chado-tools 0.0.4

Tools to access CHADO databases

# chado-tools

Python3 command line script providing various tools for accessing CHADO databases

[](https://travis-ci.org/sanger-pathogens/chado-tools)

## Prerequisites

* PostgreSQL
* Python 3.6 or higher

## Installation

Download the latest release from this github repository, or clone the repository.

Change the file with [default connection settings](pychado/data/defaultDatabase.yml) 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 `template0`.

Then run the tests:

python3 setup.py test

If the tests all pass, install:

python3 setup.py install

## 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 |
|-----------------------|----------------------------------------------------------------------|
| 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 |
| import | import data from a text file into a table of a CHADO database |
| export | export data from a table of a CHADO database into a text file |

## Examples

Create a new database called `insects` according to the current GMOD schema:

chado create insects

Dump this database into an archive called `insects.dump`:

chado dump insects insects.dump

## Note

Unless explicitly specified by the flag `-c`, all commands employ the [default connection settings](pychado/data/defaultDatabase.yml) also used to run the tests.