Ejemplo n.º 1
0
def main():
    print('\nRunning copyCaller.py')

    args = parseArgs() 
    varFile = utility.getProgramPath('varScan.jar')
    rScript = utility.getProgramPath('segmentation.R')
    cnFile = '%s/output.cn.call' %(args.outputFolder)

    sTime = utility.startTime()

    adjustment = 0
    correction = 0
    counter = -1

    while not adjustment == 'Centered':
        counter = counter + 1
        correction = correction + adjustment

        copyCall(varFile, 
                 args.inputFile,
                 cnFile,
                 correction)
        removeCommas(cnFile)
        adjustment = runRScript(rScript,
                                cnFile,
                                args.outputFolder)
        
    print('\nFinal correction value is %s' %(str(correction)))
    print('Number of adjustments: %s' %(str(counter)))

    eTime = utility.endTime()
    utility.executionTime(sTime, eTime)
    return
Ejemplo n.º 2
0
def main():
    print('\nRunning multipleCopyCall.py')

    args = parseArgs()

    sTime = utility.startTime()

    tList = []
    tmpDir = utility.createDirectory(args.outputFolder, 'copyCalls')

    for i in range(args.iteration):
        ccDir = utility.createDirectory(tmpDir, str(i))
        t = threading.Thread(target=runCopyCall,
                             args=(
                                 args.inputFile,
                                 ccDir,
                             ))
        t.start()
        tList.append(t)

        while len(threading.enumerate()) > 5:
            time.sleep(1)

    for t in tList:
        t.join()

    eTime = utility.endTime()
    utility.executionTime(sTime, eTime)
    return
Ejemplo n.º 3
0
def main():
    print('\nRunning mergePatients.py')
    args = parseArgs()
    if not args.inputFiles:
        sys.exit('No files found in path')
    sTime = utility.startTime()

    createCumulative(args.inputFiles, args.outputFile)

    eTime = utility.endTime()
    utility.executionTime(sTime, eTime)
Ejemplo n.º 4
0
def main():
    print('\nRunning annoteSegments.py')
    args = parseArgs()

    sTime = utility.startTime()

    genesDict = getAnnotationInfo(args.annotationFile)
    segments = annoteSegments(args.inputFile, genesDict)
    utility.writeOutput(segments, args.outputFile)

    eTime = utility.endTime()
    utility.executionTime(sTime, eTime)
Ejemplo n.º 5
0
def main():
    print('\nRunning summaryCopyCalls.py\n')

    args = parseArgs()

    sTime = utility.startTime()

    genesDict, iterations = iterateFiles(args.inputDir)
    genesList = geneStatistic(genesDict, iterations)
    printOutput(genesList, args.outputFile)

    eTime = utility.endTime()
    utility.executionTime(sTime, eTime)
Ejemplo n.º 6
0
def main():
    print('\nRunning cancerFilter.py')
    
    args = parseArgs()

    sTime = utility.startTime()

    geneList =  getGenes(args.geneFile)
    filteredSegs = filterSegmentGenes(args.inputFile, geneList)
    utility.writeOutput(filteredSegs, args.outputFile)

    eTime = utility.endTime()
    utility.executionTime(sTime, eTime)
Ejemplo n.º 7
0
def main():
    print('\nRunning mergeCopyCalls.py\n')

    args = parseArgs()
    sTime = utility.startTime()

    segmentsDict = segmentsCollector(args.inputFiles, args.patientId)
    total = len(args.inputFiles)
    segments = filterDict(segmentsDict, args.threshold, total)
    utility.writeOutput(segments, args.outputFile)

    eTime = utility.endTime()
    utility.executionTime(sTime, eTime)
Ejemplo n.º 8
0
def main():
    print('\nRunning mergeSegments.py\n')

    args = parseArgs()

    sTime = utility.startTime()

    armsDict = getArmsInfo(args.armRef)
    mergedSegs = getMergedSegments(args.inputFile, armsDict, args.maximum,
                                   args.minimum)
    utility.writeOutput(mergedSegs, args.outputFile)

    eTime = utility.endTime()
    utility.executionTime(sTime, eTime)
Ejemplo n.º 9
0
def main():
    print('\nRunning runCNVAnalysis.py\n')

    configFile = parseArgs()
    config = getArgsFromFIle(configFile.configFile)

    sTime = utility.startTime()

    copyNumFile = runCopyNumber(config['Input']['controlBam'],
                                config['Input']['tumoralBam'],
                                config['References']['bedFile'],
                                config['References']['refFile'],
                                config['Output']['outputFolder'],
                                config['Analysis'].getboolean('copyNumber'))

    multipleCCDir = runMultipleCopyCall(
        copyNumFile, config['Parameters']['iterations'],
        config['Output']['outputFolder'],
        config['Analysis'].getboolean('copyCalls'))

    cumulativeCC = runMergeCopyCalls(
        multipleCCDir, 'output.r.tsv', config['Parameters']['genePercentage'],
        config['Input']['patient'], config['Output']['outputFolder'],
        config['Analysis'].getboolean('mergeCopyCalls'))

    coverageFile = runCoverageFilter(
        cumulativeCC, config['Input']['controlbam'],
        config['Input']['tumoralbam'], config['References']['bedfile'],
        config['References']['reffile'], config['Parameters']['minCoverage'],
        config['Output']['outputfolder'],
        config['Analysis'].getboolean('coverageFilter'))

    mergedFile = runMergeSegments(
        coverageFile, config['References']['armreffile'],
        config['Parameters']['upperlimit'], config['Parameters']['lowerlimit'],
        config['Output']['outputfolder'],
        config['Analysis'].getboolean('mergeSegments'))

    annotedFile = runAnnoteSegments(
        mergedFile, config['References']['annotationfile'],
        config['Output']['outputfolder'],
        config['Analysis'].getboolean('annoteSegments'))

    cancerFile = runGeneFilter(annotedFile,
                               config['References']['cancerGenesReference'],
                               config['Output']['outputfolder'],
                               config['Analysis'].getboolean('geneFilter'))

    eTime = utility.endTime()
    utility.executionTime(sTime, eTime)
Ejemplo n.º 10
0
def main():
    print('\nRunning copyNumber.py')

    args = parseArgs()
    varFile = utility.getProgramPath('varScan.jar')

    sTime = utility.startTime()

    os.chdir(args.outputFolder)
    pileUpBams(varFile, args.controlFile, args.tumoralFile, args.bedFile,
               args.refFile, args.outputFolder)

    eTime = utility.endTime()
    utility.executionTime(sTime, eTime)
    return
Ejemplo n.º 11
0
def main():
    print('\nRunning createCsv.py')

    args = parseArgs()
    sTime = utility.startTime()

    genes, variationTypes, patients = getGenes(args.inputFiles)
    lines = createCsv (genes, variationTypes, patients)
    line1, line2 = csvHeader(patients, variationTypes)
    lines.insert(0, line2)
    lines.insert(0, line1)
    writeCsv(lines, args.outputFile)

    eTime = utility.endTime()
    utility.executionTime(sTime, eTime)
Ejemplo n.º 12
0
def main():
    print('\nRunning coverageFilter.py')
    args = parseArgs()

    sTime = utility.startTime()

    segments = getSegments(args.inputFile)
    tList = []
    for segment in segments:
        t = threading.Thread(target=coverageMeans,
                             args=(segment, args.controlFile, args.tumoralFile,
                                   args.bedFile, args.refFile, args.minCov))
        t.start()
        tList.append(t)

        while len(threading.enumerate()) > 5:
            time.sleep(1)

    for t in tList:
        t.join()
    utility.writeOutput(filteredSegs, args.outputFile)

    eTime = utility.endTime()
    utility.executionTime(sTime, eTime)