Outputs and columns

Tables, CSV, and TSV

By default, query and values commands print rich terminal tables.

Use --csv or --tsv to print delimited output to standard output. This supports shell pipelines:

ehitk specimens query --host-lineage Reptilia --csv
ehitk hologenomes values --field country --tsv | head

Add --output-file to write the CSV or TSV output to a file instead:

ehitk specimens query --host-lineage Reptilia --csv --output-file specimens.csv
ehitk hologenomes values --field country --tsv --output-file countries.tsv
ehitk mags query --quality high --columns mag_id,quality,url --csv --output-file high-quality-mags.csv

Use only one export format at a time.

Query column presets

All query commands support --columns.

--columns default

Use the compact default column set for the resource. This is also the behavior when --columns is omitted.

--columns all

Include every available query column for the resource.

--columns url

Include URL-focused columns. This preset is available for hologenomes and mags.

--columns a,b,c

Include only the named columns.

Examples:

ehitk specimens query --columns specimen_id,host_species,sex
ehitk hologenomes query --columns url --csv --output-file hologenome-urls.csv
ehitk mags query --columns all --limit 1
ehitk mags query --columns url --tsv --output-file mag-urls.tsv

Default columns

specimens

specimen_id, host_taxid, host_species, host_order, sex.

hologenomes

hologenome_id, specimen_id, sample_type, host_species, biome_envo_id, biome_name, data_gb.

mags

mag_id, host_taxid, host_species, host_genus, host_family, quality, completeness, contamination, mag_family, mag_genus, mag_species.

Identifier namespaces

Identifier columns keep their original namespace. EHI catalog identifiers such as specimen_id, hologenome_id, and mag_id resolve inside the EHItk catalog; host_taxid values resolve in NCBI Taxonomy; and biome_envo_id values resolve in ENVO. See Identifier namespaces for the full field-by-field list and resolver examples.

Value fields and counts

The fields action lists the names accepted by values --field:

ehitk specimens fields
ehitk hologenomes fields
ehitk mags fields --csv

The values action counts distinct values for any listed field:

ehitk specimens values --field host_order
ehitk hologenomes values --field biome_name
ehitk hologenomes values --field data_gb
ehitk mags values --field genus

For MAGs, genus and species are aliases for mag_genus and mag_species. quality is a derived field.

Statistics

The stats action prints summaries after applying filters. Hologenome and MAG statistics include available hologenome data volume in gigabases.