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}
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}