bio-restriction_enzyme 1.0.0

data/test/test_bio-restriction_enzyme.rb

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+require 'helper'
+
+class TestBioRestrictionEnzyme < Test::Unit::TestCase
+  def setup
+    @t = Bio::RestrictionEnzyme
+  end
+
+  def test_rebase
+    assert_equal(@t.rebase.respond_to?(:enzymes), true)
+    assert_not_nil @t.rebase['AarI']
+    assert_nil @t.rebase['blah']
+  end
+
+  def test_enzyme_name
+    assert_equal(@t.enzyme_name?('AarI'), true)
+    assert_equal(@t.enzyme_name?('atgc'), false)
+    assert_equal(@t.enzyme_name?('aari'), true)
+    assert_equal(@t.enzyme_name?('EcoRI'), true)
+    assert_equal(@t.enzyme_name?('EcoooRI'), false)
+  end
+end

metadata

@@ -0,0 +1,153 @@
+--- !ruby/object:Gem::Specification
+name: bio-restriction_enzyme
+version: !ruby/object:Gem::Version
+  version: 1.0.0
+  prerelease: 
+platform: ruby
+authors:
+- Trevor Wennblom
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2011-09-10 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: bio-data-restriction_enzyme
+  requirement: &70186296288220 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: *70186296288220
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: &70186296284380 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.0.0
+  type: :development
+  prerelease: false
+  version_requirements: *70186296284380
+- !ruby/object:Gem::Dependency
+  name: jeweler
+  requirement: &70186296295900 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.6.4
+  type: :development
+  prerelease: false
+  version_requirements: *70186296295900
+- !ruby/object:Gem::Dependency
+  name: rcov
+  requirement: &70186296290660 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: *70186296290660
+- !ruby/object:Gem::Dependency
+  name: bio
+  requirement: &70186296304160 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.4.1
+  type: :development
+  prerelease: false
+  version_requirements: *70186296304160
+description: Digests DNA based on restriction enzyme cut patterns
+email: trevor@well.com
+executables: []
+extensions: []
+extra_rdoc_files:
+- LICENSE.txt
+- README.rdoc
+files:
+- .document
+- COPYING.txt
+- Gemfile
+- LICENSE.txt
+- README.rdoc
+- Rakefile
+- VERSION
+- bio-restriction_enzyme.gemspec
+- lib/bio-restriction_enzyme.rb
+- lib/bio/util/restriction_enzyme.rb
+- lib/bio/util/restriction_enzyme/analysis.rb
+- lib/bio/util/restriction_enzyme/analysis_basic.rb
+- lib/bio/util/restriction_enzyme/cut_symbol.rb
+- lib/bio/util/restriction_enzyme/double_stranded.rb
+- lib/bio/util/restriction_enzyme/double_stranded/aligned_strands.rb
+- lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb
+- lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair_in_enzyme_notation.rb
+- lib/bio/util/restriction_enzyme/double_stranded/cut_locations.rb
+- lib/bio/util/restriction_enzyme/double_stranded/cut_locations_in_enzyme_notation.rb
+- lib/bio/util/restriction_enzyme/range/cut_range.rb
+- lib/bio/util/restriction_enzyme/range/cut_ranges.rb
+- lib/bio/util/restriction_enzyme/range/horizontal_cut_range.rb
+- lib/bio/util/restriction_enzyme/range/sequence_range.rb
+- lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb
+- lib/bio/util/restriction_enzyme/range/sequence_range/fragment.rb
+- lib/bio/util/restriction_enzyme/range/sequence_range/fragments.rb
+- lib/bio/util/restriction_enzyme/range/vertical_cut_range.rb
+- lib/bio/util/restriction_enzyme/single_strand.rb
+- lib/bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb
+- lib/bio/util/restriction_enzyme/single_strand_complement.rb
+- lib/bio/util/restriction_enzyme/string_formatting.rb
+- test/bio-restriction_enzyme/analysis/test_calculated_cuts.rb
+- test/bio-restriction_enzyme/analysis/test_cut_ranges.rb
+- test/bio-restriction_enzyme/analysis/test_sequence_range.rb
+- test/bio-restriction_enzyme/double_stranded/test_aligned_strands.rb
+- test/bio-restriction_enzyme/double_stranded/test_cut_location_pair.rb
+- test/bio-restriction_enzyme/double_stranded/test_cut_location_pair_in_enzyme_notation.rb
+- test/bio-restriction_enzyme/double_stranded/test_cut_locations.rb
+- test/bio-restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb
+- test/bio-restriction_enzyme/single_strand/test_cut_locations_in_enzyme_notation.rb
+- test/bio-restriction_enzyme/test_analysis.rb
+- test/bio-restriction_enzyme/test_cut_symbol.rb
+- test/bio-restriction_enzyme/test_double_stranded.rb
+- test/bio-restriction_enzyme/test_single_strand.rb
+- test/bio-restriction_enzyme/test_single_strand_complement.rb
+- test/bio-restriction_enzyme/test_string_formatting.rb
+- test/helper.rb
+- test/test_bio-restriction_enzyme.rb
+homepage: http://github.com/trevor/bioruby-restriction_enzyme
+licenses:
+- CC0
+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: 1162168444368907343
+required_rubygems_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 1.8.10
+signing_key: 
+specification_version: 3
+summary: Digests DNA based on restriction enzyme cut patterns
+test_files: []