Genes

Genes is a Django app to represent genes.

Download and Install

This package is registered as django-genes in PyPI and is pip installable:

pip install django-genes

If any of the following dependency packages are not found on your system, pip will install them too:

• django 1.8 or later (Django web framework)
• django-organisms (Organisms model, which is required by Genes model)
• django-haystack (see Search Indexes and Data Template section.)
• django-fixtureless (for unittest, see tests.py)

Quick Start

1. Add 'genes' and 'organisms' to your INSTALLED_APPS setting like this:

INSTALLED_APPS = (
    ...
    'organisms',
    'genes',
)

2. Run python manage.py migrate command to create genes and organisms models.

3. (Optional) The following step is only needed if you have django-tastypie installed to create a REST API for your project and would like to have API endpoints for django-organisms and django-genes.

Add the following to your project's urls.py file:

# There are probably already other imports here, such as:
# from django.conf.urls import url, patterns, include

# If you have not already done so, import the tastypie API:
from tastypie.api import Api

# Import the API Resources for Organisms and Genes:
from organisms.api import OrganismResource
from genes.api import GeneResource

# If you have not already done so, initialize your API and
# add the Organism and Gene Resources to it. You can also register
# the CrossRefResource and CrossRefDBResource if you want to have
# API endpoints for them as well.
v0_api = Api()
v0_api.register(OrganismResource())
v0_api.register(GeneResource())
v0_api.register(CrossRefResource())
v0_api.register(CrossRefDBResource())

# In the urlpatterns, include the urls for this api:
urlpatterns = patterns('',
    ...
    (r'^api/', include(v0_api.urls))
)

Search Indexes and Data Template

The module search_indexes.py can be used by django haystack (https://github.com/django-haystack/django-haystack) to search genes. It includes the Gene fields that should be included in the search index, and how they should be weighted. The text field refers to a document that is built for the search engine to index. The location of data template for this document is: genes/templates/search/indexes/gene_text.txt.

For more information, see: http://django-haystack.readthedocs.org/en/latest/tutorial.html#handling-data

Usage of Management Commands

This app includes five management commands in management/commands/ sub-directory:

1. genes_add_xrdb

2. genes_load_geneinfo

3. genes_load_uniprot.py

4. genes_load_wb.py

5. genes_load_gene_history.py