Output formats

atb supports several output formats for query results; the default adapts to whether you are writing to a terminal or a pipe.

By default, output is a pretty table when writing to a terminal, and TSV when piped. Override with --format:

atb query --species "Escherichia coli" --limit 5 --format tsv     # tab-separated
atb query --species "Escherichia coli" --limit 5 --format csv     # comma-separated
atb query --species "Escherichia coli" --limit 5 --format json    # JSON array
atb query --species "Escherichia coli" --limit 5 --format table   # pretty table

When writing to a file with -o, the format is inferred from the filename if --format is not given (.csv -> csv, .tsv -> tsv, .json -> json). Append .gz to any of these and the output is gzipped on the fly:

atb query --species "Escherichia coli" --hq-only -o results.csv.gz   # gzipped CSV
atb amr   --species "Escherichia coli" --hq-only -o ecoli_amr.tsv.gz # gzipped TSV

See also: Available columns for the full list of fields that can appear in query output.