bio-dbsnp 0.1.1

data/.document

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+lib/**/*.rb
+bin/*
+- 
+features/**/*.feature
+LICENSE.txt

data/.rspec

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+--color
+--format documentation

data/Gemfile

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+source "http://rubygems.org"
+# Add dependencies required to use your gem here.
+# Example:
+#   gem "activesupport", ">= 2.3.5"
+
+# Add dependencies to develop your gem here.
+# Include everything needed to run rake, tests, features, etc.
+group :development do
+  gem "rspec", "~> 2.3.0"
+  gem "bundler", "~> 1.0.0"
+  gem "jeweler", "~> 1.6.4"
+  gem "rcov", ">= 0"
+  gem "bio", ">= 1.4.1"
+end

data/Gemfile.lock

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+GEM
+  remote: http://rubygems.org/
+  specs:
+    bio (1.4.2)
+    diff-lcs (1.1.3)
+    git (1.2.5)
+    jeweler (1.6.4)
+      bundler (~> 1.0)
+      git (>= 1.2.5)
+      rake
+    rake (0.9.2)
+    rcov (0.9.10)
+    rspec (2.3.0)
+      rspec-core (~> 2.3.0)
+      rspec-expectations (~> 2.3.0)
+      rspec-mocks (~> 2.3.0)
+    rspec-core (2.3.1)
+    rspec-expectations (2.3.0)
+      diff-lcs (~> 1.1.2)
+    rspec-mocks (2.3.0)
+
+PLATFORMS
+  ruby
+
+DEPENDENCIES
+  bio (>= 1.4.1)
+  bundler (~> 1.0.0)
+  jeweler (~> 1.6.4)
+  rcov
+  rspec (~> 2.3.0)

data/LICENSE.txt

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+Copyright (c) 2011 Hiroyuki Mishima
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

data/README.rdoc

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+= bio-dbsnp
+
+A library to decode "bitfield" information in dbSNP. In VCF format, bitfiled is contained in the "VP" field in the INFO column.
+
+Further details of the format is shown in ftp://ftp.ncbi.nlm.nih.gov/snp/specs/dbSNP_BitField_latest.pdf  
+
+= how to install
+ gem install bio-dbsnp
+
+= how to use
+ require 'bio-dbsnp'
+
+ vp = "050000000000000000000200"
+ bf = Bio::NCBI::Dbsnp::Bitfield.parse vp
+ bf.version #=> 5
+ bf.variation_class #=> :dips
+
+See lib/bio/ncbi/dbsnp/bitfield.rb for implementation. spec/bio-dbsnp_spec.rb also describes a usage.
+
+== Copyright
+
+Copyright (c) 2011 Hiroyuki Mishima (missy at be.to, @mishimahryk at Twitter).
+See LICENSE.txt (the MIT Licence) for further details.

data/Rakefile

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+# encoding: utf-8
+
+require 'rubygems'
+require 'bundler'
+begin
+  Bundler.setup(:default, :development)
+rescue Bundler::BundlerError => e
+  $stderr.puts e.message
+  $stderr.puts "Run `bundle install` to install missing gems"
+  exit e.status_code
+end
+require 'rake'
+
+require 'jeweler'
+Jeweler::Tasks.new do |gem|
+  # gem is a Gem::Specification...
+  # see http://docs.rubygems.org/read/chapter/20 for more options
+  gem.name = "bio-dbsnp"
+  gem.homepage = "http://github.com/misshie/bioruby-dbsnp"
+  gem.license = "MIT"
+  gem.summary = %Q{decoding the dbSNP bitfield}
+  gem.description = %Q{decoding the dbSNP bitfield containg detaild information}
+  gem.email = "missy@be.to"
+  gem.authors = ["Hiroyuki Mishima"]
+  # dependencies defined in Gemfile
+end
+Jeweler::RubygemsDotOrgTasks.new
+
+require 'rspec/core'
+require 'rspec/core/rake_task'
+RSpec::Core::RakeTask.new(:spec) do |spec|
+  spec.pattern = FileList['spec/**/*_spec.rb']
+end
+
+RSpec::Core::RakeTask.new(:rcov) do |spec|
+  spec.pattern = 'spec/**/*_spec.rb'
+  spec.rcov = true
+end
+
+task :default => :spec
+
+require 'rake/rdoctask'
+Rake::RDocTask.new do |rdoc|
+  version = File.exist?('VERSION') ? File.read('VERSION') : ""
+
+  rdoc.rdoc_dir = 'rdoc'
+  rdoc.title = "bio-dbsnp #{version}"
+  rdoc.rdoc_files.include('README*')
+  rdoc.rdoc_files.include('lib/**/*.rb')
+end

data/VERSION

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+0.1.1

data/bio-dbsnp.gemspec

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+# Generated by jeweler
+# DO NOT EDIT THIS FILE DIRECTLY
+# Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
+# -*- encoding: utf-8 -*-
+
+Gem::Specification.new do |s|
+  s.name = %q{bio-dbsnp}
+  s.version = "0.1.1"
+
+  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
+  s.authors = [%q{Hiroyuki Mishima}]
+  s.date = %q{2011-11-03}
+  s.description = %q{decoding the dbSNP bitfield containg detaild information}
+  s.email = %q{missy@be.to}
+  s.extra_rdoc_files = [
+    "LICENSE.txt",
+    "README.rdoc"
+  ]
+  s.files = [
+    ".document",
+    ".rspec",
+    "Gemfile",
+    "Gemfile.lock",
+    "LICENSE.txt",
+    "README.rdoc",
+    "Rakefile",
+    "VERSION",
+    "bio-dbsnp.gemspec",
+    "lib/bio-dbsnp.rb",
+    "lib/bio/ncbi/dbsnp.rb",
+    "lib/bio/ncbi/dbsnp/bitfield.rb",
+    "spec/bio-dbsnp_spec.rb",
+    "spec/spec_helper.rb"
+  ]
+  s.homepage = %q{http://github.com/misshie/bioruby-dbsnp}
+  s.licenses = [%q{MIT}]
+  s.require_paths = [%q{lib}]
+  s.rubygems_version = %q{1.8.6}
+  s.summary = %q{decoding the dbSNP bitfield}
+
+  if s.respond_to? :specification_version then
+    s.specification_version = 3
+
+    if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
+      s.add_development_dependency(%q<rspec>, ["~> 2.3.0"])
+      s.add_development_dependency(%q<bundler>, ["~> 1.0.0"])
+      s.add_development_dependency(%q<jeweler>, ["~> 1.6.4"])
+      s.add_development_dependency(%q<rcov>, [">= 0"])
+      s.add_development_dependency(%q<bio>, [">= 1.4.1"])
+    else
+      s.add_dependency(%q<rspec>, ["~> 2.3.0"])
+      s.add_dependency(%q<bundler>, ["~> 1.0.0"])
+      s.add_dependency(%q<jeweler>, ["~> 1.6.4"])
+      s.add_dependency(%q<rcov>, [">= 0"])
+      s.add_dependency(%q<bio>, [">= 1.4.1"])
+    end
+  else
+    s.add_dependency(%q<rspec>, ["~> 2.3.0"])
+    s.add_dependency(%q<bundler>, ["~> 1.0.0"])
+    s.add_dependency(%q<jeweler>, ["~> 1.6.4"])
+    s.add_dependency(%q<rcov>, [">= 0"])
+    s.add_dependency(%q<bio>, [">= 1.4.1"])
+  end
+end
+

data/lib/bio-dbsnp.rb

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+# Please require your code below, respecting the bioruby directory tree. 
+# For instance, perhaps the only uncommented line in this file might 
+# be something like this:
+#
+#   require 'bio/sequence/awesome_sequence_plugin_thingy'
+#
+# and then create the ruby file 'lib/bio/sequence/awesome_sequence_thingy.rb'
+# and put your plugin's code there. It is bad practice to write other code 
+# directly into this file, because doing so causes confusion if this biogem 
+# was ever to get merged into the main bioruby tree.
+
+require 'bio/ncbi/dbsnp'

data/lib/bio/ncbi/dbsnp.rb

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+require 'bio/ncbi/dbsnp/bitfield'

data/lib/bio/ncbi/dbsnp/bitfield.rb

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+module Bio
+  module NCBI
+    module Dbsnp
+
+      class Bitfield
+        def initialize(byte_stream)
+          @byte_stream = byte_stream
+          ver = version
+          raise "Unsupported bitfield version (ver.#{ver})" unless ver == 5
+        end
+
+        attr_reader :byte_stream
+        
+        def self.parse(bitfield_str)
+          byte_stream = Array.new
+          bitfield_str.tr("_","").chars.each_slice(2) do |byte_str|
+            byte_stream << Integer("0x#{byte_str.join("")}")
+          end
+          self.new(byte_stream)
+        end
+
+        def field(fnum)
+          case fnum
+          when 0
+            byte_stream[0]
+          when 1
+            (byte_stream[2] << 8) + byte_stream[1]
+          when 2
+            (byte_stream[4] << 8) + byte_stream[3]
+        else
+            byte_stream[fnum + 2]
+          end
+        end
+
+        # field F0
+        def version
+          field(0) & 0b0000_1111
+        end
+
+        # field F1
+        def resource_link
+          fld = field(1)
+          res = Array.new
+          res << :clinical               if bit? fld, 0b100_0000_0000_0000
+          res << :precious               if bit? fld, 0b010_0000_0000_0000
+          res << :provisional_tpa        if bit? fld, 0b001_0000_0000_0000
+          res << :pubmed_central_article if bit? fld, 0b000_1000_0000_0000
+          res << :short_read_archive     if bit? fld, 0b000_0100_0000_0000
+          res << :organism_dblink        if bit? fld, 0b000_0010_0000_0000
+          res << :mgc_clone              if bit? fld, 0b000_0001_0000_0000
+          res << :trace_archive          if bit? fld, 0b000_0000_1000_0000
+          res << :assemby_archive        if bit? fld, 0b000_0000_0100_0000
+          res << :entrez_geo             if bit? fld, 0b000_0000_0010_0000
+          res << :peobe_db               if bit? fld, 0b000_0000_0001_0000
+          res << :entrez_gene            if bit? fld, 0b000_0000_0000_1000
+          res << :entrez_sts             if bit? fld, 0b000_0000_0000_0100
+          res << :threed_structure       if bit? fld, 0b000_0000_0000_0010
+          res << :submitter_link_out     if bit? fld, 0b000_0000_0000_0001
+          res
+        end
+
+        # field F2
+        def gene_function
+          fld = field(2)
+          res = Array.new
+          res << :stop_loss                 if bit? fld, 0b10_0000_0000_0000
+          res << :non_synonymous_frameshift if bit? fld, 0b01_0000_0000_0000
+          res << :non_synonymous_missense   if bit? fld, 0b00_1000_0000_0000
+          res << :stop_gain                 if bit? fld, 0b00_0100_0000_0000
+          res << :reference                 if bit? fld, 0b00_0010_0000_0000
+          res << :synonymous                if bit? fld, 0b00_0001_0000_0000
+          res << :utr_3p                    if bit? fld, 0b00_0000_1000_0000
+          res << :utr_5p                    if bit? fld, 0b00_0000_0100_0000
+          res << :acceptor_splice_site      if bit? fld, 0b00_0000_0010_0000
+          res << :donor_splice_site         if bit? fld, 0b00_0000_0001_0000
+          res << :intron                    if bit? fld, 0b00_0000_0000_1000
+          res << :gene_region_3p            if bit? fld, 0b00_0000_0000_0100
+          res << :gene_region_5p            if bit? fld, 0b00_0000_0000_0010
+          res << :gene_segment              if bit? fld, 0b00_0000_0000_0001
+          res
+        end
+
+        # field F3
+        def mapping
+          fld = field(3)
+          res = Array.new
+          res << :other_snp         if bit? fld, 0b1_0000
+          res << :assembly_conflict if bit? fld, 0b0_1000
+          res << :assembly_specific if bit? fld, 0b0_0100
+          res << :weight3           if bit? fld, 0b0_0011
+          res << :weight2           if bit? fld, 0b0_0010
+          res << :weight1           if bit? fld, 0b0_0001
+          res << :unmapped if (fld & 0b0000_0011) == 0
+          res
+        end
+
+        # field F4
+        def allele_frequency
+          fld = field(4)
+          res = Array.new
+          res << :mutation                         if bit? fld, 0b1000
+          res << :validated                        if bit? fld, 0b0100
+          res << :maf_gt5_each_and_all_populations if bit? fld, 0b0010
+          res << :maf_gt5_in_1plus_populations     if bit? fld, 0b0001
+          res
+        end
+
+        # field F5
+        def genotype
+          fld = field(5)
+          res = Array.new
+          res << :high_density          if bit? fld, 0b0100
+          res << :haplotype_tagging_set if bit? fld, 0b0010
+          res << :available             if bit? fld, 0b0001
+          res
+        end
+
+        # field F6
+        def validation
+          fld = field(6)
+          res = Array.new
+          res << :tgp_2010_production if bit? fld, 0b100_0000
+          res << :tgp_validated       if bit? fld, 0b010_0000
+          res << :tgp_2010_pilot      if bit? fld, 0b001_0000
+          res << :tgp_2009_phase1     if bit? fld, 0b000_1000
+          res << :phase_3_genotyped   if bit? fld, 0b000_0100
+          res << :phase_2_genotyped   if bit? fld, 0b000_0010
+          res << :phase_1_genotyped   if bit? fld, 0b000_0001
+          res
+        end
+
+        # field F7
+        def phenotype
+          fld = field(7)
+          res = Array.new
+          res << :mesh_disease            if bit? fld, 0b1000_0000
+          res << :clinical_diagnosis      if bit? fld, 0b0100_0000
+          res << :transciption_factor     if bit? fld, 0b0010_0000
+          res << :locus_specific_database if bit? fld, 0b0001_0000
+          res << :dbgap_p_valued          if bit? fld, 0b0000_1000
+          res << :dbgap_lod               if bit? fld, 0b0000_0100
+          res << :tpa_gwas_page           if bit? fld, 0b0000_0010
+          res << :omim_omia               if bit? fld, 0b0000_0001
+          res
+        end
+
+        # field F8
+        def variation_class
+          case (field(8) & 0b0000_1111)
+          when 0b0001
+            :snp
+          when 0b0010
+            :dips
+          when 0b0011
+            :heterozygous
+          when 0b0100
+            :microsatellite
+          when 0b0101
+            :named_variation
+          when 0b0110
+            :novariation
+          when 0b0111
+            :mixed_class
+          when 0b1000
+            :multibase_polymorphism
+          else
+            raise "Should not happen! Check bitfield verison."
+          end
+        end
+      
+       # field F9
+        def quality_check
+          fld = field(9)
+          res = Array.new
+          res << :suspect                           if bit? fld, 0b00_0000_0100_0000
+          res << :somatic                           if bit? fld, 0b00_0000_0010_0000
+          res << :reference_allele_missing          if bit? fld, 0b00_0000_0001_0000
+          res << :withdrawn_by_submitter            if bit? fld, 0b00_0000_0000_1000
+          res << :no_allele_overlap                 if bit? fld, 0b00_0000_0000_0100
+          res << :strain_specific_fiexed_defference if bit? fld, 0b00_0000_0000_0010
+          res << :genotype_conflict                 if bit? fld, 0b00_0000_0000_0001
+          res
+        end
+
+        private
+
+        def bit?(subj, bit)
+          if (subj & bit) == bit
+            true
+          else
+            false
+          end
+        end
+      end # class Bitfield
+
+    end # module Dbsnp
+  end # module NCBI
+end #module Bio

data/spec/bio-dbsnp_spec.rb

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+require File.expand_path(File.dirname(__FILE__) + '/spec_helper')
+
+describe "Dbsnp" do
+  describe "Bitfield" do
+
+    describe ".parse" do
+      context "given a string '050000000009000110000100'" do
+        it "returns a new instance of Bio::NCBI::Dbsnp" do
+          obj = Bio::NCBI::Dbsnp::Bitfield.parse('050000000009000110000100')
+          obj.should be_an_instance_of(Bio::NCBI::Dbsnp::Bitfield)
+        end
+      end
+
+      context "given a string '010000000009000110000100' for .parse" do
+        it "raises RuntimeError" do
+          str = '010000000009000110000100'
+          expect { Bio::NCBI::Dbsnp::Bitfield.parse(str) }.to raise_error(RuntimeError)
+        end
+      end
+
+    end
+
+    describe "#byte_stream" do 
+      context "given a string '050000000009000110000100' for .parse" do
+        it "returns an array ary[0] == 5" do
+          obj = Bio::NCBI::Dbsnp::Bitfield.parse('050000000009000110000100')
+          obj.byte_stream[0].should == 5
+        end
+      end
+    end
+
+    describe "#field" do 
+      context "given (1) with a string '050102030405060708090A0B' for .parse" do
+        it "returns 0x0201" do
+          obj = Bio::NCBI::Dbsnp::Bitfield.parse('050102030405060708090A0B')
+          obj.field(1).should == 0x0201
+        end
+      end
+    end
+
+   describe "#bit? (private method)" do
+      context "given (0b0010, 0b0010)" do
+        it "returns true" do
+          obj = Bio::NCBI::Dbsnp::Bitfield.parse('050000000000000000000200')
+          obj.__send__(:bit?, 0b0010, 0b0010).should be_true
+        end
+      end
+
+      context "given (0b0010, 0b0111)" do
+        it "returns false" do
+          obj = Bio::NCBI::Dbsnp::Bitfield.parse('050000000000000000000200')
+          obj.__send__(:bit?, 0b0010, 0b0111).should be_false
+        end
+      end
+
+      context "given (0b1111, 0b0111)" do
+        it "returns true" do
+          obj = Bio::NCBI::Dbsnp::Bitfield.parse('050000000000000000000200')
+          obj.__send__(:bit?, 0b1111, 0b0111).should be_true
+        end
+      end
+    end
+
+    describe "[F0] #version" do
+      context "given a string '050000000009000110000100' for .parse" do
+        it "returns 5" do 
+          obj = Bio::NCBI::Dbsnp::Bitfield.parse('050000000009000110000100')
+          obj.version.should == 5
+        end
+      end
+    end
+
+    describe "[F1] #resource_link" do
+      context "given a string '050300000301040400000100' of rs55874132 for .parse" do
+        it "returns an array containing :threed_structure and :submitter_link_out" do
+          obj = Bio::NCBI::Dbsnp::Bitfield.parse('050300000301040400000100')
+          obj.resource_link.should include(:threed_structure, :submitter_link_out)
+        end
+      end
+    end
+
+    describe "[F2] #gene_function" do
+      context "given a string '050300000301040400000100' of rs55874132 for .parse" do
+        it "returns an array containing :reference, :synonymous" do
+          obj = Bio::NCBI::Dbsnp::Bitfield.parse('050300000301040400000100')
+          obj.gene_function.should include(:reference, :synonymous)
+        end
+      end
+    end
+
+    describe "[F3] #mapping" do
+      context "given a string '05_0300_0003_01_04_04_00_00_01_00' of rs55874132 for .parse" do
+        it "returns an array containing :weight1" do
+          obj = Bio::NCBI::Dbsnp::Bitfield.parse('05_0300_0003_01_04_04_00_00_01_00')
+          obj.mapping.should include(:weight1)
+        end
+      end
+    end
+
+    describe "[F4] #allele_frequency" do
+      context "given a string '05_0300_0003_01_04_04_00_00_01_00' of rs55874132 for .parse" do
+        it "returns an array containing :validated" do
+          obj = Bio::NCBI::Dbsnp::Bitfield.parse('05_0300_0003_01_04_04_00_00_01_00')
+          obj.allele_frequency.should include(:validated)
+        end
+      end
+    end
+
+    describe "[F5] #genotype" do
+      context "given a string '05_0300_0003_01_04_04_00_00_01_00' of rs55874132 for .parse" do
+        it "returns an array containing :high_density" do
+          obj = Bio::NCBI::Dbsnp::Bitfield.parse('05_0300_0003_01_04_04_00_00_01_00')
+          obj.genotype.should include(:high_density)
+        end
+      end
+    end
+
+    describe "[F6] #validation" do
+      context "given a string '05_0000_0000_05_03_00_10_00_01_00' of rs117577454 for .parse" do
+        it "returns an array containing :tgp_2010_pilot" do
+          obj = Bio::NCBI::Dbsnp::Bitfield.parse('05_0000_0000_05_03_00_10_00_01_00')
+          obj.validation.should include(:tgp_2010_pilot)
+        end
+      end
+    end
+
+    describe "[F7] #phenotype" do
+      context "given a string '05_0128_0000_01_03_05_12_02_01_00' of rs3934834 for .parse" do
+        it "returns an array containing :tpa_gwas_page" do
+          obj = Bio::NCBI::Dbsnp::Bitfield.parse('05_0128_0000_01_03_05_12_02_01_00')
+          obj.phenotype.should include(:tpa_gwas_page)
+        end
+      end
+    end
+
+    describe "[F8] #variation_class" do
+      context "given a string '05_0000_0000_00_00_00_00_00_02_00' for .parse" do
+        it "returns ':indel'" do
+          obj = Bio::NCBI::Dbsnp::Bitfield.parse('05_0000_0000_00_00_00_00_00_02_00')
+          obj.variation_class.should == :dips
+        end
+      end
+    end
+
+    describe "[F9] #quality_check" do
+      context "given a string '05_0000_0000_01_00_00_10_00_01_40' of rs62637813 for .parse" do
+        it "returns an array containing ':suspect'" do
+          obj = Bio::NCBI::Dbsnp::Bitfield.parse('05_0000_0000_01_00_00_10_00_01_40')
+          # 0x40 = 0b0100_0000
+          obj.quality_check.should include(:suspect)
+        end
+      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 'bio-dbsnp'
+
+# 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 +1,119 @@
+--- !ruby/object:Gem::Specification
+name: bio-dbsnp
+version: !ruby/object:Gem::Version
+  version: 0.1.1
+  prerelease: 
+platform: ruby
+authors:
+- Hiroyuki Mishima
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2011-11-03 00:00:00.000000000Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: rspec
+  requirement: &96529700 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 2.3.0
+  type: :development
+  prerelease: false
+  version_requirements: *96529700
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: &96529100 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.0.0
+  type: :development
+  prerelease: false
+  version_requirements: *96529100
+- !ruby/object:Gem::Dependency
+  name: jeweler
+  requirement: &96528600 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.6.4
+  type: :development
+  prerelease: false
+  version_requirements: *96528600
+- !ruby/object:Gem::Dependency
+  name: rcov
+  requirement: &96528080 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: *96528080
+- !ruby/object:Gem::Dependency
+  name: bio
+  requirement: &96527500 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.4.1
+  type: :development
+  prerelease: false
+  version_requirements: *96527500
+description: decoding the dbSNP bitfield containg detaild information
+email: missy@be.to
+executables: []
+extensions: []
+extra_rdoc_files:
+- LICENSE.txt
+- README.rdoc
+files:
+- .document
+- .rspec
+- Gemfile
+- Gemfile.lock
+- LICENSE.txt
+- README.rdoc
+- Rakefile
+- VERSION
+- bio-dbsnp.gemspec
+- lib/bio-dbsnp.rb
+- lib/bio/ncbi/dbsnp.rb
+- lib/bio/ncbi/dbsnp/bitfield.rb
+- spec/bio-dbsnp_spec.rb
+- spec/spec_helper.rb
+homepage: http://github.com/misshie/bioruby-dbsnp
+licenses:
+- MIT
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+      segments:
+      - 0
+      hash: 3024424425824902007
+required_rubygems_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 1.8.6
+signing_key: 
+specification_version: 3
+summary: decoding the dbSNP bitfield
+test_files: []