no forget that they change during a generation.
for node in allNodes :
if(node.label == fatherId) :
n=node
if(n is not None):
son=n.new_child(label=sonId)
son.edge_length = 1
sonI= son.label.split(' ')[1]
gene = son.label.split(' ')[0]
if((int(timeStamp) > beg + int(step) -1) and quick ):#used to cut everythng no more useful
ancestor=son.parent_node
while( (int(getGen(son))-int(getGen(ancestor))) != int(step ) ):
ancestor = ancestor.parent_node
ancestorId = ancestor.label.split(' ')[1]
#Create a new tree using the ancestor as root
new_tree = Tree(tree)
mrca_node = new_tree.find_node_with_label(ancestor.label)
new_tree.seed_node=mrca_node
new_tree.seed_node.parent_node = None
addTree(new_tree,newAllPhy)
table[int(timeStamp)][int(sonI)]=ancestorId
else :
newAllPhy = allPhy
print "# Parsing done. #"
print "############################"
if(quick):
s=""
allFather=0
for i in table:
for j in i :
s+= str(j)+","
allFather=list(set(i))
try :
allFather.remove(-1)
except ValueError:
#if the script goes here it's because all genomes are transmitted
None
allAlive=list(i)
allAlive = filter (lambda a: a != -1, allAlive)
s+=str(len(allFather))+","+str(len(allAlive)) #The count of robots which have transmitted ther genome is bind at the end of the matrix
s+="\n"
csvFilname="./ancestorsRawData/"+baseName+".csv"
print "#\t write the csv file in "+csvFilname
out=open(csvFilname,"w" )
out.write(s)
out.close()
print "#\tdone"
print "#------------------------#"
return allPhy
