chado-tools 0.1.0

Tools to access CHADO databases

chado-tools

Python3 command line script providing various tools for accessing CHADO databases

Prerequisites

• Python 3.6 or higher
• PostgreSQL 9.6 or higher
• SQLite (for testing only)

Installation from source

Download the latest release from this github repository, or clone the repository to obtain the most recent updates.

Modify the file with default connection settings such that it contains an existing PostgreSQL database to which you can connect. Note: This database is only used for housekeeping purposes, it will never be changed or removed by chado-tools. You can thus simply use one of the built-in PostgreSQL databases, such as postgres.

Then run the tests:

python3 setup.py test

If the tests all pass, install:

python3 setup.py install

Alternative installations

You can install the program from the Python Package Index (PyPI) using the command

pip install chado-tools

The program is also available as Bioconda package. Install it with the command

conda install -c bioconda chado-tools

Now change the default connection parameters by running chado init. You can always reset them to the original state by running chado reset.

Usage

The installation will put a single script called chado in your PATH. The usage is:

chado <command> [options]

• To list the available commands and brief descriptions, just run chado -h or chado --help.
• To display the version of the program, type chado -v or chado --version.
• Use chado <command> -h or chado <command> --help to get a detailed description and the usage of that command.

Available commands

---

Command	Description
init	set the default connection parameters
reset	reset the default connection parameters to factory settings
connect	connect to a CHADO database for an interactive session
create	create a new instance of the CHADO schema
dump	dump a CHADO database into an archive file
restore	restore a CHADO database from an archive file
query	query a CHADO database and export the result into a text file
stats	obtain statistics to updates in a CHADO database
list	list all entities of a specified type in the CHADO database
insert	insert a new entity of a specified type into the CHADO database
delete	delete an entity of a specified type from the CHADO database
import	import entities of a specified type into the CHADO database

---

Examples

Create a new CHADO database called eukaryotes according to the current GMOD schema:

chado create eukaryotes

Dump this database into an archive called eukaryotes.dump:

chado dump eukaryotes eukaryotes.dump

List all organisms in the eukaryotes database:

chado list organisms eukaryotes

Query the database to check the meaning of a certain cvterm_id:

chado query -q "SELECT name FROM cvterm WHERE cvterm_id = 25" eukaryotes

Note

Unless explicitly specified by the flag -c, all commands employ the default connection settings. You can change these by running chado init.