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.