bio-restriction_enzyme 1.0.0
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- data/.document +5 -0
- data/COPYING.txt +121 -0
- data/Gemfile +10 -0
- data/LICENSE.txt +7 -0
- data/README.rdoc +22 -0
- data/Rakefile +53 -0
- data/VERSION +1 -0
- data/bio-restriction_enzyme.gemspec +99 -0
- data/lib/bio-restriction_enzyme.rb +1 -0
- data/lib/bio/util/restriction_enzyme.rb +218 -0
- data/lib/bio/util/restriction_enzyme/analysis.rb +241 -0
- data/lib/bio/util/restriction_enzyme/analysis_basic.rb +209 -0
- data/lib/bio/util/restriction_enzyme/cut_symbol.rb +99 -0
- data/lib/bio/util/restriction_enzyme/double_stranded.rb +313 -0
- data/lib/bio/util/restriction_enzyme/double_stranded/aligned_strands.rb +127 -0
- data/lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb +95 -0
- data/lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair_in_enzyme_notation.rb +30 -0
- data/lib/bio/util/restriction_enzyme/double_stranded/cut_locations.rb +68 -0
- data/lib/bio/util/restriction_enzyme/double_stranded/cut_locations_in_enzyme_notation.rb +99 -0
- data/lib/bio/util/restriction_enzyme/range/cut_range.rb +16 -0
- data/lib/bio/util/restriction_enzyme/range/cut_ranges.rb +39 -0
- data/lib/bio/util/restriction_enzyme/range/horizontal_cut_range.rb +59 -0
- data/lib/bio/util/restriction_enzyme/range/sequence_range.rb +249 -0
- data/lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb +236 -0
- data/lib/bio/util/restriction_enzyme/range/sequence_range/fragment.rb +43 -0
- data/lib/bio/util/restriction_enzyme/range/sequence_range/fragments.rb +33 -0
- data/lib/bio/util/restriction_enzyme/range/vertical_cut_range.rb +69 -0
- data/lib/bio/util/restriction_enzyme/single_strand.rb +193 -0
- data/lib/bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb +127 -0
- data/lib/bio/util/restriction_enzyme/single_strand_complement.rb +15 -0
- data/lib/bio/util/restriction_enzyme/string_formatting.rb +103 -0
- data/test/bio-restriction_enzyme/analysis/test_calculated_cuts.rb +281 -0
- data/test/bio-restriction_enzyme/analysis/test_cut_ranges.rb +87 -0
- data/test/bio-restriction_enzyme/analysis/test_sequence_range.rb +223 -0
- data/test/bio-restriction_enzyme/double_stranded/test_aligned_strands.rb +84 -0
- data/test/bio-restriction_enzyme/double_stranded/test_cut_location_pair.rb +58 -0
- data/test/bio-restriction_enzyme/double_stranded/test_cut_location_pair_in_enzyme_notation.rb +56 -0
- data/test/bio-restriction_enzyme/double_stranded/test_cut_locations.rb +35 -0
- data/test/bio-restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb +87 -0
- data/test/bio-restriction_enzyme/single_strand/test_cut_locations_in_enzyme_notation.rb +66 -0
- data/test/bio-restriction_enzyme/test_analysis.rb +228 -0
- data/test/bio-restriction_enzyme/test_cut_symbol.rb +27 -0
- data/test/bio-restriction_enzyme/test_double_stranded.rb +98 -0
- data/test/bio-restriction_enzyme/test_single_strand.rb +131 -0
- data/test/bio-restriction_enzyme/test_single_strand_complement.rb +131 -0
- data/test/bio-restriction_enzyme/test_string_formatting.rb +43 -0
- data/test/helper.rb +17 -0
- data/test/test_bio-restriction_enzyme.rb +21 -0
- metadata +153 -0
@@ -0,0 +1,21 @@
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require 'helper'
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class TestBioRestrictionEnzyme < Test::Unit::TestCase
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def setup
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@t = Bio::RestrictionEnzyme
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end
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def test_rebase
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assert_equal(@t.rebase.respond_to?(:enzymes), true)
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assert_not_nil @t.rebase['AarI']
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assert_nil @t.rebase['blah']
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end
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def test_enzyme_name
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assert_equal(@t.enzyme_name?('AarI'), true)
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assert_equal(@t.enzyme_name?('atgc'), false)
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assert_equal(@t.enzyme_name?('aari'), true)
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assert_equal(@t.enzyme_name?('EcoRI'), true)
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assert_equal(@t.enzyme_name?('EcoooRI'), false)
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end
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end
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metadata
ADDED
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--- !ruby/object:Gem::Specification
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name: bio-restriction_enzyme
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version: !ruby/object:Gem::Version
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version: 1.0.0
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prerelease:
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platform: ruby
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authors:
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- Trevor Wennblom
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autorequire:
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bindir: bin
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cert_chain: []
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date: 2011-09-10 00:00:00.000000000 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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name: bio-data-restriction_enzyme
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requirement: &70186296288220 !ruby/object:Gem::Requirement
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none: false
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requirements:
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19
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- - ! '>='
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20
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- !ruby/object:Gem::Version
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version: '0'
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type: :runtime
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prerelease: false
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version_requirements: *70186296288220
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- !ruby/object:Gem::Dependency
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name: bundler
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27
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requirement: &70186296284380 !ruby/object:Gem::Requirement
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28
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none: false
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requirements:
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30
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- - ~>
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- !ruby/object:Gem::Version
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version: 1.0.0
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type: :development
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prerelease: false
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version_requirements: *70186296284380
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36
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- !ruby/object:Gem::Dependency
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name: jeweler
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requirement: &70186296295900 !ruby/object:Gem::Requirement
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39
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none: false
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requirements:
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41
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- - ~>
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- !ruby/object:Gem::Version
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43
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version: 1.6.4
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type: :development
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prerelease: false
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version_requirements: *70186296295900
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47
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- !ruby/object:Gem::Dependency
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48
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name: rcov
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49
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requirement: &70186296290660 !ruby/object:Gem::Requirement
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none: false
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51
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requirements:
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52
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- - ! '>='
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53
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- !ruby/object:Gem::Version
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54
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version: '0'
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55
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type: :development
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56
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prerelease: false
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57
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version_requirements: *70186296290660
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58
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- !ruby/object:Gem::Dependency
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name: bio
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requirement: &70186296304160 !ruby/object:Gem::Requirement
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none: false
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62
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requirements:
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63
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+
- - ! '>='
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64
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- !ruby/object:Gem::Version
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65
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version: 1.4.1
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66
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type: :development
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67
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prerelease: false
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68
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version_requirements: *70186296304160
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description: Digests DNA based on restriction enzyme cut patterns
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email: trevor@well.com
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executables: []
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extensions: []
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extra_rdoc_files:
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- LICENSE.txt
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- README.rdoc
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files:
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77
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- .document
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78
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- COPYING.txt
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79
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- Gemfile
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80
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- LICENSE.txt
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81
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- README.rdoc
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82
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- Rakefile
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83
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- VERSION
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84
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- bio-restriction_enzyme.gemspec
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85
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- lib/bio-restriction_enzyme.rb
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86
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- lib/bio/util/restriction_enzyme.rb
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87
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- lib/bio/util/restriction_enzyme/analysis.rb
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88
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- lib/bio/util/restriction_enzyme/analysis_basic.rb
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89
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- lib/bio/util/restriction_enzyme/cut_symbol.rb
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90
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+
- lib/bio/util/restriction_enzyme/double_stranded.rb
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91
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- lib/bio/util/restriction_enzyme/double_stranded/aligned_strands.rb
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92
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+
- lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb
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93
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+
- lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair_in_enzyme_notation.rb
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94
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- lib/bio/util/restriction_enzyme/double_stranded/cut_locations.rb
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95
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- lib/bio/util/restriction_enzyme/double_stranded/cut_locations_in_enzyme_notation.rb
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96
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- lib/bio/util/restriction_enzyme/range/cut_range.rb
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97
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- lib/bio/util/restriction_enzyme/range/cut_ranges.rb
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98
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- lib/bio/util/restriction_enzyme/range/horizontal_cut_range.rb
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99
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- lib/bio/util/restriction_enzyme/range/sequence_range.rb
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100
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- lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb
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101
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- lib/bio/util/restriction_enzyme/range/sequence_range/fragment.rb
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102
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- lib/bio/util/restriction_enzyme/range/sequence_range/fragments.rb
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103
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- lib/bio/util/restriction_enzyme/range/vertical_cut_range.rb
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104
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- lib/bio/util/restriction_enzyme/single_strand.rb
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105
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- lib/bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb
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106
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- lib/bio/util/restriction_enzyme/single_strand_complement.rb
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107
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- lib/bio/util/restriction_enzyme/string_formatting.rb
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108
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- test/bio-restriction_enzyme/analysis/test_calculated_cuts.rb
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109
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- test/bio-restriction_enzyme/analysis/test_cut_ranges.rb
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110
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- test/bio-restriction_enzyme/analysis/test_sequence_range.rb
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111
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- test/bio-restriction_enzyme/double_stranded/test_aligned_strands.rb
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112
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- test/bio-restriction_enzyme/double_stranded/test_cut_location_pair.rb
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113
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- test/bio-restriction_enzyme/double_stranded/test_cut_location_pair_in_enzyme_notation.rb
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114
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- test/bio-restriction_enzyme/double_stranded/test_cut_locations.rb
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115
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- test/bio-restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb
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116
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- test/bio-restriction_enzyme/single_strand/test_cut_locations_in_enzyme_notation.rb
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117
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- test/bio-restriction_enzyme/test_analysis.rb
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118
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- test/bio-restriction_enzyme/test_cut_symbol.rb
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119
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- test/bio-restriction_enzyme/test_double_stranded.rb
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120
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- test/bio-restriction_enzyme/test_single_strand.rb
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121
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- test/bio-restriction_enzyme/test_single_strand_complement.rb
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122
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- test/bio-restriction_enzyme/test_string_formatting.rb
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123
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- test/helper.rb
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124
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- test/test_bio-restriction_enzyme.rb
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125
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homepage: http://github.com/trevor/bioruby-restriction_enzyme
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licenses:
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127
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- CC0
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128
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post_install_message:
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129
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rdoc_options: []
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130
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require_paths:
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131
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- lib
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132
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required_ruby_version: !ruby/object:Gem::Requirement
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133
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none: false
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134
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requirements:
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135
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- - ! '>='
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136
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- !ruby/object:Gem::Version
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137
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version: '0'
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138
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segments:
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139
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- 0
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140
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hash: 1162168444368907343
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141
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required_rubygems_version: !ruby/object:Gem::Requirement
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142
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none: false
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143
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requirements:
|
144
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- - ! '>='
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145
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- !ruby/object:Gem::Version
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146
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version: '0'
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147
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requirements: []
|
148
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rubyforge_project:
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149
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rubygems_version: 1.8.10
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150
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signing_key:
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151
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specification_version: 3
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152
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summary: Digests DNA based on restriction enzyme cut patterns
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153
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test_files: []
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