Metadata-Version: 2.1
Name: chado-tools
Version: 0.1.0
Summary: Tools to access CHADO databases
Home-page: https://github.com/sanger-pathogens/chado-tools/
Author: Christoph Puethe
Author-email: path-help@sanger.ac.uk
License: GPLv3
Description: # chado-tools
        
        Python3 command line script providing various tools for accessing CHADO databases
        
        [![Build Status](https://travis-ci.org/sanger-pathogens/chado-tools.svg?branch=master)](https://travis-ci.org/sanger-pathogens/chado-tools)
        
        ## 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](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 `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](pychado/data/defaultDatabase.yml).
        You can change these by running `chado init`.
        
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Operating System :: OS Independent
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Development Status :: 2 - Pre-Alpha
Description-Content-Type: text/markdown
