Python Pipeline.submitの例

コード例 #1

ファイル: pipeline_scrnaseq.py プロジェクト: snsansom/scseq

def estimateCopyNumber(infiles, outfile):
    '''Estimate copy numbers based on standard
       curves constructed from the spike-ins'''

    P.submit(os.path.join(code_dir, "PipelineScRnaseq.py"),
             "estimateCopyNumber",
             infiles=infiles,
             outfiles=outfile,
             params=[code_dir])

コード例 #2

def estimateCopyNumber(infiles, outfile):
    '''Estimate copy numbers based on standard
       curves constructed from the spike-ins'''

    P.submit(os.path.join(code_dir, "PipelineScRnaseq.py"),
             "estimateCopyNumber",
             infiles=infiles,
             outfiles=outfile,
             params=[code_dir])

コード例 #3

def splitPooledBamfiles(infile, sentinel):
    infile = P.snip(infile, ".sentinel") + ".bam"
    outfile = P.snip(sentinel, ".sentinel")
    params = '2'
    try:
        module = P.snip(IDR.__file__, ".py")
    except ValueError:
        module = P.snip(IDR.__file__, ".pyc")

    P.submit(module, "splitBam", params, infile, outfile)

    P.touch(sentinel)

コード例 #4

def findNPeaksForPooledPseudoreplicates(infiles, outfile):
    idr_thresh = PARAMS["idr_options_pooled_consistency_threshold"]
    try:
        module = P.snip(IDR.__file__, ".py")
    except ValueError:
        module = P.snip(IDR.__file__, ".pyc")

    P.submit(module,
             "findNPeaks",
             params=[str(idr_thresh), ],
             infiles=infiles,
             outfiles=outfile)

コード例 #5

def findNPeaksForIndividualReplicates(infiles, outfile):
    idr_thresh = PARAMS["idr_options_inter_replicate_threshold"]
    try:
        module = P.snip(IDR.__file__, ".py")
    except ValueError:
        module = P.snip(IDR.__file__, ".pyc")

    P.submit(module,
             "findNPeaks",
             params=[str(idr_thresh), ],
             infiles=infiles,
             outfiles=outfile)

コード例 #6

def splitBamfiles(infile, sentinel):
    """
    For all tracks, split the filtered bamfile in two using pysam
    """
    infile = P.snip(infile, ".sentinel") + ".bam"
    outfile = P.snip(sentinel, ".sentinel")
    params = '2'
    try:
        module = P.snip(IDR.__file__, ".py")
    except ValueError:
        module = P.snip(IDR.__file__, ".pyc")

    P.submit(module, "splitBam", params, infile, outfile)

    P.touch(sentinel)

コード例 #7

ファイル: pipeline_idr.py プロジェクト: gjaime/CGATPipelines

def splitPooledBamfiles(infile, sentinel):
    infile = P.snip(infile, ".sentinel") + ".bam"
    outfile = P.snip(sentinel, ".sentinel")
    params = '2'
    try:
        module = P.snip(IDR.__file__, ".py")
    except ValueError:
        module = P.snip(IDR.__file__, ".pyc")

    P.submit(module,
             "splitBam",
             params,
             infile,
             outfile)

    P.touch(sentinel)

コード例 #8

ファイル: pipeline_idr.py プロジェクト: gjaime/CGATPipelines

def splitBamfiles(infile, sentinel):
    """
    For all tracks, split the filtered bamfile in two using pysam
    """
    infile = P.snip(infile, ".sentinel") + ".bam"
    outfile = P.snip(sentinel, ".sentinel")
    params = '2'
    try:
        module = P.snip(IDR.__file__, ".py")
    except ValueError:
        module = P.snip(IDR.__file__, ".pyc")

    P.submit(module,
             "splitBam",
             params,
             infile,
             outfile)

    P.touch(sentinel)