Metadata-Version: 1.1
Name: dotplot
Version: 0.4.3
Summary: Small bioinformatic package for dotplot's generation (in command line and in GUI)
Home-page: https://github.com/kn-bibs/dotplot
Author: kn_bibs
Author-email: bibs.kn@uw.edu.pl
License: LGPL-3.0
Download-URL: https://github.com/kn-bibs/dotplot/tarball/v0.4.3-alpha
Description: Dotplot
        =======
        
        |Build Status| |Code Climate| |Coverage Status|
        
        Idea
        ----
        
        Dotplot is a plot used mainly in biology for graphical visualisations of
        sequences' similarity. [Read more on Wikipedia]
        (https://en.wikipedia.org/wiki/Dot\_plot\_%28bioinformatics%29).
        
        Why to create a new package?
        ----------------------------
        
        There are many programs that attempt to create dotplots already.
        Unfortunately most of these programs was created long time ago and
        written in old versions of Java. This Python3 package will allow new
        generations of bioinformaticians to generate dotplots much easier.
        
        Installation & usage
        --------------------
        
        Instalation with pip
        ~~~~~~~~~~~~~~~~~~~~
        
        The easiest way to install this package with all dependencis is to use
        pip:
        
        .. code:: bash
        
            pip install dotplot
        
        Manual installation
        ~~~~~~~~~~~~~~~~~~~
        
        .. code:: bash
        
            git clone https://github.com/kn-bibs/dotplot
        
        To use graphical user interface, you will need to have pyqt5 installed,
        e.g. with:
        
        .. code:: python3
        
            sudo apt-get install python3-pyqt5
        
        To use matplotlib for drawing, you need to have it installed, e.g. with:
        
        .. code:: bash
        
            sudo pip3 install matplotlib
        
        Note: If you have chosen manual installation, use ``python3 dotplot``
        command to run the program (while in the ``dotplot`` directory) instead
        of sole ``dotplot``.
        
        Basic usage
        ~~~~~~~~~~~
        
        .. code:: bash
        
            dotplot --fasta 1.fa 2.fa
        
        To use graphical user interface, type:
        
        .. code:: bash
        
            dotplot --fasta 1.fa 2.fa --gui
        
        You can also fetch sequences from various sources (at once):
        
        .. code:: bash
        
            dotplot --gui --ncbi NP_001009852 --uniprot P03086
        
        Advanced options
        ^^^^^^^^^^^^^^^^
        
        You can set window size to be used in plot creation:
        
        .. code:: bash
        
            dotplot --fasta 1.fa 2.fa --gui --window_size 2
        
        Furthermore, you can combine it with stringency:
        
        .. code:: bash
        
            dotplot --fasta 1.fa 2.fa --gui --window_size 2 --stringency 2
        
        And you can use a similarity matrix to compare aminoacids:
        
        .. code:: bash
        
            dotplot --fasta 1.fa 2.fa --gui --window_size 2 --stringency 2 --matrix PAM120
        
        Getting help
        ^^^^^^^^^^^^
        
        To access list of available options run command above with added option
        ``-h``.
        
        What will it do?
        ----------------
        
        In the future our application will be able to read a wide range of input
        formats, and users will be able to parametrize alignment process and
        output format to their liking.
        
        Dependencies & development
        --------------------------
        
        We are writing in ``Python3`` and strict on code styling, with pep8 and
        pylint validation. We require all code merging to master to have at
        least 7,5 pylint score. To check this, at first install pytlint with
        pip3 and then, run the following command:
        ``python3 -m pylint dotplot.py``, where in place of ``dotplot.py`` use
        any name of the module to be tested.
        
        .. |Build Status| image:: https://travis-ci.org/kn-bibs/dotplot.svg?branch=master
           :target: https://travis-ci.org/kn-bibs/dotplot
        .. |Code Climate| image:: https://codeclimate.com/github/kn-bibs/dotplot/badges/gpa.svg
           :target: https://codeclimate.com/github/kn-bibs/dotplot
        .. |Coverage Status| image:: https://coveralls.io/repos/github/kn-bibs/dotplot/badge.svg
           :target: https://coveralls.io/github/kn-bibs/dotplot
        
Keywords: dotplot,bioinformatic,gui
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: License :: OSI Approved :: GNU Lesser General Public License v3 (LGPLv3)
Classifier: Operating System :: Microsoft :: Windows
Classifier: Operating System :: POSIX :: Linux
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Utilities
Classifier: Environment :: X11 Applications :: Qt
Classifier: Environment :: Console
Classifier: Intended Audience :: Education
Classifier: Intended Audience :: Science/Research
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
