pyani report

The report subcommand reports the contents of a local SQLite3 database, located at dbpath. Output files will be written to the outdir directory.

usage: pyani report [-h] [-l LOGFILE] [-v] [–debug] [–disable_tqdm] [–version]

[–citation] -o OUTDIR [–dbpath DBPATH] [–runs] [–genomes] [–runs_genomes] [–genomes_runs] [–run_results RUN_ID [RUN_ID …]] [–run_matrices RUN_ID [RUN_ID …]] [–no_matrix_labels] [–formats FORMAT [FORMAT …]]

Flagged arguments

--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 report process runs. This is useful when testing to avoid aesthetic problems with test output.

--formats FORMAT [FORMAT ...]

Space-separated list of output formats (in addition to .tab); possible values: {html, excel,stdout}. (default: None)

--genomes

Report table of genomes in database. (default: False)

--genomes_runs

Report table of all runs in which each genome in the database participates. (default: False)

--no_matrix_labels

Turn off row/column labels in output matrix files (default: False)

-o OUTDIR, --outdir OUTDIR

Directory where output analysis reports will be written.

--runs

Report table of analysis runs in database. (default: False)

--runs_genomes

Report table of all genomes for each run in database. (default: False)

--run_matrices RUN_ID [RUN_ID ...]

Report matrices of results for space-separated list of runs. (default: None)

--run_results RUN_ID [RUN_ID ...]

Report table of results for space-separated list of runs. (default: None)

-v, --verbose

Provide verbose output to STDOUT.