diff --git a/propka/lib.py b/propka/lib.py index 8d2fc93..8f4d5c4 100644 --- a/propka/lib.py +++ b/propka/lib.py @@ -159,7 +159,6 @@ def build_parser(parser=None): group = parser group.add_argument("input_pdb", help="read data from ") - group.add_argument("-f", "--file", action="append", dest="filenames", default=[], help="read data from , i.e. is added to arguments") group.add_argument("-r", "--reference", dest="reference", default="neutral", @@ -186,10 +185,8 @@ def build_parser(parser=None): group.add_argument("-p", "--parameters", dest="parameters", default=pkg_resources.resource_filename(__name__, "propka.cfg"), help="set the parameter file [%(default)s]") - group.add_argument("-z", "--verbose", dest="verbosity", action="store_const", - const=2, help="output debugging information") - group.add_argument("-q", "--quiet", dest="verbosity", action="store_const", - const=0, default=1, help="inhibit printing to stdout") + group.add_argument("--log-level", choices=["DEBUG", "INFO", "WARNING", "ERROR", "CRITICAL"], + help="logging level verbosity", default="INFO") group.add_argument("-o", "--pH", dest="pH", type=float, default=7.0, help="setting pH-value used in e.g. stability calculations [7.0]") group.add_argument("-w", "--window", dest="window", nargs=3, type=float, @@ -262,14 +259,8 @@ def loadOptions(*args): # Set the no-print variable - if options.verbosity == 0: - logger.setLevel(logging.CRITICAL) - elif options.verbosity == 1: - logger.setLevel(logging.INFO) - elif options.verbosity == 2: - logger.setLevel(logging.DEBUG) - else: - logger.warning("Invalid verbosity level, using default") + level = getattr(logging, options.log_level) + logger.setLevel(level) # done! return options