bio-ucsc-api 0.0.1 → 0.0.3
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- data/README.rdoc +9 -2
- data/Rakefile +1 -1
- data/VERSION +1 -1
- data/bio-ucsc-api.gemspec +29 -7
- data/lib/bio-ucsc.rb +2 -2
- data/lib/bio-ucsc/hg18.rb +3 -0
- data/lib/bio-ucsc/hg18/reference.rb +171 -0
- data/lib/bio-ucsc/hg19.rb +46 -9
- data/lib/bio-ucsc/hg19/description.rb +23 -0
- data/lib/bio-ucsc/hg19/gbcdnainfo.rb +24 -0
- data/lib/bio-ucsc/hg19/kgxref.rb +19 -0
- data/lib/bio-ucsc/hg19/reference.rb +171 -0
- data/lib/bio-ucsc/hg19/refseqsummary.rb +23 -0
- data/lib/bio-ucsc/hg19/trnas.rb +20 -0
- data/samples/hg19-2bit-retrieve.rb +39 -0
- data/samples/hg19-sample.rb +22 -1
- data/samples/symbol2summary.rb +47 -0
- data/spec/hg18/reference_spec.rb +144 -0
- data/spec/hg19/description_spec.rb +25 -0
- data/spec/hg19/gbcdnainfo_spec.rb +25 -0
- data/spec/hg19/kgxref_spec.rb +14 -0
- data/spec/hg19/reference_spec.rb +137 -0
- data/spec/hg19/refseqsummary_spec.rb +15 -0
- data/spec/hg19/trnas_spec.rb +23 -0
- metadata +29 -56
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@@ -0,0 +1,25 @@
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1
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require 'bio-ucsc'
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2
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describe "Bio::Ucsc::Hg19::Description" do
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3
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4
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describe "#find" do
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5
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context "given range *(0..9)" do
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6
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it "returens an array of results" do
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7
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Bio::Ucsc::Hg19::DBConnection.default
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8
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Bio::Ucsc::Hg19::DBConnection.connect
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9
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Bio::Ucsc::Hg19::Description.find([*(0..9)]).should have(10).items
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10
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end
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11
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end
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12
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end
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13
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14
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describe ".gbCndaInfo.acc" do
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15
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context "given id==1" do
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it 'returens "AB004856"' do
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Bio::Ucsc::Hg19::DBConnection.default
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Bio::Ucsc::Hg19::DBConnection.connect
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19
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Bio::Ucsc::Hg19::Description.find(1).gbCdnaInfo.acc.should == "AB004856"
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20
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end
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21
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end
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22
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end
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25
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end
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@@ -0,0 +1,25 @@
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1
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require 'bio-ucsc'
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2
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describe "Bio::Ucsc::Hg19::GbCdnaInfo" do
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3
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4
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describe "#find" do
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5
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context "given range *(1..9)" do
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6
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it "returens an array of results" do
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7
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Bio::Ucsc::Hg19::DBConnection.default
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8
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Bio::Ucsc::Hg19::DBConnection.connect
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9
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Bio::Ucsc::Hg19::GbCdnaInfo.find([*(1..9)]).should have(9).items
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10
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end
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11
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end
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12
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end
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13
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14
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describe ".description.name" do
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15
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context "given id==1" do
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it 'returens 1' do
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Bio::Ucsc::Hg19::DBConnection.default
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18
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Bio::Ucsc::Hg19::DBConnection.connect
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19
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r = Bio::Ucsc::Hg19::GbCdnaInfo.find(1, :include => :description)
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20
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r.description.id.should == 1
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21
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end
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22
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end
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23
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end
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25
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end
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@@ -0,0 +1,14 @@
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1
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require 'bio-ucsc'
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describe "Bio::Ucsc::Hg19::KgXref" do
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3
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4
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describe "#find_by_geneSymbol" do
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5
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context 'given "TP53"' do
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it "returens an array of results" do
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Bio::Ucsc::Hg19::DBConnection.default
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Bio::Ucsc::Hg19::DBConnection.connect
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Bio::Ucsc::Hg19::KgXref.find_all_by_geneSymbol("TP53").should have(13).item
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10
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end
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11
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end
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12
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end
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13
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14
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end
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@@ -0,0 +1,137 @@
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1
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require 'bio-ucsc'
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2
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3
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describe "Bio::Ucsc::Hg19::Reference" do
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4
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5
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describe ".load" do
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context 'given "../samples/hg19.2bit"' do
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it "returns true" do
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Bio::Ucsc::Hg19::Reference.load("samples/hg19.2bit")
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9
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end
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10
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end
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11
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end
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12
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13
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describe ".header.signarue" do
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14
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context 'given "../samples/hg19.2bit"' do
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it "returns 0x1A412743" do
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Bio::Ucsc::Hg19::Reference.load("samples/hg19.2bit")
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Bio::Ucsc::Hg19::Reference.header.signature.should == 0x1A412743
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end
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19
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end
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20
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end
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21
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22
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describe ".header.version" do
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23
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context 'given "../samples/hg19.2bit"' do
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it "returns 0" do
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Bio::Ucsc::Hg19::Reference.load("samples/hg19.2bit")
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26
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Bio::Ucsc::Hg19::Reference.header.version.should == 0
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27
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end
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28
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end
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29
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end
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30
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31
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describe ".header.sequence_count" do
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32
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context 'given "../samples/hg19.2bit"' do
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33
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it "returns 0x5d" do
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34
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Bio::Ucsc::Hg19::Reference.load("samples/hg19.2bit")
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35
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Bio::Ucsc::Hg19::Reference.header.sequence_count.should == 0x5d
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end
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end
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end
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39
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40
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describe '.offsets["chr1"]' do
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41
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context 'given "../samples/hg19.2bit"' do
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it "returns 0x0687" do
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43
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Bio::Ucsc::Hg19::Reference.load("samples/hg19.2bit")
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Bio::Ucsc::Hg19::Reference.offsets["chr1"].should == 0x0687
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45
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end
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46
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end
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47
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end
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48
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49
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describe ".records" do
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50
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context 'given "chr1"' do
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51
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it 'returns (TwoBitRecord.reserved == 0)' do
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52
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Bio::Ucsc::Hg19::Reference.load("samples/hg19.2bit")
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53
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Bio::Ucsc::Hg19::Reference.records("chr1").reserved == 0
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54
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end
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55
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end
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56
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end
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57
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58
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describe ".records" do
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59
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context 'given "chr1"' do
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60
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it 'returns (TwoBitRecord.dna_size == 249_250_621)' do
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61
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Bio::Ucsc::Hg19::Reference.load("samples/hg19.2bit")
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62
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Bio::Ucsc::Hg19::Reference.records("chr1").dna_size.should == 249_250_621
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63
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end
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64
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end
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65
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end
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66
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67
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describe ".byte_to_nucleotides" do
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68
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context 'given 0b00011011' do
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69
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it 'returns "TCAG"' do
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70
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r = Bio::Ucsc::Hg19::Reference.byte_to_nucleotides(0b00011011)
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71
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r.should == "TCAG"
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72
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end
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73
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end
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74
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end
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75
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76
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describe ".bytes_to_nucleotides" do
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77
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context 'given [0b00011011, 0b11100100]' do
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78
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it 'returns "TCAGGACT"' do
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79
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ary = [0b00011011, 0b11100100]
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80
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r = Bio::Ucsc::Hg19::Reference.bytes_to_nucleotides(ary)
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81
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r.should == "TCAGGACT"
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82
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end
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83
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end
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84
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end
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85
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86
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describe ".find_by_interval_raw" do
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87
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context "given range chr1:1,000,000-1,000,030" do
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88
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it 'returens "TGGGCACAGCCTCACCCAGGAAAGCAGCTGG"' do
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89
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Bio::Ucsc::Hg19::Reference.load("samples/hg19.2bit")
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90
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itv = Bio::GenomicInterval.parse("chr1:1,000,000-1,000,030")
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91
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r = Bio::Ucsc::Hg19::Reference.find_by_interval_raw(itv)
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92
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r.should == "TGGGCACAGCCTCACCCAGGAAAGCAGCTGG"
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93
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end
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94
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end
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95
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96
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context "given range chr2:1,123,456-1,123,499" do
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97
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it 'returens "GTACTTAGAACACTATTGATTTCTGTACGTTGATTTTGTATTCT"' do
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98
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Bio::Ucsc::Hg19::Reference.load("samples/hg19.2bit")
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99
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itv = Bio::GenomicInterval.parse("chr2:1,123,456-1,123,499")
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100
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r = Bio::Ucsc::Hg19::Reference.find_by_interval_raw(itv)
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101
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r.should == "GTACTTAGAACACTATTGATTTCTGTACGTTGATTTTGTATTCT"
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102
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end
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103
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end
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104
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|
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105
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context "given range chr2:1,123,456-1,123,456" do
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106
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it 'returens "G"' do
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107
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Bio::Ucsc::Hg19::Reference.load("samples/hg19.2bit")
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108
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itv = Bio::GenomicInterval.parse("chr2:1,123,456-1,123,456")
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109
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r = Bio::Ucsc::Hg19::Reference.find_by_interval_raw(itv)
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110
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r.should == "G"
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111
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end
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112
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end
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113
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end
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114
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115
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describe ".find_by_interval" do
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116
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context "given range chr1:9,980-10,020" do
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117
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it 'returns "NNNNNNNNNNNNNNNNNNNNNTAACCCTAACCCTAACCCTA"' do
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118
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Bio::Ucsc::Hg19::Reference.load("samples/hg19.2bit")
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119
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itv = Bio::GenomicInterval.parse("chr1:9,980-10,020")
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120
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r = Bio::Ucsc::Hg19::Reference.find_by_interval(itv)
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121
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r.should == "NNNNNNNNNNNNNNNNNNNNNTAACCCTAACCCTAACCCTA"
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122
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end
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123
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end
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124
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125
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# N-block => chr1:267,720-317,719
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126
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context "given range chr1:267,690-267,735" do
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127
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it 'returns "GGGACTACAGGCGCCCGCATCCAGCTGGATNNNNNNNNNNNNNNNN' do
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128
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Bio::Ucsc::Hg19::Reference.load("samples/hg19.2bit")
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129
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itv = Bio::GenomicInterval.parse("chr1:267,690-267,735")
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130
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r = Bio::Ucsc::Hg19::Reference.find_by_interval(itv)
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131
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r.should == "GGGACTACAGGCGCCCGCATCCAGCTGGATNNNNNNNNNNNNNNNN"
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132
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end
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133
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end
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134
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end
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135
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end
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136
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137
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@@ -0,0 +1,15 @@
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1
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require 'bio-ucsc'
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2
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describe "Bio::Ucsc::Hg19::RefSeqSummary" do
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3
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4
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describe "#find_all_by_mrnaAcc" do
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5
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context 'given "NR_036941"' do
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6
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it "returens an array of results" do
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7
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Bio::Ucsc::Hg19::DBConnection.default
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8
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Bio::Ucsc::Hg19::DBConnection.connect
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9
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r = Bio::Ucsc::Hg19::RefSeqSummary.find_all_by_mrnaAcc("NR_036941")
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10
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r.should have(1).item
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11
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end
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12
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end
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13
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end
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14
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15
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end
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@@ -0,0 +1,23 @@
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1
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require 'bio-ucsc'
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2
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describe "Bio::Ucsc::Hg19::TRNAs" do
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3
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4
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describe "#find_by_interval" do
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5
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context "given range chr1:1-10,000,000" do
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6
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it "returens an array of results" do
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7
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Bio::Ucsc::Hg19::DBConnection.default
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8
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Bio::Ucsc::Hg19::DBConnection.connect
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9
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i = Bio::GenomicInterval.parse("chr1:1-10,000,000")
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10
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Bio::Ucsc::Hg19::TRNAs.find_by_interval(i).should have(1).items
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11
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end
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12
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13
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it "returens an array of results with column accessors" do
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14
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Bio::Ucsc::Hg19::DBConnection.default
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15
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Bio::Ucsc::Hg19::DBConnection.connect
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16
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i = Bio::GenomicInterval.parse("chr1:1-10,000,000")
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17
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r = Bio::Ucsc::Hg19::TRNAs.find_by_interval(i)
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18
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r[0].chrom.should == "chr1"
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19
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end
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20
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end
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21
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end
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22
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23
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end
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metadata
CHANGED
|
@@ -1,12 +1,8 @@
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1
1
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--- !ruby/object:Gem::Specification
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2
2
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name: bio-ucsc-api
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|
3
3
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version: !ruby/object:Gem::Version
|
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4
|
-
prerelease:
|
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5
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-
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6
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-
- 0
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7
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-
- 0
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8
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- 1
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9
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-
version: 0.0.1
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4
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prerelease:
|
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5
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version: 0.0.3
|
|
10
6
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platform: ruby
|
|
11
7
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authors:
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12
8
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- MISHIMA, Hiroyuki
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|
@@ -16,8 +12,7 @@ autorequire:
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16
12
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bindir: bin
|
|
17
13
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cert_chain: []
|
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18
14
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|
|
19
|
-
date: 2011-04-
|
|
20
|
-
default_executable:
|
|
15
|
+
date: 2011-04-25 00:00:00 Z
|
|
21
16
|
dependencies:
|
|
22
17
|
- !ruby/object:Gem::Dependency
|
|
23
18
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name: activerecord
|
|
@@ -26,10 +21,6 @@ dependencies:
|
|
|
26
21
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requirements:
|
|
27
22
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- - ">="
|
|
28
23
|
- !ruby/object:Gem::Version
|
|
29
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-
segments:
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30
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-
- 3
|
|
31
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-
- 0
|
|
32
|
-
- 7
|
|
33
24
|
version: 3.0.7
|
|
34
25
|
type: :runtime
|
|
35
26
|
prerelease: false
|
|
@@ -41,10 +32,6 @@ dependencies:
|
|
|
41
32
|
requirements:
|
|
42
33
|
- - ">="
|
|
43
34
|
- !ruby/object:Gem::Version
|
|
44
|
-
segments:
|
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45
|
-
- 2
|
|
46
|
-
- 8
|
|
47
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-
- 1
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|
48
35
|
version: 2.8.1
|
|
49
36
|
type: :runtime
|
|
50
37
|
prerelease: false
|
|
@@ -56,10 +43,6 @@ dependencies:
|
|
|
56
43
|
requirements:
|
|
57
44
|
- - ">="
|
|
58
45
|
- !ruby/object:Gem::Version
|
|
59
|
-
segments:
|
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60
|
-
- 0
|
|
61
|
-
- 1
|
|
62
|
-
- 2
|
|
63
46
|
version: 0.1.2
|
|
64
47
|
type: :runtime
|
|
65
48
|
prerelease: false
|
|
@@ -71,10 +54,6 @@ dependencies:
|
|
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