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 testCase(folderName):
print "Debugging: preprocessingRepeatInfo ---------------"
dataList = ioLib.preprocessingRepeatInfo(folderName)
#dataList= ioLib.filterData(dataList)
testRepeat = dataList[2]
# E.g. ['EcoliK12/long_repeats.txt', 3465034, 2724834, 3027]
### Plot distance between consecutive rise
print "Debugging: findapproxrepeatLength ---------------"
startIndex1, startIndex2, lapprox, mutationRate = approximateRepeatLib.findapproxrepeatLength(folderName+ "/oneLine.fasta", folderName+ "/oneLine2.fasta" , testRepeat[1], testRepeat[2], testRepeat[3])
# E.g. [2724708 3464908 3154 0.000317057704502]
testApproxRepeat = [startIndex1, startIndex2, lapprox, mutationRate,testRepeat[3], testRepeat[1], testRepeat[2]]
print "Debugging: plotdetailedPatternForTopRepeats2 ---------------"
#approximateRepeatLib.plotdetailedPatternForTopRepeats(folderName, 1, [testApproxRepeat],inverted = False)
approximateRepeatLib.plotdetailedPatternForTopRepeats(folderName, 1, [testApproxRepeat],inverted = False)
### Plot sliding hamming window
print "Debugging: extractApproxRepeatStatistics ---------------"
plt.figure(3)
graphPlottingLib.plotPatternBeyondRepeat( folderName+ "/oneLine.fasta",folderName+ "/oneLine2.fasta", startIndex1 - int( 1.5*lapprox), startIndex1 - int( 1.5*lapprox), startIndex2 - int( 1.5*lapprox) , startIndex2 - int( 1.5*lapprox) ,int(lapprox*5/10))
### Outputing values
print "Debugging: reportPatternBeyondRepeat ---------------"
approximateRepeatLib.reportPatternBeyondRepeat(folderName+ "/oneLine.fasta",folderName+ "/oneLine2.fasta", startIndex1 - int( 1.5*lapprox), startIndex1 - int( 1.5*lapprox), startIndex2 - int( 1.5*lapprox) , startIndex2 - int( 1.5*lapprox) ,int(lapprox*5/10),folderName+"\outputResult.txt")
### Edit distance Plot
print "Debugging: findapproxrepeatLengthEditDistance ---------------"
plt.figure(4)
approximateRepeatLib.findapproxrepeatLengthEditDistance(folderName+ "/oneLine.fasta",folderName+ "/oneLine2.fasta", testRepeat[1],testRepeat[2], testRepeat[3])
###
plt.show()
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))
