rbfam 0.2.2 → 12.0.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: db1fe9d517d0eb5e3648d3d2dd966d97901bac6c
-  data.tar.gz: 5397ae4f4d371e7218ecfab08c86de6eda735c4c
+  metadata.gz: 73c4a2c6bb2e20a1eeddd818c01199c6aceca461
+  data.tar.gz: 7ba0aa6f44ba94fbbf35cc234b7ad257c9dcdf00
 SHA512:
-  metadata.gz: 0522f496a7a88c9fe02ec5ab26a6b19a423094f0b08a9d27c9a47d6321cbd07805e76977182009764d48cce81f859bb4c52867b40836b8402bdbb5373d5f60e3
-  data.tar.gz: 84de980e4ec86fd94aaa7ff6c305e758ecae1600d02dcc6c1319c05295a0980b41a124f7b7cdaae09efca0c411064201c06b6c37497f0be5f611e982a2ed5bf3
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+  data.tar.gz: 8c32403f117ed54c391c456b6125aa08949fab7ee6dd9f6de25a51028e829300010110135d7393709e2d0e206bbc9ad42827a37a6ba697ee3fdb831c3916719f

data/Gemfile.lock

@@ -1,93 +1,107 @@
 PATH
   remote: .
   specs:
-    rbfam (0.2.2)
-      activerecord
-      activesupport
+    rbfam (12.0.0)
+      active_record_migrations (~> 4.2, >= 4.2.0.1)
+      activerecord (~> 4.2, >= 4.2.0)
+      activerecord-import (~> 0.7, >= 0.7.0)
+      activesupport (~> 4.2, >= 4.2.0)
       bio (~> 1.4, >= 1.4.2)
       bio-stockholm (~> 0.0, >= 0.0.1)
-      entrez (~> 0.5, >= 0.5.8.1)
-      httparty (~> 0.8, >= 0.8.3)
       mysql2 (~> 0.3, >= 0.3.14)
-      nokogiri (~> 1.6, >= 1.6.1)
       parallel (~> 1.3, >= 1.3.2)
+      ruby-progressbar (~> 1.7, >= 1.7.0)
+      virtus (~> 1.0, >= 1.0.3)
 
 GEM
   remote: https://rubygems.org/
   specs:
-    actionpack (3.2.21)
-      activemodel (= 3.2.21)
-      activesupport (= 3.2.21)
-      builder (~> 3.0.0)
+    actionpack (4.2.0)
+      actionview (= 4.2.0)
+      activesupport (= 4.2.0)
+      rack (~> 1.6.0)
+      rack-test (~> 0.6.2)
+      rails-dom-testing (~> 1.0, >= 1.0.5)
+      rails-html-sanitizer (~> 1.0, >= 1.0.1)
+    actionview (4.2.0)
+      activesupport (= 4.2.0)
+      builder (~> 3.1)
       erubis (~> 2.7.0)
-      journey (~> 1.0.4)
-      rack (~> 1.4.5)
-      rack-cache (~> 1.2)
-      rack-test (~> 0.6.1)
-      sprockets (~> 2.2.1)
-    activemodel (3.2.21)
-      activesupport (= 3.2.21)
-      builder (~> 3.0.0)
-    activerecord (3.2.21)
-      activemodel (= 3.2.21)
-      activesupport (= 3.2.21)
-      arel (~> 3.0.2)
-      tzinfo (~> 0.3.29)
-    activesupport (3.2.21)
-      i18n (~> 0.6, >= 0.6.4)
-      multi_json (~> 1.0)
-    arel (3.0.3)
+      rails-dom-testing (~> 1.0, >= 1.0.5)
+      rails-html-sanitizer (~> 1.0, >= 1.0.1)
+    active_record_migrations (4.2.0.1)
+      activerecord (= 4.2.0)
+      railties (= 4.2.0)
+      rake
+    activemodel (4.2.0)
+      activesupport (= 4.2.0)
+      builder (~> 3.1)
+    activerecord (4.2.0)
+      activemodel (= 4.2.0)
+      activesupport (= 4.2.0)
+      arel (~> 6.0)
+    activerecord-import (0.7.0)
+      activerecord (>= 3.0)
+    activesupport (4.2.0)
+      i18n (~> 0.7)
+      json (~> 1.7, >= 1.7.7)
+      minitest (~> 5.1)
+      thread_safe (~> 0.3, >= 0.3.4)
+      tzinfo (~> 1.1)
+    arel (6.0.0)
     awesome_print (1.2.0)
+    axiom-types (0.1.1)
+      descendants_tracker (~> 0.0.4)
+      ice_nine (~> 0.11.0)
+      thread_safe (~> 0.3, >= 0.3.1)
     bio (1.4.3.0001)
     bio-stockholm (0.0.1)
-    builder (3.0.4)
-    entrez (0.5.8.1)
-      httparty
+    builder (3.2.2)
+    coercible (1.0.0)
+      descendants_tracker (~> 0.0.1)
+    descendants_tracker (0.0.4)
+      thread_safe (~> 0.3, >= 0.3.1)
+    equalizer (0.0.9)
     erubis (2.7.0)
     gem-release (0.7.3)
-    hike (1.2.3)
-    httparty (0.13.3)
-      json (~> 1.8)
-      multi_xml (>= 0.5.2)
-    i18n (0.6.11)
-    journey (1.0.4)
+    i18n (0.7.0)
+    ice_nine (0.11.1)
     json (1.8.1)
-    mini_portile (0.6.1)
-    multi_json (1.10.1)
-    multi_xml (0.5.5)
+    loofah (2.0.1)
+      nokogiri (>= 1.5.9)
+    mini_portile (0.6.2)
+    minitest (5.5.0)
     mysql2 (0.3.17)
     nokogiri (1.6.5)
       mini_portile (~> 0.6.0)
     parallel (1.3.3)
-    rack (1.4.5)
-    rack-cache (1.2)
-      rack (>= 0.4)
-    rack-ssl (1.3.4)
-      rack
+    rack (1.6.0)
     rack-test (0.6.2)
       rack (>= 1.0)
-    railties (3.2.21)
-      actionpack (= 3.2.21)
-      activesupport (= 3.2.21)
-      rack-ssl (~> 1.3.2)
+    rails-deprecated_sanitizer (1.0.3)
+      activesupport (>= 4.2.0.alpha)
+    rails-dom-testing (1.0.5)
+      activesupport (>= 4.2.0.beta, < 5.0)
+      nokogiri (~> 1.6.0)
+      rails-deprecated_sanitizer (>= 1.0.1)
+    rails-html-sanitizer (1.0.1)
+      loofah (~> 2.0)
+    railties (4.2.0)
+      actionpack (= 4.2.0)
+      activesupport (= 4.2.0)
       rake (>= 0.8.7)
-      rdoc (~> 3.4)
-      thor (>= 0.14.6, < 2.0)
+      thor (>= 0.18.1, < 2.0)
     rake (10.4.2)
-    rdoc (3.12.2)
-      json (~> 1.4)
-    sprockets (2.2.3)
-      hike (~> 1.2)
-      multi_json (~> 1.0)
-      rack (~> 1.0)
-      tilt (~> 1.1, != 1.3.0)
-    standalone_migrations (2.1.5)
-      activerecord (~> 3.2)
-      railties (~> 3.2)
-      rake (~> 10.0)
+    ruby-progressbar (1.7.1)
     thor (0.19.1)
-    tilt (1.4.1)
-    tzinfo (0.3.42)
+    thread_safe (0.3.4)
+    tzinfo (1.2.2)
+      thread_safe (~> 0.1)
+    virtus (1.0.3)
+      axiom-types (~> 0.1)
+      coercible (~> 1.0)
+      descendants_tracker (~> 0.0, >= 0.0.3)
+      equalizer (~> 0.0, >= 0.0.9)
 
 PLATFORMS
   ruby
@@ -98,4 +112,3 @@ DEPENDENCIES
   gem-release (~> 0.7, >= 0.7.3)
   rake (~> 10.0)
   rbfam!
-  standalone_migrations (~> 2.1, >= 2.1.5)

data/Rakefile

@@ -1,3 +1,8 @@
 require "bundler/gem_tasks"
-require "standalone_migrations"
-StandaloneMigrations::Tasks.load_tasks
+require "active_record_migrations"
+require "rbfam"
+
+ActiveRecordMigrations.load_tasks
+
+ActiveRecord::Base.configurations      = ActiveRecord::Tasks::DatabaseTasks.database_configuration = Rbfam.db.config
+ActiveRecord::Tasks::DatabaseTasks.env = Rbfam.db.env

data/db/config.yml

@@ -1,4 +1,4 @@
-development:
+rbfam:
   adapter: mysql2
   database: rbfam
   username: root

data/db/migrate/20140114232757_add_alignment_table.rb

@@ -1,7 +1,7 @@
 class AddAlignmentTable < ActiveRecord::Migration
   def up
     create_table :alignments do |table|
-      table.timestamps
+      table.timestamps null: false
       table.belongs_to :family
       table.text :stockholm, limit: 4294967295
       table.text :consensus_structure

data/db/migrate/20140114232805_add_sequence_table.rb

@@ -1,7 +1,7 @@
 class AddSequenceTable < ActiveRecord::Migration
   def up
     create_table :sequences do |table|
-      table.timestamps
+      table.timestamps null: false
       table.belongs_to :alignment
       table.string :accession
       table.text :stripped_sequence

data/db/migrate/20140114232810_add_family_table.rb

@@ -1,7 +1,7 @@
 class AddFamilyTable < ActiveRecord::Migration
   def up
     create_table :families do |table|
-      table.timestamps
+      table.timestamps null: false
       table.string :name
       table.string :description
     end

data/db/migrate/20150102185134_drop_alignments.rb

@@ -0,0 +1,6 @@
+class DropAlignments < ActiveRecord::Migration
+  def change
+    drop_table :alignments
+    rename_column :sequences, :alignment_id, :family_id
+  end
+end

data/db/migrate/20150102185348_add_consensus_structure_to_families.rb

@@ -0,0 +1,5 @@
+class AddConsensusStructureToFamilies < ActiveRecord::Migration
+  def change
+    add_column :families, :consensus_structure, :text
+  end
+end

data/db/migrate/20150102192407_rename_table_and_columns_for_sequence.rb

@@ -0,0 +1,7 @@
+class RenameTableAndColumnsForSequence < ActiveRecord::Migration
+  def change
+    rename_table :sequences, :rnas
+    rename_column :rnas, :stripped_sequence, :sequence
+    rename_column :rnas, :alignment_sequence, :gapped_sequence
+  end
+end

data/db/schema.rb

@@ -9,36 +9,29 @@
 # from scratch. The latter is a flawed and unsustainable approach (the more migrations
 # you'll amass, the slower it'll run and the greater likelihood for issues).
 #
-# It's strongly recommended to check this file into your version control system.
+# It's strongly recommended that you check this file into your version control system.
 
-ActiveRecord::Schema.define(:version => 20140114232810) do
+ActiveRecord::Schema.define(version: 20150102192407) do
 
-  create_table "alignments", :force => true do |t|
-    t.datetime "created_at",                                :null => false
-    t.datetime "updated_at",                                :null => false
-    t.integer  "family_id"
-    t.text     "stockholm",           :limit => 2147483647
-    t.text     "consensus_structure"
+  create_table "families", force: :cascade do |t|
+    t.datetime "created_at",                        null: false
+    t.datetime "updated_at",                        null: false
+    t.string   "name",                limit: 255
+    t.string   "description",         limit: 255
+    t.text     "consensus_structure", limit: 65535
   end
 
-  create_table "families", :force => true do |t|
-    t.datetime "created_at",  :null => false
-    t.datetime "updated_at",  :null => false
-    t.string   "name"
-    t.string   "description"
-  end
-
-  add_index "families", ["name"], :name => "index_families_on_name", :unique => true
+  add_index "families", ["name"], name: "index_families_on_name", unique: true, using: :btree
 
-  create_table "sequences", :force => true do |t|
-    t.datetime "created_at",         :null => false
-    t.datetime "updated_at",         :null => false
-    t.integer  "alignment_id"
-    t.string   "accession"
-    t.text     "stripped_sequence"
-    t.text     "alignment_sequence"
-    t.integer  "from"
-    t.integer  "to"
+  create_table "rnas", force: :cascade do |t|
+    t.datetime "created_at",                    null: false
+    t.datetime "updated_at",                    null: false
+    t.integer  "family_id",       limit: 4
+    t.string   "accession",       limit: 255
+    t.text     "sequence",        limit: 65535
+    t.text     "gapped_sequence", limit: 65535
+    t.integer  "from",            limit: 4
+    t.integer  "to",              limit: 4
   end
 
 end

data/db/seeds.rb

@@ -0,0 +1,22 @@
+require "rbfam"
+require "activerecord-import/base"
+
+puts "Parsing %s to load in DB." % Rbfam.db.rfam_file
+entries = Bio::Stockholm::Reader.parse_from_file(Rbfam.db.rfam_file) and nil
+puts "Loading up %d RFam families." % entries.size
+
+Parallel.each(entries, progress: "Populating MySQL") do |stockholm|
+  family = Rbfam::Family.find_or_create_by(name: stockholm.gf_features["AC"], description: stockholm.gf_features["DE"], consensus_structure: stockholm.gc_features["SS_cons"])
+    
+  existing_sequences = family.rnas.map { |sequence| sequence.instance_eval { "%s/%d-%d" % [accession, from, to] } }.to_set
+  sequences          = stockholm.records.reject { |key, _| key == ?# || existing_sequences.include?(key) }.map do |identifier, record|
+    accession, from, to = identifier.split(/[\/-]/)
+
+    Rbfam::Rna.find_or_initialize_by(family: family, accession: accession, from: from, to: to) do |sequence|
+      sequence.gapped_sequence = record.sequence.upcase
+      sequence.sequence        = sequence.gapped_sequence.gsub(/[^AUGC]/, "")
+    end
+  end
+  
+  Rbfam::Rna.import(sequences.select(&:new_record?))
+end and nil

data/lib/rbfam.rb

@@ -2,24 +2,19 @@ require "active_record"
 require "active_support/inflector"
 require "bio"
 require "bio-stockholm"
-require "entrez"
-require "httparty"
-require "json"
 require "mysql2"
 require "parallel"
+require "rake"
+require "ruby-progressbar"
+require "singleton"
+require "virtus"
 
-%W|helpers modules|.each do |folder|
-  Dir[File.join(File.dirname(__FILE__), "rbfam", folder, "*.rb")].each { |name| require "rbfam/#{folder}/#{File.basename(name, '.rb')}" }
-end
+require "rbfam/db_config"
+require "rbfam/family"
+require "rbfam/rna"
 
 module Rbfam
-  def self.connect(config: nil)
-    ActiveRecord::Base.establish_connection(config || YAML.load_file(File.join(File.dirname(__FILE__), "..", "db", "config.yml"))["development"])
-  end
-  
-  def self.script(name)
-    require "rbfam/scripts/#{File.basename(name, '.rb')}"
+  def self.db
+    DbConfig.instance
   end
 end
-
-Rbfam::Family.const_set(:READABLE, JSON.parse(File.read(File.join(File.dirname(__FILE__), "rbfam", "helpers", "simple_names.json"))))

data/lib/rbfam/db_config.rb

@@ -0,0 +1,41 @@
+module Rbfam
+  class DbConfig
+    include Singleton, Virtus.model
+
+    attribute :rfam_file, String, default: ->(_, _) { File.join(File.dirname(__FILE__), "..", "..", "rfam_12.seed.utf8") }
+    attribute :env, String, default: "rbfam"
+    attribute :config, Hash[String => String], default: ->(_, _) { YAML.load_file(File.join(File.dirname(__FILE__), "..", "..", "db", "config.yml")) }
+  
+    def scoped_config
+      config[env]
+    end
+  
+    def bootstrap!
+      load_rakefile
+      Rake::Task["db:reset"].invoke
+      true
+    end
+    
+    def seed!
+      load_rakefile
+      Rake::Task["db:seed"].invoke
+      true
+    end
+    
+    def clear!
+      load_rakefile
+      Rake::Task["db:drop"].invoke
+      true
+    end
+  
+    def connect
+      ActiveRecord::Base.establish_connection(scoped_config)
+    end
+    
+    private
+    
+    def load_rakefile
+      Rake.load_rakefile(File.join(File.dirname(__FILE__), "..", "..", "Rakefile"))
+    end
+  end
+end

data/lib/rbfam/family.rb

@@ -0,0 +1,17 @@
+module Rbfam
+  class Family < ActiveRecord::Base
+    has_many :rnas
+    
+    validates :name, :description, :consensus_structure, presence: true
+    validates :name, uniqueness: true
+    
+    def self.rf(id)
+      int_id = id.to_i
+      find_by_name("RF%s%d" % [?0 * (5 - Math.log10(int_id).ceil), int_id])
+    end
+    
+    def self.named(string)
+      where(arel_table[:description].matches("%#{string}%"))
+    end
+  end
+end

data/lib/rbfam/rna.rb

@@ -0,0 +1,47 @@
+module Rbfam
+  class Rna < ActiveRecord::Base
+    belongs_to :family
+
+    validates :accession, :from, :to, :sequence, :gapped_sequence, presence: true
+    validates :from, :to, numericality: { only_integer: true, greater_than_or_equal_to: 0 }
+    validates :accession, uniqueness: { scope: [:sequence, :from, :to] }
+    
+    def strand
+      plus_strand? ? :plus : :minus
+    end
+
+    def plus_strand?
+      to > from
+    end
+
+    def minus_strand?
+      !plus_strand?
+    end
+    
+    def seq_from
+      [from, to].min
+    end
+
+    def seq_to
+      [from, to].max
+    end
+
+    alias_method :seq, def sequence
+     as_bioseq(read_attribute(:sequence))
+    end
+    
+    def gapped_sequence
+     as_bioseq(read_attribute(:gapped_sequence))
+    end
+    
+    def _id
+      ("%s %s %s" % [accession, from, to]).gsub(/\W+/, "_")
+    end
+    
+    private
+    
+    def as_bioseq(string)
+      Bio::Sequence::NA.new(string).upcase
+    end
+  end
+end

data/lib/rbfam/version.rb

@@ -1,3 +1,3 @@
 module Rbfam
-  VERSION = "0.2.2"
+  VERSION = "12.0.0"
 end

data/rbfam.gemspec

@@ -20,19 +20,19 @@ Gem::Specification.new do |spec|
   
   spec.required_ruby_version = ">= 2.0"
 
-  spec.add_development_dependency "awesome_print",         "~> 1.2.0"
-  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 "standalone_migrations", "~> 2.1", ">= 2.1.5"
+  spec.add_development_dependency "awesome_print", "~> 1.2.0"
+  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_runtime_dependency "activerecord"
-  spec.add_runtime_dependency "activesupport"
-  spec.add_runtime_dependency "bio",           "~> 1.4", ">= 1.4.2"
-  spec.add_runtime_dependency "bio-stockholm", "~> 0.0", ">= 0.0.1"
-  spec.add_runtime_dependency "entrez",        "~> 0.5", ">= 0.5.8.1"
-  spec.add_runtime_dependency "httparty",      "~> 0.8", ">= 0.8.3"
-  spec.add_runtime_dependency "mysql2",        "~> 0.3", ">= 0.3.14"
-  spec.add_runtime_dependency "nokogiri",      "~> 1.6", ">= 1.6.1"
-  spec.add_runtime_dependency "parallel",      "~> 1.3", ">= 1.3.2"
+  spec.add_runtime_dependency "activerecord",             "~> 4.2", ">= 4.2.0"
+  spec.add_runtime_dependency "activerecord-import",      "~> 0.7", ">= 0.7.0"
+  spec.add_runtime_dependency "active_record_migrations", "~> 4.2", ">= 4.2.0.1"
+  spec.add_runtime_dependency "activesupport",            "~> 4.2", ">= 4.2.0"
+  spec.add_runtime_dependency "bio",                      "~> 1.4", ">= 1.4.2"
+  spec.add_runtime_dependency "bio-stockholm",            "~> 0.0", ">= 0.0.1"
+  spec.add_runtime_dependency "mysql2",                   "~> 0.3", ">= 0.3.14"
+  spec.add_runtime_dependency "parallel",                 "~> 1.3", ">= 1.3.2"
+  spec.add_runtime_dependency "ruby-progressbar",         "~> 1.7", ">= 1.7.0"
+  spec.add_runtime_dependency "virtus",                   "~> 1.0", ">= 1.0.3"
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbfam
 version: !ruby/object:Gem::Version
-  version: 0.2.2
+  version: 12.0.0
 platform: ruby
 authors:
 - Evan Senter
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-12-12 00:00:00.000000000 Z
+date: 2015-01-02 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: awesome_print
@@ -73,193 +73,205 @@ dependencies:
       - !ruby/object:Gem::Version
         version: '10.0'
 - !ruby/object:Gem::Dependency
-  name: standalone_migrations
+  name: activerecord
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '2.1'
+        version: '4.2'
     - - ">="
       - !ruby/object:Gem::Version
-        version: 2.1.5
-  type: :development
+        version: 4.2.0
+  type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '2.1'
+        version: '4.2'
     - - ">="
       - !ruby/object:Gem::Version
-        version: 2.1.5
+        version: 4.2.0
 - !ruby/object:Gem::Dependency
-  name: activerecord
+  name: activerecord-import
   requirement: !ruby/object:Gem::Requirement
     requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.7'
     - - ">="
       - !ruby/object:Gem::Version
-        version: '0'
+        version: 0.7.0
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.7'
     - - ">="
       - !ruby/object:Gem::Version
-        version: '0'
+        version: 0.7.0
 - !ruby/object:Gem::Dependency
-  name: activesupport
+  name: active_record_migrations
   requirement: !ruby/object:Gem::Requirement
     requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '4.2'
     - - ">="
       - !ruby/object:Gem::Version
-        version: '0'
+        version: 4.2.0.1
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '4.2'
     - - ">="
       - !ruby/object:Gem::Version
-        version: '0'
+        version: 4.2.0.1
 - !ruby/object:Gem::Dependency
-  name: bio
+  name: activesupport
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.4'
+        version: '4.2'
     - - ">="
       - !ruby/object:Gem::Version
-        version: 1.4.2
+        version: 4.2.0
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.4'
+        version: '4.2'
     - - ">="
       - !ruby/object:Gem::Version
-        version: 1.4.2
+        version: 4.2.0
 - !ruby/object:Gem::Dependency
-  name: bio-stockholm
+  name: bio
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '0.0'
+        version: '1.4'
     - - ">="
       - !ruby/object:Gem::Version
-        version: 0.0.1
+        version: 1.4.2
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '0.0'
+        version: '1.4'
     - - ">="
       - !ruby/object:Gem::Version
-        version: 0.0.1
+        version: 1.4.2
 - !ruby/object:Gem::Dependency
-  name: entrez
+  name: bio-stockholm
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '0.5'
+        version: '0.0'
     - - ">="
       - !ruby/object:Gem::Version
-        version: 0.5.8.1
+        version: 0.0.1
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '0.5'
+        version: '0.0'
     - - ">="
       - !ruby/object:Gem::Version
-        version: 0.5.8.1
+        version: 0.0.1
 - !ruby/object:Gem::Dependency
-  name: httparty
+  name: mysql2
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '0.8'
+        version: '0.3'
     - - ">="
       - !ruby/object:Gem::Version
-        version: 0.8.3
+        version: 0.3.14
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '0.8'
+        version: '0.3'
     - - ">="
       - !ruby/object:Gem::Version
-        version: 0.8.3
+        version: 0.3.14
 - !ruby/object:Gem::Dependency
-  name: mysql2
+  name: parallel
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '0.3'
+        version: '1.3'
     - - ">="
       - !ruby/object:Gem::Version
-        version: 0.3.14
+        version: 1.3.2
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '0.3'
+        version: '1.3'
     - - ">="
       - !ruby/object:Gem::Version
-        version: 0.3.14
+        version: 1.3.2
 - !ruby/object:Gem::Dependency
-  name: nokogiri
+  name: ruby-progressbar
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.6'
+        version: '1.7'
     - - ">="
       - !ruby/object:Gem::Version
-        version: 1.6.1
+        version: 1.7.0
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.6'
+        version: '1.7'
     - - ">="
       - !ruby/object:Gem::Version
-        version: 1.6.1
+        version: 1.7.0
 - !ruby/object:Gem::Dependency
-  name: parallel
+  name: virtus
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.3'
+        version: '1.0'
     - - ">="
       - !ruby/object:Gem::Version
-        version: 1.3.2
+        version: 1.0.3
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.3'
+        version: '1.0'
     - - ">="
       - !ruby/object:Gem::Version
-        version: 1.3.2
+        version: 1.0.3
 description: Light wrapper for RFam data in Ruby.
 email:
 - evansenter@gmail.com
@@ -276,17 +288,16 @@ files:
 - db/migrate/20140114232757_add_alignment_table.rb
 - db/migrate/20140114232805_add_sequence_table.rb
 - db/migrate/20140114232810_add_family_table.rb
+- db/migrate/20150102185134_drop_alignments.rb
+- db/migrate/20150102185348_add_consensus_structure_to_families.rb
+- db/migrate/20150102192407_rename_table_and_columns_for_sequence.rb
 - db/schema.rb
+- db/seeds.rb
 - lib/rbfam.rb
-- lib/rbfam/helpers/common.rb
-- lib/rbfam/helpers/simple_names.json
-- lib/rbfam/modules/alignment.rb
-- lib/rbfam/modules/family.rb
-- lib/rbfam/modules/sequence.rb
-- lib/rbfam/modules/utils.rb
-- lib/rbfam/scripts/sequences_in_mysql.rb
+- lib/rbfam/db_config.rb
+- lib/rbfam/family.rb
+- lib/rbfam/rna.rb
 - lib/rbfam/version.rb
-- load_rbfam_seed.rb
 - rbfam.gemspec
 - rfam_12.seed.utf8
 homepage: ''

data/lib/rbfam/helpers/common.rb

@@ -1,18 +0,0 @@
-module Rbfam
-  module CommonHelpers
-    def self.included(base)
-      base.send(:include, InstanceMethods)
-    end
-    
-    module InstanceMethods
-      def bootstrap!(options = {})
-        tap { load_entries!(options) }
-      end
-      
-      def entries!(options = {})
-        remove_instance_variable(:@parsed_entries)
-        entries(options)
-      end
-    end
-  end
-end

data/lib/rbfam/helpers/simple_names.json

@@ -1,11 +0,0 @@
-{
-  "purine":       "RF00167",
-  "tpp":          "RF00059",
-  "secis_1":      "RF00031",
-  "trna":         "RF00005",
-  "let_7":        "RF00027",
-  "snora71":      "RF00056",
-  "u7":           "RF00066",
-  "rose":         "RF00435",
-  "hammerhead_3": "RF00008"
-}

data/lib/rbfam/modules/alignment.rb

@@ -1,60 +0,0 @@
-module Rbfam
-  class Alignment
-    include Rbfam::CommonHelpers
-
-    LINE_REGEXP = /^([\w\.]+)\/(\d+)\-(\d+)\s+([AUGC\.]+)$/
-
-    attr_reader :family, :seed
-
-    def initialize(family)
-      @family = family
-    end
-
-    def entries(options = {})
-      options = { alignment: :seed, limit: false }.merge(options)
-
-      @parsed_entries ||= (pull_from_server(options[:alignment]) || "").split(/\n/).reject do |line|
-        line =~ /^#/
-      end.select do |line|
-        line =~ LINE_REGEXP
-      end[options[:limit] ? 0...options[:limit] : 0..-1].map(&method(:parse_line)).tap do
-        @seed = options[:alignment] == :seed
-      end
-    end
-
-    def save_entries!
-      entries.each { |sequence| sequence.save!(seed: seed) }
-    end
-
-    def load_entries!(options = {})
-      @parsed_entries = family.load_entries!(options)
-    end
-
-    private
-
-    def pull_from_server(alignment)
-      url = "http://rfam.sanger.ac.uk/family/alignment/download/format?acc=%s&alnType=%s&nseLabels=1&format=pfam&download=0" % [
-        family.family_name,
-        alignment
-      ]
-      puts "GET: %s" % url unless @reponse
-
-      @response ||= if (party = HTTParty.get(url)).response.code == "200"
-        puts "RESPONSE: 200 OK"
-        party.parsed_response
-      else
-        raise RuntimeError.new("HTTParty raised the following error when retrieving alignment %s: %s %s" % [
-          family_name,
-          party.response.code,
-          party.response.message
-        ])
-      end
-    end
-
-    def parse_line(line)
-      line_match = line.match(LINE_REGEXP)
-
-      Rbfam::Sequence.new(family, line_match[1], line_match[2].to_i, line_match[3].to_i, autoload: true)
-    end
-  end
-end

data/lib/rbfam/modules/family.rb

@@ -1,70 +0,0 @@
-module Rbfam
-  class Family
-    include Rbfam::CommonHelpers
-
-    attr_reader :family_name, :description
-
-    class << self
-      def method_missing(name, *args, &block)
-        READABLE[name.to_s] ? new(READABLE[name.to_s]) : super
-      end
-    end
-
-    def initialize(family_name, description = "")
-      @family_name = family_name
-      @description = description
-    end
-
-    def id
-      ("%s %s" % [family_name, description.downcase]).strip.gsub(/\W+/, "_")
-    end
-
-    def alignment
-      Rbfam::Alignment.new(self)
-    end
-
-    def entries(options = {})
-      options = { limit: false }.merge(options)
-
-      @parsed_entries ||= pull_from_server.split(/\n/).reject { |line| line =~ /^#/ }[options[:limit] ? 0...options[:limit] : 0..-1].map(&method(:parse_line))
-    end
-
-    def load_entries!(options = {})
-      Rbfam.script("sequences_in_mysql")
-
-      Rbfam::DB::Sequence.joins(alignment: :family).where(families: { name: family_name }.merge(options)).map do |entry|
-        entry.to_rbfam(self)
-      end
-    end
-
-    def save_entries!
-      entries.each(&:save!)
-    end
-
-    private
-
-    def pull_from_server
-      # It isn't the greatest design pattern to memoize a block where a branch has unmanaged exception raising, but for my uses that should never
-      # happen and needs to blow up hard if it does.
-      url = "http://rfam.sanger.ac.uk/family/regions?entry=%s" % family_name
-      puts "GET: %s" % url unless @reponse
-
-      @reponse ||= if (party = HTTParty.get(url)).response.code == "200"
-        puts "RESPONSE: 200 OK"
-        party.parsed_response
-      else
-        raise RuntimeError.new("HTTParty raised the following error when retrieving family %s: %s %s" % [
-          family_name,
-          party.response.code,
-          party.response.message
-        ])
-      end
-    end
-
-    def parse_line(line)
-      split_line = line.split(/\t/)
-
-      Rbfam::Sequence.new(self, split_line[0], split_line[2].to_i, split_line[3].to_i, autoload: true)
-    end
-  end
-end

data/lib/rbfam/modules/sequence.rb

@@ -1,114 +0,0 @@
-module Rbfam
-  class Sequence < ActiveRecord::Base
-    attr_reader :family, :accession, :from, :to, :coord_options
-
-    def initialize(family, accession, from, to, options = {})
-      @family        = family
-      @accession     = accession
-      @from          = from
-      @to            = to
-      @coord_options = options[:autoload].is_a?(Hash) ? options[:autoload] : {}
-      
-      if options[:sequence]
-        @raw_sequence = (options[:sequence].is_a?(String) ? Bio::Sequence::NA.new(options[:sequence]) : options[:sequence]).upcase
-      end
-      
-      if options[:autoload]
-        sequence
-      end
-    end
-    
-    def save!(options = {})
-      unless extended?
-        Rbfam.script("sequences_in_mysql")
-      
-        SequenceTable.create({ 
-          family:          family.family_name, 
-          accession:       accession, 
-          sequence:        sequence, 
-          sequence_length: sequence.length, 
-          from:            from, 
-          to:              to, 
-          seq_from:        seq_from, 
-          seq_to:          seq_to,
-          seed:            options[:seed]
-        })
-      else
-        tap { puts "ERROR: at this time you can not save #{self.class.name}#extend! objects to protect against DB redundancy (and I'm lazy)." }
-      end
-    end
-    
-    def up_coord
-      [from, to].min
-    end
-
-    def down_coord
-      [from, to].max
-    end
-    
-    def seq_from
-      up_coord + coord_window.min
-    end
-    
-    def seq_to
-      up_coord + coord_window.max
-    end
-    
-    def strand
-      plus_strand? ? :plus : :minus
-    end
-
-    def plus_strand?
-      to > from
-    end
-
-    def minus_strand?
-      !plus_strand?
-    end
-
-    alias_method :seq, def sequence
-      @raw_sequence ||= Rbfam::Utils.rna_sequence_from_entrez(accession, up_coord, coord_window)
-      @raw_sequence   = minus_strand? ? @raw_sequence.complement : @raw_sequence
-    end
-    
-    def description
-      ("%s %s %s" % [accession, from, to]).gsub(/\W+/, "_")
-    end
-    
-    def extend!(coord_options = {})
-      tap do
-        @extended      = true
-        @coord_options = coord_options
-        remove_instance_variable(:@raw_sequence)
-        sequence
-      end
-    end
-    
-    def extended?
-      @extended
-    end
-    
-    def coord_window
-      # Options from coord_options ex: { length: 300, extend: 3 }, or { length: 250, extend: :both }
-      range = 0..(down_coord - up_coord)
-      
-      if coord_options[:length] && coord_options[:direction]
-        if coord_options[:direction] == :both
-          Range.new(range.min - coord_options[:length], range.max + coord_options[:length])
-        else
-          case [coord_options[:direction], strand]
-          when [3, :plus], [5, :minus] then Range.new(range.min, range.max + coord_options[:length])
-          when [5, :plus], [3, :minus] then Range.new(range.min - coord_options[:length], range.max)
-          else puts "WARNING: value for :direction key in sequence retrieval needs to be one of 5, 3, :both - found (%s)" % coord_options[:direction].inspect
-          end
-        end
-      else
-        range
-      end
-    end
-    
-    def inspect
-      "#<Rbfam::Sequence #{description} #{seq[0, 20] + ('...' if seq.length > 20)}>"
-    end
-  end
-end

data/lib/rbfam/modules/utils.rb

@@ -1,38 +0,0 @@
-module Rbfam
-  module Utils
-    class << self
-      def simple_rna_sequence(id, from, to)
-        sequence = rna_sequence_from_entrez(id, [from, to].min, 0..((to - from).abs))
-          
-        to < from ? sequence.complement : sequence
-      end
-      
-      def rna_sequence_from_entrez(id, position, window, buffer_size = 0)
-        na_sequence_from_entrez(id, position, window, buffer_size).rna
-      end
-      
-      def na_sequence_from_entrez(id, position, window, buffer_size = 0)
-        Bio::Sequence::NA.new(sequence_from_entrez(id, position, Range.new(window.min - buffer_size, window.max + buffer_size)).seq)
-      end
-
-      def aa_sequence_from_entrez(id, position, window)
-        Bio::Sequence::AA.new(sequence_from_entrez(id, position, window).seq)
-      end
-
-      def sequence_from_entrez(id, position, window)
-        puts "Retrieving sequence from Entrez: using nuccore DB (id: #{id}, seq_start: #{position + window.min}, seq_stop: #{position + window.max})"
-        puts "> True starting position: #{position} with window #{window.min} to #{window.max}"
-
-        fasta = Entrez.EFetch("nuccore", {
-          id:        id, 
-          seq_start: position + window.min, 
-          seq_stop:  position + window.max, 
-          retmode:   :fasta, 
-          rettype:   :text
-        }).response.body
-
-        Bio::FastaFormat.new(fasta)
-      end
-    end
-  end
-end

data/lib/rbfam/scripts/sequences_in_mysql.rb

@@ -1,46 +0,0 @@
-require "mysql2"
-require "active_record"
-
-module Rbfam
-  module DB
-    class Sequence < ActiveRecord::Base
-      belongs_to :alignment
-
-      validates_uniqueness_of :accession, scope: [:stripped_sequence, :from, :to]
-
-      def self.connect
-        ActiveRecord::Base.establish_connection(config = { adapter: "mysql2", username: "root", reconnect: true })
-
-        unless ActiveRecord::Base.connection.execute("show databases").to_a.inject(&:+).include?("rbfam")
-          ActiveRecord::Base.connection.create_database("rbfam")
-        end
-
-        ActiveRecord::Base.establish_connection(config.merge(database: "rbfam"))
-
-        inline_rails if defined?(inline_rails)
-      end
-
-      def to_rbfam(family = nil)
-        # Should use a singleton pattern here to look up the family.
-        ::Rbfam::Sequence.new(family || Rbfam::Family.new(family), accession, from, to, { sequence: stripped_sequence })
-      end
-    end
-
-    class Alignment < ActiveRecord::Base
-      belongs_to :family
-      has_many :sequences
-
-      self.table_name = "alignments"
-    end
-
-    class Family < ActiveRecord::Base
-      has_many :alignments
-      has_many :sequences, through: :alignment
-
-      self.table_name = "families"
-    end
-
-  end
-end
-
-Rbfam::DB::Sequence.connect

data/load_rbfam_seed.rb

@@ -1,28 +0,0 @@
-require "rbfam"
-
-entries = Bio::Stockholm::Reader.parse_from_file("rfam_12.seed.utf8") and nil
-
-Rbfam.connect(config: { adapter: "mysql2", database: "rbfam", username: "root", password: "" })
-
-class Family < ActiveRecord::Base; has_one :alignment; end
-class Alignment < ActiveRecord::Base; belongs_to :family; end
-class Sequence < ActiveRecord::Base; belongs_to :alignment; end
-
-Parallel.each(entries, progress: "Populating MySQL") do |stockholm|
-  family = Family.find_or_create_by(name: stockholm.gf_features["AC"], description: stockholm.gf_features["DE"])
-  
-  alignment = Alignment.find_or_create_by(family: family) do |alignment|
-    alignment.stockholm           = stockholm.to_yaml
-    alignment.consensus_structure = stockholm.gc_features["SS_cons"].gsub(?<, ?().gsub(?>, ?))
-  end
-  
-  stockholm.records.reject { |key, _| key == ?# }.each do |identifier, record|
-    accession, from, to = identifier.split(/[\/-]/)
-    
-    Sequence.find_or_create_by(alignment: alignment, accession: accession, from: from, to: to) do |sequence|
-      raw_sequence                = record.sequence.upcase
-      sequence.stripped_sequence  = raw_sequence.gsub(/[^AUGC]/, "")
-      sequence.alignment_sequence = raw_sequence
-    end
-  end
-end and nil