Ejemplos de R_package_path en Python

Ejemplo n.º 1

Archivo: sailfish.py Proyecto: dlorson/bcbio-nextgen

def _sleuthify_sailfish(sailfish_dir):
    """
    if installed, use wasabi to create abundance.h5 output for use with
    sleuth
    """
    if not R_package_path("wasabi"):
        return None
    else:
        rscript = Rscript_cmd()
        cmd = """{rscript} -e 'library("wasabi"); prepare_fish_for_sleuth(c("{sailfish_dir}"))'"""
        do.run(cmd.format(**locals()), "Converting Sailfish to Sleuth format.")
    return os.path.join(sailfish_dir, "abundance.h5")

Ejemplo n.º 2

Archivo: dexseq.py Proyecto: olingerc/bcbio-nextgen

def _dexseq_count_path():
    package_path = R_package_path("DEXSeq")
    if not package_path:
        return None
    return os.path.join(package_path, "python_scripts", "dexseq_count.py")