dependency=[trimReadsJobID]) ################################################################################ ## Generate RSEM Transcript alignment command ################################################################################ # Generate file names args['rsemTranPrefix'] = os.path.join(args['rsemTranSampleDir'], args['name']) args['rsemTranLog'] = args['rsemTranPrefix'] + '_RSEM.log' args['rsemTranBam'] = args['rsemTranPrefix'] + '.transcript.bam' args['rsemTranGenomeBam'] = args['rsemTranPrefix'] + '.genome.bam' # Generate rsem transcript alignment command rsemAlignCommand = fastqAlign.rsemBowtie2Align( read1=args['trimRead1'], read2=args['trimRead2'], index=args['<rsemtranindex>'], outPrefix=args['rsemTranPrefix'], rsemPath=paths['rsem'], bowtie2Path=re.sub('[^/]*$', '', paths['bowtie2']), threads=args['--threads'], forProb=args['--forprob'], genomeBam=True) # Submit rsem transcript command rsemAlignJobID = moabJobs.add(command=rsemAlignCommand, processors=args['--threads'], stdout=args['rsemTranLog'], stderr=args['rsemTranLog'], dependency=[trimReadsJobID]) ################################################################################ ## Generate RSEM Spike-In Alignment command ################################################################################ # Generate file names
################################################################################ ## Generate RSEM Transcript alignment command ################################################################################ # Generate file names args['rsemTranPrefix'] = os.path.join(args['rsemTranSampleDir'], args['name']) args['rsemTranLog'] = args['rsemTranPrefix'] + '_RSEM.log' args['rsemTranBam'] = args['rsemTranPrefix'] + '.transcript.bam' args['rsemTranGenomeBam'] = args['rsemTranPrefix'] + '.genome.bam' # Generate rsem transcript alignment command rsemAlignCommand = fastqAlign.rsemBowtie2Align( read1 = args['trimRead1'], read2 = args['trimRead2'], index = args['<rsemtranindex>'], outPrefix = args['rsemTranPrefix'], rsemPath = paths['rsem'], bowtie2Path = re.sub('[^/]*$', '', paths['bowtie2']), threads = args['--threads'], forProb = args['--forprob'], genomeBam = True ) # Submit rsem transcript command rsemAlignJobID = moabJobs.add( command = rsemAlignCommand, processors = args['--threads'], stdout = args['rsemTranLog'], stderr = args['rsemTranLog'], dependency = [trimReadsJobID] ) ################################################################################
) ############################################################################### ## Generate RSEM Transcript alignment command ############################################################################### # Generate file names args['rsemTranPrefix'] = os.path.join(args['rsemTranSampleDir'], args['name']) args['rsemTranLog'] = args['rsemTranPrefix'] + '_rsem.log' args['rsemTranBam'] = args['rsemTranPrefix'] + '.transcript.bam' args['rsemTranGenomeBam'] = args['rsemTranPrefix'] + '.genome.bam' # Generate rsem transcript alignment command rsemAlignCommand = fastqAlign.rsemBowtie2Align( read1 = args['trimRead1'], read2 = args['trimRead2'], index = args['<rsemtranindex>'], outPrefix = args['rsemTranPrefix'], rsemPath = pmDict[('rsem', 'path')], threads = args['--threads'], forProb = args['--forprob'], genomeBam = False ) # Submit rsem transcript command rsemAlignJobID = slurmJobs.add( command = rsemAlignCommand, processors = args['--threads'], stdout = args['rsemTranLog'], stderr = args['rsemTranLog'], depend = [trimReadsJobID], modules = pmDict[('rsem', 'modules')] ) ###############################################################################
inDir, inPrefix = os.path.split(args['<inprefix>']) outDir = os.path.join(args['<outdir>'], args['<samplename>']) if not os.path.isdir(outDir): os.mkdir(outDir) outPrefix = os.path.join(outDir, args['<samplename>']) outLog = outPrefix + '.rsem.log' # Create job dictionary # Extract fastq files and generate output file names read1, read2 = fastqFind.findFastq(prefix=inPrefix, dirList=[inDir], pair=True, gzip=True) rsemCommand = fastqAlign.rsemBowtie2Align(index=args['<index>'], outPrefix=outPrefix, read1=read1, read2=read2, rsemPath=args['--rsem'], bowtie2Path=args['--bowtie2'], threads=args['--threads'], forProb=args['--forprob'], genomeBam=args['--genomebam'], estimateRspd=False, check=True) print rsemCommand jobID = moab.submitJob(rsemCommand, processor=args['--threads'], stdout=outLog, stderr=outLog) print args['<samplename>'], jobID
""" # Import required modules import os from ngs_python.fastq import fastqFind, fastqAlign from general_python import docopt, toolbox, moab # Extract and process arguments args = docopt.docopt(__doc__,version = 'v1') args['--threads'] = int(args['--threads']) args['--forprob'] = float(args['--forprob']) toolbox.check_var(args['--forprob'], 'num', mn = 0, mx = 1) inDir, inPrefix = os.path.split(args['<inprefix>']) outDir = os.path.join(args['<outdir>'], args['<samplename>']) if not os.path.isdir(outDir): os.mkdir(outDir) outPrefix = os.path.join(outDir, args['<samplename>']) outLog = outPrefix + '.rsem.log' # Create job dictionary # Extract fastq files and generate output file names read1, read2 = fastqFind.findFastq(prefix = inPrefix, dirList = [inDir], pair = True, gzip = True) rsemCommand = fastqAlign.rsemBowtie2Align(index = args['<index>'], outPrefix = outPrefix, read1 = read1, read2 = read2, rsemPath = args['--rsem'], bowtie2Path = args['--bowtie2'], threads = args['--threads'], forProb = args['--forprob'], genomeBam = args['--genomebam'], estimateRspd = False, check = True) print rsemCommand jobID = moab.submitJob(rsemCommand, processor = args['--threads'], stdout = outLog, stderr = outLog) print args['<samplename>'], jobID