Metadata-Version: 1.1
Name: FsnViz
Version: 0.2.0
Summary: Tool for plotting gene fusion events detected by various tools using Circos.
Home-page: http://bow.web.id
Author: Wibowo Arindrarto
Author-email: bow@bow.web.id
License: BSD
Description: FsnViz
        ======
        
        |ci| |coverage| |pypi|
        
        .. |ci| image:: https://travis-ci.org/bow/fsnviz.svg?branch=master
            :target: https://travis-ci.org/bow/fsnviz
        
        .. |coverage| image:: https://codecov.io/gh/bow/fsnviz/branch/master/graph/badge.svg
            :target: https://codecov.io/gh/bow/fsnviz
        
        .. |pypi| image:: https://badge.fury.io/py/FsnViz.svg
            :target: http://badge.fury.io/py/fsnviz
        
        
        FsnViz is a Python tool for plotting RNA-seq fusion events using Circos plots.
        It parses outputs of gene fusion finding tools and creates Circos plots out of
        it.
        
        Currently it accepts outputs of the following gene fusion finding tool:
        
        * `STAR-Fusion <https://github.com/STAR-Fusion/STAR-Fusion>`_ hits table
          (``star-fusion``)
        * `FusionCatcher <https://github.com/ndaniel/fusioncatcher>`_ final table
          (``fusioncatcher``)
        
        
        Requirements
        ------------
        
        FsnViz runs on Python 3.5 and was tested on Circos 0.69-2. Other Circos
        versions may or may not work.
        
        
        Installation
        ------------
        
        You can download the latest version via pip:
        
            $ pip install fsnviz
        
        Circos needs to be installed separately.
        
        
        Usage
        -----
        
        FsnViz needs only a result file of the gene fusion finding tool:
        
            $ fsnviz star-fusion /path/to/result/file
        
        With the invocation above, it will create the Circos plot as an SVG image
        called ``fsnviz.svg`` in the current directory. You can adjust the output
        behavior using some flags such as:
        
            * The ``--output-dir`` flag to set the output directory. If it does not
              exist, it will be created for you.
            * The ``--base-name`` flag to set the base name of the Circos plot
              (the default is ``fsnviz``). Filename extensions are added accordingly.
            * The ``--karyotype`` flag to set the Circos reference karyotype.
              Currently only ``human.hg19`` and ``human.hg38`` are available.
        
        For a complete list, check out the help via ``fsnviz --help``.
        
        
        Credits
        -------
        
        * Initial circos templates were based on the Circos templates of
          `viewFusion <https://github.com/riverlee/viewFusion>`_, written by Jiang Li.
        
        
        License
        -------
        
        FsnViz is BSD-licensed. Refer to the ``LICENSE`` file for the full license.
        
        
        Changelog
        =========
        
        
        Versions 0.2
        ------------
        
        Release 0.2.0
        ^^^^^^^^^^^^^
        
        `release date: 30 January 2016`
        
        * Adds support for plotting FusionCatcher output.
        
        
        Versions 0.1
        ------------
        
        Release 0.1.0
        ^^^^^^^^^^^^^
        
        `release date: 20 April 2016`
        
        * First release.
        * Support for plotting STAR-fusion output on human.hg19 and human.hg38.
Keywords: rnaseq fusion circos plot bioinformatics visualization
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Environment :: Console
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: BSD License
Classifier: Operating System :: POSIX
Classifier: Programming Language :: Python :: 3.5
Classifier: Topic :: Utilities
Classifier: Topic :: Scientific/Engineering :: Visualization
