pyani classify

The classify subcommand identifies cliques (k-complete) graphs of genomes from a larger set. This is helpful for circumscribing potentially meaningful groups of genomes that can not be described using traditional taxonomy.

usage: classify [-h] [-l LOGFILE] [-v] [--debug] [--disable_tqdm]
                     [--version] [--citation] -o OUTDIR --run_id RUN_ID
                     [--dbpath DBPATH] [--cov_min COV_MIN] [--id_min ID_MIN]
                     [--min_id MIN_ID] [--max_id MAX_ID]
                     [--resolution RESOLUTION] [--show_all]

Flagged arguments

--cov_min COV_MIN
Minimum percent coverage required to draw an edge between two nodes (genomes). (default: 0.5)
--dbpath DBPATH
Path to the location of the local pyani database to be used. Default: .pyani/pyanidb
Disable the tqdm progress bar while the download process runs. This is useful when testing to avoid aesthetic problems with test output. (default: False)
--formats FORMATS
Graphics output format(s); more than one can be specified. Valid options are: (pdf/png/svg/jpg). (default: png)
--id_min ID_MIN
Minimum percent identity required to draw an edge between two nodes (genomes). (default: 0.8)
-l LOGFILE, --logfile LOGFILE
Provide the location LOGFILE to which a logfile of the download process will be written.
--max_id MAX_ID
Maximum identity threshold to test. (default: None)
--method {seaborn,mpl,plotly}
Graphics method to use for plotting. (default: seaborn)
--min_id MIN_ID
Minimum identity threshold to test. (default: None)
-o OUTDIR, --outdir OUTDIR
Path to a directory where comparison output files will be written.
--resolution RESOLUTION
Number of identity thresholds to test. (default: 0.0001)
--run_id RUN_ID
Unique database ID of the run to be plotted.
Report all intervals in log. (default: only intervals where all subgraphs are k-complete) (default: False)
-v, --verbose
Provide verbose output to STDOUT.