def _trna_annotation(data): """ use tDRmapper to quantify tRNAs """ trna_ref = op.join(dd.get_srna_trna_file(data)) name = dd.get_sample_name(data) work_dir = utils.safe_makedir( os.path.join(dd.get_work_dir(data), "trna", name)) in_file = op.basename(data["clean_fastq"]) tdrmapper = os.path.join(os.path.dirname(sys.executable), "TdrMappingScripts.pl") perl_export = utils.get_perl_exports() if not file_exists(trna_ref) or not file_exists(tdrmapper): logger.info("There is no tRNA annotation to run TdrMapper.") return work_dir out_file = op.join(work_dir, in_file + ".hq_cs.mapped") if not file_exists(out_file): with tx_tmpdir(data) as txdir: with utils.chdir(txdir): utils.symlink_plus(data["clean_fastq"], op.join(txdir, in_file)) cmd = ("{perl_export} && perl {tdrmapper} {trna_ref} {in_file}" ).format(**locals()) do.run(cmd, "tRNA for %s" % name) for filename in glob.glob("*mapped*"): shutil.move(filename, work_dir) return work_dir
def _trna_annotation(data): """ use tDRmapper to quantify tRNAs """ trna_ref = op.join(dd.get_srna_trna_file(data)) name = dd.get_sample_name(data) work_dir = utils.safe_makedir(os.path.join(dd.get_work_dir(data), "trna", name)) in_file = op.basename(data["clean_fastq"]) tdrmapper = os.path.join(os.path.dirname(sys.executable), "TdrMappingScripts.pl") perl_export = utils.get_perl_exports() if not file_exists(trna_ref) or not file_exists(tdrmapper): logger.info("There is no tRNA annotation to run TdrMapper.") return work_dir out_file = op.join(work_dir, in_file + ".hq_cs.mapped") if not file_exists(out_file): with tx_tmpdir(data) as txdir: with utils.chdir(txdir): utils.symlink_plus(data["clean_fastq"], op.join(txdir, in_file)) cmd = ("{perl_export} && perl {tdrmapper} {trna_ref} {in_file}").format(**locals()) do.run(cmd, "tRNA for %s" % name) for filename in glob.glob("*mapped*"): shutil.move(filename, work_dir) return work_dir