From df8fedf86073a2e8d5e1a0e1e9cd2f321920ef4e Mon Sep 17 00:00:00 2001 From: Olga Botvinnik Date: Thu, 13 Sep 2018 15:52:43 -0700 Subject: [PATCH] Explicitly state default thresholds in help text --- sourmash/commands.py | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/sourmash/commands.py b/sourmash/commands.py index ddee5ac411..feb065e8af 100644 --- a/sourmash/commands.py +++ b/sourmash/commands.py @@ -735,7 +735,7 @@ def search(args): parser.add_argument('-q', '--quiet', action='store_true', help='suppress non-error output') parser.add_argument('--threshold', default=0.08, type=float, - help='minimum threshold for reporting matches') + help='minimum threshold for reporting matches (default=0.08)') parser.add_argument('--save-matches', type=argparse.FileType('wt'), help='output matching signatures to this file.') parser.add_argument('--best-only', action='store_true', @@ -836,7 +836,8 @@ def categorize(args): parser.add_argument('-q', '--quiet', action='store_true', help='suppress non-error output') parser.add_argument('-k', '--ksize', type=int, default=None) - parser.add_argument('--threshold', default=0.08, type=float) + parser.add_argument('--threshold', default=0.08, type=float, + help='minimum threshold for reporting matches (default=0.08)') parser.add_argument('--traverse-directory', action="store_true") sourmash_args.add_moltype_args(parser) @@ -917,7 +918,7 @@ def gather(args): parser.add_argument('--save-matches', type=argparse.FileType('wt'), help='save the matched signatures from the database to this file.') parser.add_argument('--threshold-bp', type=float, default=5e4, - help='threshold (in bp) for reporting results') + help='threshold (in bp) for reporting results (default=50,000)') parser.add_argument('--output-unassigned', type=argparse.FileType('wt'), help='output unassigned portions of the query as a signature to this file') parser.add_argument('--scaled', type=float, default=0, @@ -1057,7 +1058,7 @@ def watch(args): parser.add_argument('-o', '--output', type=argparse.FileType('wt'), help='save signature generated from data here') parser.add_argument('--threshold', default=0.05, type=float, - help='minimum threshold for matches') + help='minimum threshold for matches (default=0.05)') parser.add_argument('--input-is-protein', action='store_true', help='Consume protein sequences - no translation needed') sourmash_args.add_construct_moltype_args(parser)