Metadata-Version: 1.1
Name: django-genome
Version: 0.7.3
Summary: Django app for syncing and storing human genome reference data
Home-page: https://github.com/genomics-geek/django-genome
Author: Michael A. Gonzalez
Author-email: genomics.geek.04.22@gmail.com
License: MIT
Description: =============================
        Django Genome
        =============================
        
        .. image:: https://badge.fury.io/py/django-genome.svg
            :target: https://badge.fury.io/py/django-genome
        
        .. image:: https://travis-ci.org/chopdgd/django-genome.svg?branch=develop
            :target: https://travis-ci.org/chopdgd/django-genome
        
        .. image:: https://codecov.io/gh/chopdgd/django-genome/branch/develop/graph/badge.svg
            :target: https://codecov.io/gh/chopdgd/django-genome
        
        .. image:: https://pyup.io/repos/github/chopdgd/django-genome/shield.svg
            :target: https://pyup.io/repos/github/chopdgd/django-genome/
            :alt: Updates
        
        .. image:: https://pyup.io/repos/github/chopdgd/django-genome/python-3-shield.svg
            :target: https://pyup.io/repos/github/chopdgd/django-genome/
            :alt: Python 3
        
        Django app for syncing and storing human genome reference data
        
        Documentation
        -------------
        
        The full documentation is at https://django-genome.readthedocs.io.
        
        Quickstart
        ----------
        
        Install Django Genome::
        
            pip install django-genome
        
        Add it to your `INSTALLED_APPS` (along with DRF and django-filters):
        
        .. code-block:: python
        
            INSTALLED_APPS = (
                ...
                'rest_framework',
                'django_filters',
                ...
                'genome',
                ...
            )
        
        Add Django Genome's URL patterns:
        
        .. code-block:: python
        
            from genome import urls as genome_urls
        
        
            urlpatterns = [
                ...
                url(r'^', include(genome_urls, namespace='genome')),
                ...
            ]
        
        Initial sync for genome models::
        
            python manage.py genome_sync
        
        Features
        --------
        
        * Includes models for Genome, Chromosome, CytoBand, Gene, Transcript, and Exons
        * Syncs data for hg18, hg19, hg38 from HGNC and UCSC
        
        Running Tests
        -------------
        
        Does the code actually work?
        
        ::
        
            source <YOURVIRTUALENV>/bin/activate
            (myenv) $ pip install tox
            (myenv) $ tox
        
        Credits
        -------
        
        Tools used in rendering this package:
        
        *  Cookiecutter_
        *  `cookiecutter-djangopackage`_
        
        .. _Cookiecutter: https://github.com/audreyr/cookiecutter
        .. _`cookiecutter-djangopackage`: https://github.com/pydanny/cookiecutter-djangopackage
        
        
        
        
        History
        -------
        
        0.1.0 (2017-12-30)
        ++++++++++++++++++
        
        * First release on PyPI.
        * Initial models and REST API
        * Syncs data from HGNC and UCSC to build database
        
        0.2.0 (2018-01-05)
        ++++++++++++++++++
        
        `Full Changelog <https://github.com/chopdgd/django-genome/compare/v0.1.0...v0.2.0>`_
        
        * Improved REST API Filters
        * made Chromosomes and Gene Symbols save as uppercase to maintain consistency
        
        
        0.2.1 (2018-01-08)
        ++++++++++++++++++
        
        `Full Changelog <https://github.com/chopdgd/django-genome/compare/v0.2.0...v0.2.1>`_
        
        * Fixed issues with migrations
        
        0.2.2 (2018-01-12)
        ++++++++++++++++++
        
        `Full Changelog <https://github.com/chopdgd/django-genome/compare/v0.2.1...v0.2.2>`_
        
        * Fixed route names for SimpleRouter
        
        0.3.0 (2018-02-09)
        ++++++++++++++++++
        
        `Full Changelog <https://github.com/chopdgd/django-genome/compare/v0.2.2...v0.3.0>`_
        
        * Updated requirements to the latest
        
        
        0.4.0 (2018-03-30)
        ++++++++++++++++++
        
        `Full Changelog <https://github.com/chopdgd/django-genome/compare/v0.3.0...v0.4.0>`_
        
        * Added API for chromosomes
        * Changed gene_symbol from being unique
        
        0.5.0 (2018-04-04)
        ++++++++++++++++++
        
        `Full Changelog <https://github.com/chopdgd/django-genome/compare/v0.4.0...v0.5.0>`_
        
        * Added GraphQL Nodes
        
        0.6.0 (2018-04-07)
        ++++++++++++++++++
        
        `Full Changelog <https://github.com/chopdgd/django-genome/compare/v0.5.0...v0.6.0>`_
        
        * Added support for Django 2 and Python 3.6
        * Dropped support for Django < 1.11 and Python 2.7, 3.3, 3.4
        
        0.6.1 (2018-04-18)
        ++++++++++++++++++
        
        `Full Changelog <https://github.com/chopdgd/django-genome/compare/v0.6.0...v0.6.1>`_
        
        * Updated 3rd party libs
        
        0.6.2 (2018-05-14)
        ++++++++++++++++++
        
        `Full Changelog <https://github.com/chopdgd/django-genome/compare/v0.6.1...v0.6.2>`_
        
        * Updated chromosomes sync to ensure lexicographic ordering of chromosomes
        
        0.6.3 (2018-05-16)
        ++++++++++++++++++
        
        `Full Changelog <https://github.com/chopdgd/django-genome/compare/v0.6.2...v0.6.3>`_
        
        * Updated sync to be able to skip sync of exons
        
        0.6.4 (2018-05-16)
        ++++++++++++++++++
        
        `Full Changelog <https://github.com/chopdgd/django-genome/compare/v0.6.3...v0.6.4>`_
        
        * Updated setup.py to read requirements.txt
        
        0.7.0 (2018-06-01)
        ++++++++++++++++++
        
        `Full Changelog <https://github.com/chopdgd/django-genome/compare/v0.6.4...v0.7.0>`_
        
        * Added Gene List model
        * Removed support for GraphQL - this is not needed here.  Applications that import this package can set up Nodes/Schema using models
        
        0.7.1 (2018-06-07)
        ++++++++++++++++++
        
        `Full Changelog <https://github.com/chopdgd/django-genome/compare/v0.7.0...v0.7.1>`_
        
        * #54 - Updated management methods to allow for updating when retrieving latest changes from RefSeq
        * #56 - Updated Gene model to have property ensembl_gene_id - which will check HGNC and Ensembl provided gene Ids
        
        0.7.2 (2018-08-13)
        ++++++++++++++++++
        
        `Full Changelog https://github.com/chopdgd/django-genome/compare/v0.7.1...v0.7.2>`_
        
        * Updated 3rd party requirements. Some requirements had changed so it was causing failures
        
        0.7.3 (2018-09-26)
        ++++++++++++++++++
        
        `Full Changelog https://github.com/chopdgd/django-genome/compare/v0.7.2...v0.7.3>`_
        
        * Updated transcript model to include preferred transcript boolean
        
Keywords: django-genome
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Framework :: Django
Classifier: Framework :: Django :: 1.11
Classifier: Framework :: Django :: 2.0
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: BSD License
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
