summarise

atb summarise

Print summary statistics for the ATB database

Synopsis

Print summary statistics for the ATB database.

By default prints total counts, HQ fraction, top species, and dataset breakdown for assemblies actually published on OSF (asm_fasta_on_osf == 1). To include unprocessed or rejected samples, run an unfiltered query and pipe it in:

atb query --format csv | atb summarise --from -

Use --by to group results by a specific column (e.g. --by sylph_species).

atb summarise [flags]

Examples

  # Default summary of the full database
  atb summarise

  # Group by species (top 20)
  atb summarise --by sylph_species --top 20

  # Summarise a previous query result
  atb summarise --from salmonella.tsv

  # Pipe query to summarise
  atb query --genus Salmonella --hq-only --limit 100 --format csv | atb summarise --from -

Options

      --by strings    group results by column(s) (e.g. --by sylph_species)
      --from string   read rows from a CSV/TSV query result file (use "-" for stdin)
  -h, --help          help for summarise
      --top int       number of top entries to show per group (default 10)

Options inherited from parent commands

      --config string     config file (default $HOME/.atb/config.toml)
      --data-dir string   directory for the local metadata index (default ~/.local/share/atb/data; override with $ATB_DATA_DIR)

SEE ALSO

• atb - Query and download AllTheBacteria genomes