bcbio_nextgen_install.py 文件源码

def _check_toolplus(x):
    """Parse options for adding non-standard/commercial tools like GATK and MuTecT.
    """
    import argparse
    Tool = collections.namedtuple("Tool", ["name", "fname"])
    std_choices = set(["data", "cadd", "dbnsfp"])
    if x in std_choices:
        return Tool(x, None)
    elif "=" in x and len(x.split("=")) == 2:
        name, fname = x.split("=")
        fname = os.path.normpath(os.path.realpath(fname))
        if not os.path.exists(fname):
            raise argparse.ArgumentTypeError("Unexpected --toolplus argument for %s. File does not exist: %s"
                                             % (name, fname))
        return Tool(name, fname)
    else:
        raise argparse.ArgumentTypeError("Unexpected --toolplus argument. Expect toolname=filename.")