def maximum_distance(tree, root):
c1 = script_tree.getChildren(tree, root)[0]
c2 = script_tree.getChildren(tree, root)[1]
name = script_tree.getBootstrap(tree, root)
if script_tree.isLeaf(tree, c1) and script_tree.isLeaf(tree, c2):
return [[name], [name]]
elif script_tree.isLeaf(tree, c1):
oo = maximum_distance(tree, c2)
return [[name] + oo[0], [name] + oo[1]]
elif script_tree.isLeaf(tree, c2):
oo = maximum_distance(tree, c1)
return [[name] + oo[0], [name] + oo[1]]
else:
orders1 = maximum_distance(tree, c1)
orders2 = maximum_distance(tree, c2)
return [[name] + orders1[0] + orders2[0], [name] + orders2[1] + orders1[1]]
def maximum_distance(tree,root):
c1 = script_tree.getChildren(tree,root)[0]
c2 = script_tree.getChildren(tree,root)[1]
name = script_tree.getBootstrap(tree,root)
if script_tree.isLeaf(tree,c1) and script_tree.isLeaf(tree,c2):
return [[name],[name]]
elif script_tree.isLeaf(tree,c1):
oo = maximum_distance(tree,c2)
return [[name] + oo[0],[name] + oo[1]]
elif script_tree.isLeaf(tree,c2):
oo = maximum_distance(tree,c1)
return [[name] + oo[0],[name] + oo[1]]
else:
orders1 = maximum_distance(tree,c1)
orders2 = maximum_distance(tree,c2)
return [[name] + orders1[0] + orders2[0],[name] + orders2[1] + orders1[1]]
def opt(tree, root):
if (script_tree.isLeaf(tree, script_tree.getChildren(tree, root)[0]) and
script_tree.isLeaf(tree, script_tree.getChildren(tree, root)[1])):
return [script_tree.getBootstrap(tree, root)]
elif script_tree.isLeaf(tree, script_tree.getChildren(tree, root)[0]):
return opt(tree, script_tree.getChildren(tree, root)[1]) + [script_tree.getBootstrap(tree, root)]
elif script_tree.isLeaf(tree, script_tree.getChildren(tree, root)[1]):
return opt(tree, script_tree.getChildren(tree, root)[0]) + [script_tree.getBootstrap(tree, root)]
else:
order1 = opt(tree, script_tree.getChildren(tree, root)[0])
order2 = opt(tree, script_tree.getChildren(tree, root)[1])
# print "level",len(order1)+len(order2),order1,order2
return mix(order1, order2) + [script_tree.getBootstrap(tree, root)]
def opt(tree,root):
if (script_tree.isLeaf(tree,script_tree.getChildren(tree,root)[0]) and
script_tree.isLeaf(tree,script_tree.getChildren(tree,root)[1])):
return [script_tree.getBootstrap(tree,root)]
elif script_tree.isLeaf(tree,script_tree.getChildren(tree,root)[0]):
return opt(tree,script_tree.getChildren(tree,root)[1])+[script_tree.getBootstrap(tree,root)]
elif script_tree.isLeaf(tree,script_tree.getChildren(tree,root)[1]):
return opt(tree,script_tree.getChildren(tree,root)[0])+[script_tree.getBootstrap(tree,root)]
else:
order1 = opt(tree,script_tree.getChildren(tree,root)[0])
order2 = opt(tree,script_tree.getChildren(tree,root)[1])
#print "level",len(order1)+len(order2),order1,order2
return mix(order1,order2) + [script_tree.getBootstrap(tree,root)]
def receptor_search(t,n):
if script_tree.isLeaf(t,n):
result = []
else:
annot = script_tree.getBootstrap(t,n)
if annot.find("T@") >= 0:
result = []
elif annot.split(".")[1][:2] == "D@":
children = script_tree.getChildren(t,n)
result = receptor_search(t,children[0]) + receptor_search(t,children[1])
else:
result = [annot.split(".")[1]]
#print result
return result
def random_order(tree, root):
c1 = script_tree.getChildren(tree, root)[0]
c2 = script_tree.getChildren(tree, root)[1]
name = script_tree.getBootstrap(tree, root)
if script_tree.isLeaf(tree, c1) and script_tree.isLeaf(tree, c2):
return [name]
elif script_tree.isLeaf(tree, c1):
return [name] + random_order(tree, c2)
elif script_tree.isLeaf(tree, c2):
return [name] + random_order(tree, c1)
else:
order1 = random_order(tree, c1)
order2 = random_order(tree, c2)
# if script_tree.isRoot(tree,root):
# print order1,order2
pos = range(len(order1) + len(order2))
for i in range(len(order2)):
index = int(random.random() * (len(pos)))
del pos[index]
# if script_tree.isRoot(tree,root):
# print pos
order = [name]
previous = 0
for i in pos:
for j in range(i - previous):
# if script_tree.isRoot(tree,root):
# print order2,i,previous
order.append(order2[0])
del order2[0]
order.append(order1[0])
del order1[0]
previous = i + 1
# if script_tree.isRoot(tree,root):
# print order1,order2,order
return order + order2
def receptor_search(t, n):
if script_tree.isLeaf(t, n):
result = []
else:
annot = script_tree.getBootstrap(t, n)
if annot.find("T@") >= 0:
result = []
elif annot.split(".")[1][:2] == "D@":
children = script_tree.getChildren(t, n)
result = receptor_search(t, children[0]) + receptor_search(
t, children[1])
else:
result = [annot.split(".")[1]]
#print result
return result
def random_order(tree,root):
c1 = script_tree.getChildren(tree,root)[0]
c2 = script_tree.getChildren(tree,root)[1]
name = script_tree.getBootstrap(tree,root)
if script_tree.isLeaf(tree,c1) and script_tree.isLeaf(tree,c2):
return [name]
elif script_tree.isLeaf(tree,c1):
return [name] + random_order(tree,c2)
elif script_tree.isLeaf(tree,c2):
return [name] + random_order(tree,c1)
else:
order1 = random_order(tree,c1)
order2 = random_order(tree,c2)
#if script_tree.isRoot(tree,root):
#print order1,order2
pos = range(len(order1)+len(order2))
for i in range(len(order2)):
index = int(random.random()*(len(pos)))
del pos[index]
#if script_tree.isRoot(tree,root):
#print pos
order = [name]
previous = 0
for i in pos:
for j in range(i - previous):
#if script_tree.isRoot(tree,root):
#print order2,i,previous
order.append(order2[0])
del order2[0]
order.append(order1[0])
del order1[0]
previous = i+1
#if script_tree.isRoot(tree,root):
#print order1,order2,order
return order + order2
parent(donnor)) + "," + str(receptor)
if not constraints_trf.has_key(c):
constraints_trf[c] = 0
constraints_trf[c] = constraints_trf[c] + 1
# 2/ calculer la contrainte selon les reconciliations
if script_tree.isLeaf(tree, n):
receptor = []
else:
if events[0][:2] != "T@":
if events[0][:2] == "D@":
species = events[0][2:]
else:
species = events[0]
receptor = [species]
else:
children = script_tree.getChildren(
tree, n)
child1 = children[0]
if script_tree.isLeaf(tree, child1):
annot_child1 = script_tree.getName(
tree, child1).split(
".")[-1].split("_")[0]
else:
annot_child1 = script_tree.getBootstrap(
tree, child1).split(".")[-1]
if annot_child1[:2] == "T@":
annot_child1 = annot_child1[
2:].split("->")[0]
if annot_child1[:2] == "D@":
annot_child1 = annot_child1[2:]
child2 = children[1]
if script_tree.isLeaf(tree, child2):
c = str(parent(donnor))+","+str(receptor)
if not constraints_trf.has_key(c):
constraints_trf[c] = 0
constraints_trf[c] = constraints_trf[c] + 1
# 2/ calculer la contrainte selon les reconciliations
if script_tree.isLeaf(tree,n):
receptor = []
else:
if events[0][:2] != "T@":
if events[0][:2] == "D@":
species = events[0][2:]
else:
species = events[0]
receptor = [species]
else:
children = script_tree.getChildren(tree,n)
child1 = children[0]
if script_tree.isLeaf(tree,child1):
annot_child1 = script_tree.getName(tree,child1).split(".")[-1].split("_")[0]
else:
annot_child1 = script_tree.getBootstrap(tree,child1).split(".")[-1]
if annot_child1[:2] == "T@":
annot_child1 = annot_child1[2:].split("->")[0]
if annot_child1[:2] == "D@":
annot_child1 = annot_child1[2:]
child2 = children[1]
if script_tree.isLeaf(tree,child2):
annot_child2 = script_tree.getName(tree,child2).split(".")[-1].split("_")[0]
else:
annot_child2 = script_tree.getBootstrap(tree,child2).split(".")[-1]
if annot_child2[:2] == "T@":
