Metadata-Version: 1.1
Name: riboplot
Version: 0.3
Summary: Plot read counts of RiboSeq data from BAM format alignment files
Home-page: https://github.com/vimalkvn/riboplot
Author: Vimalkumar Velayudhan
Author-email: vimalkumarvelayudhan@gmail.com
License: GPL
Description: =====
        About
        =====
        
        .. 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: http://pythonhosted.org/riboplot.
        
        PyPI: https://pypi.python.org/pypi/riboplot.
        
        Github Repository: https://github.com/vimalkvn/riboplot.
        
        Online: http://ribogalaxy.ucc.ie (under RiboSeq Analysis/RiboPlot).
        
        
        
        
        
        History
        =======
        0.3 (2015-12-10)
        ----------------
        * Support for multiple read lengths and corresponding offsets.
        * Optional arguments check is now split into multiple steps.
        * Remove the calculation of read lengths present in the BAM alignment. 
        
        0.2.5 (2015-11-30)
        ------------------
        * Bugfix: Use known versions of libraries as dependencies in setup.py.
          Otherwise, pip installs latest versions which haven't been tested.
        * Remove Codons label, change START to AUG [riboplot].
        
        0.2.4 (2015-11-25)
        ------------------
        * Bugfix: ribocount now returns correct read counts if an offset is provided.
        * Bugfix: Don't include read counts in the longest ORF start or stop positions
          i.e., only include reads upstream or downstream of the start or stop positions.
        
        0.2.3 (2015-11-24)
        ------------------
        * Bugfix: Recalculate read frame positions after applying offset.
        * Add sequence to CSV output.
        
        0.2.2 (2015-10-29)
        ------------------
        * Use default linewidth (riboplot), Minor changes to default plot style.
        * Use 'Agg' as the default matplotlib backend (prevent $DISPLAY errors).
        * Use smaller images for the help section.
        * Fix typo in HISTORY.rst.
        * Update Github repository URL.
        
        0.2.1 (2015-10-16)
        ------------------
        Fix: Add mock again to setup requirements. Matplolib install under Galaxy fails otherwise.
        
        0.2.0 (2015-10-15)
        ------------------
        **riboplot**
        
        * Support for color schemes - options: default, colorbrewer, rgb, greyorfs.
        * Plot changes - colored, light background for ORF architecture, legend moved down.
        * Image DPI change 300 |srarr| 600.
        * Sample scripts to plot multiple transcripts and multiple color schemes.
        
        **ribocount**
        
        * Ability to output read counts in 5'(``-v``) and 3'(``-r``) leader region.
               
        Bugfixes
        
        1. Report error if a bam index could not be generated (ex. bam sorted using 
           reference names instead of chromosome coordinates).
        2. No start/stop values when transcript sequences are in lower case.
        
        Tests
        
        * Split into three different files.
        * Updated test configuration.
        
        Minor
        
        * XML wrapper changes - remove 'leader', add help text and output label change [ribocount].
        * Remove unused pysam import [riboplot].
        * Replace doc includes with sym links (breaks Galaxy toolshed otherwise).
        * Updated CSS/Table styles (removed number column from table).
        * y limit is now 1.25x [riboplot].
        * Removed line width on bars [riboplot].
        
        0.1.1 (2015-09-08)
        ------------------
        * Remove invalid Python 3 version (whl).
        * Remove unused test data files.
        * Remove strict dependence on matplotlib and pysam versions.
        * Cleanup MANIFEST.
        
        0.1.0 (2015-08-24)
        ------------------
        * First release on PyPI.
        
        .. substitutions  
        .. |srarr|    unicode:: U+02192 .. RIGHTWARDS ARROW
        
Keywords: riboplot
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: License :: OSI Approved :: GNU General Public License (GPL)
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 2
Classifier: Programming Language :: Python :: 2.6
Classifier: Programming Language :: Python :: 2.7
