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            "Environment :: Console",
            "Environment :: X11 Applications :: Qt",
            "Intended Audience :: Education",
            "Intended Audience :: Science/Research",
            "License :: OSI Approved :: GNU Lesser General Public License v3 (LGPLv3)",
            "Operating System :: Microsoft :: Windows",
            "Operating System :: POSIX :: Linux",
            "Programming Language :: Python :: 3.5",
            "Programming Language :: Python :: 3.6",
            "Topic :: Scientific/Engineering :: Bio-Informatics",
            "Topic :: Utilities"
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        "description": "Dotplot\n=======\n\n|Build Status| |Code Climate| |Coverage Status|\n\nIdea\n----\n\nDotplot is a plot used mainly in biology for graphical visualisations of\nsequences' similarity. [Read more on Wikipedia]\n(https://en.wikipedia.org/wiki/Dot\\_plot\\_%28bioinformatics%29).\n\nWhy to create a new package?\n----------------------------\n\nThere are many programs that attempt to create dotplots already.\nUnfortunately most of these programs was created long time ago and\nwritten in old versions of Java. This Python3 package will allow new\ngenerations of bioinformaticians to generate dotplots much easier.\n\nInstallation & usage\n--------------------\n\nInstalation with pip\n~~~~~~~~~~~~~~~~~~~~\n\nThe easiest way to install this package with all dependencis is to use\npip:\n\n.. code:: bash\n\n    pip install dotplot\n\nManual installation\n~~~~~~~~~~~~~~~~~~~\n\n.. code:: bash\n\n    git clone https://github.com/kn-bibs/dotplot\n\nTo use graphical user interface, you will need to have pyqt5 installed,\ne.g. with:\n\n.. code:: python3\n\n    sudo apt-get install python3-pyqt5\n\nTo use matplotlib for drawing, you need to have it installed, e.g. with:\n\n.. code:: bash\n\n    sudo pip3 install matplotlib\n\nNote: If you have chosen manual installation, use ``python3 dotplot``\ncommand to run the program (while in the ``dotplot`` directory) instead\nof sole ``dotplot``.\n\nBasic usage\n~~~~~~~~~~~\n\n.. code:: bash\n\n    dotplot --fasta 1.fa 2.fa\n\nTo use graphical user interface, type:\n\n.. code:: bash\n\n    dotplot --fasta 1.fa 2.fa --gui\n\nYou can also fetch sequences from various sources (at once):\n\n.. code:: bash\n\n    dotplot --gui --ncbi NP_001009852 --uniprot P03086\n\nAdvanced options\n^^^^^^^^^^^^^^^^\n\nYou can set window size to be used in plot creation:\n\n.. code:: bash\n\n    dotplot --fasta 1.fa 2.fa --gui --window_size 2\n\nFurthermore, you can combine it with stringency:\n\n.. code:: bash\n\n    dotplot --fasta 1.fa 2.fa --gui --window_size 2 --stringency 2\n\nAnd you can use a similarity matrix to compare aminoacids:\n\n.. code:: bash\n\n    dotplot --fasta 1.fa 2.fa --gui --window_size 2 --stringency 2 --matrix PAM120\n\nGetting help\n^^^^^^^^^^^^\n\nTo access list of available options run command above with added option\n``-h``.\n\nWhat will it do?\n----------------\n\nIn the future our application will be able to read a wide range of input\nformats, and users will be able to parametrize alignment process and\noutput format to their liking.\n\nDependencies & development\n--------------------------\n\nWe are writing in ``Python3`` and strict on code styling, with pep8 and\npylint validation. We require all code merging to master to have at\nleast 7,5 pylint score. To check this, at first install pytlint with\npip3 and then, run the following command:\n``python3 -m pylint dotplot.py``, where in place of ``dotplot.py`` use\nany name of the module to be tested.\n\n.. |Build Status| image:: https://travis-ci.org/kn-bibs/dotplot.svg?branch=master\n   :target: https://travis-ci.org/kn-bibs/dotplot\n.. |Code Climate| image:: https://codeclimate.com/github/kn-bibs/dotplot/badges/gpa.svg\n   :target: https://codeclimate.com/github/kn-bibs/dotplot\n.. |Coverage Status| image:: https://coveralls.io/repos/github/kn-bibs/dotplot/badge.svg\n   :target: https://coveralls.io/github/kn-bibs/dotplot\n",
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