a tool to generate composition-matched background sequence sets
Project description
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 biasawayThis 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 biopythonpip install numpyInstall 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 installInstall 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 installHow to use BiasAway
Once you have installed biasaway, you can type:
biasaway --helpThis 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 exitto 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 --helpInteractive 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
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