def updateReconciliation(guiltyTransferList, HostTree, ParasiteTree, reconciliation):
"""This function takes as input a list guiltyTransferList of transfers
that are responsible for cycles, a host tree and parasite tree, and the
original reconciliation of host and parasite. It returns a new
reconciliation in which all of the guilty transfers have been marked as a
new event 'GT'."""
parents = ReconciliationGraph.parentsDict(HostTree, ParasiteTree)
newReconciliation = copy.deepcopy(reconciliation)
for transfer in guiltyTransferList:
for key in newReconciliation.keys():
if reconciliation[key][0] == "T":
if transfer[0] == key[0]:
newReconciliation[key] = ["GT"] + reconciliation[key][1:]
return newReconciliation
def updateReconciliation(guiltyTransferList, HostTree, ParasiteTree, \
reconciliation):
"""This function takes as input a list guiltyTransferList of transfers
that are responsible for cycles, a host tree and parasite tree, and the
original reconciliation of host and parasite. It returns a new
reconciliation in which all of the guilty transfers have been marked as a
new event 'GT'."""
parents = ReconciliationGraph.parentsDict(HostTree, ParasiteTree)
newReconciliation = copy.deepcopy(reconciliation)
for transfer in guiltyTransferList:
for key in newReconciliation.keys():
if reconciliation[key][0] == 'T':
if transfer[0] == key[0]:
newReconciliation[key] = ['GT'] + reconciliation[key][1:]
return newReconciliation
def buildReconciliation(HostTree, ParasiteTree, reconciliation):
"""Takes as input a host tree, a parasite tree, and a reconciliation,
and returns a graph where the keys are host or parasite nodes, and the
values are a list of the children of a particular node. The graph
represents temporal relationships between events."""
parents = ReconciliationGraph.parentsDict(HostTree, ParasiteTree)
H = ReconciliationGraph.treeFormat(HostTree)
P = ReconciliationGraph.treeFormat(ParasiteTree)
reconGraph = H
reconGraph.update(P)
transferList = []
for key in reconciliation:
if reconciliation[key][0] == 'T':
reconGraph[key[0]] = P[key[0]] + [reconciliation[key][1][1], \
reconciliation[key][2][1]]
parent1 = parents[reconciliation[key][1][1]]
parent2 = parents[reconciliation[key][2][1]]
reconGraph[parent1] = reconGraph[parent1] + [key[0]]
reconGraph[parent2] = reconGraph[parent2] + [key[0]]
transferEdge1 = reconciliation[key][1][1]
transferEdge2 = reconciliation[key][2][1]
transferList.append([key[0], parent1, transferEdge1, parent2, \
transferEdge2])
elif reconciliation[key][0] == 'S':
parent = parents[key[0]]
if parent != 'Top':
reconGraph[parent] = reconGraph[parent] + [key[1]]
reconGraph[key[1]] = reconGraph[key[1]] + reconGraph[key[0]]
elif reconciliation[key][0] == 'D':
parent = parents[key[1]]
if parent != 'Top':
reconGraph[parent] = reconGraph[parent] + [key[0]]
reconGraph[key[0]] = reconGraph[key[0]] + [key[1]]
elif reconciliation[key][0] == 'C':
reconGraph[key[1]] = [None]
reconGraph[key[0]] = [None]
for key in reconGraph:
reconGraph[key] = ReconciliationGraph.uniquify(reconGraph[key])
return reconGraph, transferList
def buildReconciliation(HostTree, ParasiteTree, reconciliation):
"""Takes as input a host tree, a parasite tree, and a reconciliation,
and returns a graph where the keys are host or parasite nodes, and the
values are a list of the children of a particular node. The graph
represents temporal relationships between events."""
parents = ReconciliationGraph.parentsDict(HostTree, ParasiteTree)
H = ReconciliationGraph.treeFormat(HostTree)
P = ReconciliationGraph.treeFormat(ParasiteTree)
reconGraph = H
reconGraph.update(P)
transferList = []
for key in reconciliation:
if reconciliation[key][0] == "T":
reconGraph[key[0]] = P[key[0]] + [reconciliation[key][1][1], reconciliation[key][2][1]]
parent1 = parents[reconciliation[key][1][1]]
parent2 = parents[reconciliation[key][2][1]]
reconGraph[parent1] = reconGraph[parent1] + [key[0]]
reconGraph[parent2] = reconGraph[parent2] + [key[0]]
transferEdge1 = reconciliation[key][1][1]
transferEdge2 = reconciliation[key][2][1]
transferList.append([key[0], parent1, transferEdge1, parent2, transferEdge2])
elif reconciliation[key][0] == "S":
parent = parents[key[0]]
if parent != "Top":
reconGraph[parent] = reconGraph[parent] + [key[1]]
reconGraph[key[1]] = reconGraph[key[1]] + reconGraph[key[0]]
elif reconciliation[key][0] == "D":
parent = parents[key[1]]
if parent != "Top":
reconGraph[parent] = reconGraph[parent] + [key[0]]
reconGraph[key[0]] = reconGraph[key[0]] + [key[1]]
elif reconciliation[key][0] == "C":
reconGraph[key[1]] = [None]
reconGraph[key[0]] = [None]
for key in reconGraph:
reconGraph[key] = ReconciliationGraph.uniquify(reconGraph[key])
return reconGraph, transferList
