biasaway 2.0.0

a tool to generate nucleotide composition-matched DNA sequences

BiasAway

a tool to generate composition-matched background sequence sets

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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 2.7, 3.4, 3.5, and 3.6.

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 six subcommands/modules: m, f, d, w, g, and c.

.. code-block:: bash

usage: biasaway <subcommand> [options]

	positional arguments <subcommand>: {m,f,d,w,g,c}

	List of subcommands
	m 	mono-nucleotide shuffling generator
	f 	mono-nucleotide shuffling within a sliding window generator
	d 	di-nucleotide shuffling generator
	w 	di-nucleotide 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 m, f, d, w, g, and c type:

.. code-block:: bash

biasaway m --help

biasaway f --help

biasaway d --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