def detectCycles(HostTree, ParasiteTree, reconciliation):
"""This function takes as input the cycle checking graph, reconGraph.
It returns a new version of reconGraph, newReconGraph, from which the
transfer events responsible for the cycles have been removed. It also
returns a list, guiltyTransferList, of the guilty transfers."""
hostTree = ReconciliationGraph.treeFormat(HostTree)
parasiteTree = ReconciliationGraph.treeFormat(ParasiteTree)
guiltyTransferList = []
markingDict = {}
reconGraph, transferList = buildReconciliation(HostTree, ParasiteTree, reconciliation)
Hroot = ReconciliationGraph.findRoot(HostTree)
markingDict[Hroot] = ["check"]
cycleNode = recurseChildren(reconGraph, markingDict, Hroot, parasiteTree)
markingDict = {}
newReconGraph, guiltyTransfer, transferList = deleteTransfer(reconGraph, transferList, cycleNode)
if guiltyTransfer != []:
guiltyTransferList.append(guiltyTransfer)
while cycleNode != None:
markingDict = {Hroot: ["check"]}
cycleNode = recurseChildren(newReconGraph, markingDict, Hroot, parasiteTree)
if cycleNode == None:
for node in newReconGraph:
if not checked(markingDict, node):
check(markingDict, node)
cycleNode = recurseChildren(newReconGraph, markingDict, node, parasiteTree)
newReconGraph, guiltyTransfer, transferList = deleteTransfer(newReconGraph, transferList, cycleNode)
if guiltyTransfer != []:
guiltyTransferList.append(guiltyTransfer)
return newReconGraph, guiltyTransferList, newReconGraph
def detectCycles(HostTree, ParasiteTree, reconciliation):
"""This function takes as input the cycle checking graph, reconGraph.
It returns a new version of reconGraph, newReconGraph, from which the
transfer events responsible for the cycles have been removed. It also
returns a list, guiltyTransferList, of the guilty transfers."""
hostTree = ReconciliationGraph.treeFormat(HostTree)
parasiteTree = ReconciliationGraph.treeFormat(ParasiteTree)
guiltyTransferList = []
markingDict = {}
reconGraph, transferList = buildReconciliation(HostTree, ParasiteTree, \
reconciliation)
Hroot = ReconciliationGraph.findRoot(HostTree)
markingDict[Hroot] = ['check']
cycleNode = recurseChildren(reconGraph, markingDict, Hroot, parasiteTree)
markingDict = {}
newReconGraph, guiltyTransfer, transferList = deleteTransfer(reconGraph, \
transferList, cycleNode)
if guiltyTransfer != []:
guiltyTransferList.append(guiltyTransfer)
while cycleNode != None:
markingDict = {Hroot: ['check']}
cycleNode = recurseChildren(newReconGraph, markingDict, Hroot,
parasiteTree)
if cycleNode == None:
for node in newReconGraph:
if not checked(markingDict, node):
check(markingDict, node)
cycleNode = recurseChildren(newReconGraph, markingDict,
node, parasiteTree)
newReconGraph, guiltyTransfer, transferList = deleteTransfer(\
newReconGraph, transferList, cycleNode)
if guiltyTransfer != []:
guiltyTransferList.append(guiltyTransfer)
return newReconGraph, guiltyTransferList, newReconGraph
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 = ReconciliationGraph.findRoot(host)
hostv = ReconciliationGraph.treeFormat(host)
Order = orderGraph.date(hostv)
# Default scoring function (if freqtype== Frequency scoring)
DTLReconGraph, numRecon = DP.DP(host, paras, phi, D, T, L)
#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 = ReconciliationGraph.buildReconstruction(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], DTLGraph, 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 = ReconciliationGraph.findRoot(host) hostv = ReconciliationGraph.treeFormat(host) Order = orderGraph.date(hostv) # Default scoring function (if freqtype== Frequency scoring) DTLReconGraph, numRecon = DP.DP(host, paras, phi, D, T, L) #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 = ReconciliationGraph.buildReconstruction(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], DTLGraph, 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
try:
host, paras, phi = newickFormatReader(fileName)
hostRoot = ReconciliationGraph.findRoot(host)
# Default scoring function (if freqtype== Frequency scoring)
DTLReconGraph, numRecon, cost = DP.DP(host, paras, phi, D, T, L)
# uses xScape scoring function
# if freqType == "xscape":
# DTLReconGraph = calcCostscapeScore.newScoreWrapper(fileName, switchLo, \
# switchHi, lossLo, lossHi, D, T, L)
# uses Unit scoring function
if freqType == "unit":
DTLReconGraph = unitScoreDTL(host, paras, phi, D, T, L)
DTLGraph = copy.deepcopy(DTLReconGraph)
scoresList, recs = Greedy.Greedy(DTLGraph, paras)
infeasible_recs = []
for rec in recs:
if orderGraph.date(ReconciliationGraph.buildReconciliation(host, paras, rec)) == False:
infeasible_recs.append(rec)
except CheetaError:
raise
except:
raise CheetaError(CheetaErrorEnum.Alg), None, sys.exc_info()[2]
return infeasible_recs, recs, cost
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 = ReconciliationGraph.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]))
print "thing"
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 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 = ReconciliationGraph.findRoot(host) # Default scoring function (if freqtype== Frequency scoring) DTLReconGraph, numRecon = DP.DP(host, paras, phi, D, T, L) #uses xScape scoring function # if freqType == "xscape": # DTLReconGraph = calcCostscapeScore.newScoreWrapper(fileName, switchLo, \ # switchHi, lossLo, lossHi, D, T, L) #uses Unit scoring function if freqType == "unit": DTLReconGraph = unitScoreDTL(host, paras, phi, D, T, L) DTLGraph = copy.deepcopy(DTLReconGraph) scoresList, recs = Greedy.Greedy(DTLGraph, paras) infeasible_recs = [] for rec in recs: if orderGraph.date(ReconciliationGraph.buildReconciliation(host, paras, rec)) == False: infeasible_recs.append(rec) return infeasible_recs, recs
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 = ReconciliationGraph.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]))
print "thing"
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()
