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'
