Mercurial > repos > vimalkumarvelayudhan > riboplot

========
RiboPlot
========

.. image:: https://img.shields.io/travis/vimalkumarvelayudhan/riboplot.svg
        :target: https://travis-ci.org/vimalkumarvelayudhan/riboplot

.. image:: https://img.shields.io/pypi/v/riboplot.svg
        :target: https://pypi.python.org/pypi/riboplot


RiboPlot includes programs to plot and output Ribo-Seq read counts from an alignment file (BAM format).

There are two programs in the package:

**riboplot**

    Plot and output read counts (csv) for a single transcript.

**ribocount**

    Output read counts for all transcripts in an alignment.

Free software: GPL license

Documentation: https://riboplot.readthedocs.org

Repository: https://github.com/vimalkumarvelayudhan/riboplot

Requirements
------------
Python packages
...............
* matplotlib ``1.3.1``
* pysam ``0.8.3``

If you have a virtualenv setup, these packages and their dependencies can be installed
using::

    pip install matplotlib==1.3.1
    pip install pysam==0.8.3

Bedtools
........
RNA coverage plot requires `bedtools <https://github.com/arq5x/bedtools2>`_ to be installed.

This release of riboplot has been tested with bedtools version ``2.17.0``.

On Ubuntu and derivatives, bedtools can be installed from the repositories using::

    sudo apt-get install bedtools
author	Vimalkumar Velayudhan <vimalkumarvelayudhan@gmail.com>
date	Mon, 31 Aug 2015 14:42:53 +0100
parents	cff63cf0dea8
children	60bbd8ebe314