From b6f7bcdc52e91ee82c793c6a6e8a019242621d35 Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Tue, 27 Feb 2024 06:27:22 -0800 Subject: [PATCH] fix misc argparse things --- .../sourmash_plugin_branchwater/__init__.py | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/src/python/sourmash_plugin_branchwater/__init__.py b/src/python/sourmash_plugin_branchwater/__init__.py index 5e50a1af..50dbedd5 100755 --- a/src/python/sourmash_plugin_branchwater/__init__.py +++ b/src/python/sourmash_plugin_branchwater/__init__.py @@ -372,10 +372,10 @@ def __init__(self, p): help='output csv file for the clusters') p.add_argument('--cluster-sizes', required=True, help='output file for the cluster size histogram') - p.add_argument('--similarity-column', type=str, default='average_ani', - choices=['containment', 'max_containment', 'jaccard', 'average_containment_ani', 'max_containment_ani'], - help='column to use as distance measure') - p.add_argument('-t', '--threshold', type=float, default=0.95, help="similarity threshold for clustering. Default: 95% ANI (0.95)") + p.add_argument('--similarity-column', type=str, default='average_containment_ani', + choices=['containment', 'max_containment', 'jaccard', 'average_containment_ani', 'max_containment_ani'], + help='column to use as distance measure') + p.add_argument('-t', '--threshold', type=float, default=0.95, help="similarity threshold for clustering. Default: 95%% ANI (0.95)") p.add_argument('-c', '--cores', default=0, type=int, help='number of cores to use (default is all available)') @@ -388,10 +388,10 @@ def main(self, args): super().main(args) status = sourmash_plugin_branchwater.do_cluster(args.pairwise_csv, - args.output, - args.cluster_sizes, - args.similarity_column, - args.threshold) + args.output, + args.cluster_sizes, + args.similarity_column, + args.threshold) if status == 0: notify(f"...clustering is done! results in '{args.output}'") notify(f" cluster counts in '{args.cluster_sizes}'")