BiasAway
a tool to generate composition-matched background sequence sets
Documentation
A detailed documentation is available in different formats: HTML | PDF | ePUB
Installation
Quick installation using conda
BiasAway is available on Bioconda for installation via conda
.
conda install -c bioconda biasaway
Install using pip
BiasAway is also available on PyPi for installation via pip
.
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.
Install development version from Bitbucket
If you have git installed, use this:
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:
biasaway --help
This will show the main help, which lists the four subcommands/modules: k
, w
, g
, and c
.
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:
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