django-genome 0.4.0

Django app for syncing and storing human genome reference data

=============================
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