unword consonants as list #322
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Nice - took me a while to understand the cluster merging, but looks good - sorry for not spotting this needed a review earlier. Is it worth addding a test for the fast pruning mode? Also based on the current CI tests it looks like the extractReferences call in __main__ is missing a merged_queries argument.
| @@ -47,7 +47,7 @@ def get_options(): | |||
| '[default = 0]', default=0, type=int) | |||
| oGroup.add_argument('--write-references', help='Write reference database isolates\' cluster assignments out too', | |||
| default=False, action='store_true') | |||
| oGroup.add_argument('--update-db', help='Update reference database with query sequences', default=False, action='store_true') | |||
| oGroup.add_argument('--update-db', help='Update reference database with query sequences', default=False, choices=['full', 'fast', False]) | |||
| oGroup.add_argument('--overwrite', help='Overwrite any existing database files', default=False, action='store_true') | |||
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Should this help change with the new options?
| @@ -279,7 +317,8 @@ def extractReferences(G, dbOrder, outPrefix, outSuffix = '', type_isolate = None | |||
| sys.exit(1) | |||
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| if use_gpu: | |||
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| if fast_mode: | |||
| raise RuntimeError("GPU graphs not yet supported with --update-db fast") | |||
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This shouldn't be hard to implement in principle, but maybe we can create a general issue for a network.py update (including the function structures identified in #328) and work out the most efficient way to get this working across all modes clearly?
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Fixes #321