def calcMutualInformation(self, TreeTable):
sumMutualInformation = 0
pairCount = 0
for i, snp in enumerate(self.SNPList):
if i < len(self.SNPList) - 1:
for j in range(i + 1, len(self.SNPList)):
hx = snp.entropy
hy = self.SNPList[j].entropy
hxy = EntropyCalculator.main(TreeTable, snp.aGenomes,snp.tGenomes,snp.cGenomes,snp.gGenomes, self.SNPList[j].aGenomes, self.SNPList[j].tGenomes, self.SNPList[j].cGenomes, self.SNPList[j].gGenomes)
sumMutualInformation += hx + hy - hxy
pairCount += 1
self.avgMutualInformation = sumMutualInformation / pairCount
def calcMutualInformation(self, TreeTable):
sumMutualInformation = 0
pairCount = 0
for i, snp in enumerate(self.SNPList):
if i < len(self.SNPList) - 1:
for j in range(i + 1, len(self.SNPList)):
hx = snp.entropy
hy = self.SNPList[j].entropy
hxy = EntropyCalculator.main(
TreeTable, snp.aGenomes, snp.tGenomes, snp.cGenomes,
snp.gGenomes, self.SNPList[j].aGenomes,
self.SNPList[j].tGenomes, self.SNPList[j].cGenomes,
self.SNPList[j].gGenomes)
sumMutualInformation += hx + hy - hxy
pairCount += 1
self.avgMutualInformation = sumMutualInformation / pairCount
def main(inputFile, treeTable):
fo = open(inputFile, "r")
ISGData = []
#read in number of genomes from file
fo.seek(12)
numGenomes = int(fo.readline().strip())
numGenomes += 1 #add one to include reference genome
#read in header row
arrLine = fo.readline().strip().split("\t")
#place genome names in array
arrGenomeName = []
intCounter = 0
for word in arrLine:
if (intCounter > 1 and intCounter < (numGenomes + 2)):
arrGenomeName.append(word)
intCounter += 1
#Determine genome group SNP differentiates
for line in fo.readlines():
arrLine = line.strip().split("\t")
strChrom = arrLine[0]
strPos = arrLine[1]
arrSNP = []
#place all SNPs into array
for i in range(2, numGenomes + 2):
arrSNP.append(arrLine[i])
#sort Genomes into groups by SNP call
arrA = []
arrT = []
arrC = []
arrG = []
intCounter = 0
for j in arrSNP:
if (arrSNP[intCounter] == 'A'):
arrA.append(arrGenomeName[intCounter])
if (arrSNP[intCounter] == 'T'):
arrT.append(arrGenomeName[intCounter])
if (arrSNP[intCounter] == 'C'):
arrC.append(arrGenomeName[intCounter])
if (arrSNP[intCounter] == 'G'):
arrG.append(arrGenomeName[intCounter])
intCounter += 1
#Checking if there at least 2 groups of at least 2 genomes
intGroups = 0
if (len(arrA) >= 1):
intGroups += 1
if (len(arrT) >= 1):
intGroups += 1
if (len(arrC) >= 1):
intGroups += 1
if (len(arrG) >= 1):
intGroups += 1
# calculate entropy values
entropy = EntropyCalculator.main(treeTable, frozenset(arrA),
frozenset(arrT), frozenset(arrC),
frozenset(arrG))
ISGData.append(
SNP(strChrom, int(strPos), entropy, arrA, arrT, arrC, arrG))
fo.close()
return ISGData
def main(inputFile, treeTable):
fo = open(inputFile, "r")
ISGData = []
#read in number of genomes from file
fo.seek(12)
numGenomes = int(fo.readline().strip())
numGenomes += 1 #add one to include reference genome
#read in header row
arrLine = fo.readline().strip().split("\t")
#place genome names in array
arrGenomeName = []
intCounter = 0
for word in arrLine:
if(intCounter > 1 and intCounter < (numGenomes + 2)):
arrGenomeName.append(word)
intCounter += 1
#Determine genome group SNP differentiates
for line in fo.readlines():
arrLine = line.strip().split("\t")
strChrom = arrLine[0]
strPos = arrLine[1]
arrSNP = []
#place all SNPs into array
for i in range(2,numGenomes+2):
arrSNP.append(arrLine[i])
#sort Genomes into groups by SNP call
arrA = []
arrT = []
arrC = []
arrG = []
intCounter = 0
for j in arrSNP:
if(arrSNP[intCounter] == 'A'):
arrA.append(arrGenomeName[intCounter])
if(arrSNP[intCounter] == 'T'):
arrT.append(arrGenomeName[intCounter])
if(arrSNP[intCounter] == 'C'):
arrC.append(arrGenomeName[intCounter])
if(arrSNP[intCounter] == 'G'):
arrG.append(arrGenomeName[intCounter])
intCounter += 1
#Checking if there at least 2 groups of at least 2 genomes
intGroups = 0
if(len(arrA) >= 1):
intGroups += 1
if(len(arrT) >= 1):
intGroups += 1
if(len(arrC) >= 1):
intGroups += 1
if(len(arrG) >= 1):
intGroups += 1
# calculate entropy values
entropy = EntropyCalculator.main(treeTable, frozenset(arrA), frozenset(arrT), frozenset(arrC), frozenset(arrG))
ISGData.append(SNP(strChrom, int(strPos), entropy, arrA, arrT, arrC, arrG))
fo.close()
return ISGData
