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 randomReconWrapper(dirName, D, T, L, numSamples, typeGen):
"""Takes in a directory of newick files, dirName, duplication, loss and
transfer costs, the number of desired random reconciliations, and the type
of generator (biased or uniform), and calls those random generators to
build a file containing the number of temporal inconsistencies found in
those randomly generated reconciliations as well as other information
relating to the file"""
totalTimeTravel = 0 # To record total number of time travels in directory
outOf = 0 # To record total number of reconciliations made
# loop through files in directory
for fileName in os.listdir(dirName):
if fileName.endswith('.newick'):
f = open(fileName[:-7]+'.txt', 'w')
f.write(typeGen+" random reconciliations"+"\n")
hostTree, parasiteTree, phi = newickFormatReader.getInput\
(dirName+"/"+fileName)
# find size of parasite and host trees
parasiteSize = len(parasiteTree)+1
hostSize = len(hostTree)+1
DTLReconGraph, numRecon = DP.DP(hostTree, parasiteTree, phi, D, T, L)
rootList = rootGenerator(DTLReconGraph, parasiteTree)
randomReconList = []
for n in range(numSamples):
timeTravelCount = 0
startRoot = random.choice(rootList)
if typeGen == "uniform":
currentRecon = uniformRecon(DTLReconGraph, [startRoot], {})
else:
normalizeDTL = normalizer(DTLReconGraph)
currentRecon = biasedRecon(normalizeDTL, [startRoot], {})
for key in currentRecon.keys():
currentRecon[key] = currentRecon[key][:-1]
randomReconList.append(currentRecon)
# make sure there are no duplicate reconciliations
uniqueReconList = []
for recon in randomReconList:
if not recon in uniqueReconList:
uniqueReconList.append(recon)
outOf += len(uniqueReconList)
for recon in uniqueReconList:
graph = reconciliationGraph.buildReconstruction\
(hostTree, parasiteTree, recon)
currentOrder = orderGraph.date(graph)
numTrans = findTransfers(recon)
if currentOrder == 'timeTravel':
f.write("Temporal Inconsistency, reconciliation has "+str(numTrans)+" transfers"+"\n")
timeTravelCount += 1
totalTimeTravel += 1
else:
f.write("No temporal inconsistencies, reconciliation has "+str(numTrans)+" transfers"+"\n")
f.write(fileName+" contains "+str(timeTravelCount)+" temporal "+ \
"inconsistencies out of "+ str(len(uniqueReconList))+ \
" reconciliations."+"\n"+"Total number of reconciliations: "+\
str(numRecon)+"\n"+"Host tree size: "+str(hostSize)+"\n"+\
"Parasite tree size: "+str(parasiteSize)+ "\n")
f.close()
print "Total fraction of temporal inconsistencies in directory: ", \
totalTimeTravel, '/', outOf
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 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