Package: django-genome
Django app for syncing and storing human genome reference dataDocumentationThe full documentation is athttps://django-genome.readthedocs.io.QuickstartInstall Django Genome:pip install django-genomeAdd it to yourINSTALLED_APPS(along with DRF and django-filters):INSTALLED_APPS=(...'rest_framework','django_filters',...'genome',...)Add Django Genome’s URL patterns:fromgenomeimporturlsasgenome_urlsurlpatterns=[...url(r'^',include(genome_urls,namespace='genome')),...]Initial sync for genome models:python manage.py genome_syncFeaturesIncludes models for Genome, Chromosome, CytoBand, Gene, Transcript, and ExonsSyncs data for hg18, hg19, hg38 from HGNC and UCSCRunning TestsDoes the code actually work?source <YOURVIRTUALENV>/bin/activate
(myenv) $ pip install tox
(myenv) $ toxCreditsTools used in rendering this package:Cookiecuttercookiecutter-djangopackageHistory0.1.0 (2017-12-30)First release on PyPI.Initial models and REST APISyncs data from HGNC and UCSC to build database0.2.0 (2018-01-05)0.2.0 ChangelogImproved REST API Filtersmade Chromosomes and Gene Symbols save as uppercase to maintain consistency0.2.1 (2018-01-08)0.2.1 ChangelogFixed issues with migrations0.2.2 (2018-01-12)0.2.2 ChangelogFixed route names for SimpleRouter0.3.0 (2018-02-09)0.3.0 ChangelogUpdated requirements to the latest0.4.0 (2018-03-30)0.4.0 ChangelogAdded API for chromosomesChanged gene_symbol from being unique0.5.0 (2018-04-04)0.5.0 ChangelogAdded GraphQL Nodes0.6.0 (2018-04-07)0.6.0 ChangelogAdded support for Django 2 and Python 3.6Dropped support for Django < 1.11 and Python 2.7, 3.3, 3.40.6.1 (2018-04-18)0.6.1 ChangelogUpdated 3rd party libs0.6.2 (2018-05-14)0.6.2 ChangelogUpdated chromosomes sync to ensure lexicographic ordering of chromosomes0.6.3 (2018-05-16)0.6.3  ChangelogUpdated sync to be able to skip sync of exons0.6.4 (2018-05-16)0.6.4 ChangelogUpdated setup.py to read requirements.txt0.7.0 (2018-06-01)0.7.0 ChangelogAdded Gene List modelRemoved support for GraphQL - this is not needed here.  Applications that import this package can set up Nodes/Schema using models0.7.1 (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 Ids0.7.2 (2018-08-13)0.7.2 ChangelogUpdated 3rd party requirements. Some requirements had changed so it was causing failures0.7.3 (2018-09-26)0.7.3 ChangelogUpdated transcript model to include preferred transcript boolean0.7.4 (2018-10-29)0.7.4 ChangelogUpdated 3rd party libs0.7.6 (2018-11-27)0.7.6 ChangelogHGNC changed their headers - so gene sync was broken.  Made reading headers case insensitive0.7.7 (2019-02-08)0.7.7 ChangelogUpdated 3rd party libsUpdated tests to use py.test fixtures correctly0.7.8 (2019-04-10)0.7.8 ChangelogUpdated 3rd party libsUpdated travis to use xenial distribution. Django 2.1 dropped support for SQLite < 3.8.30.8.0 (2019-05-31)0.8.0 ChangelogRefactored sync to use UCSC MySQL database connectionUpdated sync to incorporate transcript refseq versionsUpdated package to use latest cookiecutter template0.8.1 (2019-06-14)0.8.1 ChangelogGene entries created from RefSeq where not setting the chromosome attributeAdded better logging functionality0.8.2 (2019-07-26)0.8.2 ChangelogUpdated 3rd party libs0.9.0 (2019-08-02)0.9.0 ChangelogUpdated Gene data model and sync to include date approved/modified.0.9.1 (2019-08-05)0.9.1 ChangelogFixed issue with bundle not being published correctly0.9.2 (2019-08-09)0.9.2 ChangelogUpdated 3rd party libs0.9.3 (2019-09-09)0.9.3 ChangelogUpdated 3rd party libs1.0.0 (2019-11-01)1.0.0 ChangelogUpdated Gene model to make sure it is unique on symbolFirst, production release1.1.0 (2019-11-26)1.1.0 ChangelogUpdated dependencies1.1.1 (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