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 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 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 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 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
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
# 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] = []
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
# useful variables
nodes1 = script_tree.getNodes(tree1)
leaves1 = script_tree.getLeavesNames(tree1)
root1 = script_tree.getRoot(tree1)
internal_nodes1 = []
nodes2 = script_tree.getNodes(tree2)
leaves2 = script_tree.getLeavesNames(tree2)
root2 = script_tree.getRoot(tree2)
internal_nodes2 = []
order_input1 = order_from_tree(tree1)
order_input2 = order_from_tree(tree2)
#value_input = value(order_input)
MINIMUM_SUPPORT_WITHIN_A_FAMILY = 0.05
MINIMUM_FAMILY_SIZE = 5
#MAXIMUM_DIFFERENCE_WITH_PROFILE = 6000
OUTPUT_FILE_REC = "constraints_from_recs"
OUTPUT_FILE_TRF = "constraints_from_transfers"
parameters = sys.argv[1:]
species_tree = script_tree.readTree(open(parameters[0], "r").readline())
extant_species = script_tree.getLeavesNames(species_tree)
gene_tree_file = parameters[1]
gene_trees = []
for gt in open(gene_tree_file, "r").readlines():
gene_trees.append(gt.strip())
nodes = script_tree.getNodes(species_tree)
for n in nodes:
script_tree.setLength(species_tree, n, 1.0)
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
MINIMUM_SUPPORT_WITHIN_A_FAMILY = 0.05
MINIMUM_FAMILY_SIZE = 5
#MAXIMUM_DIFFERENCE_WITH_PROFILE = 6000
OUTPUT_FILE_REC = "constraints_from_recs"
OUTPUT_FILE_TRF = "constraints_from_transfers"
parameters = sys.argv[1:]
species_tree = script_tree.readTree(open(parameters[0],"r").readline())
extant_species = script_tree.getLeavesNames(species_tree)
gene_tree_file = parameters[1]
gene_trees = []
for gt in open(gene_tree_file,"r").readlines():
gene_trees.append(gt.strip())
nodes = script_tree.getNodes(species_tree)
for n in nodes:
script_tree.setLength(species_tree,n,1.0)
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:
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
# 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] = []