Python tophat2Align 예제들

예제 #1

###############################################################################
# Generate file names
args['tempSam'] = os.path.join(args['tophatSampleDir'],
                               args['name'] + '_sample.sam')
args['nsortBam'] = os.path.join(args['tophatSampleDir'],
                                args['name'] + '_sample_nsort.bam')
args['tophatLog'] = os.path.join(args['tophatSampleDir'],
                                 args['name'] + '_Tophat2.log')
# Generate command for single-end samples
if args['--singleend']:
    # Generate command to perform tophat2 alignment
    tophat2Complete = fastqAlign.tophat2Align(
        read1=args['trimRead1'],
        genomeIndex=args['<bwt2genindex>'],
        transcriptIndex=args['<bwt2tranindex>'],
        outDir=args['tophatSampleDir'],
        path=paths['tophat2'],
        forProb=args['--forprob'],
        threads=args['--threads'],
        readGroup='1',
        sampleName=args['name'])
# Generate command for paired-end samples
else:
    # Generate command to align first 1e6 reads to transcriptome
    alignSampleCommand = fastqAlign.bowtie2Align(
        read1=args['trimRead1'],
        read2=args['trimRead2'],
        index=args['<bwt2tranindex>'],
        bowtie2Path=paths['bowtie2'],
        samtoolsPath=paths['samtools'],
        outFile=args['nsortBam'],
        threads=args['--threads'],

예제 #2

    modules = pmDict[('rsem', 'modules')]
)

###############################################################################
## Generate Tophat2 Alignment Command
###############################################################################
# Generate file names
args['tophatLog'] = os.path.join(args['tophatSampleDir'],
    args['name'] + '_tophat2.log')
# Generate tophat command
tophat2AlignCommand = fastqAlign.tophat2Align(
    read1 = args['trimRead1'],
    read2 = args['trimRead2'],
    genomeIndex = args['<bwt2genindex>'],
    transcriptIndex = args['<bwt2tranindex>'],
    outDir = args['tophatSampleDir'],
    path = pmDict[('tophat2', 'path')],
    forProb = args['--forprob'],
    threads = args['--threads'],
    readGroup = '1',
    sampleName = args['name']
)
# Submit tophat2 commands
tophat2AlignJobID = slurmJobs.add(
    command = tophat2AlignCommand,
    processors = args['--threads'],
    stdout = args['tophatLog'],
    stderr = args['tophatLog'],
    depend = [trimReadsJobID],
    modules = pmDict[('tophat2', 'modules')]
)

예제 #3

파일: RNASeqAlign.py 프로젝트: adam-rabinowitz/ngs_python

# Generate file names
args['tempSam'] = os.path.join(args['tophatSampleDir'],
    args['name'] + '_sample.sam')
args['nsortBam'] = os.path.join(args['tophatSampleDir'],
    args['name'] + '_sample_nsort.bam')
args['tophatLog'] = os.path.join(args['tophatSampleDir'],
    args['name'] + '_Tophat2.log')
# Generate command for single-end samples
if args['--singleend']:
    # Generate command to perform tophat2 alignment
    tophat2Complete = fastqAlign.tophat2Align(
        read1 = args['trimRead1'],
        genomeIndex = args['<bwt2genindex>'],
        transcriptIndex = args['<bwt2tranindex>'],
        outDir = args['tophatSampleDir'],
        path = paths['tophat2'],
        forProb = args['--forprob'],
        threads = args['--threads'],
        readGroup = '1',
        sampleName = args['name']
    )
# Generate command for paired-end samples
else:
    # Generate command to align first 1e6 reads to transcriptome
    alignSampleCommand = fastqAlign.bowtie2Align(
        read1 = args['trimRead1'],
        read2 = args['trimRead2'],
        index = args['<bwt2tranindex>'],
        bowtie2Path = paths['bowtie2'],
        samtoolsPath = paths['samtools'],
        outFile = args['nsortBam'],

예제 #4

파일: RNASeqAlignCamp.py 프로젝트: adam-rabinowitz/ngs_python

    modules = pmDict[('rsem', 'modules')]
)

###############################################################################
## Generate Tophat2 Alignment Command
###############################################################################
# Generate file names
args['tophatLog'] = os.path.join(args['tophatSampleDir'],
    args['name'] + '_tophat2.log')
# Generate tophat command
tophat2AlignCommand = fastqAlign.tophat2Align(
    read1 = args['trimRead1'],
    read2 = args['trimRead2'],
    genomeIndex = args['<bwt2genindex>'],
    transcriptIndex = args['<bwt2tranindex>'],
    outDir = args['tophatSampleDir'],
    path = pmDict[('tophat2', 'path')],
    forProb = args['--forprob'],
    threads = args['--threads'],
    readGroup = '1',
    sampleName = args['name']
)
# Submit tophat2 commands
tophat2AlignJobID = slurmJobs.add(
    command = tophat2AlignCommand,
    processors = args['--threads'],
    stdout = args['tophatLog'],
    stderr = args['tophatLog'],
    depend = [trimReadsJobID],
    modules = pmDict[('tophat2', 'modules')]
)