django-genome 1.1.1

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)

0.2.0 Changelog

• Improved REST API Filters

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

0.2.1 (2018-01-08)

0.2.1 Changelog

• Fixed issues with migrations

0.2.2 (2018-01-12)

0.2.2 Changelog

• Fixed route names for SimpleRouter

0.3.0 (2018-02-09)

0.3.0 Changelog

• Updated requirements to the latest

0.4.0 (2018-03-30)

0.4.0 Changelog

• Added API for chromosomes

• Changed gene_symbol from being unique

0.5.0 (2018-04-04)

0.5.0 Changelog

• Added GraphQL Nodes

0.6.0 (2018-04-07)

0.6.0 Changelog

• 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)

0.6.1 Changelog

• Updated 3rd party libs

0.6.2 (2018-05-14)

0.6.2 Changelog

• Updated chromosomes sync to ensure lexicographic ordering of chromosomes

0.6.3 (2018-05-16)

0.6.3 Changelog

• Updated sync to be able to skip sync of exons

0.6.4 (2018-05-16)

0.6.4 Changelog

• Updated setup.py to read requirements.txt

0.7.0 (2018-06-01)

0.7.0 Changelog

• 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)

0.7.1 Changelog

• #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)

0.7.2 Changelog

• Updated 3rd party requirements. Some requirements had changed so it was causing failures

0.7.3 (2018-09-26)

0.7.3 Changelog

• Updated transcript model to include preferred transcript boolean

0.7.4 (2018-10-29)

0.7.4 Changelog

• Updated 3rd party libs

0.7.6 (2018-11-27)

0.7.6 Changelog

• HGNC changed their headers - so gene sync was broken. Made reading headers case insensitive

0.7.7 (2019-02-08)

0.7.7 Changelog

• Updated 3rd party libs

• Updated tests to use py.test fixtures correctly

0.7.8 (2019-04-10)

0.7.8 Changelog

• Updated 3rd party libs

• Updated travis to use xenial distribution. Django 2.1 dropped support for SQLite < 3.8.3

0.8.0 (2019-05-31)

0.8.0 Changelog

• Refactored sync to use UCSC MySQL database connection

• Updated sync to incorporate transcript refseq versions

• Updated package to use latest cookiecutter template

0.8.1 (2019-06-14)

0.8.1 Changelog

• Gene entries created from RefSeq where not setting the chromosome attribute

• Added better logging functionality

0.8.2 (2019-07-26)

0.8.2 Changelog

• Updated 3rd party libs

0.9.0 (2019-08-02)

0.9.0 Changelog

• Updated Gene data model and sync to include date approved/modified.

0.9.1 (2019-08-05)

0.9.1 Changelog

• Fixed issue with bundle not being published correctly

0.9.2 (2019-08-09)

0.9.2 Changelog

• Updated 3rd party libs

0.9.3 (2019-09-09)

0.9.3 Changelog

• Updated 3rd party libs

1.0.0 (2019-11-01)

1.0.0 Changelog

• Updated Gene model to make sure it is unique on symbol

• First, production release

1.1.0 (2019-11-26)

1.1.0 Changelog

• Updated dependencies

1.1.1 (2020-03-12)

1.1.1 Changelog

• #149 - Updated the genome sync to deal with new headers

• #144 - preferred transcript sync will now use version numbers