Metadata-Version: 1.1
Name: GOcats
Version: 1.1.4
Summary: A tool for categorizing Gene Ontology into subgraphs of user-defined emergent concepts
Home-page: https://github.com/MoseleyBioinformaticsLab/GOcats
Author: Eugene W. Hinderer III
Author-email: ehinderer01@gmail.com
License: The Clear BSD License
Description: GOcats
        ======
        
        .. image:: _static/images/GOcats_logo.png
           :width: 50%
           :align: center
           :target: http://gocats.readthedocs.io/
        
        `GOcats` is an Open Biomedical Ontology (OBO) parser and categorizing utility--currently specialized for the Gene
        Ontology (GO)--which can help scientists interpret large-scale experimental results by organizing redundant and highly-
        specific annotations into customizable, biologically-relevant concept categories. Concept subgraphs are defined by lists
        of keywords created by the user.
        
        Currently, the `GOcats` package can be used to:
           * Create subgraphs of GO which each represent a user-specified concept.
           * Map specific, or fine-grained, GO terms in a Gene Annotation File (GAF) to an arbitrary number of concept
             categories.
           * Explore the Gene Ontology graph within a Python interpreter.
        
        Citation
        ~~~~~~~~
        Please cite the GitHub repository until our manuscript is accepted for publication: https://github.com/MoseleyBioinformaticsLab/GOcats.git
        
        Installation
        ~~~~~~~~~~~~
        
        `GOcats` runs under Python 3.4+ and is available through python3-pip. Install via pip or clone the git repo and install
        the following dependencies and you are ready to go!
        
        Install on Linux
        ----------------
        
        Pip installation
        ................
        
        Dependencies should be automatically installed using this method. It is strongly recommended that you install with this
        method.
        .. code:: bash
        
           pip3 install gocats
        
        GitHub Package installation
        ...........................
        
        Make sure you have git_ installed:
        
        .. code:: bash
        
           cd ~/
           git clone https://github.com/MoseleyBioinformaticsLab/GOcats.git
        
        Dependencies
        ............
        
        `GOcats` requires the following Python libraries:
        
           * docopt_ for creating the :mod:`gocats` command-line interface.
           * JSONPickle_ for saving Python objects in a JSON serializable form and outputting to a file.
        
        To install dependencies manually:
        
        .. code:: bash
        
           pip3 install docopt
           pip3 install jsonpickle
        
        Install on Windows
        ------------------
        Windows version not yet available; sorry about that.
        
        Quickstart
        ~~~~~~~~~~
        
        For instructions on how to format your keyword list and advanced argument usage, consult the `tutorial <doc/tutorial.rst>`_, `guide <doc/guide.rst>`_, and `API <doc/api.rst>`_
        
        Subgraphs can be created from the command line.
        
        .. code:: bash
        
           python3 -m gocats create_subgraphs /path_to_ontology_file ~/GOcats/gocats/exampledata/examplecategories.csv ~/Output --supergraph_namespace=cellular_component --subgraph_namespace=cellular_component --output_termlist
        
        Mapping files can be found in the output directory:
        
           - GC_content_mapping.json_pickle  # A python dictionary with category-defining GO terms as keys and a list of all subgraph contents as values.
           - GC_id_mapping.json_pickle  # A python dictionary with every GO term of the specified namespace as keys and a list of category root terms as values.
        
        GAF mappings can also be made from the command line:
        
        .. code:: bash
        
           python3 -m gocats categorize_dataset YOUR_GAF.goa YOUR_OUTPUT_DIRECTORY/GC_id_mapping.json_pickle YOUR_OUTPUT_DIRECTORY MAPPED_DATASET_NAME.goa
        
        
        License
        ~~~~~~~
        
        Made available under the terms of The Clear BSD License. See full license in LICENSE.
        
        The Clear BSD License
        
        Copyright (c) 2017, Eugene W. Hinderer III, Hunter N.B. Moseley
        All rights reserved.
        
        Redistribution and use in source and binary forms, with or without
        modification, are permitted (subject to the limitations in the disclaimer
        below) provided that the following conditions are met:
        
        * Redistributions of source code must retain the above copyright notice, this
          list of conditions and the following disclaimer.
        
        * Redistributions in binary form must reproduce the above copyright notice,
          this list of conditions and the following disclaimer in the documentation
          and/or other materials provided with the distribution.
        
        * Neither the name of the copyright holder nor the names of its contributors may be used
          to endorse or promote products derived from this software without specific
          prior written permission.
        
        NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE GRANTED BY THIS
        LICENSE. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
        "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
        THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
        ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
        LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
        CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE
        GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
        HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
        LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
        OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
        DAMAGE.
        
        Authors
        ~~~~~~~
        
        * **Eugene W. Hinderer III** - ehinderer_
        * **Hunter N.B. Moseley** - hunter-moseley_
        
        .. _git: https://git-scm.com/book/en/v2/Getting-Started-Installing-Git/
        .. _ehinderer: https://github.com/ehinderer
        .. _hunter-moseley: https://github.com/hunter-moseley
        
Keywords: biomedical ontology analysis
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Information Analysis
Classifier: License :: OSI Approved :: BSD License
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.3
Classifier: Programming Language :: Python :: 3.4
Classifier: Programming Language :: Python :: 3.5
