bio-ucsc-api 0.0.1

data/spec/hg19/snp132mult_spec.rb

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+require 'bio-ucsc'
+describe "Bio::Ucsc::Hg19::Snp132Mult" 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::Snp132Mult.find_by_interval(i).should have(51).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::Snp132Mult.find_by_interval(i)
+        r[0].chrom.should == "chr1"
+      end
+    end
+  end
+
+end

data/spec/hg19/wgrna_spec.rb

@@ -0,0 +1,23 @@
+require 'bio-ucsc'
+describe "Bio::Ucsc::Hg19::WgRna" do 
+
+  describe "#find_by_slice" 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::WgRna.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("chr1:1-1,000,000")
+        r = Bio::Ucsc::Hg19::WgRna.find_by_interval(i)
+        r[0].chrom.should == "chr1"
+      end
+    end
+  end
+
+end

data/spec/spec_helper.rb

@@ -0,0 +1,12 @@
+$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
+$LOAD_PATH.unshift(File.dirname(__FILE__))
+require 'rspec'
+#require 'cover_me'
+
+# Requires supporting files with custom matchers and macros, etc,
+# in ./support/ and its subdirectories.
+Dir["#{File.dirname(__FILE__)}/support/**/*.rb"].each {|f| require f}
+
+RSpec.configure do |config|
+  
+end

metadata

@@ -0,0 +1,368 @@
+--- !ruby/object:Gem::Specification 
+name: bio-ucsc-api
+version: !ruby/object:Gem::Version 
+  prerelease: false
+  segments: 
+  - 0
+  - 0
+  - 1
+  version: 0.0.1
+platform: ruby
+authors: 
+- MISHIMA, Hiroyuki
+- Francesco Strozzi
+- Jan Aerts
+autorequire: 
+bindir: bin
+cert_chain: []
+
+date: 2011-04-22 00:00:00 +09:00
+default_executable: 
+dependencies: 
+- !ruby/object:Gem::Dependency 
+  name: activerecord
+  requirement: &id001 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        segments: 
+        - 3
+        - 0
+        - 7
+        version: 3.0.7
+  type: :runtime
+  prerelease: false
+  version_requirements: *id001
+- !ruby/object:Gem::Dependency 
+  name: mysql
+  requirement: &id002 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        segments: 
+        - 2
+        - 8
+        - 1
+        version: 2.8.1
+  type: :runtime
+  prerelease: false
+  version_requirements: *id002
+- !ruby/object:Gem::Dependency 
+  name: bio-genomic-interval
+  requirement: &id003 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        segments: 
+        - 0
+        - 1
+        - 2
+        version: 0.1.2
+  type: :runtime
+  prerelease: false
+  version_requirements: *id003
+- !ruby/object:Gem::Dependency 
+  name: rspec
+  requirement: &id004 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ~>
+      - !ruby/object:Gem::Version 
+        segments: 
+        - 2
+        - 5
+        - 0
+        version: 2.5.0
+  type: :development
+  prerelease: false
+  version_requirements: *id004
+- !ruby/object:Gem::Dependency 
+  name: bundler
+  requirement: &id005 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ~>
+      - !ruby/object:Gem::Version 
+        segments: 
+        - 1
+        - 0
+        - 0
+        version: 1.0.0
+  type: :development
+  prerelease: false
+  version_requirements: *id005
+- !ruby/object:Gem::Dependency 
+  name: jeweler
+  requirement: &id006 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ~>
+      - !ruby/object:Gem::Version 
+        segments: 
+        - 1
+        - 5
+        - 2
+        version: 1.5.2
+  type: :development
+  prerelease: false
+  version_requirements: *id006
+- !ruby/object:Gem::Dependency 
+  name: rcov
+  requirement: &id007 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        segments: 
+        - 0
+        version: "0"
+  type: :development
+  prerelease: false
+  version_requirements: *id007
+- !ruby/object:Gem::Dependency 
+  name: bio
+  requirement: &id008 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        segments: 
+        - 1
+        - 4
+        - 1
+        version: 1.4.1
+  type: :development
+  prerelease: false
+  version_requirements: *id008
+- !ruby/object:Gem::Dependency 
+  name: activerecord
+  requirement: &id009 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        segments: 
+        - 3
+        - 0
+        - 0
+        version: 3.0.0
+  type: :runtime
+  prerelease: false
+  version_requirements: *id009
+- !ruby/object:Gem::Dependency 
+  name: activesupport
+  requirement: &id010 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        segments: 
+        - 3
+        - 0
+        - 0
+        version: 3.0.0
+  type: :runtime
+  prerelease: false
+  version_requirements: *id010
+- !ruby/object:Gem::Dependency 
+  name: bio-genomic-interval
+  requirement: &id011 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        segments: 
+        - 0
+        - 1
+        - 1
+        version: 0.1.1
+  type: :runtime
+  prerelease: false
+  version_requirements: *id011
+description: "A Bioruby plugin: an API for UCSC Genome Browser (experimental)"
+email: missy@be.to
+executables: []
+
+extensions: []
+
+extra_rdoc_files: 
+- README.rdoc
+files: 
+- .document
+- .rspec
+- COPYING
+- COPYING.ja
+- Gemfile
+- Gemfile.lock
+- README.rdoc
+- Rakefile
+- VERSION
+- bio-ucsc-api.gemspec
+- lib/bio-ucsc.rb
+- lib/bio-ucsc/hg18.rb
+- lib/bio-ucsc/hg18/activerecord.rb
+- lib/bio-ucsc/hg18/cnpiafrate2.rb
+- lib/bio-ucsc/hg18/cnplocke.rb
+- lib/bio-ucsc/hg18/cnpredon.rb
+- lib/bio-ucsc/hg18/cnpsebat2.rb
+- lib/bio-ucsc/hg18/cnpsharp2.rb
+- lib/bio-ucsc/hg18/db_connection.rb
+- lib/bio-ucsc/hg18/dgv.rb
+- lib/bio-ucsc/hg18/refgene.rb
+- lib/bio-ucsc/hg18/rmsk.rb
+- lib/bio-ucsc/hg18/tables.rb
+- lib/bio-ucsc/hg19.rb
+- lib/bio-ucsc/hg19/activerecord.rb
+- lib/bio-ucsc/hg19/ccdsgene.rb
+- lib/bio-ucsc/hg19/cytoband.rb
+- lib/bio-ucsc/hg19/db_connection.rb
+- lib/bio-ucsc/hg19/dgv.rb
+- lib/bio-ucsc/hg19/ensgene.rb
+- lib/bio-ucsc/hg19/gwascatalog.rb
+- lib/bio-ucsc/hg19/hapmapalleleschimp.rb
+- lib/bio-ucsc/hg19/hapmapallelesmacaque.rb
+- lib/bio-ucsc/hg19/hapmapsnpsasw.rb
+- lib/bio-ucsc/hg19/hapmapsnpsceu.rb
+- lib/bio-ucsc/hg19/hapmapsnpschb.rb
+- lib/bio-ucsc/hg19/hapmapsnpschd.rb
+- lib/bio-ucsc/hg19/hapmapsnpsgih.rb
+- lib/bio-ucsc/hg19/hapmapsnpsjpt.rb
+- lib/bio-ucsc/hg19/hapmapsnpslwk.rb
+- lib/bio-ucsc/hg19/hapmapsnpsmex.rb
+- lib/bio-ucsc/hg19/hapmapsnpsmkk.rb
+- lib/bio-ucsc/hg19/hapmapsnpstsi.rb
+- lib/bio-ucsc/hg19/hapmapsnpsyri.rb
+- lib/bio-ucsc/hg19/knowngene.rb
+- lib/bio-ucsc/hg19/omimgene.rb
+- lib/bio-ucsc/hg19/phastconselements46wayprimates.rb
+- lib/bio-ucsc/hg19/phylop46wayprimates.rb
+- lib/bio-ucsc/hg19/refgene.rb
+- lib/bio-ucsc/hg19/rmsk.rb
+- lib/bio-ucsc/hg19/snp131.rb
+- lib/bio-ucsc/hg19/snp132.rb
+- lib/bio-ucsc/hg19/snp132codingdbsnp.rb
+- lib/bio-ucsc/hg19/snp132common.rb
+- lib/bio-ucsc/hg19/snp132flagged.rb
+- lib/bio-ucsc/hg19/snp132mult.rb
+- lib/bio-ucsc/hg19/wgrna.rb
+- lib/bio-ucsc/ucsc_bin.rb
+- samples/hg19-sample.rb
+- spec/hg18/cnpiafrate2_spec.rb
+- spec/hg18/cnplocke_spec.rb
+- spec/hg18/cnpredon_spec.rb
+- spec/hg18/cnpsebat2_spec.rb
+- spec/hg18/cnpsharp2_spec.rb
+- spec/hg18/db_connection_spec.rb
+- spec/hg18/dgv_spec.rb
+- spec/hg18/refgene_spec.rb
+- spec/hg18/rmsk_spec.rb
+- spec/hg19/ccdsgene_spec.rb
+- spec/hg19/cytoband_spec.rb
+- spec/hg19/db_connection_spec.rb
+- spec/hg19/dgv_spec.rb
+- spec/hg19/ensgene_spec.rb
+- spec/hg19/gwascatalog_spec.rb
+- spec/hg19/hapmapalleleschimp_spec.rb
+- spec/hg19/hapmapallelesmacaque_spec.rb
+- spec/hg19/hapmapsnpsasw_spec.rb
+- spec/hg19/hapmapsnpsceu_spec.rb
+- spec/hg19/hapmapsnpschb_spec.rb
+- spec/hg19/hapmapsnpschd_spec.rb
+- spec/hg19/hapmapsnpsgih_spec.rb
+- spec/hg19/hapmapsnpsjpt_spec.rb
+- spec/hg19/hapmapsnpslwk_spec.rb
+- spec/hg19/hapmapsnpsmex_spec.rb
+- spec/hg19/hapmapsnpsmkk_spec.rb
+- spec/hg19/hapmapsnpstsi_spec.rb
+- spec/hg19/hapmapsnpsyri_spec.rb
+- spec/hg19/knowngene_spec.rb
+- spec/hg19/omimGene_spec.rb
+- spec/hg19/phastconselements46wayprimates_spec.rb
+- spec/hg19/phyloP46wayPrimates_spec.rb
+- spec/hg19/refgene_spec.rb
+- spec/hg19/rmsk_spec.rb
+- spec/hg19/snp132Flagged_spec.rb
+- spec/hg19/snp132_spec.rb
+- spec/hg19/snp132codingdbsnp_spec.rb
+- spec/hg19/snp132common_spec.rb
+- spec/hg19/snp132mult_spec.rb
+- spec/hg19/wgrna_spec.rb
+- spec/spec_helper.rb
+has_rdoc: true
+homepage: http://github.com/misshie/bioruby-ucsc-api
+licenses: 
+- Ruby (Ruby's/GPLv2 dual)
+post_install_message: 
+rdoc_options: []
+
+require_paths: 
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement 
+  none: false
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      hash: -300095872068821190
+      segments: 
+      - 0
+      version: "0"
+required_rubygems_version: !ruby/object:Gem::Requirement 
+  none: false
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      segments: 
+      - 0
+      version: "0"
+requirements: []
+
+rubyforge_project: 
+rubygems_version: 1.3.7
+signing_key: 
+specification_version: 3
+summary: "A Bioruby plugin: an API for UCSC Genome Browser (experimental)"
+test_files: 
+- spec/hg18/cnpiafrate2_spec.rb
+- spec/hg18/cnplocke_spec.rb
+- spec/hg18/cnpredon_spec.rb
+- spec/hg18/cnpsebat2_spec.rb
+- spec/hg18/cnpsharp2_spec.rb
+- spec/hg18/db_connection_spec.rb
+- spec/hg18/dgv_spec.rb
+- spec/hg18/refgene_spec.rb
+- spec/hg18/rmsk_spec.rb
+- spec/hg19/ccdsgene_spec.rb
+- spec/hg19/cytoband_spec.rb
+- spec/hg19/db_connection_spec.rb
+- spec/hg19/dgv_spec.rb
+- spec/hg19/ensgene_spec.rb
+- spec/hg19/gwascatalog_spec.rb
+- spec/hg19/hapmapalleleschimp_spec.rb
+- spec/hg19/hapmapallelesmacaque_spec.rb
+- spec/hg19/hapmapsnpsasw_spec.rb
+- spec/hg19/hapmapsnpsceu_spec.rb
+- spec/hg19/hapmapsnpschb_spec.rb
+- spec/hg19/hapmapsnpschd_spec.rb
+- spec/hg19/hapmapsnpsgih_spec.rb
+- spec/hg19/hapmapsnpsjpt_spec.rb
+- spec/hg19/hapmapsnpslwk_spec.rb
+- spec/hg19/hapmapsnpsmex_spec.rb
+- spec/hg19/hapmapsnpsmkk_spec.rb
+- spec/hg19/hapmapsnpstsi_spec.rb
+- spec/hg19/hapmapsnpsyri_spec.rb
+- spec/hg19/knowngene_spec.rb
+- spec/hg19/omimGene_spec.rb
+- spec/hg19/phastconselements46wayprimates_spec.rb
+- spec/hg19/phyloP46wayPrimates_spec.rb
+- spec/hg19/refgene_spec.rb
+- spec/hg19/rmsk_spec.rb
+- spec/hg19/snp132Flagged_spec.rb
+- spec/hg19/snp132_spec.rb
+- spec/hg19/snp132codingdbsnp_spec.rb
+- spec/hg19/snp132common_spec.rb
+- spec/hg19/snp132mult_spec.rb
+- spec/hg19/wgrna_spec.rb
+- spec/spec_helper.rb