bio-ucsc-api 0.1.0 → 0.2.0

data/lib/bio-ucsc/uniprot.rb

@@ -0,0 +1,19 @@
+#
+# = AUTOMATIC Table Definition of Uniprot
+# Copyright::   Copyright (C) 2011
+#               MISHIMA, Hiroyuki
+#               <missy at be.to / hmishima at nagasaki-u.ac.jp> 
+# License::     The Ruby licence (Ryby's / GPLv2 dual)
+#
+
+require "#{File.dirname(__FILE__)}/uniprot/db_connection"
+require "#{File.dirname(__FILE__)}/table_class_detector"
+
+module Bio
+  module Ucsc
+    module UniProt
+      extend TableClassDetector
+      base = "#{File.dirname(__FILE__)}/uniprot"
+    end
+  end
+end

data/lib/bio-ucsc/uniprot/db_connection.rb

@@ -0,0 +1,61 @@
+#
+# = lib/ucsc/uniprot/db_connection.rb - UCSC UniProt DB connection
+#
+# Copyright::   Cioyrught (C) 2011
+#               MISHIMA, Hiroyuki <missy at be.to / hmishima at nagasaki-u.ac.jp> 
+# Copyright::   Copyright (C) 2010
+#               Jan Aerts <jan.aerts@gmail.com>
+# License::     Ruby licence (Ryby's / GPLv2 dual)
+
+require 'rubygems'
+require 'active_record'
+
+module Bio
+  module Ucsc
+
+    module UniProt
+      # = DESCRIPTION
+      # The Ucsc::Uniplot::DBConnection is the actual connection established
+      # with the UCSC mysql server.
+
+      class DBConnection < ActiveRecord::Base
+        # = DESCRIPTION
+        # The Bin::Ucsc::Uniplot::DBConnection#connect method makes the connection
+        # to the UCSC uniprot database.
+        #
+        # = USAGE
+        #  # Connect to the uniplot
+        #  Bin::Ucsc::Uniprot::DBConnection.connect
+        #
+        # ---
+        # *Arguments*: none
+        @@db_adapter  ||= 'mysql'
+        @@db_host     ||= 'genome-mysql.cse.ucsc.edu'
+        @@db_username ||= 'genome'
+        @@db_password ||= ''
+
+        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 => 'uniProt',
+                               :username => @@db_username,
+                               :password => @@db_password
+                               )
+        end
+      end
+    end # module Uniprot
+    
+  end # module Ucsc
+end # module Bio

data/lib/bio-ucsc/visigene.rb

@@ -0,0 +1,19 @@
+#
+# = AUTOMATIC Table Definition of VisiGene
+# Copyright::   Copyright (C) 2011
+#               MISHIMA, Hiroyuki
+#               <missy at be.to / hmishima at nagasaki-u.ac.jp> 
+# License::     The Ruby licence (Ryby's / GPLv2 dual)
+#
+
+require "#{File.dirname(__FILE__)}/visigene/db_connection"
+require "#{File.dirname(__FILE__)}/table_class_detector"
+
+module Bio
+  module Ucsc
+    module VisiGene
+      extend TableClassDetector
+      base = "#{File.dirname(__FILE__)}/visigene"
+    end
+  end
+end

data/lib/bio-ucsc/visigene/db_connection.rb

@@ -0,0 +1,56 @@
+#
+# = db_connection.rb - UCSC DB connection
+#
+# Copyright::   Cioyrught (C) 2011
+#               MISHIMA, Hiroyuki <missy at be.to / hmishima at nagasaki-u.ac.jp> 
+# Copyright::   Copyright (C) 2010
+#               Jan Aerts <jan.aerts@gmail.com>
+# License::     Ruby licence (Ryby's / GPLv2 dual)
+
+require 'rubygems'
+require 'active_record'
+
+module Bio
+  module Ucsc
+
+    module VisiGene
+      # = DESCRIPTION
+      # Actual connection established to the UCSC mysql server.
+      class DBConnection < ActiveRecord::Base
+        # = DESCRIPTION
+        # The #connect method make the connection
+        #
+        # = USAGE
+        #  Bin::Ucsc::DB_NAME::DBConnection.connect
+        #
+        # ---
+        # *Arguments*: none
+        @@db_adapter  ||= 'mysql'
+        @@db_host     ||= 'genome-mysql.cse.ucsc.edu'
+        @@db_username ||= 'genome'
+        @@db_password ||= ''
+
+        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 => 'visiGene',
+                               :username => @@db_username,
+                               :password => @@db_password, )
+        end
+      end
+    end # module
+    
+  end # module Ucsc
+end # module Bio

data/spec/ce6_spec.rb

@@ -0,0 +1,1238 @@
+require "bio-ucsc"
+require "pp"
+
+describe "Bio::Ucsc::Ce6" do
+
+  before(:all) do
+    Bio::Ucsc::Ce6::DBConnection.connect
+  end
+
+  describe "Bio::Ucsc::Ce6::T25mersRepeats" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Ce6::T25mersRepeats.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::AlgBindGenic" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Ce6::AlgBindGenic.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::AlgBindSites" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Ce6::AlgBindSites.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::All_est" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Ce6::All_est.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::All_mrna" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Ce6::All_mrna.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::Author" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Ce6::Author.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::BlastSGPep01" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Ce6::BlastSGPep01.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::BlastSGRef01" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Ce6::BlastSGRef01.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::Cds" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Ce6::Cds.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::Cell" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Ce6::Cell.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::ChainCaeJap1" do
+    context ".find_by_interval" do
+      it 'returns the first records' do
+        gi = Bio::GenomicInterval.parse("chrI:1-15,072,421")
+        result = Bio::Ucsc::Ce6::ChainCaeJap1.find_by_interval gi
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::ChainCaeJap1Link" do
+    context ".find_by_interval" do
+      it 'returns the first records' do
+        gi = Bio::GenomicInterval.parse("chrI:1-15,072,421")
+        result = Bio::Ucsc::Ce6::ChainCaeJap1Link.find_by_interval gi
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::ChainCaePb2" do
+    context ".first" do
+      it 'returns the first records' do
+        gi = Bio::GenomicInterval.parse("chrI:1-15,072,421")
+        result = Bio::Ucsc::Ce6::ChainCaePb2.find_by_interval gi
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::ChainCaePb2Link" do
+    context ".first" do
+      it 'returns the first records' do
+        gi = Bio::GenomicInterval.parse("chrI:1-15,072,421")
+        result = Bio::Ucsc::Ce6::ChainCaePb2Link.find_by_interval gi
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::ChainCaeRem3" do
+    context ".first" do
+      it 'returns the first records' do
+        gi = Bio::GenomicInterval.parse("chrI:1-15,072,421")
+        result = Bio::Ucsc::Ce6::ChainCaeRem3.find_by_interval gi
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::ChainCaeRem3Link" do
+    context ".first" do
+      gi = Bio::GenomicInterval.parse("chrI:1-15,072,421")
+      it 'returns the first records' do
+        result = Bio::Ucsc::Ce6::ChainCaeRem3Link.find_by_interval gi
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::ChainCb3" do
+    context ".first" do
+      it 'returns the first records' do
+        gi = Bio::GenomicInterval.parse("chrI:1-15,072,421")
+        result = Bio::Ucsc::Ce6::ChainCb3.find_by_interval gi
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::ChainCb3Link" do
+    context ".first" do
+      it 'returns the first records' do
+        gi = Bio::GenomicInterval.parse("chrI:1-15,072,421")
+        result = Bio::Ucsc::Ce6::ChainCb3Link.find_by_interval gi
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::ChainPriPac1" do
+    context ".first" do
+      it 'returns the first records' do
+        gi = Bio::GenomicInterval.parse("chrI:1-15,072,421")
+        result = Bio::Ucsc::Ce6::ChainPriPac1.find_by_interval gi
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::ChainPriPac1Link" do
+    context ".first" do
+      it 'returns the first records' do
+        gi = Bio::GenomicInterval.parse("chrI:1-15,072,421")
+        result = Bio::Ucsc::Ce6::ChainPriPac1Link.find_by_interval gi
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::ChainSelf" do
+    context ".first" do
+      it 'returns the first records' do
+        gi = Bio::GenomicInterval.parse("chrI:1-15,072,421")
+        result = Bio::Ucsc::Ce6::ChainSelf.find_by_interval gi
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::ChainSelfLink" do
+    context ".first" do
+      it 'returns the first records' do
+        gi = Bio::GenomicInterval.parse("chrI:1-15,072,421")
+        result = Bio::Ucsc::Ce6::ChainSelfLink.find_by_interval gi
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::ChromInfo" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Ce6::ChromInfo.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::Description" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Ce6::Description.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::Development" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Ce6::Development.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::DmBlastTab" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Ce6::DmBlastTab.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::DrBlastTab" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Ce6::DrBlastTab.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::EnsGene" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Ce6::EnsGene.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::EnsGtp" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Ce6::EnsGtp.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::EnsPep" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Ce6::EnsPep.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::Est" do
+    context ".find_by_interval" do
+      it 'returns the first records' do
+        gi = Bio::GenomicInterval.parse("chrI:1-15,072,421")
+        result = Bio::Ucsc::Ce6::Est.find_by_interval gi
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::EstOrientInfo" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Ce6::EstOrientInfo.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::ExtFile" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Ce6::ExtFile.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::Gap" do
+    context ".find_by_interval" do
+      it 'returns nil (the first records)' do
+        gi = Bio::GenomicInterval.parse("chrII:1-15,072,421")
+        result = Bio::Ucsc::Ce6::Gap.find_by_interval gi
+        pp result
+        result.should be_nil
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::GbCdnaInfo" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Ce6::GbCdnaInfo.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::GbExtFile" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Ce6::GbExtFile.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::GbLoaded" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Ce6::GbLoaded.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::GbMiscDiff" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Ce6::GbMiscDiff.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::GbSeq" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Ce6::GbSeq.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::GbStatus" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Ce6::GbStatus.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::GbWarn" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Ce6::GbWarn.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::Gc5Base" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Ce6::Gc5Base.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::GeneName" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Ce6::GeneName.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::Gold" do
+    context ".find_by_interval" do
+      it 'returns the first records' do
+        gi = Bio::GenomicInterval.parse("chrV:1-200,000")
+        result = Bio::Ucsc::Ce6::Gold.find_by_interval gi
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::Grp" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Ce6::Grp.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::HgBlastTab" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Ce6::HgBlastTab.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::HgFindSpec" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Ce6::HgFindSpec.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::History" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Ce6::History.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::ImageClone" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Ce6::ImageClone.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::IntronEst" do
+    context ".find_by_interval" do
+      it 'returns the first records' do
+        gi = Bio::GenomicInterval.parse("chrI:1-15,072,421")
+        result = Bio::Ucsc::Ce6::IntronEst.find_by_interval gi
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::Keyword" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Ce6::Keyword.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::KimExpDistance" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Ce6::KimExpDistance.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::Library" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Ce6::Library.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::MmBlastTab" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Ce6::MmBlastTab.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::MonoNucleosomesAntiSense" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Ce6::MonoNucleosomesAntiSense.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::MonoNucleosomesSense" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Ce6::MonoNucleosomesSense.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::Mrna" do
+    context ".first" do
+      it 'returns the first records' do
+        gi = Bio::GenomicInterval.parse("chrV:1-200,000")
+        result = Bio::Ucsc::Ce6::Mrna.find_by_interval gi
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::MrnaClone" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Ce6::MrnaClone.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::MrnaOrientInfo" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Ce6::MrnaOrientInfo.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::Mt1Forward" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Ce6::Mt1Forward.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::Mt1Reverse" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Ce6::Mt1Reverse.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::Mt2Forward" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Ce6::Mt2Forward.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::Mt2Reverse" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Ce6::Mt2Reverse.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::Mt3Forward" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Ce6::Mt3Forward.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::Mt3Reverse" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Ce6::Mt3Reverse.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::Multiz6way" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Ce6::Multiz6way.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::Multiz6wayFrames" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Ce6::Multiz6wayFrames.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::Multiz6waySummary" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Ce6::Multiz6waySummary.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::NestedRepeats" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Ce6::NestedRepeats.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::NetCaeJap1" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Ce6::NetCaeJap1.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::NetCaePb2" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Ce6::NetCaePb2.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::NetCaeRem3" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Ce6::NetCaeRem3.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::NetCb3" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Ce6::NetCb3.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::NetPriPac1" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Ce6::NetPriPac1.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::NucleosomeAdjustedCoverage" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Ce6::NucleosomeAdjustedCoverage.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::NucleosomeControl" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Ce6::NucleosomeControl.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::NucleosomeControlAntisenseCoverage" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Ce6::NucleosomeControlAntisenseCoverage.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::NucleosomeControlSenseCoverage" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Ce6::NucleosomeControlSenseCoverage.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::NucleosomeFragmentsAntisense" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Ce6::NucleosomeFragmentsAntisense.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::NucleosomeFragmentsSense" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Ce6::NucleosomeFragmentsSense.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::NucleosomeStringency" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Ce6::NucleosomeStringency.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::OrfToGene" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Ce6::OrfToGene.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::Organism" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Ce6::Organism.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::PhastCons6way" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Ce6::PhastCons6way.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::PhastConsElements6way" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Ce6::PhastConsElements6way.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::ProductName" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Ce6::ProductName.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::RefFlat" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Ce6::RefFlat.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::RefGene" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Ce6::RefGene.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::RefLink" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Ce6::RefLink.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::RefSeqAli" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Ce6::RefSeqAli.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::RefSeqStatus" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Ce6::RefSeqStatus.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::RefSeqSummary" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Ce6::RefSeqSummary.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::Rmsk" do
+    context ".find_by_interval" do
+      it 'returns the first records' do
+        gi = Bio::GenomicInterval.parse("chrV:1-200,000")
+        result = Bio::Ucsc::Ce6::Rmsk.find_by_interval gi
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::RnBlastTab" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Ce6::RnBlastTab.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::SangerBlastTab" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Ce6::SangerBlastTab.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::SangerCanonical" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Ce6::SangerCanonical.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::SangerGene" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Ce6::SangerGene.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::SangerGeneToWBGeneID" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Ce6::SangerGeneToWBGeneID.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::SangerIsoforms" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Ce6::SangerIsoforms.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::SangerLinks" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Ce6::SangerLinks.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::SangerPep" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Ce6::SangerPep.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::SangerPseudoGene" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Ce6::SangerPseudoGene.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::SangerRnaGene" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Ce6::SangerRnaGene.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::SangerToRefSeq" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Ce6::SangerToRefSeq.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::ScBlastTab" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Ce6::ScBlastTab.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::Sex" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Ce6::Sex.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::SimpleRepeat" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Ce6::SimpleRepeat.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::Source" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Ce6::Source.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::TableDescriptions" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Ce6::TableDescriptions.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::Tissue" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Ce6::Tissue.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::TrackDb" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Ce6::TrackDb.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::Wt1Forward" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Ce6::Wt1Forward.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::Wt1Reverse" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Ce6::Wt1Reverse.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::Wt2Forward" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Ce6::Wt2Forward.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::Wt2Reverse" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Ce6::Wt2Reverse.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::Wt3Forward" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Ce6::Wt3Forward.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::Wt3Reverse" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Ce6::Wt3Reverse.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::XenoMrna" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Ce6::XenoMrna.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::XenoRefFlat" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Ce6::XenoRefFlat.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::XenoRefGene" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Ce6::XenoRefGene.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Ce6::XenoRefSeqAli" do
+    context ".first" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Ce6::XenoRefSeqAli.first
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+end