bio-ucsc-api 0.0.1

data/spec/hg19/hapmapsnpschd_spec.rb

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+require 'bio-ucsc'
+describe "Bio::Ucsc::Hg19::HapMapSnpsCHD" 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::HapMapSnpsCHD.find_by_interval(i).should have(5).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::HapMapSnpsCHD.find_by_interval(i)
+        r[0].chrom.should == "chr1"
+      end
+    end
+  end
+
+end

data/spec/hg19/hapmapsnpsgih_spec.rb

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+require 'bio-ucsc'
+describe "Bio::Ucsc::Hg19::HapMapSnpsGIH" 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::HapMapSnpsGIH.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("chr1:1-600,000")
+        r = Bio::Ucsc::Hg19::HapMapSnpsGIH.find_by_interval(i)
+        r[0].chrom.should == "chr1"
+      end
+    end
+  end
+
+end

data/spec/hg19/hapmapsnpsjpt_spec.rb

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+require 'bio-ucsc'
+describe "Bio::Ucsc::Hg19::HapMapSnpsJPT" 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::HapMapSnpsJPT.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::HapMapSnpsJPT.find_by_interval(i)
+        r[0].chrom.should == "chr1"
+      end
+    end
+  end
+
+end

data/spec/hg19/hapmapsnpslwk_spec.rb

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+require 'bio-ucsc'
+describe "Bio::Ucsc::Hg19::HapMapSnpsLWK" 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::HapMapSnpsLWK.find_by_interval(i).should have(3).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::HapMapSnpsLWK.find_by_interval(i)
+        r[0].chrom.should == "chr1"
+      end
+    end
+  end
+
+end

data/spec/hg19/hapmapsnpsmex_spec.rb

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+require 'bio-ucsc'
+describe "Bio::Ucsc::Hg19::HapMapSnpsMEX" 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::HapMapSnpsMEX.find_by_interval(i).should have(1).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::HapMapSnpsMEX.find_by_interval(i)
+        r[0].chrom.should == "chr1"
+      end
+    end
+  end
+
+end

data/spec/hg19/hapmapsnpsmkk_spec.rb

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+require 'bio-ucsc'
+describe "Bio::Ucsc::Hg19::HapMapSnpsMKK" 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::HapMapSnpsMKK.find_by_interval(i).should have(3).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::HapMapSnpsMKK.find_by_interval(i)
+        r[0].chrom.should == "chr1"
+      end
+    end
+  end
+
+end

data/spec/hg19/hapmapsnpstsi_spec.rb

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+require 'bio-ucsc'
+describe "Bio::Ucsc::Hg19::HapMapSnpsTSI" 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::HapMapSnpsTSI.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("chr1:1-600,000")
+        r = Bio::Ucsc::Hg19::HapMapSnpsTSI.find_by_interval(i)
+        r[0].chrom.should == "chr1"
+      end
+    end
+  end
+
+end

data/spec/hg19/hapmapsnpsyri_spec.rb

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+require 'bio-ucsc'
+describe "Bio::Ucsc::Hg19::HapMapSnpsYRI" 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::HapMapSnpsYRI.find_by_interval(i).should have(45).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::HapMapSnpsYRI.find_by_interval(i)
+        r[0].chrom.should == "chr1"
+      end
+    end
+  end
+
+end

data/spec/hg19/knowngene_spec.rb

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+require 'bio-ucsc'
+describe "Bio::Ucsc::Hg19::KnownGene" do 
+
+  describe "#find_by_interval" do
+    context "given range chr1:1-20000" do
+      it "returens an array of results" do
+        Bio::Ucsc::Hg19::DBConnection.default
+        Bio::Ucsc::Hg19::DBConnection.connect
+        i = Bio::GenomicInterval.parse("chr1:1-20000")
+        Bio::Ucsc::Hg19::KnownGene.find_by_interval(i).should have(24).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("chr1:1-20000")
+        r = Bio::Ucsc::Hg19::KnownGene.find_by_interval(i)
+        r[0].chrom.should == "chr1"
+      end
+    end
+  end
+
+end

data/spec/hg19/omimGene_spec.rb

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+require 'bio-ucsc'
+describe "Bio::Ucsc::Hg19::OmimGene" 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::OmimGene.find_by_interval(i).should have(4).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::OmimGene.find_by_interval(i)
+        r[0].chrom.should == "chr1"
+      end
+    end
+  end
+
+end

data/spec/hg19/phastconselements46wayprimates_spec.rb

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+require 'bio-ucsc'
+describe "Bio::Ucsc::Hg19::PhastConsElements46wayPrimates" do 
+
+  describe "#find_by_interval" do
+    context "given range chr1:1-80,000" do
+      it "returens an array of results" do
+        Bio::Ucsc::Hg19::DBConnection.default
+        Bio::Ucsc::Hg19::DBConnection.connect
+        i = Bio::GenomicInterval.parse("chr1:1-80,000")
+        Bio::Ucsc::Hg19::PhastConsElements46wayPrimates.find_by_interval(i).should have(4).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("chr1:1-80,000")
+        r = Bio::Ucsc::Hg19::PhastConsElements46wayPrimates.find_by_interval(i)
+        r[0].chrom.should == "chr1"
+      end
+    end
+  end
+
+end

data/spec/hg19/phyloP46wayPrimates_spec.rb

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+require 'bio-ucsc'
+describe "Bio::Ucsc::Hg19::PhyloP46wayPrimates" do 
+
+  describe "#find_by_interval" do
+    context "given range chr1:1-50,000" do
+      it "returens an array of results" do
+        Bio::Ucsc::Hg19::DBConnection.default
+        Bio::Ucsc::Hg19::DBConnection.connect
+        i = Bio::GenomicInterval.parse("chr1:1-50,000")
+        Bio::Ucsc::Hg19::PhyloP46wayPrimates.find_by_interval(i).should have(39).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("chr1:1-50,000")
+        r = Bio::Ucsc::Hg19::PhyloP46wayPrimates.find_by_interval(i)
+        r[0].chrom.should == "chr1"
+      end
+    end
+  end
+
+end

data/spec/hg19/refgene_spec.rb

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+require 'bio-ucsc'
+describe "Bio::Ucsc::Hg19::RefGene" do 
+
+  describe "#find_by_interval" do
+    context "given range chr1:1-100,000" do
+      it "returens an array of results" do
+        Bio::Ucsc::Hg19::DBConnection.default
+        Bio::Ucsc::Hg19::DBConnection.connect
+        i = Bio::GenomicInterval.parse("chr1:1-100,000")
+        Bio::Ucsc::Hg19::RefGene.find_by_interval(i).should have(4).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("chr1:1-100,000")
+        r = Bio::Ucsc::Hg19::RefGene.find_by_interval(i)
+        r[0].chrom.should == "chr1"
+      end
+    end
+  end
+
+end

data/spec/hg19/rmsk_spec.rb

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+require 'bio-ucsc'
+describe "Bio::Ucsc::Hg19::Rmsk" do 
+
+  describe "#find_by_interval" do
+    context "given range chr1:1-100,000" do
+      it "returens an array of results" do
+        Bio::Ucsc::Hg19::DBConnection.default
+        Bio::Ucsc::Hg19::DBConnection.connect
+        i = Bio::GenomicInterval.parse("chr1:1-100,000")
+        Bio::Ucsc::Hg19::Rmsk.find_by_interval(i).should have(146).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("chr1:1-100,000")
+        r = Bio::Ucsc::Hg19::Rmsk.find_by_interval(i)
+        r[0].genoName.should == "chr1"
+      end
+    end
+  end
+
+end

data/spec/hg19/snp132Flagged_spec.rb

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+require 'bio-ucsc'
+describe "Bio::Ucsc::Hg19::Snp132Flagged" do 
+
+  describe "#find_by_interval" do
+    context "given range chr1:1-2,000,000" do
+      it "returens an array of results"  do
+        Bio::Ucsc::Hg19::DBConnection.default
+        Bio::Ucsc::Hg19::DBConnection.connect
+        i = Bio::GenomicInterval.parse("chr1:1-2,000,000")
+        Bio::Ucsc::Hg19::Snp132Flagged.find_by_interval(i).should have(3).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("chr1:1-2,000,000")
+        r = Bio::Ucsc::Hg19::Snp132Flagged.find_by_interval(i)
+        r[0].chrom.should == "chr1"
+      end
+    end
+  end
+
+end
+

data/spec/hg19/snp132_spec.rb

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+require 'bio-ucsc'
+describe "Bio::Ucsc::Hg19::Snp132" do 
+
+  describe "#find_by_interval" do
+    context "given range chr1:1-12,000" do
+      it "returens an array of results" do
+        Bio::Ucsc::Hg19::DBConnection.default
+        Bio::Ucsc::Hg19::DBConnection.connect
+        i = Bio::GenomicInterval.parse("chr1:1-12,000")
+        Bio::Ucsc::Hg19::Snp132.find_by_interval(i).should have(67).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("chr1:1-12,000")
+        r = Bio::Ucsc::Hg19::Snp132.find_by_interval(i)
+        r[0].chrom.should == "chr1"
+      end
+    end
+  end
+
+end

data/spec/hg19/snp132codingdbsnp_spec.rb

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+require 'bio-ucsc'
+describe "Bio::Ucsc::Hg19::Snp132CodingDbSnp" do 
+
+  describe "#find_by_interval" do
+    context "given range chr1:1-50,000" do
+      it "returens an array of results" do
+        Bio::Ucsc::Hg19::DBConnection.default
+        Bio::Ucsc::Hg19::DBConnection.connect
+        i = Bio::GenomicInterval.parse("chr1:1-50,000")
+        Bio::Ucsc::Hg19::Snp132CodingDbSnp.find_by_interval(i).should have(23).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("chr1:1-50,000")
+        r = Bio::Ucsc::Hg19::Snp132CodingDbSnp.find_by_interval(i)
+        r[0].chrom.should == "chr1"
+      end
+    end
+  end
+
+end

data/spec/hg19/snp132common_spec.rb

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+require 'bio-ucsc'
+describe "Bio::Ucsc::Hg19::Snp132Common" do 
+
+  describe "#find_by_interval" do
+    context "given range chr1:1-20000" do
+      it "returens an array of results"  do
+        Bio::Ucsc::Hg19::DBConnection.default
+        Bio::Ucsc::Hg19::DBConnection.connect
+        i = Bio::GenomicInterval.parse("chr1:1-20000")
+        Bio::Ucsc::Hg19::Snp132Common.find_by_interval(i).should have(4).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("chr1:1-20000") 
+        r = Bio::Ucsc::Hg19::Snp132Common.find_by_interval(i)
+        r[0].chrom.should == "chr1"
+      end
+    end
+  end
+
+end
+