Function runShellCommand

src/python/Tools/bcftools.py:27–54

Run a shell command (e.g. bcf tools), and return output

(*args)

def runShellCommand(*args):
    """ Run a shell command (e.g. bcf tools), and return output
    """
    qargs = []
    for a in args:
        if a.strip() != "|":
            qargs.append(pipes.quote(a))
        else:
            qargs.append("|")

    cmd_line = " ".join(qargs)
    logging.info(cmd_line)

    po = subprocess.Popen(cmd_line,
                          shell=True,
                          stdout=subprocess.PIPE,
                          stderr=subprocess.PIPE)

    stdout, stderr = po.communicate()

    po.wait()

    return_code = po.returncode

    if return_code != 0:
        raise Exception("Command line {} got return code {}.\nSTDOUT: {}\nSTDERR: {}".format(cmd_line, return_code, stdout, stderr))

    return stdout


def runBcftools(*args):