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        "author": "Mitchell Sullivan",
        "author_email": "mjsull@gmail.com",
        "bugtrack_url": null,
        "classifiers": [
            "Development Status :: 4 - Beta",
            "Environment :: X11 Applications",
            "Intended Audience :: Science/Research",
            "License :: OSI Approved",
            "Natural Language :: English",
            "Operating System :: POSIX :: Linux",
            "Programming Language :: Python",
            "Programming Language :: Python :: 2.7",
            "Programming Language :: Python :: 2 :: Only",
            "Topic :: Scientific/Engineering :: Bio-Informatics",
            "Topic :: Scientific/Engineering :: Visualization"
        ],
        "description": "DiscoPlot\n=========\n\n.. image:: https://pypip.in/version/DiscoPlot/badge.svg\n        :target: https://pypi.python.org/pypi/DiscoPlot/\n        :alt: Latest Version\n\n.. image:: https://pypip.in/download/DiscoPlot/badge.svg\n        :target: https://pypi.python.org/pypi/DiscoPlot/\n        :alt: Downloads\n\n.. image:: https://travis-ci.org/BeatsonLab-MicrobialGenomics/DiscoPlot.svg?branch=master\n        :target: https://travis-ci.org/BeatsonLab-MicrobialGenomics/DiscoPlot\n        :alt: Build status\n\n\nDiscoPlot allows the user to quickly identify genomic rearrangements, \nmisassemblies and sequencing artefacts by providing a scalable method for \nvisualising large sections of the genome. It reads single-end or paired read \nalignments in SAM, BAM or standard BLAST tab format and creates a scatter \nplot of opaque crosses representing the alignments to a reference. \nDiscoPlot is freely available (under a GPL license) for download (Mac OS \nX, Unix and Windows) at: \nhttps://github.com/BeatsonLab-MicrobialGenomics/DiscoPlot/releases.\n\n.. image:: https://raw.githubusercontent.com/BeatsonLab-MicrobialGenomics/DiscoPlot/master/pictures/Figure_3_lowres.gif\n        :target: https://raw.githubusercontent.com/BeatsonLab-MicrobialGenomics/DiscoPlot/master/pictures/Figure_3.gif\n        :alt: DiscoPlot figure\n\n**DiscoPlot of a mock genome.** A mock genome was created by adding genomic \nrearrangements to the chromosome of E. coli str. UTI89.  Paired-end reads \ngenerated from the mock genome (query) with GemSim and mapped back to UTI89 \n(reference). The first ~500 Kbp were then visualised using DiscoPlot.\n\n\nDocumentation\n-------------\n\nPlease use this README.rst as the core DiscoPlot user documentation. \n\n\nCitation\n--------\n\nCite this Github repository if you use DiscoPlot to generate figures \nfor publications:: \n\n    SULLIVAN MJ & BEATSON SA^. \n    DiscoPlot - Visualising discordant reads.\n    https://github.com/BeatsonLab-MicrobialGenomics/DiscoPlot.\n\n\nTODO\n----\n\nOn the roadmap:\n    * Sam compatibility\n    * Print selected read names, alignments or sequences\n\n\nInstallation\n------------\n\nDiscoPlot is a commandline application. If you're not familiar with the \ncommandline we recommend you ask local IT support to help you install it.\n\nYou will need to install/have installed:\n    * python >= 2.7 (**Python 3 is not supported**)\n\nTo automatically generate BLAST aligments (For long read DiscoPlots) using DiscoPlot you will need to install/have installed:\n    * ncbiblast+ >= 2.2.27\n\nYou can check these are installed by::\n\n    $ python --version\n    $ blastn -version\n\nInstallation of python or blastn (without a package manager) is beyond the \nscope of this document.\n\nIf you have both python and blastn you need to (if not already present) \ninstall pip_.\n\nYou can check if pip_ exists with::\n\n    $ which pip\n\nIf you get a \"not found\", please read the `pip installation instructions`_. \n\n**If you already have pip we do suggest you upgrade it.** We are using version \n1.5.6 at the time of writing this document. \n\nYou can upgrade pip_ like this::\n\n    $ pip install --upgrade pip\n\n\nThe following python libraries_ should be installed (automatically) if you follow \nthe installation instructions detailed below.\n\nWe use the following python libraries_:\n    * numpy >= 1.8.1\n    * matplotlib >= 1.3.1\n    * pysam >= 0.8.1\n\nPysam is only required for generating DiscoPlots with BAM files. SAM \ncompatability has been included to allow windows users to generate \nDiscoPlots. PySam will not install on Windows, don't bother trying (or if \nyou've succeeded please let me know how).\n\n\nLinux (Ubuntu)\n~~~~~~~~~~~~~~\n\nDiscoplot uses 3rd party packages that are extremely important for scientific \ncomputing but may be difficult to install. While *pip install * \n*--user DiscoPlot* may work we recommend you install these 3rd party packages \nusing apt-get.\n\nRun::\n\n    $ sudo apt-get install python-numpy python-matplotlib \n\nNow pip_ install DiscoPlot::\n\n    $ pip install --user DiscoPlot\n\nWe use the --user option of pip_ to put DiscoPlot in: /home/$USER/.local/bin/\nYou need to add this location to you ~/.bash_profile. \n\nAdd DiscoPlot to your path::\n\n    $ echo 'export PATH=$PATH:/home/$USER/.local/bin/' >> ~/.bash_profile\n\nFinally install BLAST+::\n\n    $ sudo apt-get install ncbi-blast+ \n\n\nMacOSX (Mavericks)\n~~~~~~~~~~~~~~~~~~\n\n**You'll need to have the equivalents of python-dev libatlas-dev liblapack-dev \ngfortran libfreetype6-dev libfreetype6 & libpng-dev installed.** We had no \nproblems installing DiscoPlot on a recently acquired OSX Mavericks machine \nusing the homebrew package manager.\n\nThe installed packages on this machine via::\n\n    $ brew list \n\nAre available at this gist_.\n\npip install DiscoPlot::\n\n    $ pip install --user DiscoPlot\n\nWe use the --user option of pip_ to put DiscoPlot in: /home/$USER/.local/bin/\nYou need to add this location to you ~/.bash_profile. \n\nAdd DiscoPlot to your path::\n\n    $ echo 'export PATH=$PATH:/home/$USER/.local/bin/' >> ~/.bash_profile\n\nFinally install BLAST+::\n\n    $ sudo brew install blast \n\n\nTesting DiscoPlot Installation\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n\nRun::\n\n    $ DiscoPlot -h \n    $ python -c 'import DiscoPlot; print DiscoPlot'\n\n\n\n\n\nUpgrading DiscoPlot\n~~~~~~~~~~~~~~~~~~~\n\nYou can upgrade like this::\n\n    pip install --upgrade DiscoPlot\n\n**Please regularly check back to make sure you're running the most recent \nDiscoPlot version.**\n\n\nExample of figures produced by DiscoPlot\n----------------------------------------\n\n.. image:: https://raw.githubusercontent.com/BeatsonLab-MicrobialGenomics/DiscoPlot/master/pictures/Figure_3_lowres.gif\n        :target: https://raw.githubusercontent.com/BeatsonLab-MicrobialGenomics/DiscoPlot/master/pictures/Figure_3.gif\n        :alt: DiscoPlot figure\n        :align: center\n\n**DiscoPlot of a mock genome.** A mock genome was created by adding genomic \nrearrangements to the chromosome of E. coli str. UTI89.  Paired-end reads \ngenerated from the mock genome (query) with GemSim (ref) and mapped back to \nUTI89 (reference). The first ~500 Kbp were then visualised using DiscoPlot.\n\n.. image:: https://raw.githubusercontent.com/BeatsonLab-MicrobialGenomics/DiscoPlot/master/pictures/Figure_4_lowres.gif\n    :target: https://raw.githubusercontent.com/BeatsonLab-MicrobialGenomics/DiscoPlot/master/pictures/Figure_4.gif\n    :alt: DiscoPlots of structural variants\n    :align: center\n\n**DiscoPlots of common structural variants.** Each box shows a common genomic \nrearrangement represented by a DiscoPlot. Rows A and B were created using \n100 bp long paired-end reads with an insert size of 300bp. Rows C and D were \ncreated using single-end reads with an average length of 1000bp. \nFor each box the rearrangement in the sequenced genome is listed, followed by \nthe scale of the gridlines in brackets.\nA1,  C1: 300 bp deletion (400 bp). A2, C2: 300 bp insertion (400 bp). \nA3, C3: 300 bp inversion (400 bp).\nA4, C4: 300 bp sequence translocated 50 Kbp upstream (10 Kbp). \nB1, D1: 3000 bp deletion (1000 bp). \nB2, D2: 3000 bp insertion (500 bp). B3, D3: 3000 bp inversion (1000 bp). \nB4, D4: 3000 bp sequence translocated 50 Kbp upstream (10 Kbp). C1) \n\n.. image:: https://raw.githubusercontent.com/BeatsonLab-MicrobialGenomics/DiscoPlot/master/pictures/Figure_5_lowres.png\n    :target: https://raw.githubusercontent.com/BeatsonLab-MicrobialGenomics/DiscoPlot/master/pictures/Figure_5.png\n    :alt: DiscoPlot of E. coli genome\n    :align: center\n\n**The dynamic nature of the genome of Escherichia coli str. UTI89.** Discoplot \nof paired-end reads from a clonal culture of UTI89 mapped back to the \npublished reference chromosome and plasmid (top). A) Zoomed region of the\nDiscoPlot, a small inversion exists in some of the sequenced bacteria. Four \nof these sites, corresponding to known prophage regions, were identified \nusing DiscoPlot. B) Close up of the plasmid in the DiscoPlot. Each entry\nin the alignment file is separated by an opaque green line. A large inversion \nhas been identified, this region corresponds to an inverted repeat found in the \nplasmid. The cross in the lower right corner indicates that this region \ncircularises.\n\n\nTutorials\n---------\n\n**Coming Soon**\n\n\nCommands\n--------\n\nTo see a full list of flags type DiscoPlot --help\n\nDetailed descriptions coming soon\n\n\n\n\n.. _pip: http://www.pip-installer.org/en/latest/\n.. _libraries: https://github.com/BeatsonLab-MicrobialGenomics/DiscoPlot/blob/master/requirements.txt\n.. _gist: https://gist.github.com/mscook/ef7499fc9d2138f17c7f\n.. _pip installation instructions: http://pip.readthedocs.org/en/latest/installing.html",
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