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
def runCopyNumber(control, tumoral, bed, ref, outFolder, toRun):
prog = utility.getProgramPath('copyNumber.py')
cmdList = [prog, '-b', bed, '-r', ref, '-o', outFolder, control, tumoral]
runCmd('CopyNumber', cmdList, toRun)
return outFolder + '/output.copynumber'
def runMultipleCopyCall(copyFile, iterations, outFolder, toRun):
prog = utility.getProgramPath('multipleCopyCall.py')
cmdList = [prog, '-o', outFolder, copyFile, iterations]
runCmd('MultipleCopyCall', cmdList, toRun)
return outFolder + '/copyCalls'
def runGeneFilter(inFile, ref, outFolder, toRun):
prog = utility.getProgramPath('filterGenes.py')
outFile = outFolder + '/output.cancer.tsv'
cmdList = [prog, '-r', ref, '-o', outFile, inFile]
runCmd('GeneFilter', cmdList, toRun)
return outFile
def runAnnoteSegments(inFile, annRef, outFolder, toRun):
prog = utility.getProgramPath('annoteSegments.py')
outFile = outFolder + '/output.annotated.tsv'
cmdList = [prog, '-r', annRef, '-o', outFile, inFile]
runCmd('AnnoteSegments', cmdList, toRun)
return outFile
def runMergeCopyCalls(ccDir, fileName, threshold, patient, outFolder, toRun):
prog = utility.getProgramPath('mergeCopyCalls.py')
filesPath = '%s/*/%s' % (ccDir, fileName)
outFile = outFolder + '/output.cumulative.tsv'
cmdList = [prog, '-o', outFile, '-n', patient, filesPath, threshold]
runCmd('MergeCopyCalls', cmdList, toRun)
return outFile
def runCopyCall(inFile, outDir):
prog = utility.getProgramPath('copyCaller.py')
cmdList = [prog, '-o', outDir, inFile]
utility.printCmdLine('copyCaller', cmdList)
subprocess.call(cmdList)
#runProg = subprocess.Popen(cmdList)
#runProg.wait()
return outDir + '/output.r.tsv'
def runMergeSegments(inFile, armRef, maxThreshold, minThreshold, outFolder,
toRun):
prog = utility.getProgramPath('mergeSegments.py')
outFile = outFolder + '/output.merged.tsv'
cmdList = [
prog, '-r', armRef, '-a', maxThreshold, '-d', minThreshold, '-o',
outFile, inFile
]
runCmd('MergeSegments', cmdList, toRun)
return outFile
def runCoverageFilter(inFile, control, tumoral, bed, ref, minCov, outFolder,
toRun):
prog = utility.getProgramPath('filterCoverage.py')
outFile = outFolder + '/output.coverage.tsv'
cmdList = [
prog, '-c', control, '-t', tumoral, '-b', bed, '-r', ref, '-m', minCov,
'-o', outFile, inFile
]
runCmd('CoverageFilter', cmdList, toRun)
return outFile
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
def runAnnoteSegments(inFile, annRef, outDir):
prog = utility.getProgramPath('annoteSegments.py')
valOut = outDir + '/output.annotated.tsv'
cmdList = [prog, '-o', valOut]
if not annRef == None:
cmdList.append('-r')
cmdList.append(annRef)
cmdList.append(inFile)
utility.printCmdLine('annoteSegment', cmdList)
subprocess.call(cmdList)
#runProg = subprocess.Popen(cmdList)
#runProg.wait()
return valOut
def runMergeSegments(inFile, armRef, tMin, tMax, patientId, outDir):
prog = utility.getProgramPath('mergeSegments.py')
valOut = outDir + '/output.merged.tsv'
cmdList = [prog, '-o', valOut, '-n', patientId]
if not armRef == None:
cmdList.append('-r')
cmdList.append(armRef)
if not tMin == None:
cmdList.append('-d')
cmdList.append(str(tMin))
if not tMax == None:
cmdList.append('-a')
cmdList.append(str(tMax))
cmdList.append(inFile)
utility.printCmdLine('mergeSegment', cmdList)
subprocess.call(cmdList)
#runProg = subprocess.Popen(cmdList)
#runProg.wait()
return valOut
