Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Explicitly state default thresholds in help text #540

Merged
merged 1 commit into from
Sep 17, 2018
Merged

Explicitly state default thresholds in help text #540

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
9 changes: 5 additions & 4 deletions sourmash/commands.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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',
Expand Down Expand Up @@ -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)
Expand Down Expand Up @@ -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,
Expand Down Expand Up @@ -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)
Expand Down