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 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
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)
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)
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)
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)
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)
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)
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)
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 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)
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)
