django-genome

============================= Django Genome

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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) ++++++++++++++++++

0.2.0 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) ++++++++++++++++++

0.2.1 Changelog <https://github.com/chopdgd/django-genome/compare/v0.2.0...v0.2.1>_

• Fixed issues with migrations

0.2.2 (2018-01-12) ++++++++++++++++++

0.2.2 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) ++++++++++++++++++

0.3.0 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) ++++++++++++++++++

0.4.0 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) ++++++++++++++++++

0.5.0 Changelog <https://github.com/chopdgd/django-genome/compare/v0.4.0...v0.5.0>_

• Added GraphQL Nodes

0.6.0 (2018-04-07) ++++++++++++++++++

0.6.0 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) ++++++++++++++++++

0.6.1 Changelog <https://github.com/chopdgd/django-genome/compare/v0.6.0...v0.6.1>_

• Updated 3rd party libs

0.6.2 (2018-05-14) ++++++++++++++++++

0.6.2 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) ++++++++++++++++++

0.6.3 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) ++++++++++++++++++

0.6.4 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) ++++++++++++++++++

0.7.0 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) ++++++++++++++++++

0.7.1 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) ++++++++++++++++++

0.7.2 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) ++++++++++++++++++

0.7.3 Changelog <https://github.com/chopdgd/django-genome/compare/v0.7.2...v0.7.3>_

• Updated transcript model to include preferred transcript boolean

0.7.4 (2018-10-29) ++++++++++++++++++

0.7.4 Changelog <https://github.com/chopdgd/django-genome/compare/v0.7.3...v0.7.4>_

• Updated 3rd party libs

0.7.6 (2018-11-27) ++++++++++++++++++

0.7.6 Changelog <https://github.com/chopdgd/django-genome/compare/v0.7.5...v0.7.6>_

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

0.7.7 (2019-02-08) ++++++++++++++++++

0.7.7 Changelog <https://github.com/chopdgd/django-genome/compare/v0.7.6...v0.7.7>_

• Updated 3rd party libs
• Updated tests to use py.test fixtures correctly

0.7.8 (2019-04-10) ++++++++++++++++++

0.7.8 Changelog <https://github.com/chopdgd/django-genome/compare/v0.7.7...v0.7.8>_

• 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 <https://github.com/chopdgd/django-genome/compare/v0.7.8...v0.8.0>_

• 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 <https://github.com/chopdgd/django-genome/compare/v0.8.0...v0.8.1>_

• 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 <https://github.com/chopdgd/django-genome/compare/v0.8.1...v0.8.2>_

• Updated 3rd party libs

0.9.0 (2019-08-02) ++++++++++++++++++

0.9.0 Changelog <https://github.com/chopdgd/django-genome/compare/v0.8.2...v0.9.0>_

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

0.9.1 (2019-08-05) ++++++++++++++++++

0.9.1 Changelog <https://github.com/chopdgd/django-genome/compare/v0.9.0...v0.9.1>_

• Fixed issue with bundle not being published correctly

0.9.2 (2019-08-09) ++++++++++++++++++

0.9.2 Changelog <https://github.com/chopdgd/django-genome/compare/v0.9.1...v0.9.2>_

• Updated 3rd party libs

0.9.3 (2019-09-09) ++++++++++++++++++

0.9.3 Changelog <https://github.com/chopdgd/django-genome/compare/v0.9.2...v0.9.3>_

• Updated 3rd party libs

1.0.0 (2019-11-01) ++++++++++++++++++

1.0.0 Changelog <https://github.com/chopdgd/django-genome/compare/v0.9.3...v1.0.0>_

• Updated Gene model to make sure it is unique on symbol
• First, production release

1.1.0 (2019-11-26) ++++++++++++++++++

1.1.0 Changelog <https://github.com/chopdgd/django-genome/compare/v1.0.0...v1.1.0>_

• Updated dependencies

1.1.1 (2020-03-12) ++++++++++++++++++

1.1.1 Changelog <https://github.com/chopdgd/django-genome/compare/v1.1.0...v1.1.1>_

• #149 - Updated the genome sync to deal with new headers
• #144 - preferred transcript sync will now use version numbers