Python plot_gene_coverage示例

示例#1

文件： qcsummary.py 项目： johnstantongeddes/bcbio-nextgen

def _run_gene_coverage(bam_file, data, out_dir):
    out_file = os.path.join(out_dir, "gene_coverage.pdf")
    ref_file = utils.get_in(data, ("genome_resources", "rnaseq", "transcripts"))
    count_file = data["count_file"]
    if utils.file_exists(out_file):
        return out_file
    with file_transaction(out_file) as tx_out_file:
        plot_gene_coverage(bam_file, ref_file, count_file, tx_out_file)
    return {"gene_coverage": out_file}

示例#2

def _run_gene_coverage(bam_file, data, out_dir):
    out_file = os.path.join(out_dir, "gene_coverage.pdf")
    ref_file = utils.get_in(data, ("genome_resources", "rnaseq", "transcripts"))
    count_file = data["count_file"]
    if utils.file_exists(out_file):
        return out_file
    with file_transaction(data, out_file) as tx_out_file:
        plot_gene_coverage(bam_file, ref_file, count_file, tx_out_file)
    return {"gene_coverage": out_file}