def Reconcile(argList):
"""Takes command-line arguments of a .newick file, duplication, transfer,
and loss costs, the type of scoring desired and possible switch and loss
ranges. Creates Files for the host, parasite, and reconciliations"""
fileName = argList[1] #.newick file
D = float(argList[2]) # Duplication cost
T = float(argList[3]) # Transfer cost
L = float(argList[4]) # Loss cost
freqType = argList[5] # Frequency type
# Optional inputs if freqType == xscape
switchLo = float(argList[6]) # Switch lower boundary
switchHi = float(argList[7]) # Switch upper boundary
lossLo = float(argList[8]) # Loss lower boundary
lossHi = float(argList[9]) # Loss upper boundary
host, paras, phi = newickFormatReader.getInput(fileName)
hostRoot = cycleCheckingGraph.findRoot(host)
hostv = cycleCheckingGraph.treeFormat(host)
Order = orderGraph.date(hostv)
# Default scoring function (if freqtype== Frequency scoring)
DTLReconGraph, numRecon = DP.DP(host, paras, phi, D, T, L)
print DTLReconGraph, numRecon
#uses xScape scoring function
if freqType == "xscape":
DTLReconGraph = calcCostscapeScore.newScoreWrapper(fileName, switchLo, \
switchHi, lossLo, lossHi, D, T, L)
#uses Unit scoring function
elif freqType == "unit":
DTLReconGraph = unitScoreDTL(host, paras, phi, D, T, L)
DTLGraph = copy.deepcopy(DTLReconGraph)
scoresList, rec = Greedy.Greedy(DTLGraph, paras)
for n in range(len(rec)):
graph = cycleCheckingGraph.buildReconciliation(host, paras, rec[n])
currentOrder = orderGraph.date(graph)
if currentOrder == "timeTravel":
rec[n], currentOrder = detectCycles.detectCyclesWrapper(
host, paras, rec[n])
currentOrder = orderGraph.date(currentOrder)
hostOrder = hOrder(hostv, currentOrder)
hostBranchs = branch(hostv, hostOrder)
if n == 0:
newickToVis.convert(fileName, hostBranchs, n, 1)
else:
newickToVis.convert(fileName, hostBranchs, n, 0)
# filename[:-7] is the file name minus the .newick
reconConversion.convert(rec[n], DTLReconGraph, paras, fileName[:-7], n)
def Reconcile(argList):
"""Takes command-line arguments of a .newick file, duplication, transfer,
and loss costs, the type of scoring desired and possible switch and loss
ranges. Creates Files for the host, parasite, and reconciliations"""
fileName = argList[1] #.newick file
D = float(argList[2]) # Duplication cost
T = float(argList[3]) # Transfer cost
L = float(argList[4]) # Loss cost
freqType = argList[5] # Frequency type
# Optional inputs if freqType == xscape
switchLo = float(argList[6]) # Switch lower boundary
switchHi = float(argList[7]) # Switch upper boundary
lossLo = float(argList[8]) # Loss lower boundary
lossHi = float(argList[9]) # Loss upper boundary
host, paras, phi = newickFormatReader.getInput(fileName)
hostRoot = cycleCheckingGraph.findRoot(host)
hostv = cycleCheckingGraph.treeFormat(host)
Order = orderGraph.date(hostv)
# Default scoring function (if freqtype== Frequency scoring)
DTLReconGraph, numRecon = DP.DP(host, paras, phi, D, T, L)
print DTLReconGraph, numRecon
#uses xScape scoring function
if freqType == "xscape":
DTLReconGraph = calcCostscapeScore.newScoreWrapper(fileName, switchLo, \
switchHi, lossLo, lossHi, D, T, L)
#uses Unit scoring function
elif freqType == "unit":
DTLReconGraph = unitScoreDTL(host, paras, phi, D, T, L)
DTLGraph = copy.deepcopy(DTLReconGraph)
scoresList, rec = Greedy.Greedy(DTLGraph, paras)
for n in range(len(rec)):
graph = cycleCheckingGraph.buildReconciliation(host, paras, rec[n])
currentOrder = orderGraph.date(graph)
if currentOrder == "timeTravel":
rec[n], currentOrder = detectCycles.detectCyclesWrapper(host, paras, rec[n])
currentOrder = orderGraph.date(currentOrder)
hostOrder = hOrder(hostv,currentOrder)
hostBranchs = branch(hostv,hostOrder)
if n == 0:
newickToVis.convert(fileName,hostBranchs, n, 1)
else:
newickToVis.convert(fileName,hostBranchs, n, 0)
# filename[:-7] is the file name minus the .newick
reconConversion.convert(rec[n], DTLReconGraph, paras, fileName[:-7], n)
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. The function also returns a list
transferList containing all the transfers in the reconciliation in the
form """
# create a dictionary with a list of parents of each host and parasite node
parents = createParentsDict(HostTree, ParasiteTree)
H = treeFormat(HostTree)
P = treeFormat(ParasiteTree)
cycleCheckingGraph = H
cycleCheckingGraph.update(P)
transferList = []
for key in reconciliation:
# deal with transfer case:
if reconciliation[key][0] == 'T':
# add the children of the parasite node to the list of children
# of the host node in cycleCheckingGraph
cycleCheckingGraph[key[0]] = P[key[0]] + \
[reconciliation[key][1][1], reconciliation[key][2][1]]
# find the parents of the take-off and landing host nodes
parent1 = parents[reconciliation[key][1][1]]
parent2 = parents[reconciliation[key][2][1]]
# add the parasite node as a child of parent1 and parent2
cycleCheckingGraph[parent1] = cycleCheckingGraph[parent1] + \
[key[0]]
cycleCheckingGraph[parent2] = cycleCheckingGraph[parent2] + \
[key[0]]
transferEdge1 = reconciliation[key][1][1]
transferEdge2 = reconciliation[key][2][1]
transferList.append([key[0], parent1, transferEdge1, parent2, \
transferEdge2])
# deal with speciation case:
elif reconciliation[key][0] == 'S':
parent = parents[key[0]]
if parent != 'Top':
cycleCheckingGraph[parent] = cycleCheckingGraph[parent] + \
[key[1]]
cycleCheckingGraph[key[1]] = cycleCheckingGraph[key[1]] + \
cycleCheckingGraph[key[0]]
# deal with duplication case:
elif reconciliation[key][0] == 'D':
parent = parents[key[1]]
if parent != 'Top':
cycleCheckingGraph[parent] = cycleCheckingGraph[parent] + \
[key[0]]
cycleCheckingGraph[key[0]] = cycleCheckingGraph[key[0]] + [key[1]]
# deal with contemporary case:
elif reconciliation[key][0] == 'C':
cycleCheckingGraph[key[1]] = [None]
cycleCheckingGraph[key[0]] = [None]
for key in cycleCheckingGraph:
cycleCheckingGraph[key] = list(set(cycleCheckingGraph[key]))
return cycleCheckingGraph, transferList