bio-genomic-interval 0.1.0

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", "~> 1.5.2"
+  gem "rcov", ">= 0"
+  gem "bio", ">= 1.4.1"
+end

data/Gemfile.lock

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+GEM
+  remote: http://rubygems.org/
+  specs:
+    bio (1.4.1)
+    diff-lcs (1.1.2)
+    git (1.2.5)
+    jeweler (1.5.2)
+      bundler (~> 1.0.0)
+      git (>= 1.2.5)
+      rake
+    rake (0.8.7)
+    rcov (0.9.9)
+    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 (~> 1.5.2)
+  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-genomic-interval
+
+Author::    MISHIMA, Hiroyuki (hmishima AT nagasaki-u.ac.jp, missy AT be.to)
+Version::   0.1.0
+Copyright:: Copyright (c) MISHIMA, Hiroyuki, 2011
+License::   the MIT/X11 license
+
+A BioRuby plugin: handling genomic intervals,such as "chr1:123-456",
+and overlaps between two intervals.
+
+= Usage
+== Generation of interval objects
+a interval object be generated by like the following:
+ a = Bio::GenomicInterval.new("chr1", 123, 456)
+ a.to_s # => "chr1:123-456"
+ b = Bio::GenomicInterval.parse("chr1:123-456")
+ b.to_s # => "chr1:123-456"
+ c = Bio::GenomicInetrval.zero_based("chr1", 122, 456)
+ c.to_s # => "chr1:123-456"
+ c.zero_start # => 122
+ 
+Last one is generated from a "Zero-based half-closed[start, end)"  interval
+, which used in UCSC Genobe Browser's BED format, instead of usual
+"One-based full-closed [start, end]" intervals.
+
+== Comparison
+ ref = Bio::GenomicInterval.parse("chr1:123-456")
+ cmp = Bio::GenomicInterval.parse("chr1:234-567")
+ ref.compare(cmp) # => :right_overlapped 
+
+ ref.adjacent # => 20
+ near = Bio::GenomicInterval.parse("chr1:458-567")
+ ref.compare(cmp) # => :right_adjacent
+
+ ref.adjacent = 1
+ ref.compare(cmp) # => :right_off
+
+== Overlap metrics
+* When a overlap exist, return a positive integers (>1) for the overlap length.
+* When a overlap does not exist, return a zero or a negative (<= 0) for the space size between the intervals.
+
+ ref = Bio::GenomicInterval.parse("chr1:10-20")
+ cmp = Bio::GenomicInterval.parse("chr1:15-25")
+ ref.overlap(cmp) # => 6
+ cmp2 = Bio::GenomicInterval.parse("chr1:25-35")
+ ref.overlap(cmp) # => -4
+
+== Expansion (or integration)
+ ref =   Bio::GenomicInterval.parse("chr1:400-600")
+ other = Bio::GenomicInterval.parse("chr1:650-800")
+ ref.expand(other).to_s # => "chr1:400-800"
+
+== Center
+ obj1 = Bio::GenomicInterval.parse("chr1:1-3")
+ obj1.center # => "chr1:2-2"
+ obj2 = Bio::GenomicInterval.parse("chr2:1-4")
+ obj2.center # => "chr1:2-2"
+
+== And others
+ ref =   Bio::GenomicInterval.parse("chr1:400-600")
+ other = Bio::GenomicInterval.parse("chr1:605-800")
+ ref.overlapped?(other) # => false
+ ref.nearly_overlapped?(other) # => true
+ ref.size # => 201
+ ref.chr_start -= 100
+ ref.chr_end += 100
+ ref.chrom = "chrX"
+ ref.to_s # => "chrX:300-700"
+
+See also the Rspec file.
+
+== Contributing to bio-genomic-interval
+Please do not hesitate to contanct the author by emails.
+
+== Copyright
+
+Copyright (c) 2011 Hiroyuki Mishima. See LICENSE.txt for
+further details.
+

data/Rakefile

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+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-genomic-interval"
+  gem.homepage = "http://github.com/misshie/bioruby-genomic-interval"
+  gem.license = "MIT"
+  gem.summary = %Q{a BioRuby plugin: handling genomic interavals and overlaps}
+  gem.description =
+    %Q{a BioRuby plugin: handling genomic intervals,such as "chr1:123-456", and overlaps between two intervalsrake }
+  gem.email = "missy@be.to"
+  gem.authors = ["Hiroyuki Mishima"]
+  # Include your dependencies below. Runtime dependencies are required when using your gem,
+  # and development dependencies are only needed for development (ie running rake tasks, tests, etc)
+  #  gem.add_runtime_dependency 'jabber4r', '> 0.1'
+  #  gem.add_development_dependency 'rspec', '> 1.2.3'
+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-genomic-interval #{version}"
+  rdoc.rdoc_files.include('README*')
+  rdoc.rdoc_files.include('lib/**/*.rb')
+end

data/VERSION

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+0.1.0

data/bio-genomic-interval.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-genomic-interval}
+  s.version = "0.1.0"
+
+  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
+  s.authors = ["Hiroyuki Mishima"]
+  s.date = %q{2011-04-07}
+  s.description = %q{a BioRuby plugin: handling genomic intervals,such as "chr1:123-456", and overlaps between two intervalsrake }
+  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-genomic-interval.gemspec",
+    "lib/bio-genomic-interval.rb",
+    "spec/bio-genomic-interval_spec.rb",
+    "spec/spec_helper.rb"
+  ]
+  s.homepage = %q{http://github.com/misshie/bioruby-genomic-interval}
+  s.licenses = ["MIT"]
+  s.require_paths = ["lib"]
+  s.rubygems_version = %q{1.6.2}
+  s.summary = %q{a BioRuby plugin: handling genomic interavals and overlaps}
+  s.test_files = [
+    "spec/bio-genomic-interval_spec.rb",
+    "spec/spec_helper.rb"
+  ]
+
+  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>, ["~> 1.5.2"])
+      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>, ["~> 1.5.2"])
+      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>, ["~> 1.5.2"])
+    s.add_dependency(%q<rcov>, [">= 0"])
+    s.add_dependency(%q<bio>, [">= 1.4.1"])
+  end
+end
+

data/lib/bio-genomic-interval.rb

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+module Bio
+
+  #
+  # =a class for manupirate genomic intervals such as "chr1:123-456"
+  #
+  class GenomicInterval
+    # a default value to determine the adjacent/very near distance in bp 
+    DEFAULT_ADJACENT = 20
+    
+    def initialize(chrom = "", chr_start = 1, chr_end = 1)
+      raise ArgumentError unless chr_start >= 1
+      raise ArgumentError unless chr_end >= 1
+      raise ArgumentError unless chr_start <= chr_end
+      @chrom = chrom
+      @chr_start = chr_start
+      @chr_end = chr_end
+      @adjacent = DEFAULT_ADJACENT
+    end
+
+    attr_accessor :chrom, :chr_start, :chr_end, :adjacent
+
+    #
+    # generate an interval object from a string expressing 
+    # one-based full-closed interval such as "chr1:123-456"
+    # 
+    def self.parse(interval)
+      chrom, start_end = interval.split(":")
+      str_start, str_end = start_end.split("-")[0..1]
+      str_end = str_start if str_end.nil?
+      chr_start = Integer(str_start)
+      chr_end   = Integer(str_end)
+      if chr_start > chr_end
+        chr_end, chr_start = chr_start, chr_end
+      end
+      self.new(chrom, chr_start, chr_end)
+  end
+
+    #
+    # generate an interval object from three atguments expressing 
+    # zero-based half-closed interval such as "chr1", 122, 456
+    # 
+    def self.zero_based(chrom = "", z_start = 0, z_end = 1)
+      z_start += 1
+      self.new(chrom, z_start, z_end)
+    end
+
+    #
+    # returns one-based full-closed interval such as "chr1:123-456"
+    #
+    def to_s
+      "#{@chrom}:#{@chr_start}-#{@chr_end}"
+    end
+
+    #
+    # returns zero-based half-closed start position
+    # 
+    def zero_start
+      @chr_start - 1
+    end
+
+    #
+    # returns zero-based half-closed end position
+    # 
+    def zero_end
+      @chr_end
+    end
+
+    #
+    # returns one of the followings:
+    #  :different_chrom, :left_adjacent, :right_adjacent
+    #  :left_off, :right_off, :equal
+    #  :contained, :containing, :left_overlapped, :right_overlapped
+    # Imagine that the receiver object is fixed on a number line
+    #
+    def compare(other)
+      case
+      when self.chrom != other.chrom
+        :different_chrom
+      when other.chr_end.between?(self.chr_start - @adjacent, self.chr_start - 1)
+        :left_adjacent
+      when other.chr_start.between?(self.chr_end + 1, self.chr_end + @adjacent)
+        :right_adjacent
+      when other.chr_end < self.chr_start
+        :left_off
+      when self.chr_end < other.chr_start
+        :right_off
+      when (self.chr_start == other.chr_start) &&
+          (self.chr_end == other.chr_end)
+        :equal
+      when (other.chr_start.between?(self.chr_start, self.chr_end)) &&
+          (other.chr_end.between?(self.chr_start, self.chr_end))
+        :contained
+      when (self.chr_start.between?(other.chr_start, other.chr_end)) &&
+          (self.chr_end.between?(other.chr_start, other.chr_end))
+        :containing
+      when (other.chr_start < self.chr_start) &&
+          (other.chr_end.between?(self.chr_start, self.chr_end))
+        :left_overlapped
+      when (other.chr_start.between?(self.chr_start, self.chr_end)) &&
+          (self.chr_end < other.chr_end)
+        :right_overlapped
+      else
+        raise Exception, "must not happen"
+      end
+    end
+
+    def nearly_overlapped?(other)
+      result = compare(other)
+      [ :left_adjacent, :right_adjacent,
+        :equal, :contained, :containing,
+        :left_overlapped, :right_overlapped].any?{|x| x == result} 
+    end
+
+    def overlapped?(other)
+      result = compare(other)
+      [ :equal, :contained, :containing,
+        :left_overlapped, :right_overlapped].any?{|x| x == result} 
+    end
+
+    def expand(other)
+      raise ArgumentError unless self.chrom == other.chrom
+      new_start = [self.chr_start, other.chr_start].min
+      new_end = [self.chr_end, other.chr_end].max
+      Bio::GenomicInterval.new(@chrom, new_start, new_end)
+    end
+
+    def size
+      chr_end - chr_start + 1
+    end
+
+    alias :length :size
+
+    def center
+      center = (chr_start + chr_end) / 2
+      Bio::GenomicInterval.new(self.chrom, center, center)
+    end
+
+    # * When a overlap exist, return a positive integers (>1) for the overlap length.
+    # * When a overlap does not exist, return a zero or a negative (<= 0) for the space size between the intervals.
+    #
+    def overlap(other)
+      case self.compare(other)
+      when :different_chrom
+        0
+      when :left_off, :left_adjacent, :left_overlapped
+        other.chr_end - self.chr_start + 1
+      when :contained, :equal
+        other.size
+      when :containing
+        self.size
+      when :right_off, :right_adjacent, :right_overlapped
+        self.chr_end - other.chr_start + 1
+      else
+        raise Exception, "must not happen"
+      end
+    end
+  end
+end

data/spec/bio-genomic-interval_spec.rb

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+require File.expand_path(File.dirname(__FILE__) + '/spec_helper')
+
+describe "Bio::GenomicInterval" do
+
+  #
+  # class methods
+  #
+
+  describe ".new" do
+    context 'given ("chr1", 1, 234)' do
+      it "is a Bio::GenomicInterval" do
+        Bio::GenomicInterval.new("chr1", 1, 234).should be_a(Bio::GenomicInterval)
+      end
+    end
+
+    context 'given ("chr1", -1, 234)' do
+      it "raises an ArgumentError" do
+        expect{Bio::GenomicInterval.new("chr1", -1, 234)}.to raise_error(ArgumentError)
+      end
+    end
+
+    context 'given ("chr1", 234, 1)' do
+      it "raise an ArgumentError" do
+        expect{Bio::GenomicInterval.new("chr1", 234, 1)}.to raise_error(ArgumentError)
+      end
+    end
+
+    context 'given no argument' do
+      it "is a Bio::GenomicInterval" do
+        Bio::GenomicInterval.new.should be_a(Bio::GenomicInterval)
+      end
+    end
+  end
+
+  describe  ".parse" do 
+    context 'given "chr1:1-123"' do
+      it 'represents "chr1:1-123" by the to_s method' do 
+        Bio::GenomicInterval.parse("chr1:1-123").to_s.should == "chr1:1-123"
+      end
+    end
+
+    context 'given "chr1:123-1"' do
+      it 'represents "chr1:1-123" by the to_s method' do 
+        Bio::GenomicInterval.parse("chr1:123-1").to_s.should == "chr1:1-123"
+      end
+    end
+
+    context 'given "chr1:123"' do
+      it 'represents "chr1:123-123" by the to_s method' do 
+        Bio::GenomicInterval.parse("chr1:123").to_s.should == "chr1:123-123"
+      end
+    end
+  end
+
+  describe ".zero_based" do
+    context 'given ("chr1", 0, 1)' do
+      it 'represents "chr1:1-1" by the to_s method' do
+        Bio::GenomicInterval.zero_based("chr1", 0, 1).to_s.should == "chr1:1-1"
+      end 
+    end
+  end
+
+  #
+  # instance methods
+  #
+  describe '#zero_start for "chr1:1-1"' do 
+    context 'when called' do
+      it 'returns 0' do
+        Bio::GenomicInterval.parse("chr1:1-1").zero_start.should == 0
+      end
+    end
+  end
+  
+  describe '#zero_end for "chr1:1-1"' do
+    context 'when called' do
+      it 'returns 1' do
+        Bio::GenomicInterval.parse("chr1:1-1").zero_end.should == 1
+      end
+    end
+  end
+
+
+  describe '#adjacent' do
+    context 'when called first' do
+      it 'returns default value' do
+        default = Bio::GenomicInterval::DEFAULT_ADJACENT
+        Bio::GenomicInterval.new.adjacent.should == default
+      end
+    end
+
+    context 'when set by #adjacent = 10' do
+      it 'returns 10' do
+        obj = Bio::GenomicInterval.new
+        obj.adjacent = 10
+        obj.adjacent.should == 10
+      end
+    end
+  end
+
+  describe '#compare for "chr1:400-600"' do 
+    context 'given "chrX:123-234"' do
+      it 'returns :different_chr' do
+        receiver = Bio::GenomicInterval.parse("chr1:400-600")
+        subject  = Bio::GenomicInterval.parse("chrX:123-234")
+        receiver.compare(subject).should == :different_chrom
+      end
+    end
+
+   context 'given "chr1:123-234"' do
+      it 'returns :left_off' do
+        receiver = Bio::GenomicInterval.parse("chr1:400-600")
+        subject  = Bio::GenomicInterval.parse("chr1:123-234")
+        receiver.compare(subject).should == :left_off
+      end
+    end
+
+   context 'given "chr1:789-890"' do
+      it 'returns :right_off' do
+        receiver = Bio::GenomicInterval.parse("chr1:400-600")
+        subject  = Bio::GenomicInterval.parse("chr1:789-890")
+        receiver.compare(subject).should == :right_off
+      end
+    end
+
+    context 'given "chr1:450-550"' do
+      it 'returns :contained' do
+        receiver = Bio::GenomicInterval.parse("chr1:400-600")
+        subject  = Bio::GenomicInterval.parse("chr1:450-550")
+        receiver.compare(subject).should == :contained
+      end
+    end
+
+    context 'given "chr1:400-400" (size == 1)' do
+      it 'returns :contained' do
+        receiver = Bio::GenomicInterval.parse("chr1:400-600")
+        subject  = Bio::GenomicInterval.parse("chr1:400-400")
+        receiver.compare(subject).should == :contained
+      end
+    end
+
+    context 'given "chr1:300-700"' do
+      it 'returns :containing' do
+        receiver = Bio::GenomicInterval.parse("chr1:400-600")
+        subject  = Bio::GenomicInterval.parse("chr1:300-700")
+        receiver.compare(subject).should == :containing
+      end
+    end
+
+    context 'given "chr1:300-500"' do
+      it 'returns :left_overlapped' do
+        receiver = Bio::GenomicInterval.parse("chr1:400-600")
+        subject  = Bio::GenomicInterval.parse("chr1:300-500")
+        receiver.compare(subject).should == :left_overlapped
+      end
+    end
+
+    context 'given "chr1:500-700"' do
+      it 'returns :right_overlapped' do
+        receiver = Bio::GenomicInterval.parse("chr1:400-600")
+        subject  = Bio::GenomicInterval.parse("chr1:500-700")
+        receiver.compare(subject).should == :right_overlapped
+      end
+    end
+
+    context 'given same interval' do
+      it 'returns :equal' do
+        receiver = subject = Bio::GenomicInterval.parse("chr1:400-600")
+        receiver.compare(subject).should == :equal
+      end
+    end
+
+    context 'given "chr1:300-398"' do
+      it 'returns :right_adjacent' do
+        receiver = Bio::GenomicInterval.parse("chr1:400-600")
+        subject  = Bio::GenomicInterval.parse("chr1:300-398")
+        receiver.compare(subject).should == :left_adjacent
+      end
+    end
+ 
+    context 'given "chr1:399-399" (size == 1)' do
+      it 'returns :right_adjacent' do
+        receiver = Bio::GenomicInterval.parse("chr1:400-600")
+        subject  = Bio::GenomicInterval.parse("chr1:399-399")
+        receiver.compare(subject).should == :left_adjacent
+      end
+    end
+
+    context 'given "chr1:603-800"' do
+      it 'returns :right_adjacent' do
+        receiver = Bio::GenomicInterval.parse("chr1:400-600")
+        subject  = Bio::GenomicInterval.parse("chr1:603-800")
+        receiver.compare(subject).should == :right_adjacent
+      end
+    end
+  end    
+
+  describe '#nearly_overlapped? for "chr1:400-600"' do
+    context 'given "chr1:300-500"' do
+      it 'returens true' do
+        receiver = Bio::GenomicInterval.parse("chr1:400-600")
+        subject  = Bio::GenomicInterval.parse("chr1:300-500")
+        receiver.nearly_overlapped?(subject).should be_true
+      end
+    end
+
+    context 'given "chr1:300-390"' do
+      it 'returens true' do
+        receiver = Bio::GenomicInterval.parse("chr1:400-600")
+        receiver.adjacent = 20
+        subject  = Bio::GenomicInterval.parse("chr1:300-390")
+        receiver.nearly_overlapped?(subject).should be_true
+      end
+    end
+  end
+
+  describe '#overlapped? for "chr1:400-600"' do
+    context 'given "chr1:300-500"' do
+      it 'returens true' do
+        receiver = Bio::GenomicInterval.parse("chr1:400-600")
+        subject  = Bio::GenomicInterval.parse("chr1:300-500")
+        receiver.overlapped?(subject).should be_true
+      end
+    end
+    context 'given "chr1:300-370"' do
+      it 'returens false' do
+        receiver = Bio::GenomicInterval.parse("chr1:400-600")
+        receiver.adjacent = 20
+        subject  = Bio::GenomicInterval.parse("chr1:300-370")
+        receiver.overlapped?(subject).should be_false
+      end
+    end
+  end
+
+  describe '#expand for "chr1:400-600"' do
+    context 'given "chr1:603-800"' do
+      it 'returns "chr1:400-800" by the to_s method' do
+        receiver = Bio::GenomicInterval.parse("chr1:400-600")
+        subject  = Bio::GenomicInterval.parse("chr1:603-800")
+        receiver.expand(subject).to_s.should == "chr1:400-800"
+      end
+    end
+
+    context 'given "chrX:603-800"' do
+      it 'raises ArgumentError' do
+        receiver = Bio::GenomicInterval.parse("chr1:400-600")
+        subject  = Bio::GenomicInterval.parse("chrX:603-800")
+        expect{receiver.expand(subject)}.to raise_error(ArgumentError)
+      end
+    end
+  end
+
+  describe '#size' do
+    context 'when initialized by "chr1:400-410"' do
+      it 'returens 11' do
+        Bio::GenomicInterval.parse("chr1:400-410").size.should == 11
+      end
+    end
+  end
+
+  describe '#center' do
+    context 'when initialized by "chr1:11-15"' do
+      it 'returns "chr1:13-13" by the to_s method' do
+        Bio::GenomicInterval.parse("chr1:11-15").center.to_s.should == "chr1:13-13"
+      end
+    end
+
+    context 'when initialize by "chr1:10-15"' do
+      it 'returns "chr1:12-12" by the to_s method' do
+        Bio::GenomicInterval.parse("chr1:10-15").center.to_s.should == "chr1:12-12"
+      end
+    end
+   end
+
+  describe '#overlap for "chr1:400-500"' do 
+    context 'given "chr1:100-200"' do
+      it 'returns -199' do
+        receiver = Bio::GenomicInterval.parse("chr1:400-500")
+        subject  = Bio::GenomicInterval.parse("chr1:100-200")
+        receiver.overlap(subject).should == -199
+      end
+    end
+
+    context 'given "chr1:100-399"' do
+      it 'returns 0' do
+        receiver = Bio::GenomicInterval.parse("chr1:400-500")
+        subject  = Bio::GenomicInterval.parse("chr1:100-399")
+        receiver.overlap(subject).should == 0
+      end
+    end
+
+    context 'given "chr1:100-400"' do
+      it 'returns 1' do
+        receiver = Bio::GenomicInterval.parse("chr1:400-500")
+        subject  = Bio::GenomicInterval.parse("chr1:100-400")
+        receiver.overlap(subject).should == 1
+      end
+    end
+
+    context 'given "chr1:410-490"' do
+      it 'returns 81' do
+        receiver = Bio::GenomicInterval.parse("chr1:400-500")
+        subject  = Bio::GenomicInterval.parse("chr1:410-490")
+        receiver.overlap(subject).should == 81
+      end
+    end
+
+    context 'given "chr1:300-600"' do
+      it 'returns 101' do
+        receiver = Bio::GenomicInterval.parse("chr1:400-500")
+        subject  = Bio::GenomicInterval.parse("chr1:300-600")
+        receiver.overlap(subject).should == 101
+      end
+    end
+
+    context 'given "chr1:400-500"' do
+      it 'returns 101' do
+        receiver = Bio::GenomicInterval.parse("chr1:400-500")
+        subject  = Bio::GenomicInterval.parse("chr1:400-500")
+        receiver.overlap(subject).should == 101
+      end
+    end
+
+    context 'given "chr1:450-550"' do
+      it 'returns 51' do
+        receiver = Bio::GenomicInterval.parse("chr1:400-500")
+        subject  = Bio::GenomicInterval.parse("chr1:450-550")
+        receiver.overlap(subject).should == 51
+      end
+    end
+
+    context 'given "chr1:501-600"' do
+      it 'returns 0' do
+        receiver = Bio::GenomicInterval.parse("chr1:400-500")
+        subject  = Bio::GenomicInterval.parse("chr1:501-600")
+        receiver.overlap(subject).should == 0
+      end
+    end
+
+    context 'given "chr1:550-600"' do
+      it 'returns -49' do
+        receiver = Bio::GenomicInterval.parse("chr1:400-500")
+        subject  = Bio::GenomicInterval.parse("chr1:550-600")
+        receiver.overlap(subject).should == -49
+      end
+    end
+
+    context 'given "chrX:100-900"' do
+      it 'returns 0' do
+        receiver = Bio::GenomicInterval.parse("chr1:400-500")
+        subject  = Bio::GenomicInterval.parse("chrX:100-900")
+        receiver.overlap(subject).should == 0
+      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-genomic-interval'
+
+# 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 +1,157 @@
+--- !ruby/object:Gem::Specification 
+name: bio-genomic-interval
+version: !ruby/object:Gem::Version 
+  hash: 27
+  prerelease: 
+  segments: 
+  - 0
+  - 1
+  - 0
+  version: 0.1.0
+platform: ruby
+authors: 
+- Hiroyuki Mishima
+autorequire: 
+bindir: bin
+cert_chain: []
+
+date: 2011-04-07 00:00:00 +09:00
+default_executable: 
+dependencies: 
+- !ruby/object:Gem::Dependency 
+  name: rspec
+  requirement: &id001 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ~>
+      - !ruby/object:Gem::Version 
+        hash: 3
+        segments: 
+        - 2
+        - 3
+        - 0
+        version: 2.3.0
+  type: :development
+  prerelease: false
+  version_requirements: *id001
+- !ruby/object:Gem::Dependency 
+  name: bundler
+  requirement: &id002 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ~>
+      - !ruby/object:Gem::Version 
+        hash: 23
+        segments: 
+        - 1
+        - 0
+        - 0
+        version: 1.0.0
+  type: :development
+  prerelease: false
+  version_requirements: *id002
+- !ruby/object:Gem::Dependency 
+  name: jeweler
+  requirement: &id003 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ~>
+      - !ruby/object:Gem::Version 
+        hash: 7
+        segments: 
+        - 1
+        - 5
+        - 2
+        version: 1.5.2
+  type: :development
+  prerelease: false
+  version_requirements: *id003
+- !ruby/object:Gem::Dependency 
+  name: rcov
+  requirement: &id004 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        hash: 3
+        segments: 
+        - 0
+        version: "0"
+  type: :development
+  prerelease: false
+  version_requirements: *id004
+- !ruby/object:Gem::Dependency 
+  name: bio
+  requirement: &id005 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        hash: 5
+        segments: 
+        - 1
+        - 4
+        - 1
+        version: 1.4.1
+  type: :development
+  prerelease: false
+  version_requirements: *id005
+description: "a BioRuby plugin: handling genomic intervals,such as \"chr1:123-456\", and overlaps between two intervalsrake "
+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-genomic-interval.gemspec
+- lib/bio-genomic-interval.rb
+- spec/bio-genomic-interval_spec.rb
+- spec/spec_helper.rb
+has_rdoc: true
+homepage: http://github.com/misshie/bioruby-genomic-interval
+licenses: 
+- MIT
+post_install_message: 
+rdoc_options: []
+
+require_paths: 
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement 
+  none: false
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      hash: 3
+      segments: 
+      - 0
+      version: "0"
+required_rubygems_version: !ruby/object:Gem::Requirement 
+  none: false
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      hash: 3
+      segments: 
+      - 0
+      version: "0"
+requirements: []
+
+rubyforge_project: 
+rubygems_version: 1.6.2
+signing_key: 
+specification_version: 3
+summary: "a BioRuby plugin: handling genomic interavals and overlaps"
+test_files: 
+- spec/bio-genomic-interval_spec.rb
+- spec/spec_helper.rb