django-genome 0.2.2

Django app for syncing and storing human genome reference data

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):

INSTALLED_APPS = (
    ...
    'rest_framework',
    'django_filters',
    ...
    'genome',
    ...
)

Add Django Genome’s URL patterns:

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

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)

• Improved REST API Filters

• made Chromosomes and Gene Symbols save as uppercase to maintain consistency

0.2.1 (2018-01-08)

• Fixed issues with migrations

0.2.2 (2018-01-12)

• Fixed route names for SimpleRouter