Metadata-Version: 2.1
Name: ddrage
Version: 1.8.0
Summary: Simulator for ddRADseq (double digest restriction site associated DNA sequencing) datasets. Generates reads (FASTQ format) that can be analyzed and validated using a ground truth file (YAML).
Author-email: Henning Timm <henning.timm@uni-due.de>
License: The MIT License (MIT)
        
        Copyright (c) 2016 Henning Timm
        
        Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
        
        The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
        
        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
        
Project-URL: Homepage, https://ddrage.readthedocs.io/en/latest/
Project-URL: Documentation, https://ddrage.readthedocs.io/en/latest/
Project-URL: Repository, https://bitbucket.org/genomeinformatics/rage
Project-URL: Bug Tracker, https://bitbucket.org/genomeinformatics/rage/issues
Project-URL: Changelog, https://ddrage.readthedocs.io/en/latest/changelog/
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
Description-Content-Type: text/x-rst
License-File: LICENSE.rst
Requires-Dist: numpy
Requires-Dist: numba
Requires-Dist: matplotlib
Requires-Dist: seaborn
Requires-Dist: scipy>=1.4.1
Requires-Dist: pyyaml
Requires-Dist: dinopy
Provides-Extra: bbd-visualization
Requires-Dist: bokeh; extra == "bbd-visualization"
Provides-Extra: documentation
Requires-Dist: sphinx>=1.5.0; extra == "documentation"

.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.4390216.svg 
   :target: https://doi.org/10.5281/zenodo.4390216

#############################
ddRAGE - ddRAD Data Generator
#############################


ddRAGE (ddRAD Data Generator) is a software to simulate double digest restriction site associated DNA sequencing reads.
The generated data sets can be used to test ddRAD analysis tools and validate their results.

The documentation, including a tutorial, can be found `here <https://ddrage.readthedocs.io/>`_.
The code is hosted on `bitbucket`_, `PyPI`_, and `bioconda`_.

.. _bitbucket: https://bitbucket.org/genomeinformatics/rage
.. _PyPI: https://pypi.python.org/pypi/ddrage/
.. _bioconda: https://bioconda.github.io/recipes/ddrage/README.html


*******************
System Requirements
*******************

- python >= 3.8
- numba
- numpy
- matplotlib
- pyyaml
- scipy
- seaborn


For the docs:

- sphinx

For parameter visualization:

- bokeh


************
Installation
************

We recommend the installation using conda:

.. code-block:: shell

   $ conda create -n ddrage -c bioconda ddrage
   $ source activate ddrage

Alternatively, you can download the source code from `bitbucket`_ and install it using pip:

.. code-block:: shell

   $ git clone https://bitbucket.org/genomeinformatics/rage.git ddrage
   $ cd ddrage
   /ddrage$ pip install .  # basic version
   # OR
   # to install with support to build the documentation and visualize bbd parameters
   /ddrage$ pip install .[documentation,BBD-visualization]


*****
Usage
*****

To simulate a ddRAD data set, call ddrage from the command line:

.. code-block:: shell

   $ ddrage

you can specify parameters to change data set parameters such as number of individuals (``-n``), nr of loci (``-l``), and coverage (``--coverage``):

.. code-block:: shell

   $ ddrage -n 6 -l 10000 --coverage 30

This creates a data set with reads from 6 individuals at 10000 loci with an expected coverage of 30.

A more detailed tutorial can be found `on readthedocs <https://ddrage.readthedocs.io/en/latest/getting-started/>`_.


*************
Citing ddRAGE
*************

Our paper describing ddRAGE has been published in `Molecular Ecology Resources <http://onlinelibrary.wiley.com/doi/10.1111/1755-0998.12743/full>`_.
You can cite it as follows:

.. code-block::

    Timm H, Weigand H, Weiss M, Leese F, Rahmann S. ddRAGE: A data set generator to evaluate ddRADseq analysis software. Mol Ecol Resour. 2018;18:681–690. https://doi.org/10.1111/1755-0998.12743

BibTeX version:

.. code-block:: latex

    @article{timm2018ddrage,
      title={ddrage: A data set generator to evaluate ddRADseq analysis software},
      author={Timm, Henning and Weigand, Hannah and Weiss, Martina and Leese, Florian and Rahmann, Sven},
      journal={Molecular Ecology Resources},
      volume={18},
      number={3},
      pages={681--690},
      year={2018},
      url = {http://dx.doi.org/10.1111/1755-0998.12743},
      doi = {10.1111/1755-0998.12743},
    }

The source code itself is also published on `Zenodo <https://zenodo.org>`_ under the DOI `10.5281/zenodo.4390216 <https://doi.org/10.5281/zenodo.4390216>`_.
