bio-genomic-interval 0.1.1 → 0.1.2

data/README.rdoc

@@ -1,12 +1,16 @@
 = bio-genomic-interval
 
 Author::    MISHIMA, Hiroyuki (hmishima AT nagasaki-u.ac.jp, missy AT be.to)
-Version::   0.1.1
+Version::   0.1.2
 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.
+= Install
+
+ $ gem install bio-genomic-interval
+ (sudo or switching to root may be required)
 
 = Usage
 == Generation of interval objects
@@ -15,6 +19,8 @@ a interval object be generated by like the following:
  a.to_s # => "chr1:123-456"
  b = Bio::GenomicInterval.parse("chr1:123-456")
  b.to_s # => "chr1:123-456"
+ b2 = Bio::GenomicInterval.parse("chr1:1,234,567-2,345,678")
+ b2.to_s # => "chr1:1234567-2345678" # ignoring ","
  c = Bio::GenomicInetrval.zero_based("chr1", 122, 456)
  c.to_s # => "chr1:123-456"
  c.zero_start # => 122
@@ -43,6 +49,11 @@ Note that size is changed to 1.
  ref.adjacent = 1
  ref.compare(cmp) # => :right_off
 
+Bio::GenomicInterval.compare returns one of the followings:
+ :different_chrom, :left_adjacent, :right_adjacent
+ :left_off, :right_off, :equal
+ :contained_by, :contains, :left_overlapped, :right_overlapped
+
 == 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.

data/VERSION

@@ -1 +1 @@
-0.1.1
+0.1.2

data/bio-genomic-interval.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = %q{bio-genomic-interval}
-  s.version = "0.1.1"
+  s.version = "0.1.2"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Hiroyuki Mishima"]
-  s.date = %q{2011-04-18}
+  s.date = %q{2011-04-20}
   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 = [

data/lib/bio-genomic-interval.rb

@@ -25,8 +25,8 @@ module Bio
       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)
+      chr_start = Integer(str_start.gsub(",",""))
+      chr_end   = Integer(str_end.gsub(",",""))
       if chr_start > chr_end
         chr_end, chr_start = chr_start, chr_end
       end

data/spec/bio-genomic-interval_spec.rb

@@ -50,6 +50,13 @@ describe "Bio::GenomicInterval" do
         Bio::GenomicInterval.parse("chr1:123").to_s.should == "chr1:123-123"
       end
     end
+
+    context 'given "chr1:1,234,567-2,345,678"' do
+      it 'ignores commas and represents "chr1:1234567-2345678"' do
+        istr = "chr1:1,234,567-2,345,678"
+        Bio::GenomicInterval.parse(istr).to_s.should == "chr1:1234567-2345678"
+      end
+    end
   end
 
   describe ".zero_based" do
@@ -360,7 +367,6 @@ describe "Bio::GenomicInterval" do
         receiver.overlap(subject).should == 0
       end
     end
-
   end
 
 end

metadata

@@ -5,8 +5,8 @@ version: !ruby/object:Gem::Version
   segments: 
   - 0
   - 1
-  - 1
-  version: 0.1.1
+  - 2
+  version: 0.1.2
 platform: ruby
 authors: 
 - Hiroyuki Mishima
@@ -14,7 +14,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2011-04-18 00:00:00 +09:00
+date: 2011-04-20 00:00:00 +09:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
@@ -126,7 +126,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
   requirements: 
   - - ">="
     - !ruby/object:Gem::Version 
-      hash: 2089191038881076262
+      hash: -73016163408757686
       segments: 
       - 0
       version: "0"