def listTopos(self):
## Outputs a file with the tree topologies in the file listed
for j in range(1,self.runNum+1):
os.chdir(self.basedir)
outfile = open(self.outprefix + "_" + str(j) + "_topolist.txt",'w')
for i in range(len(self.treelist)):
treek = self.treelist[i] + str(j)
outfile.write(treek + "\n")
treeline = ""
for m in range(len(self.modellist)):
treedir = self.basedir + "/" + treek + "/" + self.modellist[m] + "/"
topofile = treek + "_" + self.modellist[m] + "_tree_topo.txt"
topoCount = countTopos(topofile, treedir)
topoline = ""
# Parse topology file:
tfile = open(treedir + topofile,'r')
for line in tfile:
temp = line.split()
if (re.search(r'([0-9][.])',temp[0]) != None):
topoline = topoline + temp[1] + ","
elif (temp[0] == "Raw"):
topoline = self.modellist[m] + "," + topoline
break
else:
continue
outfile.write(treeline + topoline.rstrip(",") + "\n")
outfile.close()
def countToposTwoModsOut(self, treelist2,headerlist2):
## Counts topologies for two different base trees (i.e. two models)
for j in range(1,self.runNum + 1):
os.chdir(self.basedir)
outfile = open("treeleafgrowstopotable" + str(j) + ".txt",'w')
header = "tree," + self.makeheadersuff(2)
outfile.write(header)
for i in range(len(self.treelist)):
treek = self.treelist[i] + str(j)
treeg = treelist2[i] + str(j)
treeline = treek
for m in range(len(self.modellist)):
treedir = self.basedir + "/" + treek + "/" + self.modellist[m] + "/"
topofile = treek + "_" + self.modellist[m] + "_tree_topo.txt"
treeline = treeline + "," + str(countTopos(topofile,treedir))
topofile = treeg + "_" + self.modellist[m] + "_tree_topo.txt"
treeline = treeline + "," + str(countTopos(topofile,treedir))
outfile.write(treeline + "\n")
outfile.close()
def countToposOut(self):
## Counts topologies found for each type of simulation
for j in range(1,self.runNum + 1):
os.chdir(self.basedir)
outfile = open(self.topooutprefix + str(j) + ".txt",'w')
header = "tree," + self.makeheadersuff()
outfile.write(header)
for i in range(len(self.treelist)):
treek = self.treelist[i] + str(j)
treeline = treek
for m in range(len(self.modellist)):
treedir = self.basedir + "/" + treek + "/" + self.modellist[m] + "/"
topofile = treek + "_" + self.modellist[m] + "_tree_topo.txt"
treeline = treeline + "," + str(countTopos(topofile,treedir))
outfile.write(treeline + "\n")
outfile.close()