def freqSummation(argList): """Takes as input an argument list containing a newick file of host and parasite trees as well as their phi mapping, duplication, transfer, and loss costs, the type of frequency scoring to be used, as well as switch and loss cost ranges for xscape scoring, and returns a file containing the list of scores for each individual reconciliation, the sum of the those scores, the total cost of those reconciliations and the number of reconciliations of those trees.""" newickFile = argList[1] D = float(argList[2]) T = float(argList[3]) L = float(argList[4]) freqType = argList[5] switchLo = float(argList[6]) switchHi = float(argList[7]) lossLo = float(argList[8]) lossHi = float(argList[9]) fileName = newickFile[:-7] f = open(fileName+"freqFile.txt", 'w') host, paras, phi = newickFormatReader.getInput(newickFile) DTL, numRecon = DP.DP(host, paras, phi, D, T, L) print numRecon if freqType == "Frequency": newDTL = DTL elif freqType == "xscape": newDTL = calcCostscapeScore.newScoreWrapper(newickFile, switchLo, \ switchHi, lossLo, lossHi, D, T, L) elif freqType == "unit": newDTL = MasterReconciliation.unitScoreDTL(host, paras, phi, D, T, L) scoresList, reconciliation = Greedy.Greedy(newDTL, paras) totalSum = 0 for score in scoresList: totalSum +=score for index in reconciliation: totalCost = 0 for key in index: if index[key][0] == "L": totalCost+=L elif index[key][0] == "T": totalCost+=T elif index[key][0] == "D": totalCost+=D f.write(str(scoresList)+'\n') f.write(str(totalSum)+'\n') f.write(str(totalCost)+'\n') f.write(str(numRecon)) f.close()
def freqSummation(argList):
"""Takes as input an argument list containing a newick file of host and
parasite trees as well as their phi mapping, duplication, transfer, and
loss costs, the type of frequency scoring to be used, as well as switch
and loss cost ranges for xscape scoring, and returns a file containing the
list of scores for each individual reconciliation, the sum of the those
scores, the total cost of those reconciliations and the number of
reconciliations of those trees."""
newickFile = argList[1]
D = float(argList[2])
T = float(argList[3])
L = float(argList[4])
freqType = argList[5]
switchLo = float(argList[6])
switchHi = float(argList[7])
lossLo = float(argList[8])
lossHi = float(argList[9])
fileName = newickFile[:-7]
f = open(fileName + "freqFile.txt", 'w')
host, paras, phi = newickFormatReader.getInput(newickFile)
DTL, numRecon = DP.DP(host, paras, phi, D, T, L)
if freqType == "Frequency":
newDTL = DTL
elif freqType == "xscape":
newDTL = calcCostscapeScore.newScoreWrapper(newickFile, switchLo,
switchHi, lossLo, lossHi,
D, T, L)
elif freqType == "unit":
newDTL = MasterReconciliation.unitScoreDTL(host, paras, phi, D, T, L)
scoresList, reconciliation = Greedy.Greedy(newDTL, paras)
totalSum = 0
for score in scoresList:
totalSum += score
for index in reconciliation:
totalCost = 0
for key in index:
if index[key][0] == "L":
totalCost += L
elif index[key][0] == "T":
totalCost += T
elif index[key][0] == "D":
totalCost += D
f.write(str(scoresList) + '\n')
f.write(str(totalSum) + '\n')
f.write(str(totalCost) + '\n')
f.write(str(numRecon))
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 = 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 freqSummation(argList):
"""Takes as input an argument list containing a newick file of host and
parasite trees as well as their phi mapping, duplication, transfer, and
loss costs, the type of frequency scoring to be used, as well as switch
and loss cost ranges for xscape scoring, and returns a file containing the
list of scores for each individual reconciliation, the sum of the those
scores, the total cost of those reconciliations and the number of
reconciliations of those trees."""
newickFile = argList[0]
costs = {}
costs['D'] = float(argList[1])
costs['T'] = float(argList[2])
costs['L'] = float(argList[3])
freqType = argList[4]
switchLo = float(argList[5])
switchHi = float(argList[6])
lossLo = float(argList[7])
lossHi = float(argList[8])
fileName = newickFile[:-7]
f = open("{}freqFile.txt".format(fileName), 'w')
host, paras, phi = newickFormatReader.getInput(newickFile)
DTL, numRecon = dp.DP(host, paras, phi, costs['D'], costs['T'], costs['L'])
if freqType == "Frequency":
newDTL = DTL
elif freqType == "xscape":
newDTL = calcCostscapeScore.newScoreWrapper(newickFile, switchLo, switchHi, lossLo, lossHi, costs['D'],
costs['T'], costs['L'])
elif freqType == "unit":
newDTL = masterReconciliation.unitScoreDTL(host, paras, phi, costs['D'], costs['T'], costs['L'])
scoresList, reconciliation = greedy.Greedy(newDTL, paras)
totalSum = sum(scoresList)
totalCost = 0
index = reconciliation[0]
for key in index:
totalCost += costs.get(index[key][0], 0)
f.write("{}\n".format(scoresList))
f.write("{}\n".format(totalSum))
f.write("{}\n".format(totalCost))
f.write("{}".format(numRecon))
f.close()