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 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
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] != "#":
# print line
# compute first and second, the donnor and receptor
if line.find(",") >= 0:
words = line.strip().split(",")
words = words[1:]
#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
#species_under_origin = []
#for l in leaves:
#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
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
else:
parent = script_tree.getBootstrap(tree,script_tree.getParent(tree,n))
child = script_tree.getName(tree,n)
graph[parent].append(child)