bio-ucsc-api 0.0.1

data/spec/hg18/cnpsebat2_spec.rb

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+require 'bio-ucsc'
+describe "Bio::Ucsc::Hg18::CnpSebat2" do 
+
+  describe "#find_by_interval" do
+    context "given range chr1:1-20,000,000" do
+      it "returns an array of results" do
+        Bio::Ucsc::Hg18::DBConnection.default
+        Bio::Ucsc::Hg18::DBConnection.connect
+        i = Bio::GenomicInterval.parse("chr1:1-20,000,000")
+        Bio::Ucsc::Hg18::CnpSebat2.find_by_interval(i).should have(1).items
+      end
+
+      it "returns an array of results with column accessors" do
+        Bio::Ucsc::Hg18::DBConnection.default
+        Bio::Ucsc::Hg18::DBConnection.connect
+        i = Bio::GenomicInterval.parse("chr1:1-20,000,000")
+        r = Bio::Ucsc::Hg18::CnpSebat2.find_by_interval(i)
+        r[0].chrom.should == "chr1"
+      end
+    end
+  end
+
+end

data/spec/hg18/cnpsharp2_spec.rb

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+require 'bio-ucsc'
+describe "Bio::Ucsc::Hg18::CnpSharp2" do 
+
+  describe "#find_by_interval" do
+    context "given range chr1:1-2,000,000" do
+      it "returns an array of results" do
+        Bio::Ucsc::Hg18::DBConnection.default
+        Bio::Ucsc::Hg18::DBConnection.connect
+        i = Bio::GenomicInterval.parse("chr1:1-2,000,000")
+        Bio::Ucsc::Hg18::CnpSharp2.find_by_interval(i).should have(1).items
+      end
+
+      it "returns an array of results with column accessors" do
+        Bio::Ucsc::Hg18::DBConnection.default
+        Bio::Ucsc::Hg18::DBConnection.connect
+        i = Bio::GenomicInterval.parse("chr1:1-2,000,000")
+        r = Bio::Ucsc::Hg18::CnpSharp2.find_by_interval(i)
+        r[0].chrom.should == "chr1"
+      end
+    end
+  end
+
+end

data/spec/hg18/db_connection_spec.rb

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+#
+# = /spec/db_connection_spec.rb - Rspec specification for Ucsc::Hg18
+#
+# Copyright::   Cioyrught (C) 2011
+#               MISHIMA, Hiroyuki <missy at be.to / hmishima at nagasaki-u.ac.jp> 
+# License::     Ruby licence (Ryby's / GPLv2 dual)
+
+require 'bio-ucsc'
+describe "Bio::Ucsc::Hg18::DBConnection" do
+
+  describe ".new" do
+    context "given no argument" do 
+      it "establishs the hg19 connection without exceptions" do
+        expect{Bio::Ucsc::Hg18::DBConnection.connect}.not_to raise_error
+      end
+    end
+  end
+
+  describe ".db_host" do 
+    context "given no atgument" do 
+      it "returns the default" do
+        Bio::Ucsc::Hg18::DBConnection.db_host.should == "genome-mysql.cse.ucsc.edu"
+      end
+    end
+  end
+
+  describe ".db_host=" do 
+    context 'given ="localhost"' do 
+      it "changes default hostname" do
+        Bio::Ucsc::Hg18::DBConnection.db_host = "localhost"
+        Bio::Ucsc::Hg18::DBConnection.db_host.should == "localhost"
+      end
+    end
+  end
+
+end

data/spec/hg18/dgv_spec.rb

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+require 'bio-ucsc'
+describe "Bio::Ucsc::Hg18::Dgv" do 
+
+  describe "#find_by_interval" do
+    context "given range chr1:1-20000" do
+      it "returens an array of results" do
+        Bio::Ucsc::Hg18::DBConnection.default
+        Bio::Ucsc::Hg18::DBConnection.connect
+        i = Bio::GenomicInterval.parse("chr1:1-20000")
+        Bio::Ucsc::Hg18::Dgv.find_by_interval(i).should have(11).items
+      end
+
+      it "returens an array of results with column accessors" do
+        Bio::Ucsc::Hg18::DBConnection.default
+        Bio::Ucsc::Hg18::DBConnection.connect
+        i = Bio::GenomicInterval.parse("chr1:1-20000")
+        r = Bio::Ucsc::Hg18::Dgv.find_by_interval(i)
+        r[0].chrom.should == "chr1"
+      end
+    end
+  end
+
+end

data/spec/hg18/refgene_spec.rb

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+require 'bio-ucsc'
+describe "Bio::Ucsc::Hg18::RefGene" do 
+
+  describe "#find_by_interval" do
+    context "given range chr1:1-100,000" do
+      it "returens an array of results" do
+        Bio::Ucsc::Hg18::DBConnection.default
+        Bio::Ucsc::Hg18::DBConnection.connect
+        i = Bio::GenomicInterval.parse("chr1:1-100,000")
+        Bio::Ucsc::Hg18::RefGene.find_by_interval(i).should have(5).items
+      end
+
+      it "returens an array of results with column accessors" do
+        Bio::Ucsc::Hg18::DBConnection.default
+        Bio::Ucsc::Hg18::DBConnection.connect
+        i = Bio::GenomicInterval.parse("chr1:1-100,000")
+        r = Bio::Ucsc::Hg18::RefGene.find_by_interval(i)
+        r[0].chrom.should == "chr1"
+      end
+    end
+  end
+
+end

data/spec/hg18/rmsk_spec.rb

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+require 'bio-ucsc'
+describe "Bio::Ucsc::Hg18::Rmsk" do 
+
+  describe "::Chr1_Rmsk#find_by_interval" do
+    context "given range chr1:1-10,000" do
+      it "returens an array of results" do
+        Bio::Ucsc::Hg18::DBConnection.default
+        Bio::Ucsc::Hg18::DBConnection.connect
+        i = Bio::GenomicInterval.parse("chr1:1-10,000")
+        Bio::Ucsc::Hg18::Rmsk::Chr1_Rmsk.find_by_interval(i).should have(8).items
+      end
+    end
+  end
+
+  describe "#find_by_interval" do
+    context "given range chr3:1-100,000" do
+      it "returens an array of results" do
+        Bio::Ucsc::Hg18::DBConnection.default
+        Bio::Ucsc::Hg18::DBConnection.connect
+        i = Bio::GenomicInterval.parse("chr3:1-100,000")
+        Bio::Ucsc::Hg18::Rmsk.find_by_interval(i).should have(126).items
+      end
+
+      it "returens an array of results with column accessors" do
+        Bio::Ucsc::Hg18::DBConnection.default
+        Bio::Ucsc::Hg18::DBConnection.connect
+        i = Bio::GenomicInterval.parse("chr3:1-100,000")
+        r = Bio::Ucsc::Hg18::Rmsk.find_by_interval(i)
+        r[0].genoName.should == "chr3"
+      end
+    end
+  end
+end

data/spec/hg19/ccdsgene_spec.rb

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+require 'bio-ucsc'
+describe "Bio::Ucsc::Hg19::CcdsGene" do 
+
+  describe "#find_by_interval" do
+    context "given range chr1:1-1,000,000" do
+      it "returens an array of results" do
+        Bio::Ucsc::Hg19::DBConnection.default
+        Bio::Ucsc::Hg19::DBConnection.connect
+        i = Bio::GenomicInterval.parse("chr1:1-1,000,000")
+        Bio::Ucsc::Hg19::RefGene.find_by_interval(i).should have(29).items
+      end
+
+      it "returens an array of results with column accessors" do
+        Bio::Ucsc::Hg19::DBConnection.default
+        Bio::Ucsc::Hg19::DBConnection.connect
+        i = Bio::GenomicInterval.parse("chr1:1-1,000,000")
+        r = Bio::Ucsc::Hg19::RefGene.find_by_interval(i)
+        r[0].chrom.should == "chr1"
+      end
+    end
+  end
+
+end

data/spec/hg19/cytoband_spec.rb

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+require 'bio-ucsc'
+describe "Bio::Ucsc::Hg19::CytoBand" do 
+
+  describe "#find_by_INTERVAL" do
+    context "given range chr1:1-5,000,000" do
+      it "returens 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::CytoBand.find_by_interval(i).should have(2).items
+      end
+
+      it "returens an array of results with column accessors" do
+        Bio::Ucsc::Hg19::DBConnection.default
+        Bio::Ucsc::Hg19::DBConnection.connect
+        i = Bio::GenomicInterval.parse("chr1:1-5,000,000")
+        r = Bio::Ucsc::Hg19::CytoBand.find_by_interval(i)
+        r[0].chrom.should == "chr1"
+      end
+    end
+  end
+
+end

data/spec/hg19/db_connection_spec.rb

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+#
+# = /spec/hg19_spec.rb - Rspec specification for Ucsc::Hg19
+#
+# Copyright::   Cioyrught (C) 2011
+#               MISHIMA, Hiroyuki <missy at be.to / hmishima at nagasaki-u.ac.jp> 
+# License::     Ruby licence (Ryby's / GPLv2 dual)
+
+require 'bio-ucsc'
+
+describe "Bio::Ucsc::Hg19::DBConnection" do
+
+  describe ".new" do
+    context "given no argument" do 
+      it "establishs the hg19 connection without exceptions" do
+        expect{Bio::Ucsc::Hg19::DBConnection.connect}.not_to raise_error
+      end
+    end
+  end
+
+  describe ".db_host" do 
+    context "given no atgument" do 
+      it "returns the default" do
+        Bio::Ucsc::Hg19::DBConnection.db_host.should == "genome-mysql.cse.ucsc.edu"
+      end
+    end
+  end
+
+  describe ".db_host=" do 
+    context 'given ="localhost"' do 
+      it "changes default hostname" do
+        Bio::Ucsc::Hg19::DBConnection.db_host = "localhost"
+        Bio::Ucsc::Hg19::DBConnection.db_host.should == "localhost"
+      end
+    end
+  end
+
+end

data/spec/hg19/dgv_spec.rb

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+require 'bio-ucsc'
+describe "Bio::Ucsc::Hg19::Dgv" do 
+
+  describe "#find_by_interval" do
+    context "given range chr1:1-20,000" do
+      it "returens an array of results" do
+        Bio::Ucsc::Hg19::DBConnection.default
+        Bio::Ucsc::Hg19::DBConnection.connect
+        s = Bio::GenomicInterval.parse("chr1:1-20,000")
+        Bio::Ucsc::Hg19::Dgv.find_by_interval(s).should have(9).items
+      end
+
+      it "returens an array of results with column accessors" do
+        Bio::Ucsc::Hg19::DBConnection.default
+        Bio::Ucsc::Hg19::DBConnection.connect
+        s = Bio::GenomicInterval.parse("chr1:1-20,000")
+        r = Bio::Ucsc::Hg19::Dgv.find_by_interval(s)
+        r[0].chrom.should == "chr1"
+      end
+    end
+  end
+
+end

data/spec/hg19/ensgene_spec.rb

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+require 'bio-ucsc'
+describe "Bio::Ucsc::Hg19::EnsGene" do 
+
+  describe "#find_by_interval" do
+    context "given range chr1:1-500,000" do
+      it "returens an array of results" do
+        Bio::Ucsc::Hg19::DBConnection.default
+        Bio::Ucsc::Hg19::DBConnection.connect
+        i = Bio::GenomicInterval.parse("chr1:1-500,000")
+        Bio::Ucsc::Hg19::EnsGene.find_by_interval(i).should have(60).items
+      end
+
+      it "returens an array of results with column accessors" do
+        Bio::Ucsc::Hg19::DBConnection.default
+        Bio::Ucsc::Hg19::DBConnection.connect
+        i = Bio::GenomicInterval.parse("chr1:1-500,000")
+        r = Bio::Ucsc::Hg19::EnsGene.find_by_interval(i)
+        r[0].chrom.should == "chr1"
+      end
+    end
+  end
+
+end

data/spec/hg19/gwascatalog_spec.rb

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+require 'bio-ucsc'
+describe "Bio::Ucsc::Hg19::GwasCatalog" do 
+
+  describe "#find_by_interval" do
+    context "given range chr1:1-5,000,000" do
+      it "returens 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_by_interval(i).should have(8).items
+      end
+
+      it "returens an array of results with column accessors" do
+        Bio::Ucsc::Hg19::DBConnection.default
+        Bio::Ucsc::Hg19::DBConnection.connect
+        i = Bio::GenomicInterval.parse("chr1:1-5,000,000")
+        r = Bio::Ucsc::Hg19::GwasCatalog.find_by_interval(i)
+        r[0].chrom.should == "chr1"
+      end
+    end
+  end
+
+end

data/spec/hg19/hapmapalleleschimp_spec.rb

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+require 'bio-ucsc'
+describe "Bio::Ucsc::Hg19::HapMapAllelesChimp" do 
+
+  describe "#find_by_interval" do
+    context "given range chr1:1-600,000" do
+      it "returens an array of results" do
+        Bio::Ucsc::Hg19::DBConnection.default
+        Bio::Ucsc::Hg19::DBConnection.connect
+        i = Bio::GenomicInterval.parse("chr1:1-600,000")
+        Bio::Ucsc::Hg19::HapMapAllelesChimp.find_by_interval(i).should have(48).items
+      end
+
+      it "returens an array of results with column accessors" do
+        Bio::Ucsc::Hg19::DBConnection.default
+        Bio::Ucsc::Hg19::DBConnection.connect
+        i = Bio::GenomicInterval.parse("chr1:1-600,000")
+        r = Bio::Ucsc::Hg19::HapMapAllelesChimp.find_by_interval(i)
+        r[0].chrom.should == "chr1"
+      end
+    end
+  end
+
+end

data/spec/hg19/hapmapallelesmacaque_spec.rb

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+require 'bio-ucsc'
+describe "Bio::Ucsc::Hg19::HapMapAllelesMacaque" do 
+
+  describe "#find_by_interval" do
+    context "given range chr1:1-600,000" do
+      it "returens an array of results" do
+        Bio::Ucsc::Hg19::DBConnection.default
+        Bio::Ucsc::Hg19::DBConnection.connect
+        i = Bio::GenomicInterval.parse("chr1:1-600,000")
+        Bio::Ucsc::Hg19::HapMapAllelesMacaque.find_by_interval(i).should have(49).items
+      end
+
+      it "returens an array of results with column accessors" do
+        Bio::Ucsc::Hg19::DBConnection.default
+        Bio::Ucsc::Hg19::DBConnection.connect
+        i = Bio::GenomicInterval.parse("chr1:1-600,000")
+        r = Bio::Ucsc::Hg19::HapMapAllelesMacaque.find_by_interval(i)
+        r[0].chrom.should == "chr1"
+      end
+    end
+  end
+
+end

data/spec/hg19/hapmapsnpsasw_spec.rb

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+require 'bio-ucsc'
+describe "Bio::Ucsc::Hg19::HapMapSnpsASW" do 
+
+  describe "#find_by_interval" do
+    context "given range chr1:1-800,000" do
+      it "returens an array of results" do
+        Bio::Ucsc::Hg19::DBConnection.default
+        Bio::Ucsc::Hg19::DBConnection.connect
+        i = Bio::GenomicInterval.parse("chr1:1-800,000")
+        Bio::Ucsc::Hg19::HapMapSnpsASW.find_by_interval(i).should have(22).items
+      end
+
+      it "returens an array of results with column accessors" do
+        Bio::Ucsc::Hg19::DBConnection.default
+        Bio::Ucsc::Hg19::DBConnection.connect
+        i = Bio::GenomicInterval.parse("chr1:1-800,000")
+        r = Bio::Ucsc::Hg19::HapMapSnpsASW.find_by_interval(i)
+        r[0].chrom.should == "chr1"
+      end
+    end
+  end
+
+end

data/spec/hg19/hapmapsnpsceu_spec.rb

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+require 'bio-ucsc'
+describe "Bio::Ucsc::Hg19::HapMapSnpsCEU" do 
+
+  describe "#find_by_interval" do
+    context "given range chr1:1-600,000" do
+      it "returens an array of results" do
+        Bio::Ucsc::Hg19::DBConnection.default
+        Bio::Ucsc::Hg19::DBConnection.connect
+        i = Bio::GenomicInterval.parse("chr1:1-600,000")
+        Bio::Ucsc::Hg19::HapMapSnpsCEU.find_by_interval(i).should have(41).items
+      end
+
+      it "returens an array of results with column accessors" do
+        Bio::Ucsc::Hg19::DBConnection.default
+        Bio::Ucsc::Hg19::DBConnection.connect
+        i = Bio::GenomicInterval.parse("chr1:1-600,000")
+        r = Bio::Ucsc::Hg19::HapMapSnpsCEU.find_by_interval(i)
+        r[0].chrom.should == "chr1"
+      end
+    end
+  end
+
+end

data/spec/hg19/hapmapsnpschb_spec.rb

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+require 'bio-ucsc'
+describe "Bio::Ucsc::Hg19::HapMapSnpsCHB" do 
+
+  describe "#find_by_interval" do
+    context "given range chr1:1-600,000" do
+      it "returens an array of results" do
+        Bio::Ucsc::Hg19::DBConnection.default
+        Bio::Ucsc::Hg19::DBConnection.connect
+        i = Bio::GenomicInterval.parse("chr1:1-600,000")
+        Bio::Ucsc::Hg19::HapMapSnpsCHB.find_by_interval(i).should have(44).items
+      end
+
+      it "returens an array of results with column accessors" do
+        Bio::Ucsc::Hg19::DBConnection.default
+        Bio::Ucsc::Hg19::DBConnection.connect
+        i = Bio::GenomicInterval.parse("chr1:1-600,000")
+        r = Bio::Ucsc::Hg19::HapMapSnpsCHB.find_by_interval(i)
+        r[0].chrom.should == "chr1"
+      end
+    end
+  end
+
+end