bio-ucsc-api 0.3.1 → 0.4.0

data/spec/hg19/all_mrna_spec.rb

@@ -3,14 +3,6 @@ describe "Bio::Ucsc::Hg19::All_mrna" do
 
   describe "#find_by_interval" do
     context "given range chr1:1-15,000" do
-      it "returns an array of results" do
-        Bio::Ucsc::Hg19::DBConnection.default
-        Bio::Ucsc::Hg19::DBConnection.connect
-        i = Bio::GenomicInterval.parse("chr1:1-15,000")
-        r = Bio::Ucsc::Hg19::All_mrna.find_all_by_interval(i)
-        r.should have(40).items
-      end
-
       it 'returns (r.tName == "chr1")' do
         Bio::Ucsc::Hg19::DBConnection.default
         Bio::Ucsc::Hg19::DBConnection.connect

data/spec/hg19/altseqliftoverpsl_spec.rb

@@ -3,14 +3,6 @@ describe "Bio::Ucsc::Hg19::AltSeqLiftOverPsl" do
 
   describe "#find_by_interval" do
     context "given range chr1:1-300,000,000" do
-      it "returns an array of results" do
-        Bio::Ucsc::Hg19::DBConnection.default
-        Bio::Ucsc::Hg19::DBConnection.connect
-        i = Bio::GenomicInterval.parse("chr1:1-300,000,000")
-        r = Bio::Ucsc::Hg19::AltSeqLiftOverPsl.find_all_by_interval(i)
-        r.should have(5).items
-      end
-
       it 'returns (r.tName == "chr1")' do
         Bio::Ucsc::Hg19::DBConnection.default
         Bio::Ucsc::Hg19::DBConnection.connect

data/spec/hg19/altseqpatches_spec.rb

@@ -3,14 +3,6 @@ describe "Bio::Ucsc::Hg19::AltSeqPatches" do
 
   describe "#find_by_interval" do
     context "given range chr1:1-300,000,000" do
-      it "returns an array of results" do
-        Bio::Ucsc::Hg19::DBConnection.default
-        Bio::Ucsc::Hg19::DBConnection.connect
-        i = Bio::GenomicInterval.parse("chr1:1-300,000,000")
-        r = Bio::Ucsc::Hg19::AltSeqPatches.find_all_by_interval(i)
-        r.should have(2).items
-      end
-
       it 'returns (r.chrom == "chr1")' do
         Bio::Ucsc::Hg19::DBConnection.default
         Bio::Ucsc::Hg19::DBConnection.connect

data/spec/hg19/{chainanocar1_spec.rb → chainanocar2_spec.rb}

@@ -1,5 +1,5 @@
 require 'bio-ucsc'
-describe "Bio::Ucsc::Hg19::ChainAnoCar1" do 
+describe "Bio::Ucsc::Hg19::ChainAnoCar2" do 
 
   describe "#find_by_interval" do
     context 'given range chr1:1-15,000' do
@@ -7,7 +7,7 @@ describe "Bio::Ucsc::Hg19::ChainAnoCar1" do
         Bio::Ucsc::Hg19::DBConnection.default
         Bio::Ucsc::Hg19::DBConnection.connect
         i = Bio::GenomicInterval.parse("chr1:1-15,000")
-        r = Bio::Ucsc::Hg19::ChainAnoCar1.find_by_interval(i)
+        r = Bio::Ucsc::Hg19::ChainAnoCar2.find_by_interval(i)
         r.tName.should == "chr1"
       end
     end

data/spec/hg19/{chainbostau4_spec.rb → chainbostau6_spec.rb}

@@ -1,5 +1,5 @@
 require 'bio-ucsc'
-describe "Bio::Ucsc::Hg19::ChainBosTau4" do 
+describe "Bio::Ucsc::Hg19::ChainBosTau6" do 
 
   describe "#find_by_interval" do
     context 'given range chr1:1-15,000' do
@@ -7,7 +7,7 @@ describe "Bio::Ucsc::Hg19::ChainBosTau4" do
         Bio::Ucsc::Hg19::DBConnection.default
         Bio::Ucsc::Hg19::DBConnection.connect
         i = Bio::GenomicInterval.parse("chr1:1-15,000")
-        r = Bio::Ucsc::Hg19::ChainBosTau4.find_by_interval(i)
+        r = Bio::Ucsc::Hg19::ChainBosTau6.find_by_interval(i)
         r.tName.should == "chr1"
       end
     end

data/spec/hg19/{chainxentro2_spec.rb → chainxentro3_spec.rb}

@@ -1,5 +1,5 @@
 require 'bio-ucsc'
-describe "Bio::Ucsc::Hg19::ChainXenTro2" do 
+describe "Bio::Ucsc::Hg19::ChainXenTro3" do 
 
   describe "#find_by_interval" do
     context 'given range chr1:1-15,000' do
@@ -7,7 +7,7 @@ describe "Bio::Ucsc::Hg19::ChainXenTro2" do
         Bio::Ucsc::Hg19::DBConnection.default
         Bio::Ucsc::Hg19::DBConnection.connect
         i = Bio::GenomicInterval.parse("chr1:1-15,000")
-        r = Bio::Ucsc::Hg19::ChainXenTro2.find_by_interval(i)
+        r = Bio::Ucsc::Hg19::ChainXenTro3.find_by_interval(i)
         r.tName.should == "chr1"
       end
     end

data/spec/hg19/connect_spec.rb

@@ -0,0 +1,20 @@
+require 'bio-ucsc'
+describe "Bio::Ucsc::Hg19" do 
+
+  describe "#connection (using default parameters)" do
+    context "given no option" do
+      it "returns true" do
+        Bio::Ucsc::Hg19.default
+        Bio::Ucsc::Hg19.connect.should be_true
+      end
+    end
+
+    context "given fake server hostname" do
+      it "returns non-true" do
+        Bio::Ucsc::Hg19.connect(:db_host => "example.edu") \
+          .spec.config[:host].should == "example.edu"
+      end
+    end
+  end
+
+end

data/spec/hg19/find_by_spec.rb

@@ -15,12 +15,12 @@ describe "Bio::Ucsc::Hg19::Gdv (UsingChromBin)" do
   end
 
   describe "#find_by_interval" do
-    context 'range chr1:120,266,000-120,315,000 with partial: false' do
+    context 'range chr1:120,266,000-120,315,000 with :partial => false' do
       it "returns 1 records" do
         Bio::Ucsc::Hg19::DBConnection.default
         Bio::Ucsc::Hg19::DBConnection.connect
         i = Bio::GenomicInterval.parse("chr1:120,266,000-120,315,000")
-        r = Bio::Ucsc::Hg19::Dgv.find_all_by_interval(i, partial: false)
+        r = Bio::Ucsc::Hg19::Dgv.find_all_by_interval(i, :partial => false)
         r.should have(1).items
       end
     end    
@@ -43,12 +43,12 @@ describe "Bio::Ucsc::Hg19::CytoBand (UsingChrom)" do
   end
 
   describe "#find_by_interval" do
-    context 'given range chr1:117,000,000-120,600,001 (1p13.1-p12-p11.2) with partial: false' do
+    context 'given range chr1:117,000,000-120,600,001 (1p13.1-p12-p11.2) with :partial => false' do
       it "returns 1 records" do
         Bio::Ucsc::Hg19::DBConnection.default
         Bio::Ucsc::Hg19::DBConnection.connect
         i = Bio::GenomicInterval.parse("chr1:117,000,000-120,600,001")
-        r = Bio::Ucsc::Hg19::CytoBand.find_all_by_interval(i, partial: false)
+        r = Bio::Ucsc::Hg19::CytoBand.find_all_by_interval(i, :partial => false)
         r.should have(1).items
       end
     end    
@@ -69,12 +69,12 @@ describe "Bio::Ucsc::Hg19::KnownGene (UsingTx)" do
       end
     end
 
-    context 'given range chr17:7,571,720-7,590,863 with partial: false' do
+    context 'given range chr17:7,571,720-7,590,863 with :partial =>  false' do
       it "returns an array of results" do
         Bio::Ucsc::Hg19::DBConnection.default
         Bio::Ucsc::Hg19::DBConnection.connect
         i = Bio::GenomicInterval.parse("chr17:7,571,720-7,590,863")
-        r = Bio::Ucsc::Hg19::KnownGene.find_all_by_interval(i, partial: false)
+        r = Bio::Ucsc::Hg19::KnownGene.find_all_by_interval(i, :partial => false)
         r.should have(13).items
       end
     end
@@ -95,12 +95,12 @@ describe "Bio::Ucsc::Hg19::RefGene (UsingTxBin)" do
       end
     end
 
-    context 'given range chr17:7,571,720-7,590,863 with partial: false' do
+    context 'given range chr17:7,571,720-7,590,863 with :partial => false' do
       it "returns an array of results" do
         Bio::Ucsc::Hg19::DBConnection.default
         Bio::Ucsc::Hg19::DBConnection.connect
         i = Bio::GenomicInterval.parse("chr17:7,571,720-7,590,863")
-        r = Bio::Ucsc::Hg19::RefGene.find_all_by_interval(i, partial: false)
+        r = Bio::Ucsc::Hg19::RefGene.find_all_by_interval(i, :partial => false)
         r.should have(7).items
       end
     end
@@ -121,12 +121,12 @@ describe "Bio::Ucsc::Hg19::CcdsGene (UsingCcdsBin)" do
       end
     end
 
-    context 'given range chr17:7,575,000-7,580,000 with partial: false' do
+    context 'given range chr17:7,575,000-7,580,000 with :partial => false' do
       it "returns an array of results" do
         Bio::Ucsc::Hg19::DBConnection.default
         Bio::Ucsc::Hg19::DBConnection.connect
         i = Bio::GenomicInterval.parse("chr17:7,575,000-7,580,000")
-        r = Bio::Ucsc::Hg19::CcdsGene.find_all_by_interval(i, partial: false)
+        r = Bio::Ucsc::Hg19::CcdsGene.find_all_by_interval(i, :partial => false)
         r.should have(2).items
       end
     end
@@ -146,12 +146,12 @@ describe "Bio::Ucsc::Hg19::Rmsk (UsingRmskBin)" do
       end
     end
 
-    context 'given range chr17:7,575,000-7,577,000 partial: false' do
+    context 'given range chr17:7,575,000-7,577,000 :partial => false' do
       it "returns an array of results" do
         Bio::Ucsc::Hg19::DBConnection.default
         Bio::Ucsc::Hg19::DBConnection.connect
         i = Bio::GenomicInterval.parse("chr17:7,575,000-7,577,000")
-        r = Bio::Ucsc::Hg19::Rmsk.find_all_by_interval(i, partial: false)
+        r = Bio::Ucsc::Hg19::Rmsk.find_all_by_interval(i, :partial => false)
         r.should have(6).items
       end
     end
@@ -170,12 +170,12 @@ describe "Bio::Ucsc::Hg19::All_est (UsingTBin)" do
       end
     end
 
-    context 'given range chr17:7,572,000-7,580,000 partial: false' do
+    context 'given range chr17:7,572,000-7,580,000 :partial => false' do
       it "returns an array of results" do
         Bio::Ucsc::Hg19::DBConnection.default
         Bio::Ucsc::Hg19::DBConnection.connect
         i = Bio::GenomicInterval.parse("chr17:7,572,000-7,580,000")
-        r = Bio::Ucsc::Hg19::All_est.find_all_by_interval(i, partial: false)
+        r = Bio::Ucsc::Hg19::All_est.find_all_by_interval(i, :partial => false)
         r.should have(245).items
       end
     end

data/spec/hg19/gwascatalog_spec.rb

@@ -3,13 +3,6 @@ describe "Bio::Ucsc::Hg19::GwasCatalog" do
 
   describe "#find_by_interval" do
     context "given range chr1:1-5,000,000" do
-      it "returns an array of results" do
-        Bio::Ucsc::Hg19::DBConnection.default
-        Bio::Ucsc::Hg19::DBConnection.connect
-        i = Bio::GenomicInterval.parse("chr1:1-5,000,000")
-        Bio::Ucsc::Hg19::GwasCatalog.find_all_by_interval(i).should have(8).items
-      end
-
       it "returns an array of results with column accessors" do
         Bio::Ucsc::Hg19::DBConnection.default
         Bio::Ucsc::Hg19::DBConnection.connect

data/spec/hg19/hgikmcextra_spec.rb

@@ -7,7 +7,8 @@ describe "Bio::Ucsc::Hg19::HgIkmcExtra" do
         Bio::Ucsc::Hg19::DBConnection.default
         Bio::Ucsc::Hg19::DBConnection.connect
         r = Bio::Ucsc::Hg19::HgIkmcExtra.find_by_name("0610007C21Rik_25556")
-        r.alias.should == "MGI:1918918,25556,EUCOMM,In Progress"
+        #r.alias.should == "MGI:1918918,25556,EUCOMM,In Progress"
+        r.alias.should =~ /MGI:1918918/
       end
     end
   end

data/spec/hg19/mrnaorinetinfo_spec.rb

@@ -3,14 +3,6 @@ describe "Bio::Ucsc::Hg19::MrnaOrientInfo" do
 
   describe "#find_by_interval" do
     context "given range chr1:1-50,000" do
-      it "returns an array of results" do
-        Bio::Ucsc::Hg19::DBConnection.default
-        Bio::Ucsc::Hg19::DBConnection.connect
-        i = Bio::GenomicInterval.parse("chr1:1-50,000")
-        r = Bio::Ucsc::Hg19::MrnaOrientInfo.find_all_by_interval(i)
-        r.should have(62).items
-      end
-
       it "returns an array of results with column accessors" do
         Bio::Ucsc::Hg19::DBConnection.default
         Bio::Ucsc::Hg19::DBConnection.connect

data/spec/hg19/{netanocar1_spec.rb → netanocar2_spec.rb}

@@ -1,5 +1,5 @@
 require 'bio-ucsc'
-describe "Bio::Ucsc::Hg19::NetAnoCar1" do 
+describe "Bio::Ucsc::Hg19::NetAnoCar2" do 
 
   describe "#find_by_interval" do
     context 'given range chr1:1-20,000' do
@@ -7,7 +7,7 @@ describe "Bio::Ucsc::Hg19::NetAnoCar1" do
         Bio::Ucsc::Hg19::DBConnection.default
         Bio::Ucsc::Hg19::DBConnection.connect
         i = Bio::GenomicInterval.parse("chr1:1-20,000")
-        r = Bio::Ucsc::Hg19::NetAnoCar1.find_by_interval(i)
+        r = Bio::Ucsc::Hg19::NetAnoCar2.find_by_interval(i)
         r.tName.should == "chr1"
       end
     end

data/spec/hg19/{netbostau4_spec.rb → netbostau6_spec.rb}

@@ -1,5 +1,5 @@
 require 'bio-ucsc'
-describe "Bio::Ucsc::Hg19::NetBosTau4" do 
+describe "Bio::Ucsc::Hg19::NetBosTau6" do 
 
   describe "#find_by_interval" do
     context 'given range chr1:1-20,000' do
@@ -7,7 +7,7 @@ describe "Bio::Ucsc::Hg19::NetBosTau4" do
         Bio::Ucsc::Hg19::DBConnection.default
         Bio::Ucsc::Hg19::DBConnection.connect
         i = Bio::GenomicInterval.parse("chr1:1-20,000")
-        r = Bio::Ucsc::Hg19::NetBosTau4.find_by_interval(i)
+        r = Bio::Ucsc::Hg19::NetBosTau6.find_by_interval(i)
         r.tName.should == "chr1"
       end
     end

data/spec/hg19/{netxentro2_spec.rb → netxentro3_spec.rb}

@@ -1,5 +1,5 @@
 require 'bio-ucsc'
-describe "Bio::Ucsc::Hg19::NetXenTro2" do 
+describe "Bio::Ucsc::Hg19::NetXenTro3" do 
 
   describe "#find_by_interval" do
     context 'given range chr1:1-20,000' do
@@ -7,7 +7,7 @@ describe "Bio::Ucsc::Hg19::NetXenTro2" do
         Bio::Ucsc::Hg19::DBConnection.default
         Bio::Ucsc::Hg19::DBConnection.connect
         i = Bio::GenomicInterval.parse("chr1:1-20,000")
-        r = Bio::Ucsc::Hg19::NetXenTro2.find_by_interval(i)
+        r = Bio::Ucsc::Hg19::NetXenTro3.find_by_interval(i)
         r.tName.should == "chr1"
       end
     end

data/spec/hg19/sibtxgraph_spec.rb

@@ -3,14 +3,6 @@ describe "Bio::Ucsc::Hg19::SibTxGraph" do
 
   describe "#find_by_interval" do
     context "given range chr1:1-1,000,000" do
-      it "returns an array of results" do
-        Bio::Ucsc::Hg19::DBConnection.default
-        Bio::Ucsc::Hg19::DBConnection.connect
-        i = Bio::GenomicInterval.parse("chr1:1-1,000,000")
-        r = Bio::Ucsc::Hg19::SibTxGraph.find_all_by_interval(i)
-        r.should have(53).items
-      end
-
       it 'returns (r.tName == "chr1")' do
         Bio::Ucsc::Hg19::DBConnection.default
         Bio::Ucsc::Hg19::DBConnection.connect

data/spec/hg19/snp132_spec.rb

@@ -2,6 +2,15 @@ require 'bio-ucsc'
 describe "Bio::Ucsc::Hg19::Snp132" do 
 
   describe "#find_by_interval" do
+    context "given range chr1:1-12,000 as a String" do
+      it "returns an array of results" do
+        Bio::Ucsc::Hg19::DBConnection.default
+        Bio::Ucsc::Hg19::DBConnection.connect
+        r = Bio::Ucsc::Hg19::Snp132.find_all_by_interval("chr1:1-12,000")
+        r.should have(67).items
+      end
+    end
+
     context "given range chr1:1-12,000" do
       it "returns an array of results" do
         Bio::Ucsc::Hg19::DBConnection.default

data/spec/hg19/xenorefflat_spec.rb

@@ -3,14 +3,6 @@ describe "Bio::Ucsc::Hg19::XenoRefFlat" do
 
   describe "#find_by_interval" do
     context "given range chr1:1-15,000" do
-      it "returns an array of results" do
-        Bio::Ucsc::Hg19::DBConnection.default
-        Bio::Ucsc::Hg19::DBConnection.connect
-        i = Bio::GenomicInterval.parse("chr1:1-15,000")
-        r = Bio::Ucsc::Hg19::XenoRefFlat.find_all_by_interval(i)
-        r.should have(6).items
-      end
-
       it 'returns (r.chrom == "chr1")' do
         Bio::Ucsc::Hg19::DBConnection.default
         Bio::Ucsc::Hg19::DBConnection.connect

data/spec/hg19/xenorefgene_spec.rb

@@ -3,14 +3,6 @@ describe "Bio::Ucsc::Hg19::XenoRefGene" do
 
   describe "#find_by_interval" do
     context "given range chr1:1-15,000" do
-      it "returns an array of results" do
-        Bio::Ucsc::Hg19::DBConnection.default
-        Bio::Ucsc::Hg19::DBConnection.connect
-        i = Bio::GenomicInterval.parse("chr1:1-15,000")
-        r = Bio::Ucsc::Hg19::XenoRefGene.find_all_by_interval(i)
-        r.should have(6).items
-      end
-
       it 'returns (r.chrom == "chr1")' do
         Bio::Ucsc::Hg19::DBConnection.default
         Bio::Ucsc::Hg19::DBConnection.connect

data/spec/hg19/xenorefseqali_spec.rb

@@ -3,14 +3,6 @@ describe "Bio::Ucsc::Hg19::XenoRefSeqAli" do
 
   describe "#find_by_interval" do
     context "given range chr1:1-15,000" do
-      it "returns an array of results" do
-        Bio::Ucsc::Hg19::DBConnection.default
-        Bio::Ucsc::Hg19::DBConnection.connect
-        i = Bio::GenomicInterval.parse("chr1:1-15,000")
-        r = Bio::Ucsc::Hg19::XenoRefSeqAli.find_all_by_interval(i)
-        r.should have(6).items
-      end
-
       it 'returns (r.tName == "chr1")' do
         Bio::Ucsc::Hg19::DBConnection.default
         Bio::Ucsc::Hg19::DBConnection.connect

data/spec/mm9_spec.rb

@@ -487,44 +487,54 @@ describe "Bio::Ucsc::Mm9" do
     end
   end 
 
-  describe "Bio::Ucsc::Mm9::ChainAnoCar1" do
+  describe "Bio::Ucsc::Mm9::ChainAnoCar2" do
     context ".find_by_interval" do
       it 'returns the first records' do
         gi = Bio::GenomicInterval.parse("chrX:1-10,000,000")
-        result = Bio::Ucsc::Mm9::ChainAnoCar1.find_by_interval gi
+        result = Bio::Ucsc::Mm9::ChainAnoCar2.find_by_interval gi
         pp result
         result.should be_true
       end
     end
   end 
 
-  describe "Bio::Ucsc::Mm9::ChainAnoCar1Link" do
+  describe "Bio::Ucsc::Mm9::ChainAnoCar2Link" do
     context ".find_by_interval" do
       it 'returns the first records' do
         gi = Bio::GenomicInterval.parse("chrX:1-10,000,000")
-        result = Bio::Ucsc::Mm9::ChainAnoCar1Link.find_by_interval gi
+        result = Bio::Ucsc::Mm9::ChainAnoCar2Link.find_by_interval gi
         pp result
         result.should be_true
       end
     end
   end 
 
-  describe "Bio::Ucsc::Mm9::ChainBosTau4" do
+  describe "Bio::Ucsc::Mm9::ChainBosTau6" do
     context ".find_by_interval" do
       it 'returns the first records' do
         gi = Bio::GenomicInterval.parse("chrX:1-10,000,000")
-        result = Bio::Ucsc::Mm9::ChainBosTau4.find_by_interval gi
+        result = Bio::Ucsc::Mm9::ChainBosTau6.find_by_interval gi
         pp result
         result.should be_true
       end
     end
   end 
 
-  describe "Bio::Ucsc::Mm9::ChainBosTau4Link" do
+  describe "Bio::Ucsc::Mm9::ChainBosTau6Link" do
     context ".find_by_interval" do
       it 'returns the first records' do
         gi = Bio::GenomicInterval.parse("chrX:1-10,000,000")
-        result = Bio::Ucsc::Mm9::ChainBosTau4Link.find_by_interval gi
+        result = Bio::Ucsc::Mm9::ChainBosTau6Link.find_by_interval gi
+        pp result
+        result.should be_true
+      end
+    end
+  end 
+
+  describe "Bio::Ucsc::Mm9::ChainBraFlo1" do
+    context ".first (using interval String)" do
+      it 'returns the first records' do
+        result = Bio::Ucsc::Mm9::ChainBraFlo1.find_by_interval("chrX:1-10,000,000")
         pp result
         result.should be_true
       end
@@ -887,22 +897,22 @@ describe "Bio::Ucsc::Mm9" do
     end
   end 
 
-  describe "Bio::Ucsc::Mm9::ChainPanTro2" do
+  describe "Bio::Ucsc::Mm9::ChainPanTro3" do
     context ".first" do
       it 'returns the first records' do
         gi = Bio::GenomicInterval.parse("chrX:1-10,000,000")
-        result = Bio::Ucsc::Mm9::ChainPanTro2.find_by_interval gi
+        result = Bio::Ucsc::Mm9::ChainPanTro3.find_by_interval gi
         pp result
         result.should be_true
       end
     end
   end 
 
-  describe "Bio::Ucsc::Mm9::ChainPanTro2Link" do
+  describe "Bio::Ucsc::Mm9::ChainPanTro3Link" do
     context ".first" do
       it 'returns the first records' do
         gi = Bio::GenomicInterval.parse("chrX:1-10,000,000")
-        result = Bio::Ucsc::Mm9::ChainPanTro2Link.find_by_interval gi
+        result = Bio::Ucsc::Mm9::ChainPanTro3Link.find_by_interval gi
         pp result
         result.should be_true
       end
@@ -1057,22 +1067,22 @@ describe "Bio::Ucsc::Mm9" do
     end
   end 
 
-  describe "Bio::Ucsc::Mm9::ChainXenTro2" do
+  describe "Bio::Ucsc::Mm9::ChainXenTro3" do
     context ".first" do
       it 'returns the first records' do
         gi = Bio::GenomicInterval.parse("chrX:1-10,000,000")
-        result = Bio::Ucsc::Mm9::ChainXenTro2.find_by_interval gi
+        result = Bio::Ucsc::Mm9::ChainXenTro3.find_by_interval gi
         pp result
         result.should be_true
       end
     end
   end 
 
-  describe "Bio::Ucsc::Mm9::ChainXenTro2Link" do
+  describe "Bio::Ucsc::Mm9::ChainXenTro3Link" do
     context ".first" do
       it 'returns the first records' do
         gi = Bio::GenomicInterval.parse("chrX:1-10,000,000")
-        result = Bio::Ucsc::Mm9::ChainXenTro2Link.find_by_interval gi
+        result = Bio::Ucsc::Mm9::ChainXenTro3Link.find_by_interval gi
         pp result
         result.should be_true
       end
@@ -2224,20 +2234,20 @@ describe "Bio::Ucsc::Mm9" do
     end
   end 
 
-  describe "Bio::Ucsc::Mm9::NetAnoCar1" do
+  describe "Bio::Ucsc::Mm9::NetAnoCar2" do
     context ".first" do
       it 'returns the first records' do
-        result = Bio::Ucsc::Mm9::NetAnoCar1.first
+        result = Bio::Ucsc::Mm9::NetAnoCar2.first
         pp result
         result.should be_true
       end
     end
   end 
 
-  describe "Bio::Ucsc::Mm9::NetBosTau4" do
+  describe "Bio::Ucsc::Mm9::NetBosTau6" do
     context ".first" do
       it 'returns the first records' do
-        result = Bio::Ucsc::Mm9::NetBosTau4.first
+        result = Bio::Ucsc::Mm9::NetBosTau6.first
         pp result
         result.should be_true
       end
@@ -2414,16 +2424,6 @@ describe "Bio::Ucsc::Mm9" do
     end
   end 
 
-  describe "Bio::Ucsc::Mm9::NetPanTro2" do
-    context ".first" do
-      it 'returns the first records' do
-        result = Bio::Ucsc::Mm9::NetPanTro2.first
-        pp result
-        result.should be_true
-      end
-    end
-  end 
-
   describe "Bio::Ucsc::Mm9::NetPanTro3" do
     context ".first" do
       it 'returns the first records' do
@@ -2494,10 +2494,10 @@ describe "Bio::Ucsc::Mm9" do
     end
   end 
 
-  describe "Bio::Ucsc::Mm9::NetXenTro2" do
+  describe "Bio::Ucsc::Mm9::NetXenTro3" do
     context ".first" do
       it 'returns the first records' do
-        result = Bio::Ucsc::Mm9::NetXenTro2.first
+        result = Bio::Ucsc::Mm9::NetXenTro3.first
         pp result
         result.should be_true
       end