a tool to generate nucleotide composition-matched DNA sequences
Project description
BiasAway
a tool to generate composition-matched background sequence sets
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.. image:: https://anaconda.org/bioconda/biasaway/badges/version.svg :target: https://anaconda.org/bioconda/biasaway
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.. image:: https://anaconda.org/bioconda/biasaway/badges/installer/conda.svg :target: https://conda.anaconda.org/bioconda
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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
Project details
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