bio-ucsc-api 0.3.1 → 0.4.0

data/lib/bio-ucsc/tetnig2.rb

@@ -1,13 +1,13 @@
 #
 # = AUTOMATIC Table Definition of the Tetraodon Mar. 2007 (Genoscope 8.0/tetNig2) assembly
-# Copyright::   Copyright (C) 2011
+# Copyright::   Copyright (C) 2011, 2012
 #               MISHIMA, Hiroyuki
 #               <missy at be.to / hmishima at nagasaki-u.ac.jp> 
 # License::     The Ruby licence (Ryby's / GPLv2 dual)
 #
 
-require "#{File.dirname(__FILE__)}/tetnig2/db_connection"
-require "#{File.dirname(__FILE__)}/table_class_detector"
+require "#{::File.dirname(__FILE__)}/db_connector"
+require "#{::File.dirname(__FILE__)}/table_class_detector"
 
 module Bio
   module Ucsc
@@ -17,8 +17,10 @@ module Bio
 Chr11 Chr12 Chr13 Chr14 Chr15 Chr16 Chr17 Chr18 Chr19 
 Chr20 Chr21 ChrM ChrUn_random)
       extend TableClassDetector
+      include DBConnector
+      DBConnection.database "tetNig2"
 
-      base = "#{File.dirname(__FILE__)}/tetnig2"
+      base = "#{::File.dirname(__FILE__)}/tetnig2"
       autoload :Mrna, "#{base}/mrna"
     end
   end

data/lib/bio-ucsc/tetnig2/mrna.rb

@@ -12,25 +12,28 @@ module Bio
     module TetNig2
 
       class Mrna
+        include DBConnector
+        DBConnection.database "tetNig2"
+
         KLASS = "Mrna"
         KLASS_S = "mrna"
 
         Bio::Ucsc::TetNig2::CHROMS.each do |chr|
           class_eval %!
             class #{chr[0..0].upcase + chr[1..-1]}_#{KLASS} < DBConnection
-              set_table_name "#{chr[0..0].downcase + chr[1..-1]}_#{KLASS_S}"
-              set_primary_key nil
-              set_inheritance_column nil
+              self.table_name = "#{chr[0..0].downcase + chr[1..-1]}_#{KLASS_S}"
+              self.primary_key = nil
+              self.inheritance_column = nil
 
-              def self.find_by_interval(interval, opt = {:partial => true})
+              def self.find_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
                 find_first_or_all_by_interval(interval, :first, opt)
               end
         
-              def self.find_all_by_interval(interval, opt = {:partial => true})
+              def self.find_all_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
                 find_first_or_all_by_interval(interval, :all, opt)
               end
 
-              def self.find_first_or_all_by_interval(interval, first_all, opt)
+              def self.find_first_or_all_by_interval(interval, first_all, opt); interval =  Bio::Ucsc::Gi.wrap(interval)
                 zstart = interval.zero_start
                 zend   = interval.zero_end
                 if opt[:partial] == true
@@ -63,13 +66,13 @@ AND  (tEnd BETWEEN :zstart AND :zend))
           !
         end # each chromosome
 
-        def self.find_by_interval(interval, opt = {:partial => true})
+        def self.find_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
           chrom = interval.chrom[0..0].upcase + interval.chrom[1..-1]
           chr_klass = self.const_get("#{chrom}_#{KLASS}")
           chr_klass.__send__(:find_by_interval, interval, opt)
         end
 
-        def self.find_all_by_interval(interval, opt = {:partial => true})
+        def self.find_all_by_interval(interval, opt = {:partial => true}); interval = Bio::Ucsc::Gi.wrap(interval)
           chrom = interval.chrom[0..0].upcase + interval.chrom[1..-1]
           chr_klass = self.const_get("#{chrom}_#{KLASS}")
           chr_klass.__send__(:find_all_by_interval, interval, opt)

data/lib/bio-ucsc/uniprot.rb

@@ -1,19 +1,22 @@
 #
 # = AUTOMATIC Table Definition of Uniprot
-# Copyright::   Copyright (C) 2011
+# Copyright::   Copyright (C) 2011, 2012
 #               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"
+require "#{::File.dirname(__FILE__)}/db_connector"
+require "#{::File.dirname(__FILE__)}/table_class_detector"
 
 module Bio
   module Ucsc
     module UniProt
       extend TableClassDetector
-      base = "#{File.dirname(__FILE__)}/uniprot"
+      include DBConnector
+      DBConnection.database "uniProt"
+
+      base = "#{::File.dirname(__FILE__)}/uniprot"
     end
   end
 end

data/lib/bio-ucsc/visigene.rb

@@ -6,14 +6,17 @@
 # License::     The Ruby licence (Ryby's / GPLv2 dual)
 #
 
-require "#{File.dirname(__FILE__)}/visigene/db_connection"
-require "#{File.dirname(__FILE__)}/table_class_detector"
+require "#{::File.dirname(__FILE__)}/db_connector"
+require "#{::File.dirname(__FILE__)}/table_class_detector"
 
 module Bio
   module Ucsc
     module VisiGene
       extend TableClassDetector
-      base = "#{File.dirname(__FILE__)}/visigene"
+      include DBConnector
+      DBConnection.database "visiGene"
+
+      base = "#{::File.dirname(__FILE__)}/visigene"
     end
   end
 end

data/lib/bio-ucsc/xentro2.rb

@@ -1,13 +1,13 @@
 #
 # = AUTOMATIC Table Definition of the X. tropicalis Aug. 2005 (JGI 4.1/xenTro2) assembly
-# Copyright::   Copyright (C) 2011
+# Copyright::   Copyright (C) 2011, 2012
 #               MISHIMA, Hiroyuki
 #               <missy at be.to / hmishima at nagasaki-u.ac.jp> 
 # License::     The Ruby licence (Ryby's / GPLv2 dual)
 #
 
-require "#{File.dirname(__FILE__)}/xentro2/db_connection"
-require "#{File.dirname(__FILE__)}/table_class_detector"
+require "#{::File.dirname(__FILE__)}/db_connector"
+require "#{::File.dirname(__FILE__)}/table_class_detector"
 
 module Bio
   module Ucsc
@@ -15,16 +15,10 @@ module Bio
       CHROMS = %w() # many scaffolds
 
       extend TableClassDetector
+      include DBConnector
+      DBConnection.database "xenTro2"
 
-      base = "#{File.dirname(__FILE__)}/xentro2"
-      # autoload :ChainGalGal3, "#{base}/chaingalgal3"
-      # autoload :ChainGalGal3Link, "#{base}/chaingalgal3link"
-      # autoload :Est, "#{base}/est"
-      # autoload :Gap, "#{base}/gap"
-      # autoload :Gold, "#{base}/gold"
-      # autoload :IntronEst, "#{base}/intronest"
-      # autoload :Mrna, "#{base}/mrna"
-      # autoload :Rmsk, "#{base}/rmsk"
+      base = "#{::File.dirname(__FILE__)}/xentro2"
     end
   end
 end

data/samples/num-gene-exon.rb

@@ -9,8 +9,7 @@
 # number of genes, and maximum number of exons.
 #
 
-#require 'bio-ucsc'
-require '../lib/bio-ucsc'
+require 'bio-ucsc'
 
 interval = Bio::GenomicInterval.parse(ARGV[0])
 

data/samples/snp2genes.rb

@@ -13,13 +13,7 @@
 
 PADDING = 60_000
 
-# require 'bio-ucsc'
-require File.dirname(__FILE__) + '/../lib/bio-ucsc'
-
-# require 'active_record'
-# require 'logger'
-# ActiveRecord::Base.logger = Logger.new("sql.log")
-# ActiveRecord::Base.logger.level = 0
+require 'bio-ucsc'
 
 include Bio
 

data/samples/symbol2summary.rb

@@ -8,9 +8,15 @@
 # License::     The Ruby licence (Ryby's / GPLv2 dual)
 #
 
-require File.dirname(__FILE__) + '/../lib/bio-ucsc'
+#require File.dirname(__FILE__) + '/../lib/bio-ucsc'
+require 'bio-ucsc'
 require 'nkf'
 
+require 'active_record'
+require 'logger'
+ActiveRecord::Base.logger = Logger.new("sql.log")
+ActiveRecord::Base.logger.level = 0
+
 class Sym2Sum
 
   def run(genesym)

data/spec/ailmel1_spec.rb

@@ -67,45 +67,45 @@ describe "Bio::Ucsc::AilMel1" do
     end
   end 
 
-  describe "Bio::Ucsc::AilMel1::ChainBraFlo1" do
-    context ".first" do
-      it 'returns the first records' do
-        result = Bio::Ucsc::AilMel1::ChainBraFlo1.first
-        pp result
-        result.should be_true
-      end
-    end
-  end 
-
-  describe "Bio::Ucsc::AilMel1::ChainBraFlo1Link" do
-    context ".first" do
-      it 'returns the first records' do
-        result = Bio::Ucsc::AilMel1::ChainBraFlo1Link.first
-        pp result
-        result.should be_true
-      end
-    end
-  end 
-
-  describe "Bio::Ucsc::AilMel1::ChainGalGal3" do
-    context ".first" do
-      it 'returns the first records' do
-        result = Bio::Ucsc::AilMel1::ChainGalGal3.first
-        pp result
-        result.should be_true
-      end
-    end
-  end 
-
-  describe "Bio::Ucsc::AilMel1::ChainGalGal3Link" do
-    context ".first" do
-      it 'returns the first records' do
-        result = Bio::Ucsc::AilMel1::ChainGalGal3Link.first
-        pp result
-        result.should be_true
-      end
-    end
-  end 
+  # describe "Bio::Ucsc::AilMel1::ChainBraFlo1" do
+  #   context ".first" do
+  #     it 'returns the first records' do
+  #       result = Bio::Ucsc::AilMel1::ChainBraFlo1.first
+  #       pp result
+  #       result.should be_true
+  #     end
+  #   end
+  # end 
+
+  # describe "Bio::Ucsc::AilMel1::ChainBraFlo1Link" do
+  #   context ".first" do
+  #     it 'returns the first records' do
+  #       result = Bio::Ucsc::AilMel1::ChainBraFlo1Link.first
+  #       pp result
+  #       result.should be_true
+  #     end
+  #   end
+  # end 
+
+  # describe "Bio::Ucsc::AilMel1::ChainGalGal3" do
+  #   context ".first" do
+  #     it 'returns the first records' do
+  #       result = Bio::Ucsc::AilMel1::ChainGalGal3.first
+  #       pp result
+  #       result.should be_true
+  #     end
+  #   end
+  # end 
+
+  # describe "Bio::Ucsc::AilMel1::ChainGalGal3Link" do
+  #   context ".first" do
+  #     it 'returns the first records' do
+  #       result = Bio::Ucsc::AilMel1::ChainGalGal3Link.first
+  #       pp result
+  #       result.should be_true
+  #     end
+  #   end
+  # end 
 
   describe "Bio::Ucsc::AilMel1::ChainHg19" do
     context ".first" do
@@ -147,25 +147,25 @@ describe "Bio::Ucsc::AilMel1" do
     end
   end 
 
-  describe "Bio::Ucsc::AilMel1::ChainOryLat2" do
-    context ".first" do
-      it 'returns the first records' do
-        result = Bio::Ucsc::AilMel1::ChainOryLat2.first
-        pp result
-        result.should be_true
-      end
-    end
-  end 
+  # describe "Bio::Ucsc::AilMel1::ChainOryLat2" do
+  #   context ".first" do
+  #     it 'returns the first records' do
+  #       result = Bio::Ucsc::AilMel1::ChainOryLat2.first
+  #       pp result
+  #       result.should be_true
+  #     end
+  #   end
+  # end 
 
-  describe "Bio::Ucsc::AilMel1::ChainOryLat2Link" do
-    context ".first" do
-      it 'returns the first records' do
-        result = Bio::Ucsc::AilMel1::ChainOryLat2Link.first
-        pp result
-        result.should be_true
-      end
-    end
-  end 
+  # describe "Bio::Ucsc::AilMel1::ChainOryLat2Link" do
+  #   context ".first" do
+  #     it 'returns the first records' do
+  #       result = Bio::Ucsc::AilMel1::ChainOryLat2Link.first
+  #       pp result
+  #       result.should be_true
+  #     end
+  #   end
+  # end 
 
   describe "Bio::Ucsc::AilMel1::ChromInfo" do
     context ".first" do
@@ -207,15 +207,15 @@ describe "Bio::Ucsc::AilMel1" do
     end
   end 
 
-  describe "Bio::Ucsc::AilMel1::ExtFile" do
-    context ".first" do
-      it 'returns the first records' do
-        result = Bio::Ucsc::AilMel1::ExtFile.first
-        pp result
-        result.should be_true
-      end
-    end
-  end 
+  # describe "Bio::Ucsc::AilMel1::ExtFile" do
+  #   context ".first" do
+  #     it 'returns the first records' do
+  #       result = Bio::Ucsc::AilMel1::ExtFile.first
+  #       pp result
+  #       result.should be_true
+  #     end
+  #   end
+  # end 
 
   describe "Bio::Ucsc::AilMel1::Gap" do
     context ".first" do
@@ -367,15 +367,15 @@ describe "Bio::Ucsc::AilMel1" do
     end
   end 
 
-  describe "Bio::Ucsc::AilMel1::IntronEst" do
-    context ".first" do
-      it 'returns the first records' do
-        result = Bio::Ucsc::AilMel1::IntronEst.first
-        pp result
-        result.should be_true
-      end
-    end
-  end 
+  # describe "Bio::Ucsc::AilMel1::IntronEst" do
+  #   context ".first" do
+  #     it 'returns the first records' do
+  #       result = Bio::Ucsc::AilMel1::IntronEst.first
+  #       pp result
+  #       result.should be_true
+  #     end
+  #   end
+  # end 
 
   describe "Bio::Ucsc::AilMel1::Keyword" do
     context ".first" do
@@ -417,25 +417,25 @@ describe "Bio::Ucsc::AilMel1" do
     end
   end 
 
-  describe "Bio::Ucsc::AilMel1::Multiz6way" do
-    context ".first" do
-      it 'returns the first records' do
-        result = Bio::Ucsc::AilMel1::Multiz6way.first
-        pp result
-        result.should be_true
-      end
-    end
-  end 
+  # describe "Bio::Ucsc::AilMel1::Multiz6way" do
+  #   context ".first" do
+  #     it 'returns the first records' do
+  #       result = Bio::Ucsc::AilMel1::Multiz6way.first
+  #       pp result
+  #       result.should be_true
+  #     end
+  #   end
+  # end 
 
-  describe "Bio::Ucsc::AilMel1::Multiz6wayFrames" do
-    context ".first" do
-      it 'returns the first records' do
-        result = Bio::Ucsc::AilMel1::Multiz6wayFrames.first
-        pp result
-        result.should be_true
-      end
-    end
-  end 
+  # describe "Bio::Ucsc::AilMel1::Multiz6wayFrames" do
+  #   context ".first" do
+  #     it 'returns the first records' do
+  #       result = Bio::Ucsc::AilMel1::Multiz6wayFrames.first
+  #       pp result
+  #       result.should be_true
+  #     end
+  #   end
+  # end 
 
   describe "Bio::Ucsc::AilMel1::NestedRepeats" do
     context ".first" do
@@ -447,25 +447,25 @@ describe "Bio::Ucsc::AilMel1" do
     end
   end 
 
-  describe "Bio::Ucsc::AilMel1::NetBraFlo1" do
-    context ".first" do
-      it 'returns the first records' do
-        result = Bio::Ucsc::AilMel1::NetBraFlo1.first
-        pp result
-        result.should be_true
-      end
-    end
-  end 
+  # describe "Bio::Ucsc::AilMel1::NetBraFlo1" do
+  #   context ".first" do
+  #     it 'returns the first records' do
+  #       result = Bio::Ucsc::AilMel1::NetBraFlo1.first
+  #       pp result
+  #       result.should be_true
+  #     end
+  #   end
+  # end 
 
-  describe "Bio::Ucsc::AilMel1::NetGalGal3" do
-    context ".first" do
-      it 'returns the first records' do
-        result = Bio::Ucsc::AilMel1::NetGalGal3.first
-        pp result
-        result.should be_true
-      end
-    end
-  end 
+  # describe "Bio::Ucsc::AilMel1::NetGalGal3" do
+  #   context ".first" do
+  #     it 'returns the first records' do
+  #       result = Bio::Ucsc::AilMel1::NetGalGal3.first
+  #       pp result
+  #       result.should be_true
+  #     end
+  #   end
+  # end 
 
   describe "Bio::Ucsc::AilMel1::NetHg19" do
     context ".first" do
@@ -487,15 +487,15 @@ describe "Bio::Ucsc::AilMel1" do
     end
   end 
 
-  describe "Bio::Ucsc::AilMel1::NetOryLat2" do
-    context ".first" do
-      it 'returns the first records' do
-        result = Bio::Ucsc::AilMel1::NetOryLat2.first
-        pp result
-        result.should be_true
-      end
-    end
-  end 
+  # describe "Bio::Ucsc::AilMel1::NetOryLat2" do
+  #   context ".first" do
+  #     it 'returns the first records' do
+  #       result = Bio::Ucsc::AilMel1::NetOryLat2.first
+  #       pp result
+  #       result.should be_true
+  #     end
+  #   end
+  # end 
 
   describe "Bio::Ucsc::AilMel1::Organism" do
     context ".first" do
@@ -507,25 +507,25 @@ describe "Bio::Ucsc::AilMel1" do
     end
   end 
 
-  describe "Bio::Ucsc::AilMel1::PhastCons6way" do
-    context ".first" do
-      it 'returns the first records' do
-        result = Bio::Ucsc::AilMel1::PhastCons6way.first
-        pp result
-        result.should be_true
-      end
-    end
-  end 
+  # describe "Bio::Ucsc::AilMel1::PhastCons6way" do
+  #   context ".first" do
+  #     it 'returns the first records' do
+  #       result = Bio::Ucsc::AilMel1::PhastCons6way.first
+  #       pp result
+  #       result.should be_true
+  #     end
+  #   end
+  # end 
 
-  describe "Bio::Ucsc::AilMel1::PhastConsElements6way" do
-    context ".first" do
-      it 'returns the first records' do
-        result = Bio::Ucsc::AilMel1::PhastConsElements6way.first
-        pp result
-        result.should be_true
-      end
-    end
-  end 
+  # describe "Bio::Ucsc::AilMel1::PhastConsElements6way" do
+  #   context ".first" do
+  #     it 'returns the first records' do
+  #       result = Bio::Ucsc::AilMel1::PhastConsElements6way.first
+  #       pp result
+  #       result.should be_true
+  #     end
+  #   end
+  # end 
 
   describe "Bio::Ucsc::AilMel1::ProductName" do
     context ".first" do
@@ -537,25 +537,25 @@ describe "Bio::Ucsc::AilMel1" do
     end
   end 
 
-  describe "Bio::Ucsc::AilMel1::Quality" do
-    context ".first" do
-      it 'returns the first records' do
-        result = Bio::Ucsc::AilMel1::Quality.first
-        pp result
-        result.should be_true
-      end
-    end
-  end 
+  # describe "Bio::Ucsc::AilMel1::Quality" do
+  #   context ".first" do
+  #     it 'returns the first records' do
+  #       result = Bio::Ucsc::AilMel1::Quality.first
+  #       pp result
+  #       result.should be_true
+  #     end
+  #   end
+  # end 
 
-  describe "Bio::Ucsc::AilMel1::RefLink" do
-    context ".first" do
-      it 'returns the first records' do
-        result = Bio::Ucsc::AilMel1::RefLink.first
-        pp result
-        result.should be_true
-      end
-    end
-  end 
+  # describe "Bio::Ucsc::AilMel1::RefLink" do
+  #   context ".first" do
+  #     it 'returns the first records' do
+  #       result = Bio::Ucsc::AilMel1::RefLink.first
+  #       pp result
+  #       result.should be_true
+  #     end
+  #   end
+  # end 
 
   describe "Bio::Ucsc::AilMel1::RefSeqStatus" do
     context ".first" do
@@ -637,95 +637,95 @@ describe "Bio::Ucsc::AilMel1" do
     end
   end 
 
-  describe "Bio::Ucsc::AilMel1::TransMapAlnMRna" do
-    context ".first" do
-      it 'returns the first records' do
-        result = Bio::Ucsc::AilMel1::TransMapAlnMRna.first
-        pp result
-        result.should be_true
-      end
-    end
-  end 
-
-  describe "Bio::Ucsc::AilMel1::TransMapAlnRefSeq" do
-    context ".first" do
-      it 'returns the first records' do
-        result = Bio::Ucsc::AilMel1::TransMapAlnRefSeq.first
-        pp result
-        result.should be_true
-      end
-    end
-  end 
-
-  describe "Bio::Ucsc::AilMel1::TransMapAlnSplicedEst" do
-    context ".first" do
-      it 'returns the first records' do
-        result = Bio::Ucsc::AilMel1::TransMapAlnSplicedEst.first
-        pp result
-        result.should be_true
-      end
-    end
-  end 
-
-  describe "Bio::Ucsc::AilMel1::TransMapAlnUcscGenes" do
-    context ".first" do
-      it 'returns the first records' do
-        result = Bio::Ucsc::AilMel1::TransMapAlnUcscGenes.first
-        pp result
-        result.should be_true
-      end
-    end
-  end 
-
-  describe "Bio::Ucsc::AilMel1::TransMapInfoMRna" do
-    context ".first" do
-      it 'returns the first records' do
-        result = Bio::Ucsc::AilMel1::TransMapInfoMRna.first
-        pp result
-        result.should be_true
-      end
-    end
-  end 
-
-  describe "Bio::Ucsc::AilMel1::TransMapInfoRefSeq" do
-    context ".first" do
-      it 'returns the first records' do
-        result = Bio::Ucsc::AilMel1::TransMapInfoRefSeq.first
-        pp result
-        result.should be_true
-      end
-    end
-  end 
-
-  describe "Bio::Ucsc::AilMel1::TransMapInfoSplicedEst" do
-    context ".first" do
-      it 'returns the first records' do
-        result = Bio::Ucsc::AilMel1::TransMapInfoSplicedEst.first
-        pp result
-        result.should be_true
-      end
-    end
-  end 
-
-  describe "Bio::Ucsc::AilMel1::TransMapInfoUcscGenes" do
-    context ".first" do
-      it 'returns the first records' do
-        result = Bio::Ucsc::AilMel1::TransMapInfoUcscGenes.first
-        pp result
-        result.should be_true
-      end
-    end
-  end 
-
-  describe "Bio::Ucsc::AilMel1::WindowmaskerSdust" do
-    context ".first" do
-      it 'returns the first records' do
-        result = Bio::Ucsc::AilMel1::WindowmaskerSdust.first
-        pp result
-        result.should be_true
-      end
-    end
-  end 
+  # describe "Bio::Ucsc::AilMel1::TransMapAlnMRna" do
+  #   context ".first" do
+  #     it 'returns the first records' do
+  #       result = Bio::Ucsc::AilMel1::TransMapAlnMRna.first
+  #       pp result
+  #       result.should be_true
+  #     end
+  #   end
+  # end 
+
+  # describe "Bio::Ucsc::AilMel1::TransMapAlnRefSeq" do
+  #   context ".first" do
+  #     it 'returns the first records' do
+  #       result = Bio::Ucsc::AilMel1::TransMapAlnRefSeq.first
+  #       pp result
+  #       result.should be_true
+  #     end
+  #   end
+  # end 
+
+  # describe "Bio::Ucsc::AilMel1::TransMapAlnSplicedEst" do
+  #   context ".first" do
+  #     it 'returns the first records' do
+  #       result = Bio::Ucsc::AilMel1::TransMapAlnSplicedEst.first
+  #       pp result
+  #       result.should be_true
+  #     end
+  #   end
+  # end 
+
+  # describe "Bio::Ucsc::AilMel1::TransMapAlnUcscGenes" do
+  #   context ".first" do
+  #     it 'returns the first records' do
+  #       result = Bio::Ucsc::AilMel1::TransMapAlnUcscGenes.first
+  #       pp result
+  #       result.should be_true
+  #     end
+  #   end
+  # end 
+
+  # describe "Bio::Ucsc::AilMel1::TransMapInfoMRna" do
+  #   context ".first" do
+  #     it 'returns the first records' do
+  #       result = Bio::Ucsc::AilMel1::TransMapInfoMRna.first
+  #       pp result
+  #       result.should be_true
+  #     end
+  #   end
+  # end 
+
+  # describe "Bio::Ucsc::AilMel1::TransMapInfoRefSeq" do
+  #   context ".first" do
+  #     it 'returns the first records' do
+  #       result = Bio::Ucsc::AilMel1::TransMapInfoRefSeq.first
+  #       pp result
+  #       result.should be_true
+  #     end
+  #   end
+  # end 
+
+  # describe "Bio::Ucsc::AilMel1::TransMapInfoSplicedEst" do
+  #   context ".first" do
+  #     it 'returns the first records' do
+  #       result = Bio::Ucsc::AilMel1::TransMapInfoSplicedEst.first
+  #       pp result
+  #       result.should be_true
+  #     end
+  #   end
+  # end 
+
+  # describe "Bio::Ucsc::AilMel1::TransMapInfoUcscGenes" do
+  #   context ".first" do
+  #     it 'returns the first records' do
+  #       result = Bio::Ucsc::AilMel1::TransMapInfoUcscGenes.first
+  #       pp result
+  #       result.should be_true
+  #     end
+  #   end
+  # end 
+
+  # describe "Bio::Ucsc::AilMel1::WindowmaskerSdust" do
+  #   context ".first" do
+  #     it 'returns the first records' do
+  #       result = Bio::Ucsc::AilMel1::WindowmaskerSdust.first
+  #       pp result
+  #       result.should be_true
+  #     end
+  #   end
+  # end 
 
   describe "Bio::Ucsc::AilMel1::XenoMrna" do
     context ".first" do