def main(): logger = multiprocessing.log_to_stderr() logger.setLevel(multiprocessing.SUBDEBUG) if len(sys.argv) >= 4: #directory containing fastq library fastqsDir = workerForBam.getAbsPath(sys.argv[1]) #directory containing other directories with fasta names fastaDir = workerForBam.getAbsPath(sys.argv[2]) #directory containing file locks lockDirPath = workerForBam.getAbsPath(sys.argv[3]) #directory containing temp output -> fastQ's, jobsFile outDir = workerForBam.getAbsPath(sys.argv[4]) #write all fastq's processing in job file combineJobPath = writeCombineBAMJobsFromSAI(outDir, fastqsDir,\ fastaDir,\ lockDirPath) #call workers to generate paired BAMs from SAIs #results = callPairedSAIToBAMWorkers(fastqsDir, fastaDir) #print results else: print 'err: files missing'
def main(): if len(sys.argv) >= 4: #directory containing fastq library fastqsDir = workerForBam.getAbsPath(sys.argv[1]) #directory containing other directories with fasta names fastaDir = workerForBam.getAbsPath(sys.argv[2]) #directory containing file locks lockDirPath = workerForBam.getAbsPath(sys.argv[3]) #directory containing temp output -> fastQ's, jobsFile outDir = workerForBam.getAbsPath(sys.argv[4]) #now for all scaffolds combined bams and look for SNPs snpsFinder(fastaDir, outDir, lockDirPath) else: print 'err: files missing'
def main(): if len(sys.argv) >= 4: #directory containing fastq library fastqsDir = workerForBam.getAbsPath(sys.argv[1]) #directory containing other directories with fasta names fastaDir = workerForBam.getAbsPath(sys.argv[2]) #directory containing file locks lockDirPath = workerForBam.getAbsPath(sys.argv[3]) #directory containing temp output -> fastQ's, jobsFile outDir = workerForBam.getAbsPath(sys.argv[4]) #initialize deafult value of threads numThreads = 12 #TODO: make the following design correct if len(sys.argv) >= 5: #TODO: exception handling for conversion to int numThreads = int(sys.argv[5]) #write all fastq's processing in job file combineJobPath = writeCombineSAIJobs(outDir, fastqsDir, fastaDir,\ lockDirPath, numThreads) print 'combine jobs path: ', combineJobPath #write all serial fastq's processing in job script file combineJobPath = writeCombineSerialSAIJobs(outDir, fastqsDir, fastaDir, numThreads) print 'combine serial jobs script: ', combineJobPath #call workers to generate SAIs #callSAIWorkers(fastqsDir, fastaDir, numThreads) else: print 'err: files missing'
def main(): logger = multiprocessing.log_to_stderr() logger.setLevel(multiprocessing.SUBDEBUG) if len(sys.argv) >= 4: #directory containing fastq library fastqsDir = workerForBam.getAbsPath(sys.argv[1]) #directory containing other directories with fasta names fastaDir = workerForBam.getAbsPath(sys.argv[2]) #directory containing file locks lockDirPath = workerForBam.getAbsPath(sys.argv[3]) #directory containing temp output -> fastQ's, jobsFile outDir = workerForBam.getAbsPath(sys.argv[4]) #initialize deafult value of threads numThreads = 12 #TODO: make the following design correct if len(sys.argv) >= 5: #TODO: exception handling for conversion to int numThreads = int(sys.argv[5]) #write all fastq's processing in job file combineJobPath = writeCombineSAIJobs(outDir, fastqsDir, fastaDir,\ lockDirPath, numThreads) #call workers to generate SAIs #TODO: take number of threads as args #results = callSAIWorkers(fastqsDir, fastaDir, numThreads) #print results else: print 'err: files missing'
def main(): logger = multiprocessing.log_to_stderr() logger.setLevel(multiprocessing.SUBDEBUG) if len(sys.argv) >= 4: #directory containing fastq library fastqsDir = workerForBam.getAbsPath(sys.argv[1]) #directory containing other directories with fasta names fastaDir = workerForBam.getAbsPath(sys.argv[2]) #directory containing file locks lockDirPath = workerForBam.getAbsPath(sys.argv[3]) #directory containing temp output -> fastQ's, jobsFile outDir = workerForBam.getAbsPath(sys.argv[4]) #write all fastq's processing in job file #combineJobPath = writeCombineFastqJobs(outDir, fastqsDir, fastaDir,\ # lockDirPath) tools = workerForBam.getToolsDict() """retcode = workerForBam.callParallelDrone(combineJobPath,\ tools['PARALLEL_DRONE']) if retcode != 0: #error occured while calling parallel drone print "parallel drone erred, in executing combined jobs" return -1 """ #now for all scaffolds combined bams and look for SNPs parallelSNPsFinder.snpsFinder(fastaDir, outDir, lockDirPath) else: print 'err: files missing'