Metadata-Version: 2.1
Name: chado-tools
Version: 0.2.10
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)   
        [![License: GPL v3](https://img.shields.io/badge/License-GPL%20v3-brightgreen.svg)](https://github.com/sanger-pathogens/chado-tools/blob/master/LICENSE)   
        [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat-square)](http://bioconda.github.io/recipes/chado-tools/README.html)   
        [![Container ready](https://img.shields.io/badge/container-ready-brightgreen.svg)](https://quay.io/repository/biocontainers/chado-tools)   
        [![codecov](https://codecov.io/gh/sanger-pathogens/chado-tools/branch/master/graph/badge.svg)](https://codecov.io/gh/sanger-pathogens/chado-tools)
        
        ## Contents
          * [Installation](#installation)
            * [Required dependencies](#required-dependencies)
            * [From source](#from-source)
            * [Using pip](#using-pip)
            * [Using Bioconda](#using-bioconda)
          * [Usage](#usage)
            * [Available commands](#available-commands)
            * [Examples](#examples)
            * [Note](#note)
          * [License](#license)
          * [Feedback/Issues](#feedbackissues)
        
        ## Installation
        
        There are a number of ways to install chado-tools and details are provided below. If you encounter an issue when installing chado-tools please contact your local system administrator. If you encounter a bug please log it [here](https://github.com/sanger-pathogens/chado-tools/issues) or email us at path-help@sanger.ac.uk.
        
        ### Required dependencies
        
        * Python 3.6 or higher
        * PostgreSQL 9.6 or higher
        
        ### 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 the settings for an existing PostgreSQL database server to which you can connect.
        
        Then run the tests:
        
            python3 setup.py test
        
        If the tests all pass, install:
        
            python3 setup.py install
        
        ### Using pip
        
        You can install the program from the *Python Package Index (PyPI)* using the command
        
            pip install 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`.
        
        ### Using Bioconda
        
        The program is also available as *Bioconda* package. Install it with the command
        
            conda install -c bioconda chado-tools
        
        ## 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               |
        | query                 | query a CHADO database and export the result into a text file        |
        | execute               | execute a function defined in a CHADO database                       |
        | extract               | run a pre-compiled query against 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 data from file into the CHADO database                        |
        | export                | export data from the CHADO database to file                          |
        | admin                 | perform admin tasks, such as creating or dumping a CHADO database    |
        ------------------------------------------------------------------------------------------------
        
        ### Examples
        
        Create a new CHADO database called `eukaryotes` according to the current GMOD schema:
        
            chado admin create eukaryotes
            chado admin setup -s gmod eukaryotes
            
        Dump this database into an archive called `eukaryotes.dump`:
        
            chado admin dump eukaryotes eukaryotes.dump
        
        List all organisms in the `eukaryotes` database:
        
            chado extract 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`.
        
        ## License
        chado-tools is free software, licensed under [GPLv3](https://github.com/sanger-pathogens/chado-tools/blob/master/LICENSE).
        
        ## Feedback/Issues
        Please report any issues to the [issues page](https://github.com/sanger-pathogens/chado-tools/issues) or email path-help@sanger.ac.uk.
        
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 :: 3 - Alpha
Description-Content-Type: text/markdown
