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django-genome-1.1.1
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مشاهده بیشترتوضیحات
Django app for syncing and storing human genome reference data
| ویژگی | مقدار |
|---|---|
| سیستم عامل | - |
| نام فایل | django-genome-1.1.1 |
| نام | django-genome |
| نسخه کتابخانه | 1.1.1 |
| نگهدارنده | [] |
| ایمیل نگهدارنده | [] |
| نویسنده | Michael A. Gonzalez |
| ایمیل نویسنده | GonzalezMA@email.chop.edu |
| آدرس صفحه اصلی | https://github.com/genomics-geek/django-genome |
| آدرس اینترنتی | https://pypi.org/project/django-genome/ |
| مجوز | MIT |
=============================
Django Genome
=============================
.. image:: https://badge.fury.io/py/django-genome.svg
:target: https://badge.fury.io/py/django-genome
.. image:: https://travis-ci.org/chopdgd/django-genome.svg?branch=develop
:target: https://travis-ci.org/chopdgd/django-genome
.. image:: https://codecov.io/gh/chopdgd/django-genome/branch/develop/graph/badge.svg
:target: https://codecov.io/gh/chopdgd/django-genome
.. image:: https://pyup.io/repos/github/chopdgd/django-genome/shield.svg
:target: https://pyup.io/repos/github/chopdgd/django-genome/
:alt: Updates
.. image:: https://pyup.io/repos/github/chopdgd/django-genome/python-3-shield.svg
:target: https://pyup.io/repos/github/chopdgd/django-genome/
:alt: Python 3
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
نیازمندی
| مقدار | نام |
|---|---|
| ==3.10.3 | djangorestframework |
| ==2.2.0 | django-filter |
| ==1.1.0 | django-genomix |
| ==3.2.0 | django-model-utils |
| ==1.4.4 | mysqlclient |
| ==4.37.0 | tqdm |
نحوه نصب
نصب پکیج whl django-genome-1.1.1:
pip install django-genome-1.1.1.whl
نصب پکیج tar.gz django-genome-1.1.1:
pip install django-genome-1.1.1.tar.gz