organism

This section is auto-generated from the help text for the chakin command organism.

add_organism command

Usage:

chakin organism add_organism [OPTIONS] GENUS SPECIES COMMON ABBR

Help

Add a new organism to the Chado database

Output

Organism information

Options:

--comment TEXT  A comment / description
-h, --help      Show this message and exit.

delete_all_organisms command

Usage:

chakin organism delete_all_organisms [OPTIONS]

Help

Delete all organisms

Output

None

Options:

--confirm   Confirm that you really do want to delete ALL of the organisms.
-h, --help  Show this message and exit.

delete_organisms command

Usage:

chakin organism delete_organisms [OPTIONS]

Help

Delete all organisms

Output

None

Options:

--organism_id INTEGER  organism_id filter
--genus TEXT           genus filter
--species TEXT         species filter
--common TEXT          common filter
--abbr TEXT            abbr filter
--comment TEXT         comment filter
-h, --help             Show this message and exit.

get_organisms command

Usage:

chakin organism get_organisms [OPTIONS]

Help

Get all or some organisms

Output

Organisms information

Options:

--organism_id INTEGER  organism_id filter
--genus TEXT           genus filter
--species TEXT         species filter
--common TEXT          common filter
--abbr TEXT            abbr filter
--comment TEXT         comment filter
-h, --help             Show this message and exit.