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 convert(fileName, HostOrder, n, writeParasite):
"""takes name of original .newick file and the dictionary of host tree branch lengths
and creates files for the host + parasite trees. Parasite tree can
be ommited if desired"""
f = open(fileName, 'r')
contents = f.read()
host, paras, phi = newickFormatReader.getInput(fileName)
hostRoot = cycleCheckingGraph.findRoot(host)
f.close()
H, P, phi = contents.split(";")
P = P.strip()
H = H.strip()
H = H + ';'
host = treelib1.parse_newick(H, HostOrder)
for key in HostOrder:
H = H.replace(str(key), str(key) + ':' + str(HostOrder[key]))
f = open(fileName[:-7] + str(n) + ".stree", 'w')
treelib1.write_newick(host, f, root_data=True)
f.close()
if writeParasite:
f = open(fileName[:-7] + '.tree', 'w')
f.write(P + ";")
f.close()
def convert(fileName, HostOrder, n, writeParasite):
"""takes name of original .newick file and the dictionary of host tree branch lengths
and creates files for the host + parasite trees. Parasite tree can
be ommited if desired"""
f = open(fileName, 'r')
contents = f.read()
host, paras, phi = newickFormatReader.getInput(fileName)
hostRoot = cycleCheckingGraph.findRoot(host)
f.close()
H,P,phi = contents.split(";")
P = P.strip()
H = H.strip()
H = H + ';'
host = treelib1.parse_newick(H, HostOrder)
for key in HostOrder:
H = H.replace(str(key), str(key) + ':' + str(HostOrder[key]))
f = open(fileName[:-7]+ str(n) +".stree", 'w')
treelib1.write_newick(host, f, root_data = True)
f.close()
if writeParasite:
f = open(fileName[:-7] + '.tree', 'w')
f.write(P + ";")
f.close()
def detectCycles(HostTree, ParasiteTree, reconciliation):
"""This function takes as input the cycle checking graph,
cycleCheckingGraph. It returns a new version of cycleCheckingGraph,
newCycleCheckingGraph, from which the transfer events responsible for the
cycles have been removed. It also returns a list, guiltyTransferList, of
the guilty transfers."""
guiltyTransferList = []
markingDict = {}
cycleCheckingGraph, transferList = buildReconciliation(HostTree,
ParasiteTree, reconciliation)
Hroot = findRoot(HostTree)
markingDict[Hroot] = ['check']
cycleEdge = recurseChildren(cycleCheckingGraph, markingDict, Hroot)
newCycleCheckingGraph, guiltyTransfer, transferList = deleteTransfer(
cycleCheckingGraph, markingDict, transferList, cycleEdge)
if guiltyTransfer:
guiltyTransferList.append(guiltyTransfer)
while cycleEdge is not None:
markingDict = {}
cycleEdge = recurseChildren(newCycleCheckingGraph,
{Hroot: ['check']}, Hroot)
if cycleEdge is None:
for node in newCycleCheckingGraph:
if not checked(markingDict, node):
check(markingDict, node)
cycleEdge = recurseChildren(newCycleCheckingGraph,
markingDict, node)
if cycleEdge is not None:
break
newCycleCheckingGraph, guiltyTransfer, transferList = deleteTransfer(
newCycleCheckingGraph, markingDict, transferList, cycleEdge)
if guiltyTransfer:
guiltyTransferList.append(guiltyTransfer)
return newCycleCheckingGraph, guiltyTransferList