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 combinedStatisticsPlot(folderName,topX,typeOferror):
dataList = ioLib.preprocessingRepeatInfo(folderName)
metaListForInterleaveRepeat, metaListForTripleRepeat = differentTypeOfRepeatLib.findDifferentTypesOfRepeat(dataList,topX)
maxInterleaveRepeatLength = metaListForInterleaveRepeat[0][-1]
maxTripleRepeatLength = metaListForTripleRepeat[0][-1]
print "maxInterleaveRepeatLength,maxTripleRepeatLength", maxInterleaveRepeatLength,maxTripleRepeatLength
listOfRepeat = ioLib.extractExactRepeats(folderName)
print listOfRepeat
listOfApproxRepeat = approximateRepeatLib.clusteringRepeatMain(folderName, listOfRepeat, topX, 'r', typeOferror , -1, [])
for eachitem in listOfApproxRepeat:
#startIndex1, startIndex2, lapprox, mutationRate,lengthOfExactRepeat, start1, start2
if eachitem[2] < eachitem[4]:
print "Errorrrrrrrrrrrrrrrr", eachitem[2] , eachitem[4]
eachitem.insert(0,'eee')
print "listOfApproxRepeat", listOfApproxRepeat
metaListForInterleaveRepeat, metaListForTripleRepeat = differentTypeOfRepeatLib.findDifferentTypesOfRepeat(listOfApproxRepeat,topX)
print "metaListForInterleaveRepeat, metaListForTripleRepeat",metaListForInterleaveRepeat, metaListForTripleRepeat
listOfInterleaveRepeat = differentTypeOfRepeatLib.extractShorterCopy(metaListForInterleaveRepeat)
if len(listOfInterleaveRepeat) > 0:
approximateRepeatLib.clusteringRepeatMain(folderName, listOfInterleaveRepeat, topX, 'i',typeOferror, maxInterleaveRepeatLength,listOfApproxRepeat)
listOfTripleRepeat = differentTypeOfRepeatLib.extractShorterCopy(metaListForTripleRepeat)
if len(listOfTripleRepeat) > 0:
approximateRepeatLib.clusteringRepeatMain(folderName, listOfTripleRepeat, topX, 't',typeOferror,maxTripleRepeatLength,listOfApproxRepeat)
'''
