rbfam

Light wrapper for RFam data in Ruby. Provides two ActiveRecord::Base models, Rbfam::Family and Rbfam::Rna. Rbfam::Rna#seq objects are cast as Bio::Sequence::NA, and support any methods provided by that class.

Rbfam::Family(id: integer, created_at: datetime, updated_at: datetime, name: string, description: string, consensus_structure: text)
Rbfam::Rna(id: integer, created_at: datetime, updated_at: datetime, family_id: integer, accession: string, sequence: text, gapped_sequence: text, from: integer, to: integer)

Versioning follows a variant of semver, where release X.Y.Z.A has RFam major version X, RFam minor version Y, minor version Z and patch level A.

Usage

require "rbfam"
Rbfam.db.connect

Rbfam::Family.count                             #=> 2450
Rbfam::Rna.count                                #=> 47218

Rbfam::Family.rf(5).name                        #=> "RF00005" 
Rbfam::Family.rf(5).description                 #=> "tRNA"
Rbfam::Family.rf(5).class.superclass            #=> ActiveRecord::Base 
Rbfam::Family.named("microRNA").count           #=> 524 
 
Rbfam::Family.rf(167).rnas.count                #=> 133
Rbfam::Family.rf(167).rnas.plus_strand.count    #=> 76
Rbfam::Family.rf(167).rnas.first.description    #=> "X83878.1/168-267"
Rbfam::Family.rf(167).rnas.first.seq.gc_content #=> (23/50)
Rbfam::Family.rf(167).rnas.first.seq.class      #=> Bio::Sequence::NA

Installation

To install via Rubygems:

gem install rbfam

To install from source:

git clone https://github.com/evansenter/rbfam.git
cd rbfam
bundle install
rake install

Configuration

The default configuration for the database resides in db/config.yml, but is easily overridable. Rbfam uses the Rbfam.db.scoped_config function to access the database, which retrieves the configuration from the Rbfam.db.config object, keyed by Rbfam.db.env. Both of these functions have writers as well for user-specific configuration.

Rbfam.db.scoped_config #=> {"adapter"=>"mysql2", "database"=>"rbfam", "username"=>"root", "password"=>nil} 
Rbfam.db.config        #=> {"rbfam"=>{"adapter"=>"mysql2", "database"=>"rbfam", "username"=>"root", "password"=>nil}} 
Rbfam.db.env           #=> "rbfam"

Initialization

The first time that you use Rbfam, you need to build and populate the database. This process takes approximately 15 minutes as all the data from Rfam 12.0 is loaded into MySQL. To do this, one does the following:

require "rbfam"
Rbfam.db.bootstrap!