def tree_from_order(order):
nodes = script_tree.getNodes(tree)
for n in nodes:
if not script_tree.isRoot(tree,n):
if script_tree.isLeaf(tree,n):
index = len(order)
else:
index = order.index(script_tree.getBootstrap(tree,n))
index_parent = order.index(script_tree.getBootstrap(tree,script_tree.getParent(tree,n)))
script_tree.setLength(tree,n,index-index_parent)
return script_tree.writeTree(tree,root,False)
def tree_from_order(order):
nodes = script_tree.getNodes(tree)
for n in nodes:
if not script_tree.isRoot(tree, n):
if script_tree.isLeaf(tree, n):
index = len(order)
else:
index = order.index(script_tree.getBootstrap(tree, n))
index_parent = order.index(script_tree.getBootstrap(tree, script_tree.getParent(tree, n)))
script_tree.setLength(tree, n, index - index_parent)
return script_tree.writeTree(tree, root, False)
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 parent(x):
#print x
nodes = script_tree.getNodes(species_tree)
for n in nodes:
if script_tree.isLeaf(species_tree,n):
name = script_tree.getName(species_tree,n)
else:
name = script_tree.getBootstrap(species_tree,n)
if name == x:
if script_tree.isRoot(species_tree,n):
result = -1
else:
result = script_tree.getBootstrap(species_tree,script_tree.getParent(species_tree,n))
return result
def parent(x):
#print x
nodes = script_tree.getNodes(species_tree)
for n in nodes:
if script_tree.isLeaf(species_tree, n):
name = script_tree.getName(species_tree, n)
else:
name = script_tree.getBootstrap(species_tree, n)
if name == x:
if script_tree.isRoot(species_tree, n):
result = -1
else:
result = script_tree.getBootstrap(
species_tree, script_tree.getParent(species_tree, n))
return result
def distance_from(x, y):
nodes = script_tree.getNodes(species_tree)
for n in nodes:
if script_tree.isLeaf(species_tree, n):
name = script_tree.getName(species_tree, n)
else:
name = script_tree.getBootstrap(species_tree, n)
if name == x:
A = n
if name == y:
B = n
return script_tree.distanceFrom(species_tree, A, B)
def distance_from(x,y):
nodes = script_tree.getNodes(species_tree)
for n in nodes:
if script_tree.isLeaf(species_tree,n):
name = script_tree.getName(species_tree,n)
else:
name = script_tree.getBootstrap(species_tree,n)
if name == x:
A = n
if name == y:
B = n
return script_tree.distanceFrom(species_tree,A,B)
def order_from_tree(tree):
order = []
nodes = script_tree.getNodes(tree)
root = script_tree.getRoot(tree)
for n in nodes:
if not script_tree.isLeaf(tree,n):
order.append(n)
#print order
order.sort(lambda x,y: cmp(script_tree.distanceFrom(tree,x,root),script_tree.distanceFrom(tree,y,root)))
for i in range(len(order)):
order[i] = script_tree.getBootstrap(tree,order[i])
return order
def order_from_tree(tree):
order = []
nodes = script_tree.getNodes(tree)
root = script_tree.getRoot(tree)
for n in nodes:
if not script_tree.isLeaf(tree, n):
order.append(n)
# print order
order.sort(lambda x, y: cmp(script_tree.distanceFrom(tree, x, root), script_tree.distanceFrom(tree, y, root)))
for i in range(len(order)):
order[i] = script_tree.getBootstrap(tree, order[i])
return order
def donnor_search(t,n):
current_node = n
result = -1
while result == -1 and not script_tree.isRoot(t,current_node):
current_node = script_tree.getParent(t,current_node)
annot = script_tree.getBootstrap(t,current_node)
event = annot[1:].split(".")[0]
if event[:2] != "T@" and event[:2] != "D@":
result = event
if annot.find("@T") >= 0:
current_node = script_tree.getRoot(t)
result = -1
return result
def donnor_search(t, n):
current_node = n
result = -1
while result == -1 and not script_tree.isRoot(t, current_node):
current_node = script_tree.getParent(t, current_node)
annot = script_tree.getBootstrap(t, current_node)
event = annot[1:].split(".")[0]
if event[:2] != "T@" and event[:2] != "D@":
result = event
if annot.find("@T") >= 0:
current_node = script_tree.getRoot(t)
result = -1
return result
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 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 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 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 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
order[i] = script_tree.getBootstrap(tree,order[i])
return order
# useful variables
degre_entrant = {}
edge = {}
graph = {}
nodes = script_tree.getNodes(tree)
leaves = script_tree.getLeavesNames(tree)
root = script_tree.getRoot(tree)
internal_nodes = []
# initialise from nodes
for n in nodes:
if (not script_tree.isLeaf(tree,n)):
node = script_tree.getBootstrap(tree,n)
graph[node] = []
degre_entrant[node] = []
internal_nodes.append(node)
else:
node = script_tree.getName(tree,n)
graph[node] = []
print "tree with ",len(internal_nodes),"internal nodes"
# parse transfers
#by_family = {}
for line in constraints:
#print line
order[i] = script_tree.getBootstrap(tree,order[i])
return order
# useful variables
degre_entrant = {}
edge = {}
graph = {}
nodes = script_tree.getNodes(tree)
leaves = script_tree.getLeavesNames(tree)
root = script_tree.getRoot(tree)
internal_nodes = []
# initialise from nodes
for n in nodes:
if (not script_tree.isLeaf(tree,n)):
node = script_tree.getBootstrap(tree,n)
graph[node] = []
degre_entrant[node] = []
internal_nodes.append(node)
else:
node = script_tree.getName(tree,n)
graph[node] = []
# initialise from branches
for n in nodes:
if (not script_tree.isLeaf(tree,n)):
if (not script_tree.isRoot(tree,n)):
parent = script_tree.getBootstrap(tree,script_tree.getParent(tree,n))
child = script_tree.getBootstrap(tree,n)
graph[parent].append(child)
edge[parent+","+child] = MAX_NUMBER
#species_under_origin.append(script_tree.getName(species_tree,l))
leaves = script_tree.getLeaves(tree,root)
#species_present = []
#for l in leaves:
#if script_tree.getName(tree,l).split("_")[0] not in species_present:
#species_present.append(script_tree.getName(tree,l).split("_")[0])
if len(leaves) > MINIMUM_FAMILY_SIZE:# and difference_symetrique(species_present,species_under_origin) < MAXIMUM_DIFFERENCE_WITH_PROFILE:
#print script_tree.writeTree(tree,root,False)
#print origination,len(leaves),len(species_present),len(species_under_origin),
#output_distr.write(str(difference_symetrique(species_present,species_under_origin))+"\n")
nodes = script_tree.getNodes(tree)
for n in nodes:
if script_tree.isLeaf(tree,n):
annot = script_tree.getName(tree,n)
else:
annot = script_tree.getBootstrap(tree,n)
#if script_tree.isLeaf(tree,n) and annot.find("T")>=0:
#print annot
# annot: evenement
events = annot.split(".")
if events[0] == "":
del events[0]
for e in events:
if e[:2] == "T@":
# on a touve un transfert
#print e
donnor = e[2:].split("->")[0]
receptor = e[2:].split("->")[1]
#print annot,donnor,receptor
# 1/ calculer la contrainte selon les transferts
if parent(donnor) != -1 and not (receptor in script_tree.getLeavesNames(species_tree)):
# useful variables
degre_entrant = {}
edge = {}
graph = {}
nodes = script_tree.getNodes(tree)
leaves = script_tree.getLeavesNames(tree)
root = script_tree.getRoot(tree)
# rootname = script_tree.getBootstrap(tree,root)
internal_nodes = []
# initialise from nodes
for n in nodes:
if (not script_tree.isLeaf(tree, n)):
node = script_tree.getBootstrap(tree, n)
graph[node] = []
degre_entrant[node] = []
internal_nodes.append(node)
else:
node = script_tree.getName(tree, n)
graph[node] = []
print
"tree with ", len(internal_nodes), "internal nodes"
# parse transfers
# by_family = {}
for line in constraints:
# print line
if (len(line.split()) >= 2 or len(line.split(",")) >= 2) and line.find("FRQ") < 0 and line[0] != "#":
#species_present = []
#for l in leaves:
#if script_tree.getName(tree,l).split("_")[0] not in species_present:
#species_present.append(script_tree.getName(tree,l).split("_")[0])
if len(
leaves
) > MINIMUM_FAMILY_SIZE: # and difference_symetrique(species_present,species_under_origin) < MAXIMUM_DIFFERENCE_WITH_PROFILE:
#print script_tree.writeTree(tree,root,False)
#print origination,len(leaves),len(species_present),len(species_under_origin),
#output_distr.write(str(difference_symetrique(species_present,species_under_origin))+"\n")
nodes = script_tree.getNodes(tree)
for n in nodes:
if script_tree.isLeaf(tree, n):
annot = script_tree.getName(tree, n)
else:
annot = script_tree.getBootstrap(tree, n)
#if script_tree.isLeaf(tree,n) and annot.find("T")>=0:
#print annot
# annot: evenement
events = annot.split(".")
if events[0] == "":
del events[0]
for e in events:
if e[:2] == "T@":
# on a touve un transfert
#print e
donnor = e[2:].split("->")[0]
receptor = e[2:].split("->")[1]
#print annot,donnor,receptor
# 1/ calculer la contrainte selon les transferts
if parent(donnor) != -1 and not (