def savingLNKFile(folderName=""):
fout = open(folderName + "dataPoints.csv", 'wb')
mywriter = csv.writer(fout)
mywriter.writerow([
"G", "N", "L", "p", "epsilon", "K", "liid", "threshold", "NKcov",
"Nbridge", "Ncov", "Nratio", "numberOfClusterRounds", "brachingDepth",
"bridgingDepth", "msaWidth", "Nbridgenoiseless", "ratioNoiseless",
"clusterRounds", "fingerPrint", "clusterRatio"
])
for index in range(5):
G, L, p = 50000, 200, 0.015
linter, ltriple = 100, 10
L = L - index * 20
epsilon = 0.05
### Noisy Compute
calculator = numericalCompute.thresholdCompute(p, G)
liid, threshold = calculator.findRoot()
threshold = threshold - 2
K = int(liid * 1.3)
calculator = numericalCompute.Ncompute(G, L, epsilon)
Ncov = int(calculator.findRoot())
calculator = numericalCompute.Ncompute(G, L - K, epsilon / 3)
NKcov = int(calculator.findRoot())
Nbridge = int(G * math.log(3 / epsilon) /
float(L - max(linter, ltriple) - 10))
#N = int ( max(NKcov, Nbridge)*1.5)
N = int(max(NKcov, Nbridge) * 1.5)
numberOfClusterRounds, brachingDepth, bridgingDepth, msaWidth = 6, liid * 2 / 3, liid * 2 / 3, liid * 2 / 3
### Noiseless Compute
calculator = numericalCompute.Ncompute(G, L, epsilon)
Nbridgenoiseless = int(G * math.log(3 / epsilon) /
float(L - max(linter, ltriple)))
Noiseless = max(Nbridgenoiseless, Ncov)
ratioNoiseless = Noiseless / float(Ncov)
clusterRounds, fingerPrint, clusterRatio = 2, 6, 1
mywriter.writerow([
G, N, L, p, epsilon, K, liid, threshold, NKcov, Nbridge, Ncov,
N / float(Ncov), numberOfClusterRounds, brachingDepth,
bridgingDepth, msaWidth, Nbridgenoiseless, ratioNoiseless,
clusterRounds, fingerPrint, clusterRatio
])
fout.close()
def savingLNKFile(folderName = ""):
fout = open(folderName+ "dataPoints.csv", 'wb')
mywriter = csv.writer(fout)
mywriter.writerow(["G", "N", "L", "p", "epsilon", "K", "liid", "threshold", "NKcov", "Nbridge", "Ncov", "Nratio" ,"numberOfClusterRounds","brachingDepth", "bridgingDepth", "msaWidth" , "Nbridgenoiseless", "ratioNoiseless" , "clusterRounds", "fingerPrint", "clusterRatio"])
for index in range(5):
G, L, p= 50000, 200, 0.015
linter , ltriple = 100, 10
L = L - index*20
epsilon = 0.05
### Noisy Compute
calculator =numericalCompute.thresholdCompute(p, G)
liid , threshold = calculator.findRoot()
threshold = threshold - 2
K = int(liid*1.3)
calculator = numericalCompute.Ncompute(G,L,epsilon)
Ncov = int(calculator.findRoot())
calculator = numericalCompute.Ncompute(G,L- K,epsilon/3)
NKcov = int(calculator.findRoot())
Nbridge = int ( G*math.log(3/epsilon)/float(L-max(linter, ltriple) - 10) )
#N = int ( max(NKcov, Nbridge)*1.5)
N = int ( max(NKcov, Nbridge)*1.5)
numberOfClusterRounds,brachingDepth,bridgingDepth,msaWidth = 6 , liid*2/3, liid*2/3 , liid*2/3
### Noiseless Compute
calculator = numericalCompute.Ncompute(G,L,epsilon)
Nbridgenoiseless = int ( G*math.log(3/epsilon)/float(L-max(linter, ltriple) ) )
Noiseless = max(Nbridgenoiseless, Ncov)
ratioNoiseless = Noiseless/ float(Ncov)
clusterRounds, fingerPrint, clusterRatio = 2 , 6 , 1
mywriter.writerow([G, N, L, p, epsilon, K, liid, threshold,NKcov, Nbridge, Ncov, N/float(Ncov),numberOfClusterRounds,brachingDepth,bridgingDepth,msaWidth, Nbridgenoiseless,ratioNoiseless,clusterRounds, fingerPrint, clusterRatio])
fout.close()
def savingGenomeSegmentFile(folderName):
fin = open(folderName+ "genomeStat.csv", 'r')
myreader = csv.reader(fin)
dataList = []
firstTime = True
for eachrow in myreader:
if firstTime:
firstTime = False
else:
dataList.append([int(eachrow[0]), int(eachrow[1]), int(eachrow[2]), int(eachrow[3]), int(eachrow[4]) , int(eachrow[5]), int(eachrow[6])])
fin.close()
fout = open(folderName+ "dataPoints.csv", 'wb')
mywriter = csv.writer(fout)
#mywriter.writerow(["G", "N", "L", "p", "epsilon", "K", "liid", "threshold", "NKcov", "Nbridge", "Ncov", "Nratio" ,"numberOfClusterRounds","brachingDepth", "bridgingDepth", "msaWidth" , "Nbridgenoiseless", "ratioNoiseless" , "clusterRounds", "fingerPrint", "clusterRatio", "approx repeat", "Lcrit", "approxinter"])
mywriter.writerow(["G", "N", "L", "p", "epsilon", "K", "liid", "threshold", "NKcov", "Nbridge", "Ncov", "Nratio" ,"numberOfClusterRounds","brachingDepth", "bridgingDepth", "msaWidth" , "Nbridgenoiseless", "ratioNoiseless" , "clusterRounds", "fingerPrint", "clusterRatio", "startIndex", "endIndex", "approxinter"])
for index in range(len(dataList)):
linter , ltriple = dataList[index][3], dataList[index][4]
G, L, p= dataList[index][1] - dataList[index][0], dataList[index][5], 0.015
epsilon = 0.05
### Noisy Compute
calculator =numericalCompute.thresholdCompute(p, G)
liid , threshold = calculator.findRoot()
#K = liid*2
K = 600
calculator = numericalCompute.Ncompute(G,L,epsilon)
Ncov = int(calculator.findRoot())
calculator = numericalCompute.Ncompute(G,L- liid,epsilon)
NKcov = int(calculator.findRoot())
Nbridge = int ( G*math.log(9/epsilon)/float(L-max(linter, ltriple) - liid) )
N = max(NKcov, Nbridge)
#numberOfClusterRounds,brachingDepth,bridgingDepth,msaWidth = 6 , liid*1/3, liid*1/3 , liid*2/3
numberOfClusterRounds,brachingDepth,bridgingDepth,msaWidth = 6 , liid*2/3, liid*2/3 , liid*2/3
### Noiseless Compute
calculator = numericalCompute.Ncompute(G,L,epsilon)
Nbridgenoiseless = int ( G*math.log(3/epsilon)/float(L-max(linter, ltriple) ) )
Noiseless = max(Nbridgenoiseless, Ncov)
ratioNoiseless = Noiseless/ float(Ncov)
clusterRounds, fingerPrint, clusterRatio = 2 , 6 , 1
#mywriter.writerow([G, N, L, p, epsilon, K, liid, threshold,NKcov, Nbridge, Ncov, N/float(Ncov),numberOfClusterRounds,brachingDepth,bridgingDepth,msaWidth, Nbridgenoiseless,ratioNoiseless,clusterRounds, fingerPrint, clusterRatio,dataList[index][2], dataList[index][3] ,dataList[index][6]])
mywriter.writerow([G, N, L, p, epsilon, K, liid, threshold,NKcov, Nbridge, Ncov, N/float(Ncov),numberOfClusterRounds,brachingDepth,bridgingDepth,msaWidth, Nbridgenoiseless,ratioNoiseless,clusterRounds, fingerPrint, clusterRatio,dataList[index][0], dataList[index][1] ,dataList[index][6]])
fout.close()
def savingGenomeSegmentFile(folderName):
fin = open(folderName + "genomeStat.csv", 'r')
myreader = csv.reader(fin)
dataList = []
firstTime = True
for eachrow in myreader:
if firstTime:
firstTime = False
else:
dataList.append([
int(eachrow[0]),
int(eachrow[1]),
int(eachrow[2]),
int(eachrow[3]),
int(eachrow[4]),
int(eachrow[5]),
int(eachrow[6])
])
fin.close()
fout = open(folderName + "dataPoints.csv", 'wb')
mywriter = csv.writer(fout)
#mywriter.writerow(["G", "N", "L", "p", "epsilon", "K", "liid", "threshold", "NKcov", "Nbridge", "Ncov", "Nratio" ,"numberOfClusterRounds","brachingDepth", "bridgingDepth", "msaWidth" , "Nbridgenoiseless", "ratioNoiseless" , "clusterRounds", "fingerPrint", "clusterRatio", "approx repeat", "Lcrit", "approxinter"])
mywriter.writerow([
"G", "N", "L", "p", "epsilon", "K", "liid", "threshold", "NKcov",
"Nbridge", "Ncov", "Nratio", "numberOfClusterRounds", "brachingDepth",
"bridgingDepth", "msaWidth", "Nbridgenoiseless", "ratioNoiseless",
"clusterRounds", "fingerPrint", "clusterRatio", "startIndex",
"endIndex", "approxinter"
])
for index in range(len(dataList)):
linter, ltriple = dataList[index][3], dataList[index][4]
G, L, p = dataList[index][1] - dataList[index][0], dataList[index][
5], 0.015
epsilon = 0.05
### Noisy Compute
calculator = numericalCompute.thresholdCompute(p, G)
liid, threshold = calculator.findRoot()
#K = liid*2
K = 600
calculator = numericalCompute.Ncompute(G, L, epsilon)
Ncov = int(calculator.findRoot())
calculator = numericalCompute.Ncompute(G, L - liid, epsilon)
NKcov = int(calculator.findRoot())
Nbridge = int(G * math.log(9 / epsilon) /
float(L - max(linter, ltriple) - liid))
N = max(NKcov, Nbridge)
#numberOfClusterRounds,brachingDepth,bridgingDepth,msaWidth = 6 , liid*1/3, liid*1/3 , liid*2/3
numberOfClusterRounds, brachingDepth, bridgingDepth, msaWidth = 6, liid * 2 / 3, liid * 2 / 3, liid * 2 / 3
### Noiseless Compute
calculator = numericalCompute.Ncompute(G, L, epsilon)
Nbridgenoiseless = int(G * math.log(3 / epsilon) /
float(L - max(linter, ltriple)))
Noiseless = max(Nbridgenoiseless, Ncov)
ratioNoiseless = Noiseless / float(Ncov)
clusterRounds, fingerPrint, clusterRatio = 2, 6, 1
#mywriter.writerow([G, N, L, p, epsilon, K, liid, threshold,NKcov, Nbridge, Ncov, N/float(Ncov),numberOfClusterRounds,brachingDepth,bridgingDepth,msaWidth, Nbridgenoiseless,ratioNoiseless,clusterRounds, fingerPrint, clusterRatio,dataList[index][2], dataList[index][3] ,dataList[index][6]])
mywriter.writerow([
G, N, L, p, epsilon, K, liid, threshold, NKcov, Nbridge, Ncov,
N / float(Ncov), numberOfClusterRounds, brachingDepth,
bridgingDepth, msaWidth, Nbridgenoiseless, ratioNoiseless,
clusterRounds, fingerPrint, clusterRatio, dataList[index][0],
dataList[index][1], dataList[index][6]
])
fout.close()
