organisms

This section is auto-generated from the help text for the arrow command organisms.

add_organism command

Usage:

arrow organisms add_organism [OPTIONS] COMMON_NAME DIRECTORY

Help

Add an organism

Output

a dictionary with information about the new organism

Options:

--blatdb TEXT      Server-side path to 2bit index of the genome for Blat
--genus TEXT       Genus
--species TEXT     Species
--public           Should the organism be public or not
--metadata TEXT    JSON formatted arbitrary metadata
--suppress_output  Suppress output of all organisms (true / false) (default
                   false)

-h, --help         Show this message and exit.

delete_features command

Usage:

arrow organisms delete_features [OPTIONS] ORGANISM_ID

Help

Remove features of an organism

Output

an empty dictionary

Options:

-h, --help  Show this message and exit.

delete_organism command

Usage:

arrow organisms delete_organism [OPTIONS] ORGANISM_ID

Help

Delete an organism

Output

A list of all remaining organisms

Options:

--suppress_output  Suppress return of all organisms (true / false) (default
                   false)

-h, --help         Show this message and exit.

get_organism_creator command

Usage:

arrow organisms get_organism_creator [OPTIONS] ORGANISM_ID

Help

Get the creator of an organism

Output

a dictionary containing user information

Options:

-h, --help  Show this message and exit.

get_organisms command

Usage:

arrow organisms get_organisms [OPTIONS]

Help

Get all organisms

Output

Organism information

Options:

--common_name TEXT  Optionally filter on common name
-h, --help          Show this message and exit.

get_sequences command

Usage:

arrow organisms get_sequences [OPTIONS] ORGANISM_ID

Help

Get the sequences for an organism

Output

The set of sequences associated with an organism

Options:

-h, --help  Show this message and exit.

show_organism command

Usage:

arrow organisms show_organism [OPTIONS] COMMON_NAME

Help

Get information about a specific organism.

Output

a dictionary containing the organism’s information

Options:

-h, --help  Show this message and exit.

update_metadata command

Usage:

arrow organisms update_metadata [OPTIONS] ORGANISM_ID METADATA

Help

Update the metadata for an existing organism.

Output

An empty, useless dictionary

Options:

-h, --help  Show this message and exit.

update_organism command

Usage:

arrow organisms update_organism [OPTIONS] ORGANISM_ID COMMON_NAME

Help

Update an organism

Output

a dictionary with information about the updated organism

Options:

--blatdb TEXT          Server-side Blat directory for the organism
--species TEXT         Species
--genus TEXT           Genus
--public               User's email
--no_reload_sequences  Set this if you don't want Apollo to reload genome
                       sequences (no change in genome sequence)

--suppress_output      Suppress output of all organisms (true / false)
                       (default false)

-h, --help             Show this message and exit.