Metadata-Version: 2.1
Name: chado-tools
Version: 0.2.14
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)   
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        [![Docker Build Status](https://img.shields.io/docker/cloud/build/sangerpathogens/chado-tools.svg)](https://hub.docker.com/r/sangerpathogens/chado-tools)   
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        [![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)
            * [Using a Docker container](#using-a-docker-container)
          * [Usage](#usage)
            * [Database connection](#database-connection)
            * [Available commands](#available-commands)
            * [Examples](#examples)
            * [Note concerning tests](#note-concerning-tests)
          * [License](#license)
          * [Feedback/Issues](#feedback/issues)
        
        ## 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
        * 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.
        Then install the software:
        
            python3 setup.py install
        
        For running tests please see the [note](#note-concerning-tests) below.
        
        ### Using pip
        You can install the program from the [Python Package Index (PyPI)](https://pypi.org/project/chado-tools/) using the command
        
            pip install chado-tools
        
        ### Using Bioconda
        The program is also available as [Bioconda package](https://anaconda.org/bioconda/chado-tools). Install it with the command
        
            conda install -c bioconda chado-tools
        
        ### Using a Docker container
        The program is also available as a standalone Docker container. The latest build can be downloaded from [DockerHub](https://hub.docker.com/r/sangerpathogens/chado-tools) with the command
        
            docker pull sangerpathogens/chado-tools
        
        When running the container with Docker, use the flags `--interactive --tty` and map all required environment variables (see below) with flag `--env`.
        
        
        ## Usage
        The installation will put a single script called `chado` in your PATH.
        The usage is:
        
            chado <command> [<subcommand>] [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.
        
        ### Database connection
        You can set up default values for database host, port and user with environment variables. To do so, add the following 
        lines to your `.bashrc` (replacing the example values):
        
            export CHADO_HOST=localhost
            export CHADO_PORT=5432
            export CHADO_USER=chadouser
        
        The software seeks for these environment variables on your system. If they do not exist, it will use the 
        [default connection settings](pychado/data/defaultDatabase.yml), which you can edit manually if you really want.
        
        Analogously, you can specify a default password with the environment variable `CHADO_PASS`.
        The flag `-p` enforces asking the user for a password, which is useful if you don't want to store a default password in your environment.
        
        Alternatively, you can supply your own YAML configuration file in the same format as the [default file](pychado/data/defaultDatabase.yml)
        with flag `-c` (including password). The software will then ignore any environment variables. 
        
        
        ### Available commands
        
        ------------------------------------------------------------------------------------------------
        | Command               | Description                                                          |
        |-----------------------|----------------------------------------------------------------------|
        | 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
        
        Export a FASTA file containing the sequences of the organism `Pfalciparum`:
        
            chado export fasta -a Pfalciparum -o Pfalciparum.fasta -t contigs eukaryotes
        
        ### Note concerning tests
        Some of the integration tests rely on access to a PostgreSQL server. In order to successfully run those tests, 
        modify the [default connection settings](pychado/data/defaultDatabase.yml) such that they describe an existing 
        PostgreSQL database server to which you can connect. The tests can then be run as `python3 setup.py test`.
        They create temporary databases on that server and clean those up when finished, so this shouldn't interfere with
        anything you have stored in any database on that server. If you are concerned about this, though, make sure to point
        the tool to an empty test server.
        
        ## 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
