OGSync sub commands

OGSync home

Open the OGSync Home Page and exit

OGSync.py home

arguments

argument	description
`-h`, `--help`	show this help message and exit
`--debug`	display debug info, for developers only

source

oglib/og_home_impl.py

OGSync init

Setup the local OGSync database in MongoDB

OGSync init [option]

arguments

argument	description
`-h`, `--help`	show this help message and exit
`-r`, `--reinstall`	force to reset the database. NOTE: THIS OPERATION WILL EMPTY THE DATABASE!!
`--debug`	display debug info, for developers only

source

oglib/og_init_impl.py

OGSync update

Sync the local OGSync list with NCBI Organelle Genome database

OGSync update [options]

arguments

argument	description
`-h`, `--help`	show this help message and exit
`-d`, `--show-diff`	if show the difference of the genome list between current and latest, False by default
`--debug`	display debug info, for developers only

source

oglib/og_update_impl.py

OGSync config

Configurate and customize OGSync.

OGSync config [options]

arguments

argument	description
-h, –help	show this help message and exit
–get {NCBI_API_KEY}	get the config parameters
–set SET	set the config parameters, in json format
–debug	display debug info, for developers only, in json format

optional config

argument	description
NCBI_API_KEY	api key for NCBI E-utilities, see this

For example, use these commands to get/set NCBI_API_KEY. Use OGSync config --get NCBI_API_KEY to get config value Use OGSync config --set '{"NCBI_API_KEY"}':"xxx"' to set config value

source

oglib/og_config_impl.py

OGSync add

Add Organelle Genomes into local database and sync with NCBI

OGSync add refSeq1[,refSeq2,...] [options]

arguments

argument	description
`refSeq`	REQUIRED. the refSeq code of the Organelle Genome in the database, NCNumber or INSDC.
`-h`, `--help`	show this help message and exit
`-f`, `--force-upgrade`	if force to upgrade the local data, False by default
`--debug`	display debug info, for developers only

source

oglib/og_add_impl.py

OGSync remove

Remove Organelle Genomes from local database

OGSync remove refSeq1[,refSeq2,...] [options]

arguments

argument	description
`refSeq`	REQUIRED. the refSeq code of the Organelle Genome in the database, NCNumber or INSDC.
`-h`, `--help`	show this help message and exit
`--debug`	display debug info, for developers only

source

oglib/og_remove_impl.py

OGSync list

List Organelle Genomes in local/remote database

OGSync list [options]

arguments

argument	description
`-h`, `--help`	show this help message and exit
`-r`, `--remote`	List Organelle Genomes in remote database, False by default.
`-l`, `--list-RefSeq-only`	List the RefSeq for Organelle Genomes, False by default
`-j`, `--output-json`	Output in json format, False by default
`--debug`	display debug info, for developers only

source

oglib/og_list_impl.py

OGSync show

Show Organelle Genomes in the local database into tree/json view.

OGSync show refSeq infoType [options]

info type

Currently, OGSync provides four types

type	description
general	show the general information of the genome, such as name, id, description and etc.
sequence	show the nucleatide sequence of the genome.
annotations	show the annotations of the genome, such as molecule_type, taxonomy, source and etc.
features	show the features of the genome, including the qualifier info.

arguments

argument	description
`refSeq`	REQUIRED. the refSeq code of the Organelle Genome in the database, NCNumber or INSDC.
`infoType`	REQUIRED. the type of info to show.
`-h`, `--help`	show this help message and exit
`-j`, `--output-json`	Output in json format, False by default
`--debug`	display debug info, for developers only

source

oglib/og_show_impl.py