From 4e2d43bb1f3e480a44704e8c04c8f96bd0fa2cdf Mon Sep 17 00:00:00 2001 From: "N. Tessa Pierce" Date: Wed, 27 Apr 2022 11:46:01 -0700 Subject: [PATCH] tax threshold arg from #1788 --- src/sourmash/cli/utils.py | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/src/sourmash/cli/utils.py b/src/sourmash/cli/utils.py index 1725518747..2063fd09de 100644 --- a/src/sourmash/cli/utils.py +++ b/src/sourmash/cli/utils.py @@ -67,10 +67,14 @@ def range_limited_float_type(arg): return f -def add_tax_threshold_arg(parser, default=0.1): +def add_tax_threshold_arg(parser, containment_default=0.1, ani_default=None): parser.add_argument( - '--containment-threshold', default=default, type=range_limited_float_type, - help=f'minimum containment threshold for classification; default={default}' + '--containment-threshold', default=containment_default, type=range_limited_float_type, + help=f'minimum containment threshold for classification; default={containment_default}', + ) + parser.add_argument( + '--ani-threshold', '--aai-threshold', default=ani_default, type=range_limited_float_type, + help=f'minimum ANI threshold (nucleotide gather) or AAI threshold (protein gather) for classification; default={ani_default}', )