Python run_sambambaの例

コード例 #1

def test_run_sambamba(tmpdir, bed_path, bam_path):
    out_path = tmpdir.join('ccds.coverage.bed')
    run_sambamba(bam_path,
                 bed_path,
                 outfile=str(out_path),
                 cov_thresholds=THRESHOLDS)
    assert out_path.exists()

コード例 #2

def test_run_sambamba_missing(tmpdir, reset_path, bed_path, bam_path):
    out_path = tmpdir.join('ccds.coverage.bed')
    with pytest.raises(OSError):
        run_sambamba(bam_path,
                     bed_path,
                     outfile=str(out_path),
                     cov_thresholds=THRESHOLDS)

コード例 #3

ファイル: sambamba.py プロジェクト: biocyberman/chanjo

def sambamba(context, bam_file, regions, cov_thresholds, outfile):
    """Run Sambamba from chanjo."""
    LOG.info("Running chanjo sambamba")
    try:
        run_sambamba(bam_file, regions, outfile, cov_thresholds)
    except Exception:
        LOG.exception('something went really wrong :_(')
        context.abort()

コード例 #4

ファイル: test_sambamba.py プロジェクト: biocyberman/chanjo

def test_run_sambamba(tmpdir, bed_path, bam_path):
    out_path = tmpdir.join('ccds.coverage.bed')
    run_sambamba(bam_path, bed_path, outfile=str(out_path),
                 cov_thresholds=THRESHOLDS)
    assert out_path.exists()

コード例 #5

ファイル: test_sambamba.py プロジェクト: biocyberman/chanjo

def test_run_sambamba_missing(tmpdir, reset_path, bed_path, bam_path):
    out_path = tmpdir.join('ccds.coverage.bed')
    with pytest.raises(OSError):
        run_sambamba(bam_path, bed_path, outfile=str(out_path),
                     cov_thresholds=THRESHOLDS)