BiasAway
--------
a tool to generate composition-matched background sequence sets
.. image:: https://travis-ci.org/asntech/biasaway.svg?branch=master
:target: https://travis-ci.org/asntech/biasaway
.. image:: https://img.shields.io/pypi/pyversions/biasaway.svg
:target: https://www.python.org
.. image:: https://img.shields.io/pypi/v/biasaway.svg
:target: https://pypi.python.org/pypi/biasaway
.. image:: https://anaconda.org/bioconda/biasaway/badges/version.svg
:target: https://anaconda.org/bioconda/biasaway
.. image:: https://anaconda.org/bioconda/biasaway/badges/downloads.svg
:target: https://bioconda.github.io/recipes/biasaway/README.html
.. image:: https://anaconda.org/bioconda/biasaway/badges/installer/conda.svg
:target: https://conda.anaconda.org/bioconda
.. image:: https://img.shields.io/github/issues/asntech/biasaway.svg
:target: https://github.com/asntech/biasaway/issues
Documentation
=============
**A detailed documentation is available in different formats:** `HTML <http://biasaway.readthedocs.org>`_ | `PDF <http://readthedocs.org/projects/biasaway/downloads/pdf/latest/>`_ | `ePUB <http://readthedocs.org/projects/biasaway/downloads/epub/latest/>`_
Installation
============
Quick installation using `conda`
--------------------------------
BiasAway is available on `Bioconda <https://anaconda.org/bioconda/biasaway>`_ for installation via ``conda``.
.. code-block:: bash
conda install -c bioconda biasaway
Install using `pip`
-------------------
BiasAway is also available on `PyPi <https://pypi.org/project/biasaway/>`_ for installation via ``pip``.
.. code-block:: bash
pip install biasaway
BiasAway is developed in Python and Python packages ``biopython`` and ``numpy``. Both ``pip`` and ``conda`` will install these dependencies and you are ready to use BiasAway. It is tested with Python versions ``3.4``, ``3.5``, ``3.6``, and ``3.7``.
Install BiasAway from source
============================
You can install a development version by using ``git`` from `bitbucket <https://bitbucket.org/CBGR/biasaway/>`_.
Install development version from `Bitbucket`
--------------------------------------------
If you have `git` installed, use this:
.. code-block:: bash
git clone https://bitbucket.org/CBGR/biasaway.git
cd biasaway
python setup.py sdist install
How to use BiasAway
===================
Once you have installed biasaway, you can type:
.. code-block:: bash
biasaway --help
This will show the main help, which lists the four subcommands/modules: ``k``, ``w``, ``g``, and ``c``.
.. code-block:: bash
usage: biasaway <subcommand> [options]
positional arguments <subcommand>: {k,w,g,c}
List of subcommands
k k-mer shuffling generator
w k-mer shuffling within a sliding window generator
g %GC distribution-based background chooser
c GC distribution and %GC composition within a sliding window background chooser
optional arguments:
-h, --help show this help message and exit
-v, --version show program's version number and exit
And to view the help for the six subcommands ``k``, ``w``, ``g``, and ``c`` type:
.. code-block:: bash
biasaway k --help
biasaway w --help
biasaway g --help
biasaway c --help
Interactive web-server
======================
BiasAway web-server is freely available at: http://biasaway.uio.no
Support
=======
If you have questions, or found any bug in the program, please write to us at ``azizk[at]uio.no`` or ``anthony.mathelier[at]ncmm.uio.no``