Command model

EHItk commands have the form:

ehitk [global options] <resource> <action> [action options]

Resources

specimens: Host and specimen metadata. This resource supports fields, query, values, and stats.
hologenomes: Shotgun sequencing datasets linked to specimens. This resource supports fields, query, values, stats, and fetch.
mags: Metagenome-assembled genomes linked to parent hologenomes and host specimens. This resource supports fields, query, values, stats, and fetch.
database: Show the SQLite catalog currently used by EHItk: whether it is the bundled catalog or an alternate catalog passed with --db, its path, size, SHA256 checksum, and its data_version / schema_version (unknown for older catalogs built before this metadata existed).

fields: Lists the field names accepted by values --field, including aliases and the canonical field each alias resolves to.
query: Prints matching records as a rich table by default, or emits CSV/TSV to standard output or --output-file.
values: Counts distinct values for one field after applying the same filters used by query.
stats: Prints a compact summary of a filtered subset.
fetch: Downloads files for matching hologenomes or MAGs, or writes a batch shell script with curl commands.

--version: Show the installed EHItk version and exit.
--db PATH: Use an alternate SQLite catalog instead of the bundled database.

All command levels include help text:

ehitk --help
ehitk specimens --help
ehitk hologenomes --help
ehitk mags --help
ehitk mags query --help