bio-restriction_enzyme 1.0.0

data/.document

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+lib/**/*.rb
+bin/*
+- 
+features/**/*.feature
+LICENSE.txt

data/COPYING.txt

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data/Gemfile

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+source "http://rubygems.org"
+
+gem 'bio-data-restriction_enzyme'
+
+group :development do
+  gem "bundler", "~> 1.0.0"
+  gem "jeweler", "~> 1.6.4"
+  gem "rcov", ">= 0"
+  gem "bio", ">= 1.4.1"
+end

data/LICENSE.txt

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+Bio::RestrictionEnzyme
+
+Written in 2005-2011 by Trevor Wennblom <trevor@well.com>
+
+To the extent possible under law, the author(s) have dedicated all copyright and related and neighboring rights to this software to the public domain worldwide. This software is distributed without any warranty.
+
+You should have received a copy of the CC0 Public Domain Dedication along with this software. If not, see <http://creativecommons.org/publicdomain/zero/1.0/>.

data/README.rdoc

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+= bio-restriction_enzyme
+
+Bio::RestrictionEnzyme
+
+Digests DNA based on restriction enzyme cut patterns
+
+
+== notes
+
+Re-implementation of Bio::RestrictionEnzyme as a BioGem.
+
+This BioGem does not include changes found in BioRuby 1.4.2. These will be added if resubmitted under a compatible license.
+
+
+== contribution
+
+Improvements encouraged, send pull requests.
+
+
+== license
+
+CC0 1.0 Universal (CC0 1.0) Public Domain Dedication

data/Rakefile

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+# encoding: utf-8
+
+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-restriction_enzyme'
+  gem.homepage = 'http://github.com/trevor/bioruby-restriction_enzyme'
+  gem.license = 'CC0'
+  gem.summary = %Q{Digests DNA based on restriction enzyme cut patterns}
+  gem.description = %Q{Digests DNA based on restriction enzyme cut patterns}
+  gem.email = 'trevor@well.com'
+  gem.authors = ['Trevor Wennblom']
+  # dependencies defined in Gemfile
+end
+Jeweler::RubygemsDotOrgTasks.new
+
+require 'rake/testtask'
+Rake::TestTask.new(:test) do |test|
+  test.libs << 'lib' << 'test'
+  test.pattern = 'test/**/test_*.rb'
+  test.verbose = true
+end
+
+require 'rcov/rcovtask'
+Rcov::RcovTask.new do |test|
+  test.libs << 'test'
+  test.pattern = 'test/**/test_*.rb'
+  test.verbose = true
+  test.rcov_opts << '--exclude "gems/*"'
+end
+
+task :default => :test
+
+require 'rake/rdoctask'
+Rake::RDocTask.new do |rdoc|
+  version = File.exist?('VERSION') ? File.read('VERSION') : ""
+
+  rdoc.rdoc_dir = 'rdoc'
+  rdoc.title = "bio-restriction_enzyme #{version}"
+  rdoc.rdoc_files.include('README*')
+  rdoc.rdoc_files.include('lib/**/*.rb')
+end

data/VERSION

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+1.0.0

data/bio-restriction_enzyme.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 = "bio-restriction_enzyme"
+  s.version = "1.0.0"
+
+  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
+  s.authors = ["Trevor Wennblom"]
+  s.date = "2011-09-10"
+  s.description = "Digests DNA based on restriction enzyme cut patterns"
+  s.email = "trevor@well.com"
+  s.extra_rdoc_files = [
+    "LICENSE.txt",
+    "README.rdoc"
+  ]
+  s.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"
+  ]
+  s.homepage = "http://github.com/trevor/bioruby-restriction_enzyme"
+  s.licenses = ["CC0"]
+  s.require_paths = ["lib"]
+  s.rubygems_version = "1.8.10"
+  s.summary = "Digests DNA based on restriction enzyme cut patterns"
+
+  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_runtime_dependency(%q<bio-data-restriction_enzyme>, [">= 0"])
+      s.add_development_dependency(%q<bundler>, ["~> 1.0.0"])
+      s.add_development_dependency(%q<jeweler>, ["~> 1.6.4"])
+      s.add_development_dependency(%q<rcov>, [">= 0"])
+      s.add_development_dependency(%q<bio>, [">= 1.4.1"])
+    else
+      s.add_dependency(%q<bio-data-restriction_enzyme>, [">= 0"])
+      s.add_dependency(%q<bundler>, ["~> 1.0.0"])
+      s.add_dependency(%q<jeweler>, ["~> 1.6.4"])
+      s.add_dependency(%q<rcov>, [">= 0"])
+      s.add_dependency(%q<bio>, [">= 1.4.1"])
+    end
+  else
+    s.add_dependency(%q<bio-data-restriction_enzyme>, [">= 0"])
+    s.add_dependency(%q<bundler>, ["~> 1.0.0"])
+    s.add_dependency(%q<jeweler>, ["~> 1.6.4"])
+    s.add_dependency(%q<rcov>, [">= 0"])
+    s.add_dependency(%q<bio>, [">= 1.4.1"])
+  end
+end
+

data/lib/bio-restriction_enzyme.rb

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+require 'bio/util/restriction_enzyme'

data/lib/bio/util/restriction_enzyme.rb

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+module Bio
+
+  autoload :REBASE, 'bio/db/rebase'
+
+# = Description
+#
+# Bio::RestrictionEnzyme allows you to fragment a DNA strand using one
+# or more restriction enzymes.  Bio::RestrictionEnzyme is aware that
+# multiple enzymes may be competing for the same recognition site and
+# returns the various possible fragmentation patterns that result in
+# such circumstances.
+#
+# When using Bio::RestrictionEnzyme you may simply use the name of common
+# enzymes to cut your sequence or you may construct your own unique enzymes
+# to use.
+#
+# Visit the documentaion for individual classes for more information.
+#
+# An examination of the unit tests will also reveal several interesting uses
+# for the curious programmer.
+#
+# = Usage
+#
+# == Basic
+#
+# EcoRI cut pattern:
+#   G|A A T T C
+#    +-------+
+#   C T T A A|G
+#
+# This can also be written as:
+#   G^AATTC
+#
+# Note that to use the method +cut_with_enzyme+ from a Bio::Sequence object
+# you currently must +require+ +bio/util/restriction_enzyme+ directly.  If
+# instead you're going to directly call Bio::RestrictionEnzyme::Analysis
+# then only +bio+ needs to be +required+.
+#
+#   require 'bio'
+#   require 'bio/util/restriction_enzyme'
+#
+#   seq = Bio::Sequence::NA.new('gaattc')
+#   cuts = seq.cut_with_enzyme('EcoRI')
+#   cuts.primary                        # => ["aattc", "g"]
+#   cuts.complement                     # => ["cttaa", "g"]
+#   cuts.inspect                        # => "[#<struct Bio::RestrictionEnzyme::Fragment primary=\"g    \", complement=\"cttaa\">, #<struct Bio::RestrictionEnzyme::Fragment primary=\"aattc\", complement=\"    g\">]"
+#
+#   seq = Bio::Sequence::NA.new('gaattc')
+#   cuts = seq.cut_with_enzyme('g^aattc')
+#   cuts.primary                        # => ["aattc", "g"]
+#   cuts.complement                     # => ["cttaa", "g"]
+#
+#   seq = Bio::Sequence::NA.new('gaattc')
+#   cuts = seq.cut_with_enzyme('g^aattc', 'gaatt^c')
+#   cuts.primary                        # => ["aattc", "c", "g", "gaatt"]
+#   cuts.complement                     # => ["c", "cttaa", "g", "ttaag"]
+#
+#   seq = Bio::Sequence::NA.new('gaattcgaattc')
+#   cuts = seq.cut_with_enzyme('EcoRI')
+#   cuts.primary                        # => ["aattc", "aattcg", "g"]
+#   cuts.complement                     # => ["cttaa", "g", "gcttaa"]
+#
+#   seq = Bio::Sequence::NA.new('gaattcgggaattc')
+#   cuts = seq.cut_with_enzyme('EcoRI')
+#   cuts.primary                        # => ["aattc", "aattcggg", "g"]
+#   cuts.complement                     # => ["cttaa", "g", "gcccttaa"]
+#
+#   cuts[0].inspect                     # => "#<struct Bio::RestrictionEnzyme::Fragment primary=\"g    \", complement=\"cttaa\">"
+#
+#   cuts[0].primary                     # => "g    "
+#   cuts[0].complement                  # => "cttaa"
+#
+#   cuts[1].primary                     # => "aattcggg    "
+#   cuts[1].complement                  # => "    gcccttaa"
+#
+#   cuts[2].primary                     # => "aattc"
+#   cuts[2].complement                  # => "    g"
+#
+# == Advanced
+#
+#   require 'bio'
+#
+#   enzyme_1 = Bio::RestrictionEnzyme.new('anna', [1,1], [3,3])
+#   enzyme_2 = Bio::RestrictionEnzyme.new('gg', [1,1])
+#   a = Bio::RestrictionEnzyme::Analysis.cut('agga', enzyme_1, enzyme_2)
+#   a.primary                           # => ["a", "ag", "g", "ga"]
+#   a.complement                        # => ["c", "ct", "t", "tc"]
+#
+#   a[0].primary                        # => "ag"
+#   a[0].complement                     # => "tc"
+#
+#   a[1].primary                        # => "ga"
+#   a[1].complement                     # => "ct"
+#
+#   a[2].primary                        # => "a"
+#   a[2].complement                     # => "t"
+#
+#   a[3].primary                        # => "g"
+#   a[3].complement                     # => "c"
+#
+# = Todo / under development
+#
+# * Circular DNA cutting
+#
+
+class RestrictionEnzyme
+
+  #require 'bio/util/restriction_enzyme/cut_symbol'
+
+  autoload :CutSymbol,               'bio/util/restriction_enzyme/cut_symbol'
+  autoload :StringFormatting,        'bio/util/restriction_enzyme/string_formatting'
+  autoload :SingleStrand,            'bio/util/restriction_enzyme/single_strand'
+  autoload :SingleStrandComplement,  'bio/util/restriction_enzyme/single_strand_complement'
+  autoload :DoubleStranded,          'bio/util/restriction_enzyme/double_stranded'
+  autoload :Analysis,                'bio/util/restriction_enzyme/analysis'
+  autoload :Range,                   'bio/util/restriction_enzyme/range/sequence_range'
+
+  include CutSymbol
+  extend CutSymbol
+
+  # See Bio::RestrictionEnzyme::DoubleStranded.new for more information.
+  #
+  # ---
+  # *Arguments*
+  # * +users_enzyme_or_rebase_or_pattern+: One of three possible parameters:  The name of an enzyme, a REBASE::EnzymeEntry object, or a nucleotide pattern with a cut mark.
+  # * +cut_locations+: The cut locations in enzyme index notation.
+  # *Returns*:: Bio::RestrictionEnzyme::DoubleStranded
+  #--
+  # Factory for DoubleStranded
+  #++
+  def self.new(users_enzyme_or_rebase_or_pattern, *cut_locations)
+    DoubleStranded.new(users_enzyme_or_rebase_or_pattern, *cut_locations)
+  end
+
+  # REBASE enzyme data information
+  #
+  # Returns a Bio::REBASE object loaded with all of the enzyme data on file.
+  #
+  # ---
+  # *Arguments*
+  # * _none_
+  # *Returns*:: Bio::REBASE
+  def self.rebase
+    enzymes_yaml_file = File.join(File.dirname(File.expand_path(__FILE__)), '..', 'data', 'enzymes.yaml')
+    @@rebase_enzymes ||= Bio::REBASE.load_yaml(enzymes_yaml_file)
+    @@rebase_enzymes
+  end
+
+  # Check if supplied name is the name of an available enzyme
+  #
+  # See Bio::REBASE.enzyme_name?
+  #
+  # ---
+  # *Arguments*
+  # * +name+: Enzyme name
+  # *Returns*:: +true+ _or_ +false+
+  def self.enzyme_name?( name )
+    self.rebase.enzyme_name?(name)
+  end
+
+  # See Bio::RestrictionEnzyme::Analysis.cut
+  def self.cut( sequence, enzymes )
+    Bio::RestrictionEnzyme::Analysis.cut( sequence, enzymes )
+  end
+
+  # A Bio::RestrictionEnzyme::Fragment is a DNA fragment composed of fused primary and
+  # complementary strands that would be found floating in solution after a full
+  # sequence is digested by one or more RestrictionEnzymes.
+  #
+  # You will notice that either the primary or complement strand will be
+  # padded with spaces to make them line up according to the original DNA
+  # configuration before they were cut.
+  #
+  # Example:
+  #
+  # Fragment 1:
+  #   primary =    "attaca"
+  #   complement = "  atga"
+  #
+  # Fragment 2:
+  #   primary =    "g  "
+  #   complement = "cta"
+  #
+  # View these with the +primary+ and +complement+ methods.
+  #
+  # Bio::RestrictionEnzyme::Fragment is a simple +Struct+ object.
+  #
+  # Note: unrelated to Bio::RestrictionEnzyme::Range::SequenceRange::Fragment
+  Fragment = Struct.new(:primary, :complement, :p_left, :p_right, :c_left, :c_right)
+
+  # Bio::RestrictionEnzyme::Fragments inherits from +Array+.
+  #
+  # Bio::RestrictionEnzyme::Fragments is a container for Fragment objects.  It adds the
+  # methods +primary+ and +complement+ which returns an +Array+ of all
+  # respective strands from it's Fragment members in alphabetically sorted
+  # order.  Note that it will
+  # not return duplicate items and does not return the spacing/padding
+  # that you would
+  # find by accessing the members directly.
+  #
+  # Example:
+  #
+  #   primary = ['attaca', 'g']
+  #   complement = ['atga', 'cta']
+  #
+  # Note: unrelated to Bio::RestrictionEnzyme::Range::SequenceRange::Fragments
+  class Fragments < Array
+    def primary; strip_and_sort(:primary); end
+    def complement; strip_and_sort(:complement); end
+
+    protected
+
+    def strip_and_sort( sym_strand )
+      self.map {|uf| uf.send( sym_strand ).tr(' ', '') }.sort
+    end
+  end
+end # RestrictionEnzyme
+end # Bio