Django app for syncing and storing human genome reference data
Project description
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:
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
Project details
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