Metadata-Version: 1.1
Name: biasaway
Version: 1.0.2
Summary: a tool to generate composition-matched background sequence sets
Home-page: https://github.com/asntech/biasaway
Author: Aziz Khan
Author-email: azez.khan@gmail.com
License: MIT
Description-Content-Type: UNKNOWN
Description: BiasAway
        --------
        
        	a tool to generate composition-matched background sequence sets
        
        .. image:: https://travis-ci.org/asntech/biasaway.svg?branch=master
            :target: https://travis-ci.org/asntech/biasaway
        
        .. image:: https://img.shields.io/pypi/pyversions/biasaway.svg
            :target: https://www.python.org
        
        .. image:: https://img.shields.io/pypi/v/biasaway.svg
            :target: https://pypi.python.org/pypi/biasaway
        
        .. image:: https://anaconda.org/bioconda/biasaway/badges/version.svg
        	:target: https://anaconda.org/bioconda/biasaway
        
        .. image:: https://anaconda.org/bioconda/biasaway/badges/downloads.svg
            :target: https://bioconda.github.io/recipes/biasaway/README.html
        
        .. image:: https://anaconda.org/bioconda/biasaway/badges/installer/conda.svg
        	:target: https://conda.anaconda.org/bioconda
        
        .. image:: https://img.shields.io/github/issues/asntech/biasaway.svg
        	:target: https://github.com/asntech/biasaway/issues
        
        
        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
        ------------------------------
        
        .. code-block:: bash
        
        	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.
        
        .. code-block:: bash
        
            pip install biopython
        
        .. code-block:: bash
        
            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:
        
        .. code-block:: bash
        
            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:
        
        .. code-block:: bash
        
            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:
        
        .. code-block:: bash
        
        	biasaway --help
        
        This will show the main help, which lists the three 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
        
        
        to see the help for the three 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 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``
        
        
Platform: linux/unix
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 2.7
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Software Development :: Libraries :: Python Modules
