rbfam 12.0.0 → 12.0.1.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 73c4a2c6bb2e20a1eeddd818c01199c6aceca461
-  data.tar.gz: 7ba0aa6f44ba94fbbf35cc234b7ad257c9dcdf00
+  metadata.gz: 5e8a9a60da5c870fecc28993c07e92ca3d4094b6
+  data.tar.gz: dff5a43d67ed40d3a5a7c7841a34da852a20ab8e
 SHA512:
-  metadata.gz: bef8054a40a26e2f58d2f2e869f3bc8741d469db958066cfd8812117a768c47e7c2b6a1eefe17d125984262f6be47351ef4299848126583328c540bc432e2c8a
-  data.tar.gz: 8c32403f117ed54c391c456b6125aa08949fab7ee6dd9f6de25a51028e829300010110135d7393709e2d0e206bbc9ad42827a37a6ba697ee3fdb831c3916719f
+  metadata.gz: b79607c06c28a80d1870c4d2d220e9ef4c2521c112f67b7e516f28c3211bb25c369ea606331cdb1e3c103d21777063582361f31253ca33a4b3448bf073b045fb
+  data.tar.gz: 821524e61a2db5a246e3edfefcf948f8040f6586001c790cf3e79551db7247b527d2169920b748131fae4df55e0fd4415b17e2eaaf644dd7faeb80ededdaa3cb

data/Gemfile.lock

@@ -1,7 +1,7 @@
 PATH
   remote: .
   specs:
-    rbfam (12.0.0)
+    rbfam (12.0.1)
       active_record_migrations (~> 4.2, >= 4.2.0.1)
       activerecord (~> 4.2, >= 4.2.0)
       activerecord-import (~> 0.7, >= 0.7.0)
@@ -97,7 +97,7 @@ GEM
     thread_safe (0.3.4)
     tzinfo (1.2.2)
       thread_safe (~> 0.1)
-    virtus (1.0.3)
+    virtus (1.0.4)
       axiom-types (~> 0.1)
       coercible (~> 1.0)
       descendants_tracker (~> 0.0, >= 0.0.3)
@@ -107,8 +107,8 @@ PLATFORMS
   ruby
 
 DEPENDENCIES
-  awesome_print (~> 1.2.0)
+  awesome_print (~> 1.2)
   bundler (~> 1.7)
-  gem-release (~> 0.7, >= 0.7.3)
-  rake (~> 10.0)
+  gem-release (~> 0.7)
+  rake (~> 10.4)
   rbfam!

data/README.md

@@ -1,4 +1,68 @@
 rbfam
 =====
 
-Light wrapper for RFam data in Ruby.
+Light wrapper for RFam data in Ruby. Provides two [`ActiveRecord::Base`](http://api.rubyonrails.org/classes/ActiveRecord/Base.html) models, `Rbfam::Family` and `Rbfam::Rna`. `Rbfam::Rna#seq` objects are cast as [`Bio::Sequence::NA`](http://bioruby.org/rdoc/Bio/Sequence/NA.html), 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
+
+```ruby
+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`](https://github.com/evansenter/rbfam/blob/master/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.
+
+```ruby
+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:
+
+```ruby
+require "rbfam"
+Rbfam.db.bootstrap!
+```

data/lib/rbfam/db_config.rb

@@ -11,21 +11,21 @@ module Rbfam
     end
   
     def bootstrap!
-      load_rakefile
-      Rake::Task["db:reset"].invoke
-      true
+      ensure_action("Are you sure you'd like to completely rebuild the database? This takes around 10 minutes.") do
+        Rake::Task["db:reset"].invoke
+      end
     end
     
     def seed!
-      load_rakefile
-      Rake::Task["db:seed"].invoke
-      true
+      ensure_action("Are you sure you'd like to re-seed the database? This is faster than bootstrap!, and won't delete data.") do
+        Rake::Task["db:seed"].invoke
+      end
     end
     
     def clear!
-      load_rakefile
-      Rake::Task["db:drop"].invoke
-      true
+      ensure_action("Are you sure you'd like drop the database? This can't be un-done.") do
+        Rake::Task["db:drop"].invoke
+      end
     end
   
     def connect
@@ -34,6 +34,19 @@ module Rbfam
     
     private
     
+    def ensure_action(string, &block)
+      puts "#{string} (y/n)"
+      response = gets.chomp.downcase
+      if response == ?y
+        load_rakefile
+        yield block
+        true
+      else 
+        puts "Bailing, no changes were made."
+        false
+      end
+    end
+    
     def load_rakefile
       Rake.load_rakefile(File.join(File.dirname(__FILE__), "..", "..", "Rakefile"))
     end

data/lib/rbfam/rna.rb

@@ -6,6 +6,9 @@ module Rbfam
     validates :from, :to, numericality: { only_integer: true, greater_than_or_equal_to: 0 }
     validates :accession, uniqueness: { scope: [:sequence, :from, :to] }
     
+    scope :plus_strand,  ->{ where(arel_table[:to].gt(arel_table[:from])) }
+    scope :minus_strand, ->{ where(arel_table[:to].lt(arel_table[:from])) }
+    
     def strand
       plus_strand? ? :plus : :minus
     end
@@ -34,14 +37,18 @@ module Rbfam
      as_bioseq(read_attribute(:gapped_sequence))
     end
     
+    def description
+      "%s/%s-%s" % [accession, from, to]
+    end
+    
     def _id
-      ("%s %s %s" % [accession, from, to]).gsub(/\W+/, "_")
+      description.gsub(/\W+/, "_")
     end
     
     private
     
     def as_bioseq(string)
-      Bio::Sequence::NA.new(string).upcase
+      Bio::Sequence::NA.new(string)
     end
   end
 end

data/lib/rbfam/version.rb

@@ -1,3 +1,3 @@
 module Rbfam
-  VERSION = "12.0.0"
+  VERSION = "12.0.1.0"
 end

data/rbfam.gemspec

@@ -20,10 +20,10 @@ Gem::Specification.new do |spec|
   
   spec.required_ruby_version = ">= 2.0"
 
-  spec.add_development_dependency "awesome_print", "~> 1.2.0"
+  spec.add_development_dependency "awesome_print", "~> 1.2"
   spec.add_development_dependency "bundler",       "~> 1.7"
-  spec.add_development_dependency "gem-release",   "~> 0.7", ">= 0.7.3"
-  spec.add_development_dependency "rake",          "~> 10.0"
+  spec.add_development_dependency "gem-release",   "~> 0.7"
+  spec.add_development_dependency "rake",          "~> 10.4"
   
   spec.add_runtime_dependency "activerecord",             "~> 4.2", ">= 4.2.0"
   spec.add_runtime_dependency "activerecord-import",      "~> 0.7", ">= 0.7.0"

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbfam
 version: !ruby/object:Gem::Version
-  version: 12.0.0
+  version: 12.0.1.0
 platform: ruby
 authors:
 - Evan Senter
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-01-02 00:00:00.000000000 Z
+date: 2015-01-04 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: awesome_print
@@ -16,14 +16,14 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 1.2.0
+        version: '1.2'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 1.2.0
+        version: '1.2'
 - !ruby/object:Gem::Dependency
   name: bundler
   requirement: !ruby/object:Gem::Requirement
@@ -45,9 +45,6 @@ dependencies:
     - - "~>"
       - !ruby/object:Gem::Version
         version: '0.7'
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: 0.7.3
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
@@ -55,23 +52,20 @@ dependencies:
     - - "~>"
       - !ruby/object:Gem::Version
         version: '0.7'
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: 0.7.3
 - !ruby/object:Gem::Dependency
   name: rake
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '10.0'
+        version: '10.4'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '10.0'
+        version: '10.4'
 - !ruby/object:Gem::Dependency
   name: activerecord
   requirement: !ruby/object:Gem::Requirement