biasaway 1.0.2

a tool to generate composition-matched background sequence sets

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

conda install -c bioconda biasaway

This will install all the dependencies and you are ready to use BiasAway.

Install using pip

You can install BiasAway from PyPi using pip.

Install from PyPi:

pip install biasaway

Note: If you install using pip, make sure to install BEDTools and R packages listed below.

BiasAway requires the following Python modules and R packages:

• Python (v2.7): https://www.python.org

• Biopython: https://biopython.org

• Numpy (<=v1.16.5): https://numpy.org

A quick installation using pip, you can also use conda.

pip install biopython

pip install numpy

Install BiasAway from source

You can install a development version by using git from GitHub or 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

Install development version from GitHub

If you have git installed, use this:

git clone https://github.com/asntech/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 three subcommands/modules: m, f, d, w, g, and c.

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

to see the help for the three subcommands m, f, d, w, g, and c type:

biasaway m --help

biasaway f --help

biasaway d --help

biasaway w --help

biasaway g --help

biasaway c --help

Interactive Web App

BiasAway Web App is freely available at:

The source code for the web app is available at https://github.com/asntech/BiasAwayApp

Support

If you have questions, or found any bug in the program, please write to us at aziz.khan[at]ncmm.uio.no