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
)
###############################################################################
## 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')]
)
###############################################################################
