Python generateOneLineFile 예제들

예제 #1

파일: approximateRepeatLib.py 프로젝트: kakitfive/approxRepeats

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))

예제 #2

파일: graphPlottingLib.py 프로젝트: kakitfive/approxRepeats

def batchComputationOfStatistics(folders):
    for eachfolder in folders:
        ioLib.generateOneLineFile(eachfolder, eachfolder + "/genome.fasta")
        batchPatternBeyondRepeat(eachfolder + "/long_repeats.txt",
                                 eachfolder + "/oneLine.fasta",
                                 eachfolder + "/oneLine2.fasta",
                                 eachfolder + "/result")

예제 #3

파일: approximateRepeatLib.py 프로젝트: AdventureCompBio/approxRepeats

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))

예제 #4

파일: graphPlottingLib.py 프로젝트: AdventureCompBio/approxRepeats

def batchComputationOfStatistics(folders):
    for eachfolder in folders:
        ioLib.generateOneLineFile(eachfolder, eachfolder+ "/genome.fasta")
        batchPatternBeyondRepeat(eachfolder + "/long_repeats.txt", eachfolder + "/oneLine.fasta", eachfolder + "/oneLine2.fasta" , eachfolder+ "/result")