def extractApproxRepeatStatistics(folderName, topX):
ioLib.generateOneLineFile(folderName, folderName + "/genome.fasta")
listOfData = ioLib.readFromMummerOutput(folderName + "/long_repeats.txt")
listOfData = sorted(listOfData, key=itemgetter(2), reverse=True)
if listOfData[0][0] == 1 and listOfData[0][1] == 1:
listOfData.pop(0)
length = listOfData[0][2]
for index in range(min(topX, len(listOfData))):
start1 = listOfData[index][0]
start2 = listOfData[index][1]
print "Starting Location 1:", start1
print "Starting Location 2:", start2
print ""
#reportPatternBeyondRepeat( folderName+ "/oneLine.fasta", folderName+ "/oneLine2.fasta", start1 - int( 1.5*length) ,start1 - int( 1.5*length) -1 , start2 - int( 1.5* length) ,start2 - int( 1.5* length) -1 , int(length*5/10),folderName+"/outputfile" + str(index)+".txt")
#graphPlottingLib.readAndPlotStat(folderName+"/outputfile" + str(index)+".txt",folderName+"/outputfile" + str(index)+".txt2",folderName, index)
graphPlottingLib.plotPatternBeyondRepeat(
folderName + "/oneLine.fasta", folderName + "/oneLine2.fasta",
start1 - int(1.5 * length), start1 - int(1.5 * length) - 1,
start2 - int(1.5 * length), start2 - int(1.5 * length),
int(length * 5 / 10))
def testreadFromMummerOutput():
listOfData = ioLib.readFromMummerOutput("ecoli536")
listOfData = sorted(listOfData, key = itemgetter(2,0,1)) ## sort by order of 2, 0, 1 in the list
for eachitem in listOfData:
print eachitem
graphPlottingLib.plotExactRepeatStatistics(listOfData)
def testIndelStatistics():
listOfData = ioLib.readFromMummerOutput("ecoli536")
listOfData = ioLib.filterData(listOfData)
listOfData =ioLib.transformMummerOutput(listOfData)
listOfData = sorted(listOfData)
listOfData= approximateRepeatLib.findApproximateIndelRepeatStatistics(listOfData, "oneLine.fasta","oneLine2.fasta")
print listOfData
def batchPatternBeyondRepeat(sourceFile,genomeSource1, genomeSource2,outputfile):
listOfData = ioLib.readFromMummerOutput(sourceFile)
listOfData= sorted(listOfData,key = itemgetter(2), reverse = True)
if listOfData[0][0] == 1 and listOfData[0][1] == 1:
listOfData.pop(0)
start1 = listOfData[0][0]
start2 = listOfData[0][1]
length = listOfData[0][2]
print listOfData
print start1
print start2
print length
graphPlottingLib.plotPatternBeyondRepeat(genomeSource1,genomeSource2, start1 + int( length/2) ,start1 + int( length/2) +1 , start2 + int( length/2) ,start2 + int( length/2) +1 , int(length*5/10))
def extractApproxRepeatStatistics(folderName, topX):
ioLib.generateOneLineFile(folderName, folderName+ "/genome.fasta")
listOfData = ioLib.readFromMummerOutput(folderName+ "/long_repeats.txt")
listOfData= sorted(listOfData,key = itemgetter(2), reverse = True)
if listOfData[0][0] == 1 and listOfData[0][1] == 1:
listOfData.pop(0)
length = listOfData[0][2]
for index in range(min(topX,len(listOfData))):
start1 = listOfData[index][0]
start2 = listOfData[index][1]
print "Starting Location 1:" , start1
print "Starting Location 2:" , start2
print ""
#reportPatternBeyondRepeat( folderName+ "/oneLine.fasta", folderName+ "/oneLine2.fasta", start1 - int( 1.5*length) ,start1 - int( 1.5*length) -1 , start2 - int( 1.5* length) ,start2 - int( 1.5* length) -1 , int(length*5/10),folderName+"/outputfile" + str(index)+".txt")
#graphPlottingLib.readAndPlotStat(folderName+"/outputfile" + str(index)+".txt",folderName+"/outputfile" + str(index)+".txt2",folderName, index)
graphPlottingLib.plotPatternBeyondRepeat( folderName+ "/oneLine.fasta",folderName+ "/oneLine2.fasta", start1 - int( 1.5*length), start1 - int( 1.5*length) -1, start2 - int( 1.5* length) , start2 - int( 1.5* length) ,int(length*5/10))
def batchGenerateApproximateRepeatStatIndel(genomeSource1,genomeSource2,mummerOutput,HDrange):
arrayOfListOfData = []
listOfData = ioLib.readFromMummerOutput(mummerOutput)
listOfData = sorted(listOfData,key = itemgetter(2))
listOfData = ioLib.filterData(listOfData)
listOfData = ioLib.transformMummerOutput(listOfData)
arrayOfListOfData.append(listOfData)
for index in range(1,HDrange):
listOfData= approximateRepeatLib.findApproximateIndelRepeatStatistics(listOfData, "oneLine.fasta","oneLine2.fasta")
listOfData = ioLib.filterData(listOfData)
arrayOfListOfData.append(listOfData)
temp = listOfData[len(listOfData)-1]
print "Approx repeat indel"
print listOfData[len(listOfData)-5:len(listOfData)-1]
#checking(temp,genomeSource1,genomeSource2 )
print listOfData[len(listOfData)-2:len(listOfData)]
plotgraph(arrayOfListOfData, HDrange)
def batchGenerateApproximateRepeatStat(genomeSource1,genomeSource2,mummerOutput,HDrange):
arrayOfListOfData = []
listOfData = ioLib.readFromMummerOutput(mummerOutput)
listOfData = sorted(listOfData,key = itemgetter(2))
listOfData = ioLib.filterData(listOfData)
arrayOfListOfData.append(listOfData)
### Checking
temp = listOfData[len(listOfData)-1]
#debuggingLib.checking(temp,genomeSource1,genomeSource2 )
### End Checking
for index in range(1,HDrange):
listOfData = approximateRepeatLib.findApproxRepeatStatistics(listOfData, genomeSource1, genomeSource2)
listOfData = ioLib.filterData(listOfData)
arrayOfListOfData.append(listOfData)
temp = listOfData[len(listOfData)-1]
print listOfData[len(listOfData)-5:len(listOfData)-1]
def batchGenerateApproximateRepeatStatIndel(genomeSource1, genomeSource2,
mummerOutput, HDrange):
arrayOfListOfData = []
listOfData = ioLib.readFromMummerOutput(mummerOutput)
listOfData = sorted(listOfData, key=itemgetter(2))
listOfData = ioLib.filterData(listOfData)
listOfData = ioLib.transformMummerOutput(listOfData)
arrayOfListOfData.append(listOfData)
for index in range(1, HDrange):
listOfData = approximateRepeatLib.findApproximateIndelRepeatStatistics(
listOfData, "oneLine.fasta", "oneLine2.fasta")
listOfData = ioLib.filterData(listOfData)
arrayOfListOfData.append(listOfData)
temp = listOfData[len(listOfData) - 1]
print "Approx repeat indel"
print listOfData[len(listOfData) - 5:len(listOfData) - 1]
#checking(temp,genomeSource1,genomeSource2 )
print listOfData[len(listOfData) - 2:len(listOfData)]
plotgraph(arrayOfListOfData, HDrange)
def batchGenerateApproximateRepeatStat(genomeSource1, genomeSource2,
mummerOutput, HDrange):
arrayOfListOfData = []
listOfData = ioLib.readFromMummerOutput(mummerOutput)
listOfData = sorted(listOfData, key=itemgetter(2))
listOfData = ioLib.filterData(listOfData)
arrayOfListOfData.append(listOfData)
### Checking
temp = listOfData[len(listOfData) - 1]
#debuggingLib.checking(temp,genomeSource1,genomeSource2 )
### End Checking
for index in range(1, HDrange):
listOfData = approximateRepeatLib.findApproxRepeatStatistics(
listOfData, genomeSource1, genomeSource2)
listOfData = ioLib.filterData(listOfData)
arrayOfListOfData.append(listOfData)
temp = listOfData[len(listOfData) - 1]
print listOfData[len(listOfData) - 5:len(listOfData) - 1]
def batchPatternBeyondRepeat(sourceFile, genomeSource1, genomeSource2,
outputfile):
listOfData = ioLib.readFromMummerOutput(sourceFile)
listOfData = sorted(listOfData, key=itemgetter(2), reverse=True)
if listOfData[0][0] == 1 and listOfData[0][1] == 1:
listOfData.pop(0)
start1 = listOfData[0][0]
start2 = listOfData[0][1]
length = listOfData[0][2]
print listOfData
print start1
print start2
print length
graphPlottingLib.plotPatternBeyondRepeat(genomeSource1, genomeSource2,
start1 + int(length / 2),
start1 + int(length / 2) + 1,
start2 + int(length / 2),
start2 + int(length / 2) + 1,
int(length * 5 / 10))
