Esempi in Python per PipelineIDR.callIDRPeaks

Esempio n. 1

def callPeaksOnIndividualReplicates(infile, outfile):
    infile = P.snip(infile, ".sentinel") + ".bam"
    # fetch peak calling parameters
    PARAMS_PEAKCALLER = get_peak_caller_parameters(
        PARAMS["options_peak_caller"])

    # call peaks
    IDR.callIDRPeaks(infile, outfile, PARAMS["options_peak_caller"],
                     PARAMS["options_control_type"], PARAMS_PEAKCALLER)

    P.touch(outfile)

Esempio n. 2

File: pipeline_idr.py Progetto: jmadzo/cgat

def callPeaksOnPseudoreplicates(infile, outfile):
    # fetch peak calling parameters
    PARAMS_PEAKCALLER = get_peak_caller_parameters(
        PARAMS["options_peak_caller"])

    # call peaks on pseudoreplicates
    IDR.callIDRPeaks(infile,
                     outfile,
                     PARAMS["options_peak_caller"],
                     PARAMS["options_control_type"],
                     PARAMS_PEAKCALLER,
                     pseudoreplicate=True)

Esempio n. 3

def callPeaksOnPseudoreplicates(infile, outfile):
    # fetch peak calling parameters
    PARAMS_PEAKCALLER = get_peak_caller_parameters(
        PARAMS["options_peak_caller"])

    # call peaks on pseudoreplicates
    IDR.callIDRPeaks(infile,
                     outfile,
                     PARAMS["options_peak_caller"],
                     PARAMS["options_control_type"],
                     PARAMS_PEAKCALLER,
                     pseudoreplicate=True)

Esempio n. 4

File: pipeline_idr.py Progetto: jmadzo/cgat

def callPeaksOnIndividualReplicates(infile, outfile):
    infile = P.snip(infile, ".sentinal") + ".bam"
    # fetch peak calling parameters
    PARAMS_PEAKCALLER = get_peak_caller_parameters(
        PARAMS["options_peak_caller"])

    # call peaks
    IDR.callIDRPeaks(infile,
                     outfile,
                     PARAMS["options_peak_caller"],
                     PARAMS["options_control_type"],
                     PARAMS_PEAKCALLER)

    P.touch(outfile)