goruby 0.0.1

data/.gitignore

@@ -0,0 +1,21 @@
+## MAC OS
+.DS_Store
+
+## TEXTMATE
+*.tmproj
+tmtags
+
+## EMACS
+*~
+\#*
+.\#*
+
+## VIM
+*.swp
+
+## PROJECT::GENERAL
+coverage
+rdoc
+pkg
+
+## PROJECT::SPECIFIC

data/LICENSE

@@ -0,0 +1,676 @@
+Copyright (c) 2009 Ben J Woodcroft
+
+                    GNU GENERAL PUBLIC LICENSE
+                       Version 3, 29 June 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
+ Everyone is permitted to copy and distribute verbatim copies
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+OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO,
+THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+PURPOSE.  THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM
+IS WITH YOU.  SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF
+ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
+
+  16. Limitation of Liability.
+
+  IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
+WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS
+THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
+GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE
+USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF
+DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
+PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
+EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
+SUCH DAMAGES.
+
+  17. Interpretation of Sections 15 and 16.
+
+  If the disclaimer of warranty and limitation of liability provided
+above cannot be given local legal effect according to their terms,
+reviewing courts shall apply local law that most closely approximates
+an absolute waiver of all civil liability in connection with the
+Program, unless a warranty or assumption of liability accompanies a
+copy of the Program in return for a fee.
+
+                     END OF TERMS AND CONDITIONS
+
+            How to Apply These Terms to Your New Programs
+
+  If you develop a new program, and you want it to be of the greatest
+possible use to the public, the best way to achieve this is to make it
+free software which everyone can redistribute and change under these terms.
+
+  To do so, attach the following notices to the program.  It is safest
+to attach them to the start of each source file to most effectively
+state the exclusion of warranty; and each file should have at least
+the "copyright" line and a pointer to where the full notice is found.
+
+    <one line to give the program's name and a brief idea of what it does.>
+    Copyright (C) <year>  <name of author>
+
+    This program is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+
+    This program is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+Also add information on how to contact you by electronic and paper mail.
+
+  If the program does terminal interaction, make it output a short
+notice like this when it starts in an interactive mode:
+
+    <program>  Copyright (C) <year>  <name of author>
+    This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
+    This is free software, and you are welcome to redistribute it
+    under certain conditions; type `show c' for details.
+
+The hypothetical commands `show w' and `show c' should show the appropriate
+parts of the General Public License.  Of course, your program's commands
+might be different; for a GUI interface, you would use an "about box".
+
+  You should also get your employer (if you work as a programmer) or school,
+if any, to sign a "copyright disclaimer" for the program, if necessary.
+For more information on this, and how to apply and follow the GNU GPL, see
+<http://www.gnu.org/licenses/>.
+
+  The GNU General Public License does not permit incorporating your program
+into proprietary programs.  If your program is a subroutine library, you
+may consider it more useful to permit linking proprietary applications with
+the library.  If this is what you want to do, use the GNU Lesser General
+Public License instead of this License.  But first, please read
+<http://www.gnu.org/philosophy/why-not-lgpl.html>.

data/README.rdoc

@@ -0,0 +1,17 @@
+= goruby
+
+Description goes here.
+
+== Note on Patches/Pull Requests
+ 
+* Fork the project.
+* Make your feature addition or bug fix.
+* Add tests for it. This is important so I don't break it in a
+  future version unintentionally.
+* Commit, do not mess with rakefile, version, or history.
+  (if you want to have your own version, that is fine but bump version in a commit by itself I can ignore when I pull)
+* Send me a pull request. Bonus points for topic branches.
+
+== Copyright
+
+Copyright (c) 2010 Ben J Woodcroft. See LICENSE for details.

data/Rakefile

@@ -0,0 +1,57 @@
+require 'rubygems'
+require 'rake'
+
+begin
+  require 'jeweler'
+  Jeweler::Tasks.new do |gem|
+    gem.name = "goruby"
+    gem.summary = "Gene Ontology (GO) interface for Ruby"
+    gem.description = "GoRuby makes it easy to interact with the Gene Ontology by using the infrastructure setup in R. By connecting to R using RSRuby, the database and methods can be interrogated. Plus, keeping the R library up to date is much simpler than having to keep a GO implementation up to date."
+    gem.email = "donttrustben near gmail.com"
+    gem.homepage = "http://github.com/wwood/goruby"
+    gem.authors = ["Ben J Woodcroft"]
+    gem.add_development_dependency "thoughtbot-shoulda", ">= 0"
+    # gem is a Gem::Specification... see http://www.rubygems.org/read/chapter/20 for additional settings
+    
+    gem.add_dependency('array_pair')
+    gem.add_dependency('rsruby')
+    gem.add_dependency('bio')
+  end
+  Jeweler::GemcutterTasks.new
+rescue LoadError
+  puts "Jeweler (or a dependency) not available. Install it with: gem install jeweler"
+end
+
+require 'rake/testtask'
+Rake::TestTask.new(:test) do |test|
+  test.libs << 'lib' << 'test'
+  test.pattern = 'test/**/test_*.rb'
+  test.verbose = true
+end
+
+begin
+  require 'rcov/rcovtask'
+  Rcov::RcovTask.new do |test|
+    test.libs << 'test'
+    test.pattern = 'test/**/test_*.rb'
+    test.verbose = true
+  end
+rescue LoadError
+  task :rcov do
+    abort "RCov is not available. In order to run rcov, you must: sudo gem install spicycode-rcov"
+  end
+end
+
+task :test => :check_dependencies
+
+task :default => :test
+
+require 'rake/rdoctask'
+Rake::RDocTask.new do |rdoc|
+  version = File.exist?('VERSION') ? File.read('VERSION') : ""
+
+  rdoc.rdoc_dir = 'rdoc'
+  rdoc.title = "goruby #{version}"
+  rdoc.rdoc_files.include('README*')
+  rdoc.rdoc_files.include('lib/**/*.rb')
+end

data/VERSION

@@ -0,0 +1 @@
+0.0.1

data/lib/go.rb

@@ -0,0 +1,165 @@
+require 'rsruby'
+require 'bio'
+require 'array_pair'
+
+module Bio
+  class Go
+    def initialize
+      @r = RSRuby.instance
+      @r.library('GO.db')
+      #      @r.print('initing') #debug to test if this is being loaded twice
+    end
+    
+    # Return an array of GO identifiers that are the offspring (all the descendents)
+    # of the given GO term from any ontology (cellular component, biological process
+    # or molecular function)
+    def go_offspring(go_id)
+      o = ontology_abbreviation(go_id)
+      case o
+      when 'MF'
+        return molecular_function_offspring(go_id)
+      when 'CC'
+        return cellular_component_offspring(go_id)
+      when 'BP'
+        return biological_process_offspring(go_id)
+      else
+        raise Exception, "Unknown ontology abbreviation found: #{o} for go id: #{go_id}"
+      end
+    end
+    
+    # Return an array of GO identifiers that are the offspring (all the descendents)
+    # of the given GO term given that it is a cellular component
+    # GO term. 
+    def cellular_component_offspring(go_term)
+      go_get(go_term, 'GOCCOFFSPRING')
+    end
+
+    # Return an array of GO identifiers that are the offspring (all the descendents)
+    # of the given GO term given that it is a molecular function
+    # GO term.     
+    def molecular_function_offspring(go_term)
+      go_get(go_term, 'GOMFOFFSPRING')
+    end
+    
+    # Return an array of GO identifiers that are the offspring (all the descendents)
+    # of the given GO term given that it is a biological process
+    # GO term. 
+    def biological_process_offspring(go_term)
+      go_get(go_term, 'GOBPOFFSPRING')
+    end
+    
+    # Generic method for retrieving
+    # e.g offspring('GO:0042717', 'GOCCCHILDREN')
+    def go_get(go_term, partition)
+      answers = @r.eval_R("get('#{go_term}', #{partition})")
+      return [] if answers.kind_of?(Bignum) # returns this for some reason when there's no children
+      return answers
+    end
+    
+    # Given a GO ID such as GO:0048253, return the GO term that is the 
+    # primary ID (GO:0050333), so that offspring functions can be used properly.
+    def primary_go_id(go_id_or_synonym_id)
+      # > get('GO:0048253', GOSYNONYM)
+      #GOID: GO:0050333
+      #Term: thiamin-triphosphatase activity
+      #Ontology: MF
+      #Definition: Catalysis of the reaction: thiamin triphosphate + H2O =
+      #    thiamin diphosphate + phosphate.
+      #Synonym: thiamine-triphosphatase activity
+      #Synonym: thiamine-triphosphate phosphohydrolase activity
+      #Synonym: ThTPase activity
+      #Synonym: GO:0048253
+      #Secondary: GO:0048253
+    
+      begin
+        # try to find the synonym
+        return @r.eval_R("GOID(get('#{go_id_or_synonym_id}', GOSYNONYM))")
+      rescue RException
+        # if no synonym is found, try to find the primary ID. raise RException if none is found
+        return @r.eval_R("GOID(get('#{go_id_or_synonym_id}', GOTERM))")
+      end
+    end
+    
+    # Retrieve the string description of the given go identifier
+    def term(go_id)
+      @r.eval_R("Term(get('#{go_id}', GOTERM))")
+    end
+    
+    # Retrieve the GO annotations associated with a PDB id,
+    # using Bio::Fetch PDB and UniprotKB at EBI
+    def cc_pdb_to_go(pdb_id)
+      # retrieve the pdb file from EBI, to extract the UniprotKB Identifiers
+      pdb = Bio::Fetch.new('http://www.ebi.ac.uk/cgi-bin/dbfetch').fetch('pdb', pdb_id)
+      
+      # parse the PDB and return the uniprot accessions (there may be >1 because of chains)
+      uniprots = Bio::PDB.new(pdb).dbref.select{|s| s.database=='UNP'}.collect{|s| s.dbAccession}
+      
+      gos = []
+      uniprots.uniq.each do |uniprot|
+        u = Bio::Fetch.new('http://www.ebi.ac.uk/cgi-bin/dbfetch').fetch('uniprot', uniprot)
+        
+        unp = Bio::SPTR.new(u)
+        
+        gos.push unp.dr('GO').select{|a|
+          a['Version'].match(/^C\:/)
+        }.collect{ |g|
+          g['Accession']
+        }
+      end
+      
+      return gos.flatten.uniq
+    end
+  
+    # Does the subsumer subsume the subsumee? i.e. Does it include
+    # the subsumee as one of its children in the GO tree?
+    # 
+    # For repetitively testing one GO term subsumes others, it might
+    # be faster to use subsume_tester
+    def subsume?(subsumer_go_id, subsumee_go_id)
+      # map the subsumee to non-synonomic id
+      primaree = self.primary_go_id(subsumee_go_id)
+      primarer = self.primary_go_id(subsumer_go_id)
+    
+      # return if they are the same - the obvious case
+      return true if primaree == primarer
+    
+      # return if subsumee is a descendent of sumsumer
+      return go_offspring(primarer).include?(primaree)
+    end
+    
+    # Return a subsume tester for a given GO term. This method is faster
+    # than repeatedly calling subsume? because the list of children is cached
+    def subsume_tester(subsumer_go_id, check_for_synonym=true)
+      Go::SubsumeTester.new(self, subsumer_go_id, check_for_synonym)
+    end
+  
+    # Return 'MF', 'CC' or 'BP' corresponding to the
+    def ontology_abbreviation(go_id)
+      @r.eval_R("Ontology(get('#{go_id}', GOTERM))")
+    end
+
+    class SubsumeTester
+      attr_reader :subsumer_offspring, :master_go_id
+    
+      def initialize(go_object, subsumer_go_id, check_for_synonym=true)
+        @go = go_object
+      
+        if check_for_synonym
+          @master_go_id = @go.primary_go_id(subsumer_go_id)
+        else
+          @master_go_id = subsumer_go_id
+        end
+        @subsumer_offspring = @go.go_offspring(@master_go_id)
+        @subsumer_offspring_hash = [@subsumer_offspring].flatten.to_hash
+      end
+    
+      def subsume?(subsumer_go_id, check_for_synonym=true)
+        primaree = check_for_synonym ?
+          @go.primary_go_id(subsumer_go_id) :
+          subsumer_go_id
+        return true if @master_go_id == primaree
+        @subsumer_offspring_hash.has_key?(primaree)
+      end
+    end
+  end
+end

data/test/helper.rb

@@ -0,0 +1,10 @@
+require 'rubygems'
+require 'test/unit'
+require 'shoulda'
+
+$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
+$LOAD_PATH.unshift(File.dirname(__FILE__))
+require 'goruby'
+
+class Test::Unit::TestCase
+end

data/test/test_goruby.rb

@@ -0,0 +1,108 @@
+$:.unshift File.join(File.dirname(__FILE__),'..','lib')
+
+require 'rubygems'
+require 'test/unit'
+require 'go'
+
+class GoTest < Test::Unit::TestCase
+  def setup
+    @go = Bio::Go.new
+  end
+  
+  def test_cellular_component_offspring
+    # test no offspring
+    # GO:0031676 does not (as of test writing) have any offspring
+    assert_equal [], @go.cellular_component_offspring('GO:0031676')
+    
+    # test multiple offspring
+    assert_equal ["GO:0030075","GO:0030077","GO:0030078","GO:0030079","GO:0030080",
+      "GO:0030081","GO:0030082","GO:0030089","GO:0030094","GO:0030096",
+      "GO:0031633","GO:0031676","GO:0031979","GO:0042717","GO:0048493",
+      "GO:0048494"
+    ],
+      @go.cellular_component_offspring('GO:0042716')
+    
+    # test not in CC
+    assert_raise RException do
+      @go.cellular_component_offspring('GO:0042716not')
+    end
+  end
+  
+  # operations below are expensive because they require
+  # multiple downloads from internet, so are commented
+  # out by default
+  #  def test_cc_pdb_to_go_some
+  #    assert_equal ['GO:0005743'],
+  #      @go.cc_pdb_to_go('2a06')
+  #  end
+  
+  def test_go_term
+    # test MF
+    assert_equal "G-protein coupled receptor activity", @go.term('GO:0004930')
+   
+    # test CC
+    assert_equal 'endoplasmic reticulum', @go.term('GO:0005783')
+  end
+  
+  def test_synonym
+    # test real synonym
+    assert_equal 'GO:0050333', @go.primary_go_id('GO:0048253')
+    
+    # test primary id
+    assert_equal 'GO:0050333', @go.primary_go_id('GO:0050333')
+    
+    # test bad id
+    assert_raise RException do
+      @go.primary_go_id('GO:AWAY')
+    end
+  end
+  
+  def test_subsume
+    # test normal truth
+    assert @go.subsume?('GO:0003824', 'GO:0050333')
+      
+    # test subsumee is synonym
+    assert @go.subsume?('GO:0003824', 'GO:0048253')
+      
+    # test equal terms
+    assert @go.subsume?('GO:0009536','GO:0009536')
+      
+    # test falsity - plastid part does not subsume plastid
+    assert_equal false, @go.subsume?('GO:0044435','GO:0009536')
+  end
+  
+  def test_subsume_tester
+    tester = @go.subsume_tester('GO:0003824')
+    assert_kind_of Bio::Go::SubsumeTester, tester
+    assert tester.subsume?('GO:0050333')
+    
+    tester = @go.subsume_tester('GO:0044435')
+    assert_equal false, tester.subsume?('GO:0009536')
+    
+    #equality
+    tester = @go.subsume_tester('GO:0044435')
+    assert tester.subsume?('GO:0044435')
+  end
+
+  def test_subsume_tester_no_check_synonym
+    # test normal truth
+    tester = @go.subsume_tester('GO:0003824')
+    assert_equal true, tester.subsume?('GO:0050333', false)
+    assert_equal true, tester.subsume?('GO:0050333', true)
+
+    # test subsumee is synonym
+    tester = @go.subsume_tester('GO:0003824')
+    assert_equal false, tester.subsume?('GO:0048253', false)
+    assert_equal true, tester.subsume?('GO:0048253', true)
+
+    # test equal terms
+    tester = @go.subsume_tester('GO:0050333')
+    assert_equal true, tester.subsume?('GO:0050333', false)
+    assert_equal true, tester.subsume?('GO:0050333', true)
+
+    # test equal that is synonym
+    tester = @go.subsume_tester('GO:0050333')
+    assert_equal false, tester.subsume?('GO:0048253', false)
+    assert_equal true, tester.subsume?('GO:0048253', true)
+  end
+end

metadata

@@ -0,0 +1,103 @@
+--- !ruby/object:Gem::Specification 
+name: goruby
+version: !ruby/object:Gem::Version 
+  version: 0.0.1
+platform: ruby
+authors: 
+- Ben J Woodcroft
+autorequire: 
+bindir: bin
+cert_chain: []
+
+date: 2010-02-11 00:00:00 +11:00
+default_executable: 
+dependencies: 
+- !ruby/object:Gem::Dependency 
+  name: thoughtbot-shoulda
+  type: :development
+  version_requirement: 
+  version_requirements: !ruby/object:Gem::Requirement 
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: "0"
+    version: 
+- !ruby/object:Gem::Dependency 
+  name: array_pair
+  type: :runtime
+  version_requirement: 
+  version_requirements: !ruby/object:Gem::Requirement 
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: "0"
+    version: 
+- !ruby/object:Gem::Dependency 
+  name: rsruby
+  type: :runtime
+  version_requirement: 
+  version_requirements: !ruby/object:Gem::Requirement 
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: "0"
+    version: 
+- !ruby/object:Gem::Dependency 
+  name: bio
+  type: :runtime
+  version_requirement: 
+  version_requirements: !ruby/object:Gem::Requirement 
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: "0"
+    version: 
+description: GoRuby makes it easy to interact with the Gene Ontology by using the infrastructure setup in R. By connecting to R using RSRuby, the database and methods can be interrogated. Plus, keeping the R library up to date is much simpler than having to keep a GO implementation up to date.
+email: donttrustben near gmail.com
+executables: []
+
+extensions: []
+
+extra_rdoc_files: 
+- LICENSE
+- README.rdoc
+files: 
+- .gitignore
+- LICENSE
+- README.rdoc
+- Rakefile
+- VERSION
+- lib/go.rb
+- test/helper.rb
+- test/test_goruby.rb
+has_rdoc: true
+homepage: http://github.com/wwood/goruby
+licenses: []
+
+post_install_message: 
+rdoc_options: 
+- --charset=UTF-8
+require_paths: 
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement 
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      version: "0"
+  version: 
+required_rubygems_version: !ruby/object:Gem::Requirement 
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      version: "0"
+  version: 
+requirements: []
+
+rubyforge_project: 
+rubygems_version: 1.3.5
+signing_key: 
+specification_version: 3
+summary: Gene Ontology (GO) interface for Ruby
+test_files: 
+- test/test_goruby.rb
+- test/helper.rb