bio-genomic-interval 0.1.0 → 0.1.1

data/README.rdoc

@@ -1,7 +1,7 @@
 = bio-genomic-interval
 
 Author::    MISHIMA, Hiroyuki (hmishima AT nagasaki-u.ac.jp, missy AT be.to)
-Version::   0.1.0
+Version::   0.1.1
 Copyright:: Copyright (c) MISHIMA, Hiroyuki, 2011
 License::   the MIT/X11 license
 
@@ -23,6 +23,14 @@ 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.
 
+ d = Bio::GenomicInetrval.zero_based("chr1", 100, 100)
+ d.to_s # => "chr1:101-101"
+ d.length # => 1
+
+In the BED format, an insertion position is like "chr1:100-100", whose size is 0.
+This interval is converted into "chr1:101-101" in the one-based format.
+Note that size is changed to 1.
+
 == Comparison
  ref = Bio::GenomicInterval.parse("chr1:123-456")
  cmp = Bio::GenomicInterval.parse("chr1:234-567")
@@ -43,7 +51,7 @@ Last one is generated from a "Zero-based half-closed[start, end)"  interval
  cmp = Bio::GenomicInterval.parse("chr1:15-25")
  ref.overlap(cmp) # => 6
  cmp2 = Bio::GenomicInterval.parse("chr1:25-35")
- ref.overlap(cmp) # => -4
+ ref.overlap(cmp2) # => -4
 
 == Expansion (or integration)
  ref =   Bio::GenomicInterval.parse("chr1:400-600")

data/Rakefile

@@ -11,17 +11,20 @@ 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 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 }
+    %Q{a BioRuby plugin: handling genomic intervals,such as "chr1:123-456", and overlap state between two intervals }
   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)
+  # 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

data/VERSION

@@ -1 +1 @@
-0.1.0
+0.1.1

data/bio-genomic-interval.gemspec

@@ -5,12 +5,12 @@
 
 Gem::Specification.new do |s|
   s.name = %q{bio-genomic-interval}
-  s.version = "0.1.0"
+  s.version = "0.1.1"
 
   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.date = %q{2011-04-18}
+  s.description = %q{a BioRuby plugin: handling genomic intervals,such as "chr1:123-456", and overlap state between two intervals }
   s.email = %q{missy@be.to}
   s.extra_rdoc_files = [
     "LICENSE.txt",
@@ -33,7 +33,7 @@ Gem::Specification.new do |s|
   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.rubygems_version = %q{1.3.7}
   s.summary = %q{a BioRuby plugin: handling genomic interavals and overlaps}
   s.test_files = [
     "spec/bio-genomic-interval_spec.rb",
@@ -41,6 +41,7 @@ Gem::Specification.new do |s|
   ]
 
   if s.respond_to? :specification_version then
+    current_version = Gem::Specification::CURRENT_SPECIFICATION_VERSION
     s.specification_version = 3
 
     if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then

data/lib/bio-genomic-interval.rb

@@ -1,12 +1,14 @@
 module Bio
 
   #
-  # =a class for manupirate genomic intervals such as "chr1:123-456"
+  # 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
     
+    attr_accessor :chrom, :chr_start, :chr_end, :adjacent
+
     def initialize(chrom = "", chr_start = 1, chr_end = 1)
       raise ArgumentError unless chr_start >= 1
       raise ArgumentError unless chr_end >= 1
@@ -17,12 +19,8 @@ module Bio
       @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]
@@ -33,45 +31,36 @@ module Bio
         chr_end, chr_start = chr_start, chr_end
       end
       self.new(chrom, chr_start, chr_end)
-  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_end += 1 if (z_start == z_end)
       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
+    #  :contained_by, :contains, :left_overlapped, :right_overlapped
     # Imagine that the receiver object is fixed on a number line
-    #
     def compare(other)
       case
       when self.chrom != other.chrom
@@ -89,10 +78,10 @@ module Bio
         :equal
       when (other.chr_start.between?(self.chr_start, self.chr_end)) &&
           (other.chr_end.between?(self.chr_start, self.chr_end))
-        :contained
+        :contained_by
       when (self.chr_start.between?(other.chr_start, other.chr_end)) &&
           (self.chr_end.between?(other.chr_start, other.chr_end))
-        :containing
+        :contains
       when (other.chr_start < self.chr_start) &&
           (other.chr_end.between?(self.chr_start, self.chr_end))
         :left_overlapped
@@ -107,13 +96,13 @@ module Bio
     def nearly_overlapped?(other)
       result = compare(other)
       [ :left_adjacent, :right_adjacent,
-        :equal, :contained, :containing,
+        :equal, :contained_by, :contains,
         :left_overlapped, :right_overlapped].any?{|x| x == result} 
     end
 
     def overlapped?(other)
       result = compare(other)
-      [ :equal, :contained, :containing,
+      [ :equal, :contained_by, :contains,
         :left_overlapped, :right_overlapped].any?{|x| x == result} 
     end
 
@@ -137,16 +126,15 @@ module Bio
 
     # * 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)
+     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
+      when :contained_by, :equal
         other.size
-      when :containing
+      when :contains
         self.size
       when :right_off, :right_adjacent, :right_overlapped
         self.chr_end - other.chr_start + 1
@@ -154,5 +142,7 @@ module Bio
         raise Exception, "must not happen"
       end
     end
-  end
-end
+
+  end # class GenomicInterval
+
+end # module Bio

data/spec/bio-genomic-interval_spec.rb

@@ -60,6 +60,15 @@ describe "Bio::GenomicInterval" do
     end
   end
 
+  describe ".zero_based" do
+    context 'given ("chr1", 100, 100) <e.g. insertion position>' do
+      it 'represents "chr1:101-101" by the to_s method' do
+        Bio::GenomicInterval.zero_based("chr1", 100, 100).to_s.should == "chr1:101-101"
+      end 
+    end
+  end
+
+
   #
   # instance methods
   #
@@ -123,26 +132,26 @@ describe "Bio::GenomicInterval" do
     end
 
     context 'given "chr1:450-550"' do
-      it 'returns :contained' do
+      it 'returns :contained_by' do
         receiver = Bio::GenomicInterval.parse("chr1:400-600")
         subject  = Bio::GenomicInterval.parse("chr1:450-550")
-        receiver.compare(subject).should == :contained
+        receiver.compare(subject).should == :contained_by
       end
     end
 
     context 'given "chr1:400-400" (size == 1)' do
-      it 'returns :contained' do
+      it 'returns :contained_by' do
         receiver = Bio::GenomicInterval.parse("chr1:400-600")
         subject  = Bio::GenomicInterval.parse("chr1:400-400")
-        receiver.compare(subject).should == :contained
+        receiver.compare(subject).should == :contained_by
       end
     end
 
     context 'given "chr1:300-700"' do
-      it 'returns :containing' do
+      it 'returns :contains' do
         receiver = Bio::GenomicInterval.parse("chr1:400-600")
         subject  = Bio::GenomicInterval.parse("chr1:300-700")
-        receiver.compare(subject).should == :containing
+        receiver.compare(subject).should == :contains
       end
     end
 

metadata

@@ -1,13 +1,12 @@
 --- !ruby/object:Gem::Specification 
 name: bio-genomic-interval
 version: !ruby/object:Gem::Version 
-  hash: 27
-  prerelease: 
+  prerelease: false
   segments: 
   - 0
   - 1
-  - 0
-  version: 0.1.0
+  - 1
+  version: 0.1.1
 platform: ruby
 authors: 
 - Hiroyuki Mishima
@@ -15,7 +14,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2011-04-07 00:00:00 +09:00
+date: 2011-04-18 00:00:00 +09:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
@@ -25,7 +24,6 @@ dependencies:
     requirements: 
     - - ~>
       - !ruby/object:Gem::Version 
-        hash: 3
         segments: 
         - 2
         - 3
@@ -41,7 +39,6 @@ dependencies:
     requirements: 
     - - ~>
       - !ruby/object:Gem::Version 
-        hash: 23
         segments: 
         - 1
         - 0
@@ -57,7 +54,6 @@ dependencies:
     requirements: 
     - - ~>
       - !ruby/object:Gem::Version 
-        hash: 7
         segments: 
         - 1
         - 5
@@ -73,7 +69,6 @@ dependencies:
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
-        hash: 3
         segments: 
         - 0
         version: "0"
@@ -87,7 +82,6 @@ dependencies:
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
-        hash: 5
         segments: 
         - 1
         - 4
@@ -96,7 +90,7 @@ dependencies:
   type: :development
   prerelease: false
   version_requirements: *id005
-description: "a BioRuby plugin: handling genomic intervals,such as \"chr1:123-456\", and overlaps between two intervalsrake "
+description: "a BioRuby plugin: handling genomic intervals,such as \"chr1:123-456\", and overlap state between two intervals "
 email: missy@be.to
 executables: []
 
@@ -132,7 +126,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
   requirements: 
   - - ">="
     - !ruby/object:Gem::Version 
-      hash: 3
+      hash: 2089191038881076262
       segments: 
       - 0
       version: "0"
@@ -141,14 +135,13 @@ required_rubygems_version: !ruby/object:Gem::Requirement
   requirements: 
   - - ">="
     - !ruby/object:Gem::Version 
-      hash: 3
       segments: 
       - 0
       version: "0"
 requirements: []
 
 rubyforge_project: 
-rubygems_version: 1.6.2
+rubygems_version: 1.3.7
 signing_key: 
 specification_version: 3
 summary: "a BioRuby plugin: handling genomic interavals and overlaps"