OGSync’s Documentation

How to use

Begin with OGSync CLI

The PATH for OGSync in the docker container is pre-configured, and user can just type OGSync to start.

Get Help

You can type -h/--help after any command to get the help info:

root@mst:/opt/OGSync# OGSync --help
usage: OGSync [-h] [-v] {home,init,add,remove,update,config,list,show} ...

optional arguments:
  -h, --help            show this help message and exit
  -v, --version         show OGSync version number and exit

avaiable commands:
  {home,init,add,remove,update,config,list,show}
    home                Display OGSync Homepage info and exit
    init                Initialize the local OGSync database
    add                 Add Organelle Genomes into local database and sync with NCBI
    remove              Remove Organelle Genomes from local database
    update              Sync the local OGSync list with NCBI Organelle Genome database
    config              Configurate and customize OGSync
    list                List Organelle Genomes in local/remote database
    show                Show detailed info of Organelle Genomes in the local database

Check OGSync Version

Use OGSync -v or OGSync --version to see the version info.

root@mst:/opt/OGSync# OGSync --version
OGSync 0.1.0

Sub commands

Currently, OGSync provides 8 sub commands:

Sub command	Description
home	Display OGSync Homepage info and exit
init	Initialize the local OGSync database
add	Add Organelle Genomes into local database and sync with NCBI
remove	Remove Organelle Genomes from local database
update	Sync the local OGSync list with NCBI Organelle Genome database
config	Configurate and customize OGSync
list	List Organelle Genomes in local/remote database
show	Show detailed info of Organelle Genomes in the local database

For Developers

Trouble Shooting

OGSync provide -d/--debug option as a global argument, and it turns on a verbose log for troubleshooting.

For example, when use update sub command, it will display a progress bar while updating, such as:

root@mst:/opt/OGSync# OGSync update
Syncing with NCBI database.
Updating: (23343/23343) 100% |▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒| Elapsed Time: 0:00:10 Time: 0:00:10
OGSync is updated: 0 Oganelle Genomes are updated.

--debug will show a more detailed update progress, which normally consume more time, such as:

root@mst:/opt/OGSync# OGSync update --debug
DEBUG MODE is set ON by options: {'show_diff': False, 'debug': True, 'callback': <function run_update_command at 0xffffa24ba040>}
Syncing with NCBI database.
Connecting to local database.
Re-formating dataset.
Updating the Organelle Genome List.
Updating: (23343/23343) 100% |▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒| Elapsed Time: 0:00:11 Time: 0:00:11
OGSync is updated: 0 Oganelle Genomes are updated.
23344  were up-to-date and not modified.

OGSync API

Developers can use OGSync as a service by adding -j/--json argument.

For example, when use show sub command, it will display a tree view in terminal, such as:

root@mst:/opt/OGSync# OGSync show NC_048988.1 general
general
├─ id: NC_048988.1
├─ name: NC_048988
├─ description: Abbottina binhi isolate AB-PEx-PiG01 mitochondrion, complete genome
├─ dbxrefs
│  └─ 0: BioProject:PRJNA642447
└─ main_feature
   ├─ location
   │  └─ FeatureLocation
   │     ├─ _start: 0
   │     ├─ _end: 16609
   │     ├─ _strand: 1
   │     ├─ ref: None
   │     └─ ref_db: None
   ├─ type: source
   ├─ id: <unknown id>
   └─ qualifiers
      ├─ organism
      │  └─ 0: Abbottina binhi
      ├─ organelle
      │  └─ 0: mitochondrion
      ├─ mol_type
      │  └─ 0: genomic DNA
      ├─ isolate
      │  └─ 0: AB-PEx-PiG01
      ├─ db_xref
      │  └─ 0: taxon:2745886
      └─ country
         └─ 0: China: Pingguo, Guangxi province

-j will parse the result as json string, which is more flexible for further development, such as:

root@mst:/opt/OGSync# OGSync show NC_048988.1 general -j
general
{
  "id": "NC_048988.1",
  "name": "NC_048988",
  "description": "Abbottina binhi isolate AB-PEx-PiG01 mitochondrion, complete genome",
  "dbxrefs": [
    "BioProject:PRJNA642447"
  ],
  "main_feature": {
    "location": {
      "FeatureLocation": {
        "_start": 0,
        "_end": 16609,
        "_strand": 1,
        "ref": null,
        "ref_db": null
      }
    },
    "type": "source",
    "id": "<unknown id>",
    "qualifiers": {
      "organism": [
        "Abbottina binhi"
      ],
      "organelle": [
        "mitochondrion"
      ],
      "mol_type": [
        "genomic DNA"
      ],
      "isolate": [
        "AB-PEx-PiG01"
      ],
      "db_xref": [
        "taxon:2745886"
      ],
      "country": [
        "China: Pingguo, Guangxi province"
      ]
    }
  }
}