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: pyani.py 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_tqdm

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.

--show_all

Report all intervals in log. (default: only intervals where all subgraphs are k-complete) (default: False)

-v, --verbose

Provide verbose output to STDOUT.