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MRG: fix argparse stuff in cluster command #245

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Feb 27, 2024
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MRG: fix argparse stuff in cluster command #245

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16 changes: 8 additions & 8 deletions src/python/sourmash_plugin_branchwater/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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)')

Expand All @@ -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}'")
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