def snpsFinder(fastaPath, outDir, lockDirPath):
#get all tools
tools = workerForBam.getToolsDict()
#get all scaffold folder names inside fasta dir
fastaDirs = workerForBam.getAllFastas(fastaPath)
#file containing snpfinder job for each scaffold
snpsFinderJobFileName = fastaPath.split('/')[-1]+"SNPFinderJobs.jobs"
print snpsFinderJobFileName + ' job file to be created '
try:
#open the snpsFinderJob file
snpsFinderJobFile = open(outDir + snpsFinderJobFileName, 'w')
for fastaDir in fastaDirs:
#get fasta file path
fastaFilePath = fastaPath + fastaDir + "/" + fastaDir + ".fasta"
writeJob(snpsFinderJobFile, fastaFilePath, lockDirPath, tools)
snpsFinderJobFile.close()
except IOError as (errno, strerror):
print "I/O error({0}): {1}".format(errno, strerror)
return -1
def writeCombineFastqJobs(outDir, fastqDir, fastaPath, lockDirPath):
combinedBAMJobsName = 'combinedBAMJob.jobs'
combinedBAMJobsPath = os.path.join(outDir, combinedBAMJobsName)
tools = workerForBam.getToolsDict()
#contained all fastas against which to map the fastqs
fastaFilePaths = []
#fastaPath contains all .fasta inside a dir with same name as fasta
#get all fasta name without ext ".fasta" in a list
fastaDirs = workerForBam.getAllFastas(fastaPath)
for fastaDir in fastaDirs:
#get fasta File Path
fastaFilePath = fastaPath + fastaDir + "/" + fastaDir + ".fasta"
fastaFilePaths.append(fastaFilePath)
print 'fastaFilePaths: ', fastaFilePaths
with open(combinedBAMJobsPath, 'w') as combinedBAMJobsFile:
dirContents = os.listdir(fastqDir)
for fileName in dirContents:
fastqPath = os.path.join(fastqDir, fileName)
if os.path.isfile(fastqPath) and\
fileName.endswith('fastq'):
for fastaFilePath in fastaFilePaths:
workerForBam.writeJob(combinedBAMJobsFile, fastaFilePath,\
fastqPath, lockDirPath, tools)
return combinedBAMJobsPath
