bio-ucsc-api 0.3.1 → 0.4.0

data/spec/aplcal1_spec.rb

@@ -67,26 +67,6 @@ describe "Bio::Ucsc::AplCal1" do
     end
   end 
 
-  describe "Bio::Ucsc::AplCal1::ChainHg19" do
-    context ".first" do
-      it 'returns the first records' do
-        result = Bio::Ucsc::AplCal1::ChainHg19.first
-        pp result
-        result.should be_true
-      end
-    end
-  end 
-
-  describe "Bio::Ucsc::AplCal1::ChainHg19Link" do
-    context ".first" do
-      it 'returns the first records' do
-        result = Bio::Ucsc::AplCal1::ChainHg19Link.first
-        pp result
-        result.should be_true
-      end
-    end
-  end 
-
   describe "Bio::Ucsc::AplCal1::ChromInfo" do
     context ".first" do
       it 'returns the first records' do
@@ -347,16 +327,6 @@ describe "Bio::Ucsc::AplCal1" do
     end
   end 
 
-  describe "Bio::Ucsc::AplCal1::NetHg19" do
-    context ".first" do
-      it 'returns the first records' do
-        result = Bio::Ucsc::AplCal1::NetHg19.first
-        pp result
-        result.should be_true
-      end
-    end
-  end 
-
   describe "Bio::Ucsc::AplCal1::Organism" do
     context ".first" do
       it 'returns the first records' do

data/spec/braflo1_spec.rb

@@ -71,7 +71,7 @@ describe "Bio::Ucsc::BraFlo1" do
     context ".find_by_interval" do
       it 'returns the first records' do
         gi = Bio::GenomicInterval.parse("chrUn:1-10,000,000")
-        result = Bio::Ucsc::BraFlo1::ChainGalGal.find_by_interval gi
+        result = Bio::Ucsc::BraFlo1::ChainGalGal3.find_by_interval gi
         pp result
         result.should be_true
       end

data/spec/canfam2_spec.rb

@@ -107,22 +107,22 @@ describe "Bio::Ucsc::CanFam2" do
     end
   end 
 
-  describe "Bio::Ucsc::CanFam2::ChainBosTau4" do
+  describe "Bio::Ucsc::CanFam2::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::CanFam2::ChainBosTau4.find_by_interval gi
+        result = Bio::Ucsc::CanFam2::ChainBosTau6.find_by_interval gi
         pp result
         result.should be_true
       end
     end
   end 
 
-  describe "Bio::Ucsc::CanFam2::ChainBosTau4Link" do
+  describe "Bio::Ucsc::CanFam2::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::CanFam2::ChainBosTau4Link.find_by_interval gi
+        result = Bio::Ucsc::CanFam2::ChainBosTau6Link.find_by_interval gi
         pp result
         result.should be_true
       end
@@ -700,10 +700,10 @@ describe "Bio::Ucsc::CanFam2" do
     end
   end 
 
-  describe "Bio::Ucsc::CanFam2::NetBosTau4" do
+  describe "Bio::Ucsc::CanFam2::NetBosTau6" do
     context ".first" do
       it 'returns the first records' do
-        result = Bio::Ucsc::CanFam2::NetBosTau4.first
+        result = Bio::Ucsc::CanFam2::NetBosTau6.first
         pp result
         result.should be_true
       end

data/spec/danrer7_spec.rb

@@ -207,20 +207,20 @@ describe "Bio::Ucsc::DanRer7" do
     end
   end 
 
-  describe "Bio::Ucsc::DanRer7::ChainXenTro2" do
+  describe "Bio::Ucsc::DanRer7::ChainXenTro3" do
     context ".first" do
       it 'returns the first records' do
-        result = Bio::Ucsc::DanRer7::ChainXenTro2.first
+        result = Bio::Ucsc::DanRer7::ChainXenTro3.first
         pp result
         result.should be_true
       end
     end
   end 
 
-  describe "Bio::Ucsc::DanRer7::ChainXenTro2Link" do
+  describe "Bio::Ucsc::DanRer7::ChainXenTro3Link" do
     context ".first" do
       it 'returns the first records' do
-        result = Bio::Ucsc::DanRer7::ChainXenTro2Link.first
+        result = Bio::Ucsc::DanRer7::ChainXenTro3Link.first
         pp result
         result.should be_true
       end
@@ -607,10 +607,10 @@ describe "Bio::Ucsc::DanRer7" do
     end
   end 
 
-  describe "Bio::Ucsc::DanRer7::NetXenTro2" do
+  describe "Bio::Ucsc::DanRer7::NetXenTro3" do
     context ".first" do
       it 'returns the first records' do
-        result = Bio::Ucsc::DanRer7::NetXenTro2.first
+        result = Bio::Ucsc::DanRer7::NetXenTro3.first
         pp result
         result.should be_true
       end

data/spec/file/twobit.rb

@@ -0,0 +1,167 @@
+require 'bio-ucsc'
+
+describe "Bio::Ucsc::File::Twobit" do 
+  describe ".open" do
+    context 'given "../samples/hg18.2bit"' do
+      it "returns a Bio::Ucsc::File::Twobit object" do
+        ref = Bio::Ucsc::File::Twobit.open("samples/hg18.2bit")
+        ref.should be_kind_of Bio::Ucsc::File::Twobit
+      end
+    end
+
+    context 'given "../samples/hg18.2bit" and a block' do
+      it "returns a Bio::Ucsc::File::Twobit object" do
+        Bio::Ucsc::File::Twobit.open("samples/hg18.2bit") do |tb|          
+          tb.should be_kind_of Bio::Ucsc::File::Twobit
+        end
+      end
+    end
+  end
+
+  describe ".load" do
+    context 'given "../samples/hg18.2bit"' do
+      it "returns a Bio::Ucsc::File::Twobit object" do
+        ref = Bio::Ucsc::File::Twobit.load("samples/hg18.2bit")
+        ref.should be_kind_of Bio::Ucsc::File::Twobit
+      end
+    end
+  end
+
+  describe "#header.signarue" do
+    context 'given "../samples/hg18.2bit"' do
+      it "returns 0x1A412743" do
+        ref = Bio::Ucsc::File::Twobit.load("samples/hg18.2bit")
+        ref.header.signature.should == 0x1A412743
+      end
+    end
+  end
+
+  describe "#header.version" do
+    context 'given "../samples/hg18.2bit"' do
+      it "returns 0" do
+        ref = Bio::Ucsc::File::Twobit.load("samples/hg18.2bit")
+        ref.header.version.should == 0
+      end
+    end
+  end
+
+  describe "#header.sequence_count" do
+    context 'given "../samples/hg18.2bit"' do
+      it "returns 0x5d" do
+        ref = Bio::Ucsc::File::Twobit.load("samples/hg18.2bit")
+        ref.header.sequence_count.should == 49
+      end
+    end
+  end
+
+  describe '#offsets["chr1"]' do
+    context 'given "../samples/hg18.2bit"' do
+      it "returns 0x100bbd2b" do 
+        ref = Bio::Ucsc::File::Twobit.load("samples/hg18.2bit")
+        ref.offsets["chr1"].should == 0x100bbd2b
+      end
+    end
+  end
+
+  describe "#records" do
+    context 'given "chr1"' do
+      it 'returns (TwoBitRecord.reserved == 0)' do
+        ref = Bio::Ucsc::File::Twobit.load("samples/hg18.2bit")
+        ref.records("chr1").reserved == 0
+      end
+    end
+
+    context 'given "chr1"' do
+      it 'returns (TwoBitRecord.dna_size == 249_250_621)' do
+        ref = Bio::Ucsc::File::Twobit.load("samples/hg18.2bit")
+        ref.records("chr1").dna_size.should == 247249719
+      end
+    end
+  end
+
+  describe "#byte_to_nucleotides" do
+    context 'given 0b00011011' do
+      it 'returns "TCAG"' do
+        ref = Bio::Ucsc::File::Twobit.load("samples/hg18.2bit")
+        ref.__send__(:byte_to_nucleotides, 0b00011011).should == "TCAG"
+      end
+    end
+  end
+
+  describe "#bytes_to_nucleotides" do
+    context 'given [0b00011011, 0b11100100]' do
+      it 'returns "TCAGGACT"' do
+        ary = [0b00011011, 0b11100100]
+        ref = Bio::Ucsc::File::Twobit.load("samples/hg18.2bit")
+        ref.__send__(:bytes_to_nucleotides, ary).should == "TCAGGACT"
+      end
+    end
+  end
+
+  describe "#find_by_interval_raw" do
+    context "given range chr1:1,000,000-1,000,030" do
+      it 'returens "TACGTGGCTGCTCTCACACATGGGCCATGTG"' do
+        ref = Bio::Ucsc::File::Twobit.load("samples/hg18.2bit")
+        itv = Bio::GenomicInterval.parse("chr1:1,000,000-1,000,030")
+        ref.find_by_interval_raw(itv).should ==
+          "TACGTGGCTGCTCTCACACATGGGCCATGTG"
+      end
+    end
+
+    context "given range chr2:1,123,456-1,123,499" do
+      it 'returens "TAATGGCATACATGTAGAAAATGCAACTCATGAAGAAGTGGTAA"' do
+        ref = Bio::Ucsc::File::Twobit.load("samples/hg18.2bit")
+        itv = Bio::GenomicInterval.parse("chr2:1,123,456-1,123,499")
+        ref.find_by_interval_raw(itv).should ==
+          "TAATGGCATACATGTAGAAAATGCAACTCATGAAGAAGTGGTAA"
+      end
+    end
+
+    context "given range chr2:1,123,456-1,123,456" do
+      it 'returens "T"' do
+        ref = Bio::Ucsc::File::Twobit.load("samples/hg18.2bit")
+        itv = Bio::GenomicInterval.parse("chr2:1,123,456-1,123,456")
+        ref.find_by_interval_raw(itv).should == "T"
+      end
+    end
+  end
+    
+  describe ".find_by_interval" do
+    context "given range chr1:217,260-217,299" do
+      it 'returns "NNNNNNNNNNNNNNNNNNNNNGATTCATGGCTGAAATCGT"' do
+        ref = Bio::Ucsc::File::Twobit.load("samples/hg18.2bit")
+        itv = Bio::GenomicInterval.parse("chr1:217,260-217,299")
+        ref.find_by_interval(itv).should ==
+          "NNNNNNNNNNNNNNNNNNNNNGATTCATGGCTGAAATCGT"
+      end
+    end
+    
+    # N-block => chr1:267,720-317,719
+    context "given range chr1:257,560-257,600" do
+      it 'returns "CAGGCGCCCGCATCCAGCTGGATNNNNNNNNNNNNNNNNNN"' do
+        ref = Bio::Ucsc::File::Twobit.load("samples/hg18.2bit")
+        itv = Bio::GenomicInterval.parse("chr1:257,560-257,600")
+        ref.find_by_interval(itv).should ==
+          "CAGGCGCCCGCATCCAGCTGGATNNNNNNNNNNNNNNNNNN"
+      end
+    end
+  end
+
+  describe ".subseq" do
+    context "given range chr1:257,560-257,600" do
+      it 'returns "CAGGCGCCCGCATCCAGCTGGATNNNNNNNNNNNNNNNNNN"' do
+        ref = Bio::Ucsc::File::Twobit.open("samples/hg18.2bit")
+        ref.subseq("chr1:257,560-257,600").should ==
+          "CAGGCGCCCGCATCCAGCTGGATNNNNNNNNNNNNNNNNNN"
+      end
+    end
+  end
+  
+end
+
+# N-Blocks
+#  chr1:167281-217280,
+#  chr1:257583-307582,
+#  chr1:461232-511231,
+#  chr1:2624081-2674080,
+ 

data/spec/galgal3_spec.rb

@@ -117,22 +117,22 @@ describe "Bio::Ucsc::GalGal3" do
     end
   end 
 
-  describe "Bio::Ucsc::GalGal3::ChainAnoCar1" do
+  describe "Bio::Ucsc::GalGal3::ChainAnoCar2" do
     context ".find_by_interval" do
       it 'returns the first records' do
         gi = Bio::GenomicInterval.parse("chrW:1-10,000,000")
-        result = Bio::Ucsc::GalGal3::ChainAnoCar1.find_by_interval gi
+        result = Bio::Ucsc::GalGal3::ChainAnoCar2.find_by_interval gi
         pp result
         result.should be_true
       end
     end
   end 
 
-  describe "Bio::Ucsc::GalGal3::ChainAnoCar1Link" do
+  describe "Bio::Ucsc::GalGal3::ChainAnoCar2Link" do
     context ".find_by_interval" do
       it 'returns the first records' do
         gi = Bio::GenomicInterval.parse("chrW:1-10,000,000")
-        result = Bio::Ucsc::GalGal3::ChainAnoCar1Link.find_by_interval gi
+        result = Bio::Ucsc::GalGal3::ChainAnoCar2Link.find_by_interval gi
         pp result
         result.should be_true
       end
@@ -440,22 +440,22 @@ describe "Bio::Ucsc::GalGal3" do
     end
   end 
 
-  describe "Bio::Ucsc::GalGal3::ChainXenTro2" do
+  describe "Bio::Ucsc::GalGal3::ChainXenTro3" do
     context ".find_by_interval" do
       it 'returns the first records' do
         gi = Bio::GenomicInterval.parse("chrW:1-10,000,000")
-        result = Bio::Ucsc::GalGal3::ChainXenTro2.find_by_interval gi
+        result = Bio::Ucsc::GalGal3::ChainXenTro3.find_by_interval gi
         pp result
         result.should be_true
       end
     end
   end 
 
-  describe "Bio::Ucsc::GalGal3::ChainXenTro2Link" do
+  describe "Bio::Ucsc::GalGal3::ChainXenTro3Link" do
     context ".find_by_interval" do
       it 'returns the first records' do
         gi = Bio::GenomicInterval.parse("chrW:1-10,000,000")
-        result = Bio::Ucsc::GalGal3::ChainXenTro2Link.find_by_interval gi
+        result = Bio::Ucsc::GalGal3::ChainXenTro3Link.find_by_interval gi
         pp result
         result.should be_true
       end
@@ -857,10 +857,10 @@ describe "Bio::Ucsc::GalGal3" do
     end
   end 
 
-  describe "Bio::Ucsc::GalGal3::NetAnoCar1" do
+  describe "Bio::Ucsc::GalGal3::NetAnoCar2" do
     context ".first" do
       it 'returns the first records' do
-        result = Bio::Ucsc::GalGal3::NetAnoCar1.first
+        result = Bio::Ucsc::GalGal3::NetAnoCar2.first
         pp result
         result.should be_true
       end
@@ -1007,10 +1007,10 @@ describe "Bio::Ucsc::GalGal3" do
     end
   end 
 
-  describe "Bio::Ucsc::GalGal3::NetXenTro2" do
+  describe "Bio::Ucsc::GalGal3::NetXenTro3" do
     context ".first" do
       it 'returns the first records' do
-        result = Bio::Ucsc::GalGal3::NetXenTro2.first
+        result = Bio::Ucsc::GalGal3::NetXenTro3.first
         pp result
         result.should be_true
       end

data/spec/gasacu1_spec.rb

@@ -67,22 +67,22 @@ describe "Bio::Ucsc::GasAcu1" do
     end
   end 
 
-  describe "Bio::Ucsc::GasAcu1::ChainAnoCar1" do
+  describe "Bio::Ucsc::GasAcu1::ChainAnoCar2" do
     context ".find_by_interval" do
       it 'returns the first records' do
         gi = Bio::GenomicInterval.parse("chrI:1-10,000,000")
-        result = Bio::Ucsc::GasAcu1::ChainAnoCar1.find_by_interval gi
+        result = Bio::Ucsc::GasAcu1::ChainAnoCar2.find_by_interval gi
         pp result
         result.should be_true
       end
     end
   end 
 
-  describe "Bio::Ucsc::GasAcu1::ChainAnoCar1Link" do
+  describe "Bio::Ucsc::GasAcu1::ChainAnoCar2Link" do
     context ".find_by_interval" do
       it 'returns the first records' do
         gi = Bio::GenomicInterval.parse("chrI:1-10,000,000")
-        result = Bio::Ucsc::GasAcu1::ChainAnoCar1Link.find_by_interval gi
+        result = Bio::Ucsc::GasAcu1::ChainAnoCar2Link.find_by_interval gi
         pp result
         result.should be_true
       end
@@ -570,10 +570,10 @@ describe "Bio::Ucsc::GasAcu1" do
     end
   end 
 
-  describe "Bio::Ucsc::GasAcu1::NetAnoCar1" do
+  describe "Bio::Ucsc::GasAcu1::NetAnoCar2" do
     context ".first" do
       it 'returns the first records' do
-        result = Bio::Ucsc::GasAcu1::NetAnoCar1.first
+        result = Bio::Ucsc::GasAcu1::NetAnoCar2.first
         pp result
         result.should be_true
       end

data/spec/hg18/find_by_spec.rb

@@ -12,15 +12,13 @@ describe "Bio::Ucsc::Hg18::Gdv (UsingChromBin)" do
         r.should have(4).items
       end
     end    
-  end
-
-  describe "#find_by_interval" do
+    
     context 'range chr1:120,266,000-120,315,000 with partial: false' do
       it "returns 1 records" do
         Bio::Ucsc::Hg18::DBConnection.default
         Bio::Ucsc::Hg18::DBConnection.connect
         i = Bio::GenomicInterval.parse("chr1:120,266,000-120,315,000")
-        r = Bio::Ucsc::Hg18::Dgv.find_all_by_interval(i, partial: false)
+        r = Bio::Ucsc::Hg18::Dgv.find_all_by_interval(i, :partial => false)
         r.should have(0).items
       end
     end    
@@ -39,16 +37,14 @@ describe "Bio::Ucsc::Hg18::CytoBand (UsingChrom)" do
         r = Bio::Ucsc::Hg18::CytoBand.find_all_by_interval(i)
         r.should have(2).items
       end
-    end    
-  end
+    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
       it "returns 1 records" do
         Bio::Ucsc::Hg18::DBConnection.default
         Bio::Ucsc::Hg18::DBConnection.connect
         i = Bio::GenomicInterval.parse("chr1:117,000,000-120,600,001")
-        r = Bio::Ucsc::Hg18::CytoBand.find_all_by_interval(i, partial: false)
+        r = Bio::Ucsc::Hg18::CytoBand.find_all_by_interval(i, :partial => false)
         r.should have(0).items
       end
     end    
@@ -69,12 +65,12 @@ describe "Bio::Ucsc::Hg18::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::Hg18::DBConnection.default
         Bio::Ucsc::Hg18::DBConnection.connect
         i = Bio::GenomicInterval.parse("chr17:7,571,720-7,590,863")
-        r = Bio::Ucsc::Hg18::KnownGene.find_all_by_interval(i, partial: false)
+        r = Bio::Ucsc::Hg18::KnownGene.find_all_by_interval(i, :partial => false)
         r.should have(0).items
       end
     end
@@ -95,12 +91,12 @@ describe "Bio::Ucsc::Hg18::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::Hg18::DBConnection.default
         Bio::Ucsc::Hg18::DBConnection.connect
         i = Bio::GenomicInterval.parse("chr17:7,571,720-7,590,863")
-        r = Bio::Ucsc::Hg18::RefGene.find_all_by_interval(i, partial: false)
+        r = Bio::Ucsc::Hg18::RefGene.find_all_by_interval(i, :partial => false)
         r.should have(0).items
       end
     end
@@ -121,12 +117,12 @@ describe "Bio::Ucsc::Hg18::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::Hg18::DBConnection.default
         Bio::Ucsc::Hg18::DBConnection.connect
         i = Bio::GenomicInterval.parse("chr17:7,575,000-7,580,000")
-        r = Bio::Ucsc::Hg18::CcdsGene.find_all_by_interval(i, partial: false)
+        r = Bio::Ucsc::Hg18::CcdsGene.find_all_by_interval(i, :partial => false)
         r.should have(0).items
       end
     end
@@ -146,12 +142,12 @@ describe "Bio::Ucsc::Hg18::Rmsk (UsingGenoBin)" 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::Hg18::DBConnection.default
         Bio::Ucsc::Hg18::DBConnection.connect
         i = Bio::GenomicInterval.parse("chr17:7,575,000-7,577,000")
-        r = Bio::Ucsc::Hg18::Rmsk.find_all_by_interval(i, partial: false)
+        r = Bio::Ucsc::Hg18::Rmsk.find_all_by_interval(i, :partial => false)
         r.should have(7).items
       end
     end
@@ -172,17 +168,15 @@ describe "Bio::Ucsc::Hg18::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::Hg18::DBConnection.default
         Bio::Ucsc::Hg18::DBConnection.connect
         i = Bio::GenomicInterval.parse("chr17:7,572,000-7,580,000")
-        r = Bio::Ucsc::Hg18::All_est.find_all_by_interval(i, partial: false)
+        r = Bio::Ucsc::Hg18::All_est.find_all_by_interval(i, :partial => false)
         r.should have(0).items
       end
     end
   end
 
 end
-
-