Python set_sample_nameの例

コード例 #1

ファイル: test_dexseq.py プロジェクト: GetBen/bcbio-nextgen

 def test_bcbio_dexseq(self):
     data = dd.set_sample_name({}, "test")
     data = dd.set_work_bam(data, test_data.BAM_FILE)
     data = dd.set_work_dir(data, self.out_dir)
     data = dd.set_dexseq_gff(data, test_data.DEXSEQ_GFF)
     data = dd.set_strandedness(data, "unstranded")
     out_file = dexseq.bcbio_run(data)
     self.assertTrue(file_exists(out_file))

コード例 #2

ファイル: test_dexseq.py プロジェクト: yong27/bcbio-nextgen

 def test_bcbio_dexseq(self):
     data = dd.set_sample_name({}, "test")
     data = dd.set_work_bam(data, test_data.BAM_FILE)
     data = dd.set_work_dir(data, self.out_dir)
     data = dd.set_dexseq_gff(data, test_data.DEXSEQ_GFF)
     data = dd.set_strandedness(data, "unstranded")
     out_file = dexseq.bcbio_run(data)
     self.assertTrue(file_exists(out_file))

コード例 #3

ファイル: umi.py プロジェクト: sdwfrost/bcbio-nextgen

def split_demultiplexed_sampledata(data, demultiplexed):
    """
    splits demultiplexed samples into separate entries in the global sample
    datadict
    """
    datadicts = []
    samplename = dd.get_sample_name(data)
    for fastq in demultiplexed:
        barcode = os.path.basename(fastq).split(".")[0]
        datadict = copy.deepcopy(data)
        datadict = dd.set_sample_name(datadict, samplename + "-" + barcode)
        datadict = dd.set_description(datadict, samplename + "-" + barcode)
        datadict["rgnames"]["rg"] = samplename + "-" + barcode
        datadict["name"] = ["", samplename + "-" + barcode]
        datadict["files"] = [fastq]
        datadicts.append(datadict)
    return datadicts

コード例 #4

def split_demultiplexed_sampledata(data, demultiplexed):
    """
    splits demultiplexed samples into separate entries in the global sample
    datadict
    """
    datadicts = []
    samplename = dd.get_sample_name(data)
    for fastq in demultiplexed:
        barcode = os.path.basename(fastq).split(".")[0]
        datadict = copy.deepcopy(data)
        datadict = dd.set_sample_name(datadict, samplename + "-" + barcode)
        datadict = dd.set_description(datadict, samplename + "-" + barcode)
        datadict["rgnames"]["rg"] = samplename + "-" + barcode
        datadict["name"]= ["", samplename + "-" + barcode]
        datadict["files"] = [fastq]
        datadicts.append(datadict)
    return datadicts