gene_ontology 0.0.1

data/.document

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

data/LICENSE

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+Copyright (c) 2011 Brigham Young University
+Authored by John T. Prince
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

data/README.rdoc

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+= gene_ontology
+
+Parses gene ontology .obo files, links terms through is_a and provides methods
+to find levels and traverse the tree.
+
+== Examples
+
+    go = GeneOntology.new.from_file("gene_ontology.obo")
+    go.header # => a GeneOntology::Header object
+    go.id_to_term # => a hash from GO id to the GeneOntology::Term
+    some_term = go.id_to_term.values.first
+
+    # traverse the tree upwards, beginning with the current Term
+    some_term.each do |term|
+      term.name =~ /Plasma Membrane/i
+    end
+    some_term.level  # => how many levels down from the top 3
+                     # molecular_function, biol comp. etc are level 0
+
+== Copyright
+
+See LICENSE
+

data/Rakefile

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+require 'rubygems'
+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 = "gene_ontology"
+  gem.homepage = "http://github.com/princelab/gene_ontology"
+  gem.license = "MIT"
+  gem.summary = %Q{parses gene ontology (GO) .obo files and provides tree traversal methods}
+  gem.description = %{Parses gene ontology (GO) .obo files, links terms through is_a and provides methods
+to find levels and traverse the tree.}
+  gem.email = "jtprince@gmail.com"
+  gem.authors = ["John T. Prince"]
+  gem.add_development_dependency "spec-more", ">= 0"
+  gem.add_development_dependency "bundler", "~> 1.0.0"
+  gem.add_development_dependency "jeweler", "~> 1.5.2"
+  gem.add_development_dependency "rcov", ">= 0"
+end
+Jeweler::RubygemsDotOrgTasks.new
+
+require 'rake/testtask'
+Rake::TestTask.new(:spec) do |spec|
+  spec.libs << 'lib' << 'spec'
+  spec.pattern = 'spec/**/*_spec.rb'
+  spec.verbose = true
+end
+
+require 'rcov/rcovtask'
+Rcov::RcovTask.new do |spec|
+  spec.libs << 'spec'
+  spec.pattern = 'spec/**/*_spec.rb'
+  spec.verbose = true
+end
+
+task :default => :spec
+
+require 'rake/rdoctask'
+Rake::RDocTask.new do |rdoc|
+  version = File.exist?('VERSION') ? File.read('VERSION') : ""
+
+  rdoc.rdoc_dir = 'rdoc'
+  rdoc.title = "gene_ontology #{version}"
+  rdoc.rdoc_files.include('README*')
+  rdoc.rdoc_files.include('lib/**/*.rb')
+end

data/VERSION

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+0.0.1

data/lib/gene_ontology.rb

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+
+# typical usage: 
+#     
+#     terms = GeneOntology.new.from_file(filename)
+class GeneOntology
+
+  attr_accessor :header
+  attr_accessor :id_to_term
+
+  # returns self
+  def from_file(filename)
+    File.open(filename) do |io|
+      @header = parse_header(io)
+      @id_to_term = parse_terms(io)
+    end
+    self
+  end
+
+  # returns a header object
+  def parse_header(io)
+    header = Header.new
+    while md=io.gets.match(/^([\w\-]+): (.*)/)
+      key, val = md[1].to_sym, md[2]
+      if key == :subsetdef
+        header.subsetdefs.push(val)
+      elsif !header.respond_to?(key)
+        header.other[key] = val
+      else
+        header[key] = val
+      end
+    end
+    header
+  end
+
+  # turns is_a links from strings to actual GeneOntology objects
+  # returns id_to_term
+  def self.link!(terms)
+    id_to_term = {} 
+    terms.each {|term| id_to_term[term.id] = term }
+    terms.each do |term|
+      term.is_a.map! {|id| id_to_term[id] }
+    end
+    id_to_term
+  end
+
+  # returns id_to_term
+  # is_a points to an array of actual objects
+  def parse_terms(io, opts={})
+    opts = {:link => true}.merge(opts)
+    terms = []
+    in_term = false
+    while line = io.gets
+      if (md=line.match(/^(\w+): (.+)/)) && (in_term)
+        key, val = md[1].to_sym, md[2].split(' ! ').first
+        if Term::PLURAL.include?(key)
+          terms.last.send(key) << val
+        else
+          terms.last.send("#{key}=", val)
+        end
+      elsif line !~ /\w/
+        in_term = false
+      elsif line =~ /\[Term\]/
+        terms << Term.new
+        in_term = true
+      end
+    end
+    id_to_term = self.class.link!(terms)
+    id_to_term.values.each {|term| term.find_level }
+    id_to_term
+  end
+
+  # synonym, xref, consider and is_a are arrays.  level is how far down the
+  # heirarchy the term is.  0 is the top level (molecular function, biological
+  # process...)
+  class Term
+    include Enumerable
+    attr_accessor *%w(id level alt_id intersection_of replaced_by created_by creation_date disjoint_from relationship name namespace def subset comment is_obsolete synonym xref consider is_a).map(&:to_sym)
+
+    PLURAL = [:synonym, :xref, :consider, :is_a]
+    def initialize
+      PLURAL.each {|k| self.send("#{k}=", []) }
+      self
+    end
+
+    def inspect
+      "<[#{level}]#{@id}: #{@name} is_a.size=#{@is_a.size}>"
+    end
+
+    # starting with that term, traverses upwards in the tree
+    def each(&block)
+      block.call(self)
+      is_a.each do |term| 
+        term.each(&block)
+      end
+    end
+
+    # returns a unique array of go terms at that level
+    def trace_to_level(n=1)
+      if self.level == n
+        [self]
+      elsif n > self.level
+        []
+      else
+        self.is_a.map {|anc| anc.trace_to_level(n) }.flatten.uniq
+      end
+    end
+
+    # returns the number of levels below the top (top 3 categories [mf, bp,
+    # cc] are at level 0)
+    def find_level
+      if @level ; @level
+      else
+        @level = 
+          if @is_a.size == 0 ; 0
+          else
+            @is_a.map {|term| term.find_level }.min + 1
+          end
+      end
+    end
+  end
+
+  # subsetdefs is an array, other is a hash for any key/value pairs not
+  # already defined here
+  Header = Struct.new( *%w(format-version date saved-by auto-generated-by synonymtypedef systematic_synonym default-namespace remark ontology subsetdefs other).map(&:to_sym) )
+  class Header
+    def initialize(*args)
+      super(*args)
+      self.subsetdefs = []
+      self.other = {}
+      self
+    end
+  end
+end
+

data/spec/gene_ontology_spec.rb

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+require 'spec_helper'
+
+describe "GeneOntology" do
+  it "fails" do
+    should.flunk "hey buddy, you should probably rename this file and start specing for real"
+  end
+end

data/spec/spec_helper.rb

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+require 'rubygems'
+require 'bacon'
+
+$LOAD_PATH.unshift(File.dirname(__FILE__))
+$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
+require 'gene_ontology'
+
+Bacon.summary_on_exit

metadata

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+--- !ruby/object:Gem::Specification 
+name: gene_ontology
+version: !ruby/object:Gem::Version 
+  prerelease: 
+  version: 0.0.1
+platform: ruby
+authors: 
+- John T. Prince
+autorequire: 
+bindir: bin
+cert_chain: []
+
+date: 2011-05-24 00:00:00 -06:00
+default_executable: 
+dependencies: 
+- !ruby/object:Gem::Dependency 
+  name: spec-more
+  prerelease: false
+  requirement: &id001 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: "0"
+  type: :development
+  version_requirements: *id001
+- !ruby/object:Gem::Dependency 
+  name: bundler
+  prerelease: false
+  requirement: &id002 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ~>
+      - !ruby/object:Gem::Version 
+        version: 1.0.0
+  type: :development
+  version_requirements: *id002
+- !ruby/object:Gem::Dependency 
+  name: jeweler
+  prerelease: false
+  requirement: &id003 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ~>
+      - !ruby/object:Gem::Version 
+        version: 1.5.2
+  type: :development
+  version_requirements: *id003
+- !ruby/object:Gem::Dependency 
+  name: rcov
+  prerelease: false
+  requirement: &id004 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: "0"
+  type: :development
+  version_requirements: *id004
+description: |-
+  Parses gene ontology (GO) .obo files, links terms through is_a and provides methods
+  to find levels and traverse the tree.
+email: jtprince@gmail.com
+executables: []
+
+extensions: []
+
+extra_rdoc_files: 
+- LICENSE
+- README.rdoc
+files: 
+- .document
+- LICENSE
+- README.rdoc
+- Rakefile
+- VERSION
+- lib/gene_ontology.rb
+- spec/gene_ontology_spec.rb
+- spec/spec_helper.rb
+has_rdoc: true
+homepage: http://github.com/princelab/gene_ontology
+licenses: 
+- MIT
+post_install_message: 
+rdoc_options: []
+
+require_paths: 
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement 
+  none: false
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      version: "0"
+required_rubygems_version: !ruby/object:Gem::Requirement 
+  none: false
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      version: "0"
+requirements: []
+
+rubyforge_project: 
+rubygems_version: 1.6.2
+signing_key: 
+specification_version: 3
+summary: parses gene ontology (GO) .obo files and provides tree traversal methods
+test_files: 
+- spec/gene_ontology_spec.rb
+- spec/spec_helper.rb