Metadata-Version: 2.0
Name: ddrage
Version: 1.1.2
Summary: Simulator for ddRADseq (double digest restriction site associdated DNA squencing) datasets. Generates reads (FASTQ format) that can be analyzed and validated using a ground truth file (YAML).
Home-page: https://bitbucket.org/genomeinformatics/rage
Author: Henning Timm
Author-email: henning.timm@uni-due.de
License: MIT
Platform: UNKNOWN
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 :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
Requires-Dist: matplotlib
Requires-Dist: numba
Requires-Dist: numpy
Requires-Dist: pyyaml
Requires-Dist: scipy
Provides-Extra: BBD-visualization
Requires-Dist: bokeh; extra == 'BBD-visualization'
Provides-Extra: documentaion
Requires-Dist: sphinx (>=1.5.0); extra == 'documentaion'
Requires-Dist: sphinx-rtd-theme; extra == 'documentaion'

RAGE - ddRAD Data Generator
============================

RAGE (ddRAD Data Generator) is a software to simulate double digest restriction site associated DNA sequencing reads.
The generated datasets 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/>`_.


System Requirements
~~~~~~~~~~~~~~~~~~~

- python >= 3.5
- numpy
- scipy
- matplotlib
- pyyaml
- numba

For the docs:

- sphinx
- sphinx_rtd_theme

For parameter visualization:

- bokeh


Installation
~~~~~~~~~~~~

We recommend the installation using conda:

.. code-block:: shell

   $ conda create -c bioconda -n rage  python rage
   $ source activate rage

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

.. code-block:: shell

   $ git clone https://bitbucket.org/genomeinformatics/rage.git
   $ cd rage
   /rage$ python setup.py install

In this case you have to install the requirements listed above.


.. _bitbucket: https://bitbucket.org/genomeinformatics/rage


Usage
~~~~~

To simulate a ddRAD dataset, call rage from the command line:

.. code-block:: shell

   $ rage

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

.. code-block:: shell

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

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


