WingenderTFClass

This gem allows to retrieve information for a transcription factor from Wingender's TFClass ontology. Necessary data come with gem but can be updated using the rake task in rake/WingenderClassification.rake. While current version works quite nice, API is going to be changed. Current version is quite preliminary. So please lock used in your app version of a gem via Gemfile.

Posibly sometimes these changes will be made (ToDo):

• Use third-party *.obo (ontology format) reader.
• Support alt_id and other tags
• More convenient data structure for an ontology.
• Less duplication in classes for obtaining family by UniprotID/UniprotAC/motif/somewhat else
• Method rename
• List monad for multiple TF classes of multiple TF motifs (just as an experiment)
• Make usage of rake task to update data more simple in use

Installation

Add this line to your application's Gemfile:

gem 'WingenderTFClass'

And then execute:

$ bundle

Or install it yourself as:

$ gem install WingenderTFClass

Usage

require 'WingenderTFClass'
class_recognizer = WingenderTFClass::ProteinFamilyRecognizers::HumanAtLevel[2]
family_recognizer = WingenderTFClass::ProteinFamilyRecognizers::HumanAtLevel[3]
class_recognizer.subfamilies_by_uniprot_id('RXRA_HUMAN')
# => [Nuclear receptors with C4 zinc fingers{2.1}]
family_recognizer.subfamilies_by_uniprot_id('RXRA_HUMAN')
# => [RXR-related receptors (NR2){2.1.3}]

subfamily_mouse_recognizer = WingenderTFClass::ProteinFamilyRecognizers::MouseAtLevel[4]
subfamily_mouse_recognizer.subfamilies_by_uniprot_id('RXRA_MOUSE')
# => [Retinoid X receptors (NR2B){2.1.3.1}]

Development

After checking out the repo, run bin/setup to install dependencies. Then, run rake test to run the tests. You can also run bin/console for an interactive prompt that will allow you to experiment.

To install this gem onto your local machine, run bundle exec rake install. To release a new version, update the version number in version.rb, and then run bundle exec rake release, which will create a git tag for the version, push git commits and tags, and push the .gem file to rubygems.org.

Contributing

Bug reports and pull requests are welcome on GitHub at https://github.com/VorontsovIE/WingenderTFClass.