bio-ucsc-api 0.6.0 → 0.6.1

checksums.yaml

@@ -0,0 +1,15 @@
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+  data.tar.gz: !binary |-
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+SHA512:
+  metadata.gz: !binary |-
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data/Gemfile.lock

@@ -1,30 +1,30 @@
 GEM
   remote: http://rubygems.org/
   specs:
-    activemodel (4.0.2)
-      activesupport (= 4.0.2)
+    activemodel (4.0.3)
+      activesupport (= 4.0.3)
       builder (~> 3.1.0)
-    activerecord (4.0.2)
-      activemodel (= 4.0.2)
+    activerecord (4.0.3)
+      activemodel (= 4.0.3)
       activerecord-deprecated_finders (~> 1.0.2)
-      activesupport (= 4.0.2)
+      activesupport (= 4.0.3)
       arel (~> 4.0.0)
     activerecord-deprecated_finders (1.0.3)
-    activesupport (4.0.2)
+    activesupport (4.0.3)
       i18n (~> 0.6, >= 0.6.4)
       minitest (~> 4.2)
       multi_json (~> 1.3)
       thread_safe (~> 0.1)
       tzinfo (~> 0.3.37)
     addressable (2.3.5)
-    arel (4.0.1)
-    atomic (1.1.14)
-    atomic (1.1.14-java)
+    arel (4.0.2)
+    atomic (1.1.15)
+    atomic (1.1.15-java)
     bio (1.4.3.0001)
     bio-genomic-interval (0.1.2)
     builder (3.1.4)
     diff-lcs (1.2.5)
-    faraday (0.8.8)
+    faraday (0.8.9)
       multipart-post (~> 1.2.0)
     git (1.2.6)
     github_api (0.10.1)
@@ -35,8 +35,7 @@ GEM
       nokogiri (~> 1.5.2)
       oauth2
     hashie (2.0.5)
-    highline (1.6.20)
-    httpauth (0.2.0)
+    highline (1.6.21)
     i18n (0.6.9)
     jeweler (1.8.8)
       builder
@@ -49,41 +48,40 @@ GEM
       rdoc
     json (1.8.1)
     json (1.8.1-java)
-    jwt (0.1.8)
+    jwt (0.1.11)
       multi_json (>= 1.5)
     minitest (4.7.5)
-    multi_json (1.8.2)
+    multi_json (1.9.0)
     multi_xml (0.5.5)
     multipart-post (1.2.0)
     mysql (2.9.1)
     nokogiri (1.5.10)
     nokogiri (1.5.10-java)
-    oauth2 (0.9.2)
-      faraday (~> 0.8)
-      httpauth (~> 0.2)
-      jwt (~> 0.1.4)
-      multi_json (~> 1.0)
+    oauth2 (0.9.3)
+      faraday (>= 0.8, < 0.10)
+      jwt (~> 0.1.8)
+      multi_json (~> 1.3)
       multi_xml (~> 0.5)
       rack (~> 1.2)
     rack (1.5.2)
-    rake (10.1.0)
-    rdoc (4.0.1)
+    rake (10.1.1)
+    rdoc (4.1.1)
       json (~> 1.4)
     rspec (2.14.1)
       rspec-core (~> 2.14.0)
       rspec-expectations (~> 2.14.0)
       rspec-mocks (~> 2.14.0)
-    rspec-core (2.14.7)
-    rspec-expectations (2.14.4)
+    rspec-core (2.14.8)
+    rspec-expectations (2.14.5)
       diff-lcs (>= 1.1.3, < 2.0)
-    rspec-mocks (2.14.4)
+    rspec-mocks (2.14.6)
     safe_attributes (1.0.10)
       activerecord (>= 3.0.0)
-    thread_safe (0.1.3)
-      atomic
-    thread_safe (0.1.3-java)
-      atomic
-    tzinfo (0.3.38)
+    thread_safe (0.2.0)
+      atomic (>= 1.1.7, < 2)
+    thread_safe (0.2.0-java)
+      atomic (>= 1.1.7, < 2)
+    tzinfo (0.3.39)
 
 PLATFORMS
   java

data/README.md

@@ -1,4 +1,4 @@
-# bio-ucsc-api version 0.6.0
+# bio-ucsc-api version 0.6.1
 
 **The Ruby UCSC API**: accessing the UCSC Genome Database using Ruby.
 
@@ -35,7 +35,7 @@ $ gem install bio-ucsc-api
 
 If your favorite databese is not supported, please do not hesitate to contact the author. 
 
-* **human** Hg19, Hg18
+* **human** Hg38, Hg19, Hg18
 * **mammals** chimp (PanTro3), orangutan (PonAbe2), rhesus (RheMac2), marmoset (CalJac3), mouse (Mm10, Mm9), rat (Rn5, Rn4), guinea pig (CavPor3), rabbit (OryCun2), cat (FelCat4), panda (AilMel1), dog (CanFam2), horse (EquCab2), pig (SusScr2), sheep (OviAri1), cow (BosTau4), elephant (LoxAfr3), opossum (MonDom5), platypus (OrnAna1)
 * **vertebrates** chicken (GalGal3), zebra finch (TaeGut1), lizard (AnoCar2), X. tropicalis (XenTro2), zebrafish (DanRer7), tetraodon (TetNig2), fugu (Fr2), stickleback (GasAcu1), medaka (OryLat2), lamprey (PetMar1)
 * **deuterostomes** lancelet (BraFlo1), sea squirt (Ci2), sea urchin (StrPur2)
@@ -53,7 +53,7 @@ This package is based on the followings:
 Supported Ruby interpreter implementations:
 
 * Ruby Version 2.0.0 or later
-* Ruby version 1.9.2 or later
+* Ruby version 1.9.3 or later
 * JRuby version 1.6.3 or later - Appropiate Java heap size may have to be specified to invoke JRuby, especially when you use Bio::Ucsc::File::Twobit. Try "jruby -J-Xmx3g your_script.rb" to keep 3G byte heap.
 
 * Ruby version 1.8.7 or earlier are no longer supported by UCSC API v0.6.0 and later because Ruby on Rails and ActiveRecord version 4.0 do not support these old Rubies. 
@@ -72,6 +72,7 @@ See also:
 * UCSCBin library - https://github.com/misshie/UCSCBin
  
 # Change Log
+ * **UPDATE** (v.0.6.1) Support new human hg38 reference. Newer tables after this release will be supported in later varsions. 
  * **NEW** (v0.6.0): Support ActiveRecord v4.0 (a part of Ruby on Ralils v4.0). Other related library dependencies are also updated. To Supress deprecation warnings for using dynamic finders such as 'find_by_name_and_chrom', use `ActiveSupport::Deprecation.silenced = true`. Because ActiveRecord v4.0 does not support Ruby v1.8.7 and earlier, Ruby UCSC API no longer supports these older Rubies. 
  * **UPDATE** (v0.6.0): Ruby UCSC API is now licensed under the MIT License. See also the LICENSE.txt file.
  

data/VERSION

@@ -1 +1 @@
-0.6.0
+0.6.1

data/bio-ucsc-api.gemspec

@@ -2,14 +2,15 @@
 # DO NOT EDIT THIS FILE DIRECTLY
 # Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
 # -*- encoding: utf-8 -*-
+# stub: bio-ucsc-api 0.6.1 ruby lib
 
 Gem::Specification.new do |s|
   s.name = "bio-ucsc-api"
-  s.version = "0.6.0"
+  s.version = "0.6.1"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Hiroyuki Mishima", "Jan Aerts"]
-  s.date = "2013-12-11"
+  s.date = "2014-03-13"
   s.description = "Ruby UCSC API: accessing the UCSC Genome Database using Ruby"
   s.email = "missy@be.to"
   s.extra_rdoc_files = [
@@ -26,7 +27,6 @@ Gem::Specification.new do |s|
     "Rakefile",
     "VERSION",
     "bio-ucsc-api.gemspec",
-    "lib/#bio-ucsc.rb#",
     "lib/bio-ucsc-api.rb",
     "lib/bio-ucsc.rb",
     "lib/bio-ucsc/ailmel1.rb",
@@ -264,6 +264,9 @@ Gem::Specification.new do |s|
     "lib/bio-ucsc/hg19.rb",
     "lib/bio-ucsc/hg19/description.rb",
     "lib/bio-ucsc/hg19/gbcdnainfo.rb",
+    "lib/bio-ucsc/hg38.rb",
+    "lib/bio-ucsc/hg38/description.rb",
+    "lib/bio-ucsc/hg38/gbcdnainfo.rb",
     "lib/bio-ucsc/hgfixed.rb",
     "lib/bio-ucsc/loxafr3.rb",
     "lib/bio-ucsc/mm10.rb",
@@ -427,6 +430,7 @@ Gem::Specification.new do |s|
     "lib/bio-ucsc/visigene.rb",
     "lib/bio-ucsc/xentro2.rb",
     "samples/bed2refseq.rb",
+    "samples/get-gene-ontology.rb",
     "samples/hg19-2bit-retrieve.rb",
     "samples/hg19-sample.rb",
     "samples/num-gene-exon.rb",
@@ -436,11 +440,11 @@ Gem::Specification.new do |s|
   s.homepage = "http://github.com/misshie/bioruby-ucsc-api"
   s.licenses = ["The MIT License"]
   s.require_paths = ["lib"]
-  s.rubygems_version = "1.8.11"
+  s.rubygems_version = "2.1.11"
   s.summary = "The Ruby UCSC API: accessing the UCSC Genome Database using Ruby"
 
   if s.respond_to? :specification_version then
-    s.specification_version = 3
+    s.specification_version = 4
 
     if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
       s.add_runtime_dependency(%q<activerecord>, ["~> 4.0.2"])

data/lib/bio-ucsc.rb

@@ -21,11 +21,12 @@ require "#{base}/gi.rb"
 
 module Bio
   module Ucsc
-    VERSION = "0.6.0"
+    VERSION = "0.6.1"
     base = "#{::File.dirname(__FILE__)}/bio-ucsc"
     
     # mammmals #####################################
     # human genome assemblies
+    autoload :Hg38, "#{base}/hg38"
     autoload :Hg19, "#{base}/hg19"
     autoload :Hg18, "#{base}/hg18"
 

data/lib/bio-ucsc/hg38.rb

@@ -0,0 +1,66 @@
+#
+# = AUTOMATIC Table Definition of Hg38
+# Copyright::   Copyright (C) 2011, 2012, 2014
+#               MISHIMA, Hiroyuki
+#               <missy at be.to / hmishima at nagasaki-u.ac.jp> 
+# License::     The MIT license
+#
+
+require "#{::File.dirname(__FILE__)}/table_class_detector"
+
+module Bio
+  module Ucsc
+    module Hg38
+      extend TableClassDetector
+
+      def self.default
+        DBConnection.default
+      end
+
+      def self.connect(param = Hash.new)
+        DBConnection.db_adapter = param[:db_adapter] if param[:db_adapter]
+        DBConnection.db_host = param[:db_host] if param[:db_host]
+        DBConnection.db_username = param[:db_username] if param[:db_username]
+        DBConnection.password = param[:password] if param[:password]
+        DBConnection.connect
+      end
+
+      class DBConnection < ActiveRecord::Base
+        include SafeAttributes
+        self.inheritance_column = 'dummy_not_to_use'
+
+        @@db_adapter  ||= 'mysql'
+        @@db_host     ||= 'genome-mysql.cse.ucsc.edu'
+        @@db_username ||= 'genome'
+        @@db_password ||= ''
+        @@db_name     ||= 'hg38'
+
+        cattr_accessor :db_adapter, :db_host, :db_username, :db_password
+
+        self.abstract_class = true
+
+        def self.default
+          @@db_adapter  = 'mysql'
+          @@db_host     = 'genome-mysql.cse.ucsc.edu'
+          @@db_username = 'genome'
+          @@db_password = ''
+        end
+
+        def self.connect
+          establish_connection({ :adapter =>  @@db_adapter,
+                                 :host =>     @@db_host,
+                                 :database => @@db_name,
+                                 :username => @@db_username,
+                                 :password => @@db_password, })
+        end
+      end # class DBConnection
+      
+      base = "#{::File.dirname(__FILE__)}/hg38"
+      # Hg19::Description has "id" colomn that is primary key
+      autoload :Description, "#{base}/description"
+      # Hg19::GbCdbaInfo has "id" colomn that is primary key
+      autoload :GbCdnaInfo, "#{base}/gbcdnainfo"
+
+    end # module Hg38
+  end
+end

data/lib/bio-ucsc/hg38/description.rb

@@ -0,0 +1,16 @@
+#
+# Hg19::Description has "id" colomn that is primary key
+#
+
+module Bio
+  module Ucsc
+    module Hg38
+      class Description < DBConnection
+        self.table_name = "description"
+        self.inheritance_column = nil
+      end
+    end
+  end
+end
+
+        

data/lib/bio-ucsc/hg38/gbcdnainfo.rb

@@ -0,0 +1,14 @@
+#
+# Hg19::GbCdnaInfo has "id" colomn that is primary key
+#
+
+module Bio
+  module Ucsc
+    module Hg38
+      class GbCdnaInfo < DBConnection
+        self.table_name = "gbCdnaInfo"
+        self.inheritance_column = nil
+      end
+    end
+  end
+end

data/samples/get-gene-ontology.rb

@@ -0,0 +1,51 @@
+require 'bio-ucsc'
+
+class GetGeneOntology
+  
+  GO   = Bio::Ucsc::Go
+  HG19 = Bio::Ucsc::Hg19
+
+  IdAspName = Struct.new(:goId, :aspect, :name)
+  ASPECTS = {
+    "F" => "Molecular Function",
+    "P" => "Biological Process",
+    "C" => "Cellular Component",
+  }
+
+  def sp_display_ids(genesym)
+    spdid =
+      HG19::KgXref.select(:spDisplayID).where(:geneSymbol => genesym).map{|x| x ? x.spDisplayID : []}
+    spdid.uniq.sort
+  end
+
+  def go_id_aspects(dids)
+    GO::GoaPart.select(:goId,:aspect).where(:dbObjectSymbol => dids).
+      map{|x| x ? IdAspName.new(x.goId, x.aspect, "") : []}
+  end
+
+  def term_names(idaspnames)
+    idaspnames.map do |ian|
+      ian.name = GO::Term.select(:name,).where(:acc => ian[:goId]).first.name
+      ian
+    end
+  end
+
+  def run(gene_symbol)
+    GO.connect
+    #GO.connect( :db_host => 'localhost',
+    #            :db_username => 'genome',
+    #            :db_password => '' )
+    HG19.connect
+    puts "# gene symbol: #{gene_symbol}"
+    dids = sp_display_ids(gene_symbol)
+    idaspnames = go_id_aspects(dids)
+    term_names(idaspnames).
+      sort_by{|x| [x.aspect, x.goId]}.
+      each{|x| puts "#{ASPECTS[x.aspect]}\t#{x.goId}\t#{x.name}"}
+  end
+
+end
+
+if $0 == __FILE__
+  ARGV.each{|x| GetGeneOntology.new.run(x)}
+end

metadata

@@ -1,8 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bio-ucsc-api
 version: !ruby/object:Gem::Version
-  version: 0.6.0
-  prerelease: 
+  version: 0.6.1
 platform: ruby
 authors:
 - Hiroyuki Mishima
@@ -10,140 +9,178 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-12-11 00:00:00.000000000 Z
+date: 2014-03-13 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: activerecord
-  requirement: &160170600 !ruby/object:Gem::Requirement
-    none: false
+  requirement: !ruby/object:Gem::Requirement
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
         version: 4.0.2
   type: :runtime
   prerelease: false
-  version_requirements: *160170600
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 4.0.2
 - !ruby/object:Gem::Dependency
   name: activesupport
-  requirement: &160169480 !ruby/object:Gem::Requirement
-    none: false
+  requirement: !ruby/object:Gem::Requirement
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
         version: 4.0.2
   type: :runtime
   prerelease: false
-  version_requirements: *160169480
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 4.0.2
 - !ruby/object:Gem::Dependency
   name: mysql
-  requirement: &160168120 !ruby/object:Gem::Requirement
-    none: false
+  requirement: !ruby/object:Gem::Requirement
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
         version: 2.9.1
   type: :runtime
   prerelease: false
-  version_requirements: *160168120
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 2.9.1
 - !ruby/object:Gem::Dependency
   name: safe_attributes
-  requirement: &160166800 !ruby/object:Gem::Requirement
-    none: false
+  requirement: !ruby/object:Gem::Requirement
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
         version: 1.0.10
   type: :runtime
   prerelease: false
-  version_requirements: *160166800
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.0.10
 - !ruby/object:Gem::Dependency
   name: activerecord-deprecated_finders
-  requirement: &160165900 !ruby/object:Gem::Requirement
-    none: false
+  requirement: !ruby/object:Gem::Requirement
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
         version: 1.0.3
   type: :runtime
   prerelease: false
-  version_requirements: *160165900
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.0.3
 - !ruby/object:Gem::Dependency
   name: bio-genomic-interval
-  requirement: &160181120 !ruby/object:Gem::Requirement
-    none: false
+  requirement: !ruby/object:Gem::Requirement
     requirements:
     - - ! '>='
       - !ruby/object:Gem::Version
         version: 0.1.2
   type: :runtime
   prerelease: false
-  version_requirements: *160181120
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 0.1.2
 - !ruby/object:Gem::Dependency
   name: rake
-  requirement: &160180180 !ruby/object:Gem::Requirement
-    none: false
+  requirement: !ruby/object:Gem::Requirement
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
         version: 10.1.0
   type: :development
   prerelease: false
-  version_requirements: *160180180
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 10.1.0
 - !ruby/object:Gem::Dependency
   name: rspec
-  requirement: &160179160 !ruby/object:Gem::Requirement
-    none: false
+  requirement: !ruby/object:Gem::Requirement
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
         version: 2.14.1
   type: :development
   prerelease: false
-  version_requirements: *160179160
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 2.14.1
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &160178180 !ruby/object:Gem::Requirement
-    none: false
+  requirement: !ruby/object:Gem::Requirement
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
         version: 1.3.5
   type: :development
   prerelease: false
-  version_requirements: *160178180
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.3.5
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &160177160 !ruby/object:Gem::Requirement
-    none: false
+  requirement: !ruby/object:Gem::Requirement
     requirements:
     - - ~>
       - !ruby/object:Gem::Version
         version: 1.8.8
   type: :development
   prerelease: false
-  version_requirements: *160177160
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.8.8
 - !ruby/object:Gem::Dependency
   name: bio
-  requirement: &160176000 !ruby/object:Gem::Requirement
-    none: false
+  requirement: !ruby/object:Gem::Requirement
     requirements:
     - - ! '>='
       - !ruby/object:Gem::Version
-        version: 1.4.3
+        version: !binary |-
+          MS40LjM=
   type: :development
   prerelease: false
-  version_requirements: *160176000
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: !binary |-
+          MS40LjM=
 - !ruby/object:Gem::Dependency
   name: rdoc
-  requirement: &160175260 !ruby/object:Gem::Requirement
-    none: false
+  requirement: !ruby/object:Gem::Requirement
     requirements:
     - - ! '>='
       - !ruby/object:Gem::Version
         version: 4.0.1
   type: :development
   prerelease: false
-  version_requirements: *160175260
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 4.0.1
 description: ! 'Ruby UCSC API: accessing the UCSC Genome Database using Ruby'
 email: missy@be.to
 executables: []
@@ -161,7 +198,6 @@ files:
 - Rakefile
 - VERSION
 - bio-ucsc-api.gemspec
-- lib/#bio-ucsc.rb#
 - lib/bio-ucsc-api.rb
 - lib/bio-ucsc.rb
 - lib/bio-ucsc/ailmel1.rb
@@ -399,6 +435,9 @@ files:
 - lib/bio-ucsc/hg19.rb
 - lib/bio-ucsc/hg19/description.rb
 - lib/bio-ucsc/hg19/gbcdnainfo.rb
+- lib/bio-ucsc/hg38.rb
+- lib/bio-ucsc/hg38/description.rb
+- lib/bio-ucsc/hg38/gbcdnainfo.rb
 - lib/bio-ucsc/hgfixed.rb
 - lib/bio-ucsc/loxafr3.rb
 - lib/bio-ucsc/mm10.rb
@@ -562,6 +601,7 @@ files:
 - lib/bio-ucsc/visigene.rb
 - lib/bio-ucsc/xentro2.rb
 - samples/bed2refseq.rb
+- samples/get-gene-ontology.rb
 - samples/hg19-2bit-retrieve.rb
 - samples/hg19-sample.rb
 - samples/num-gene-exon.rb
@@ -570,29 +610,25 @@ files:
 homepage: http://github.com/misshie/bioruby-ucsc-api
 licenses:
 - The MIT License
+metadata: {}
 post_install_message: 
 rdoc_options: []
 require_paths:
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement
-  none: false
   requirements:
   - - ! '>='
     - !ruby/object:Gem::Version
       version: '0'
-      segments:
-      - 0
-      hash: -3654614311172701481
 required_rubygems_version: !ruby/object:Gem::Requirement
-  none: false
   requirements:
   - - ! '>='
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 1.8.11
+rubygems_version: 2.1.11
 signing_key: 
-specification_version: 3
+specification_version: 4
 summary: ! 'The Ruby UCSC API: accessing the UCSC Genome Database using Ruby'
 test_files: []

data/lib/#bio-ucsc.rb#

@@ -1,209 +0,0 @@
-#
-# = bio-ucsc.rb
-# Copyright::   Copyright (C) 2011-2013
-#               MISHIMA, Hiroyuki <missy at be.to / hmishima at nagasaki-u.ac.jp> 
-# License::     Ruby licence (Ryby's / GPLv2 dual)
-
-base = "#{::File.dirname(__FILE__)}/bio-ucsc"
-
-require 'rubygems'
-gem 'activerecord', "~> 4.0.2"
-require "active_record"
-gem "safe_attributes"
-require "safe_attributes"
-gem "activerecord-deprecated_finders"
-require "active_record/deprecated_finders"
-#ActiveSupport::Deprecation.silenced = true
-
-require "#{base}/ucsc_bin"
-require "#{base}/genomic-interval-bin"
-require "#{base}/gi.rb"
-
-module Bio
-  module Ucsc
-    VERSION = "0.6.0"
-    base = "#{::File.dirname(__FILE__)}/bio-ucsc"
-    
-    # mammmals #####################################
-    # human genome assemblies
-    autoload :Hg19, "#{base}/hg19"
-    autoload :Hg18, "#{base}/hg18"
-
-    # chimp genome assemblies
-    autoload :PanTro3, "#{base}/pantro3"
-
-    # orangutan genome assemblies
-    autoload :PonAbe2, "#{base}/ponabe2"
-
-    # rhesus macaque genome assemblies
-    autoload :RheMac2, "#{base}/rhemac2"
-
-    # marmoset genome assemblies
-    autoload :CalJac3, "#{base}/caljac3"
-
-    # mouse genome assemblies
-    autoload :Mm9,  "#{base}/mm9"
-    autoload :Mm10, "#{base}/mm10"
-
-    # rat genome assemblies
-    autoload :Rn5, "#{base}/rn5"
-    autoload :Rn4, "#{base}/rn4"
-
-    # guinea pig genome assemblies
-    autoload :CavPor3, "#{base}/cavpor3"
-
-    # rabbit genome assemblies
-    autoload :OryCun2, "#{base}/orycun2"
-
-    # cat genome assemblies
-    autoload :FelCat4, "#{base}/felcat4"
-
-    # panda genome assemblies
-    autoload :AilMel1, "#{base}/ailmel1"
-    
-    # dog genome assemblies
-    autoload :CanFam2, "#{base}/canfam2"
-
-    # horse genome assemblies
-    autoload :EquCab2, "#{base}/equcab2"
-
-    # pig genome assemblies
-    autoload :SusScr2, "#{base}/susscr2"
-
-    # sheep genome assemblies
-    autoload :OviAri1, "#{base}/oviari1"
-
-    # cow genome assemblies
-    autoload :BosTau4, "#{base}/bostau4"
-
-    # elephant genome assemblies
-    autoload :LoxAfr3, "#{base}/loxafr3"
-
-    # opossum genome assemblies
-    autoload :MonDom5, "#{base}/mondom5"
-
-    # platypus genome assemblies
-    autoload :OrnAna1, "#{base}/ornana1"
-
-    # vertebrates #################################
-    # chiken genome assemblies
-    autoload :GalGal4, "#{base}/galgal4"
-
-    # zebra finch genome assemblies
-    autoload :TaeGut1, "#{base}/taegut1"
-
-    # lizard genome assemblies
-    autoload :AnoCar2, "#{base}/anocar2"
-
-    # X. tropicalis genome assemblies
-    autoload :XenTro2, "#{base}/xentro2"
-
-    # zebrafish genome assemblies
-    autoload :DanRer7, "#{base}/danrer7"
-
-    # tetraodon genome assemblies
-    autoload :TetNig2, "#{base}/tetnig2"
-
-    # fugu genome assemblies
-    autoload :Fr2, "#{base}/fr2"
-
-    # stickleback genome assemblies
-    autoload :GasAcu1, "#{base}/gasacu1"
-
-    # medaka genome assemblies
-    autoload :OryLat2, "#{base}/orylat2"
-
-    # lamprey genome assemblies
-    autoload :PetMar1, "#{base}/petmar1"
-
-    # deuterostomes ###############################
-    # lancelet genome assemblies
-    autoload :BraFlo1, "#{base}/braflo1.rb"
-
-    # sea squirt genome assemblies
-    autoload :Ci2, "#{base}/ci2"
-
-    # sea urchin genome assemblies
-    autoload :StrPur2, "#{base}/strpur2"
-
-    # insects  ####################################
-    # D. melanogaster genome assemblies
-    autoload :Dm3, "#{base}/dm3" 
-
-    # D. silulans genome assemblies
-    autoload :DroSim1, "#{base}/drosim1"
-
-    # D. sechellia genome assemblies
-    autoload :DroSec1, "#{base}/drosec1"
-
-    # D. yakuba genome assemblies
-    autoload :DroYak2, "#{base}/droyak2"
-
-    # D. erecta genome assemblies
-    autoload :DroEre1, "#{base}/droere1"
-
-    # D. ananassae genome assemblies
-    autoload :DroAna2, "#{base}/droana2"
-
-    # D. pseudoobscura genome assemblies
-    autoload :Dp3, "#{base}/dp3"
-
-    # D. persimilis genome assemblies
-    autoload :DroPer1, "#{base}/droper1"
-
-    # D. virilis genome assemblies
-    autoload :DroVir2, "#{base}/drovir2"
-
-    # D. mojavensis genome assemblies
-    autoload :DroMoj2, "#{base}/dromoj2"
-
-    # D. grimshawi genome assemblies
-    autoload :DroGri1, "#{base}/drogri1"
-
-    # Anopheles mosquito genome assemblies
-    autoload :AnoGam1, "#{base}/anogam1"
-
-    # honey bee genome assemblies
-    autoload :ApiMel2, "#{base}/apimel2"
-
-    # nematodes ###################################
-    # C. elegans genome assemblies
-    autoload :Ce6, "#{base}/ce6"
-
-    # C. brenneri genome assemblies
-    autoload :CaePb2, "#{base}/caepb2"
-
-    # C. briggsae genome assemblies
-    autoload :Cb3, "#{base}/cb3"
-
-    # C. remanei genome assemblies
-    autoload :CaeRem3, "#{base}/caerem3"
-
-    # C. japonica genome assemblies
-    autoload :CaeJap1, "#{base}/caejap1"
-
-    # P. pacificus genome assemblies
-    autoload :PriPac1, "#{base}/pripac1"
-
-    # others  #####################################
-    # sea hare genome assemblies
-    autoload :AplCal1, "#{base}/aplcal1"
-
-    # yeast genome assemblies
-    autoload :SacCer2, "#{base}/saccer2"
-
-    # genome assembly independent dababases #######
-    autoload :UniProt, "#{base}/uniprot"
-    autoload :Proteome,  "#{base}/proteome"
-    autoload :Go, "#{base}/go"
-    autoload :HgFixed, "#{base}/hgfixed"
-    autoload :VisiGene, "#{base}/visigene"
-
-    # utility classes #############################
-    # accessing genome sequences in the 2bit format 
-    # after version 0.4.0, UCSC::Reference is moved to UCSC::File::Twobit
-    autoload :File, "#{base}/file"
-    autoload :Reference, "#{base}/reference"
-    autoload :Schema, "#{base}/schema"
-  end
-end