Exemple #1
0
def _mint_trna_annotation(data):
    """
    use MINTmap to quantify tRNAs
    """
    trna_lookup = op.join(dd.get_srna_mint_lookup(data))
    trna_space = op.join(dd.get_srna_mint_space(data))
    trna_other = op.join(dd.get_srna_mint_other(data))
    name = dd.get_sample_name(data)
    work_dir = utils.safe_makedir(os.path.join(dd.get_work_dir(data), "trna_mint", name))
    in_file = op.basename(data["clean_fastq"])
    mintmap = os.path.realpath(os.path.join(os.path.dirname(sys.executable), "MINTmap.pl"))
    perl_export = utils.get_perl_exports()
    if not file_exists(trna_lookup) or not file_exists(mintmap):
        logger.info("There is no tRNA annotation to run MINTmap.")
        return work_dir
    jar_folder = os.path.join(os.path.dirname(mintmap), "MINTplates")
    out_file = op.join(work_dir, name + "-MINTmap_v1-exclusive-tRFs.expression.txt")
    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} && {mintmap} -f {in_file} -p {name} "
                       "-l {trna_lookup} -s {trna_space} -j {jar_folder} "
                       "-o {trna_other}").format(**locals())
                do.run(cmd, "tRNA for %s" % name)
                for filename in glob.glob("*MINTmap*"):
                    shutil.move(filename, work_dir)
    return work_dir
Exemple #2
0
def _mint_trna_annotation(data):
    """
    use MINTmap to quantify tRNAs
    """
    trna_lookup = op.join(dd.get_srna_mint_lookup(data))
    trna_space = op.join(dd.get_srna_mint_space(data))
    trna_other = op.join(dd.get_srna_mint_other(data))
    name = dd.get_sample_name(data)
    work_dir = utils.safe_makedir(os.path.join(dd.get_work_dir(data), "trna_mint", name))
    in_file = op.basename(data["clean_fastq"])
    mintmap = os.path.realpath(os.path.join(os.path.dirname(sys.executable), "MINTmap.pl"))
    perl_export = utils.get_perl_exports()
    if not file_exists(trna_lookup) or not file_exists(mintmap):
        logger.info("There is no tRNA annotation to run MINTmap.")
        return work_dir
    jar_folder = os.path.join(os.path.dirname(mintmap), "MINTplates")
    out_file = op.join(work_dir, name + "-MINTmap_v1-exclusive-tRFs.expression.txt")
    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} && {mintmap} -f {in_file} -p {name} "
                       "-l {trna_lookup} -s {trna_space} -j {jar_folder} "
                       "-o {trna_other}").format(**locals())
                do.run(cmd, "tRNA for %s" % name)
                for filename in glob.glob("*MINTmap*"):
                    shutil.move(filename, work_dir)
    return work_dir