gene_ontology 0.0.1 → 0.1.1

checksums.yaml

@@ -0,0 +1,7 @@
+---
+SHA1:
+  metadata.gz: '03399bf5f91610a8fa66a1c410cf7366da691aad'
+  data.tar.gz: 561304a916e6839afba04eebba5cd02f27d5fa86
+SHA512:
+  metadata.gz: ae6e94c568240a3550ff0779488d82e178d8e26711b0db1959f284bb774b786e7750f291de1faa34b41704faf1e93f5c38dbaa81ca9fd4db7d788636a48f1662
+  data.tar.gz: af7118dfb8b6921bfe24ed607e210b2c7e3b4c28b9611c600a92a7693572e9426c78578f9c52876a379b79cb676c3cf9ebd323755bed5c1c8d61a786e93aad23

data/.gitignore

@@ -0,0 +1,10 @@
+/.bundle/
+/.yardoc
+/_yardoc/
+/coverage/
+/doc/
+/pkg/
+/spec/reports/
+/tmp/
+
+go.obo

data/README.md

@@ -0,0 +1,55 @@
+# GeneOntology
+
+Parses gene ontology .obo files, links terms through `is_a` and provides
+methods to find levels and traverse the tree.
+
+## Installation
+
+Add this line to your application's Gemfile:
+
+```ruby
+gem 'gene_ontology'
+```
+
+And then execute:
+
+    $ bundle
+
+Or install it yourself as:
+
+    $ gem install gene_ontology
+
+## Usage
+
+```
+require 'gene_ontology'
+
+# download from http://purl.obolibrary.org/obo/go.obo
+go = GeneOntology.from_file("go.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
+```
+
+## Testing
+
+```
+rake test
+```
+
+Note: will download http://purl.obolibrary.org/obo/go.obo to a tempfile unless
+'go.obo' is already in package root.  Just for testing.
+
+## License
+
+[MIT License](https://opensource.org/licenses/MIT) -- see LICENSE for
+copyright info.

data/Rakefile

@@ -1,46 +1,10 @@
-require 'rubygems'
-require 'rake'
+require "bundler/gem_tasks"
+require "rake/testtask"
 
-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"
+Rake::TestTask.new(:test) do |t|
+  t.libs << "test"
+  t.libs << "lib"
+  t.test_files = FileList["test/**/*_test.rb"]
 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
+task :default => :test

data/gene_ontology.gemspec

@@ -0,0 +1,27 @@
+
+lib = File.expand_path("../lib", __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require "gene_ontology/version"
+
+Gem::Specification.new do |spec|
+  spec.name          = "gene_ontology"
+  spec.version       = GeneOntology::VERSION
+  spec.authors       = ["John T. Prince"]
+  spec.email         = ["jtprince@gmail.com"]
+
+  spec.summary       = %q{Parses gene ontology .obo files}
+  spec.description   = %q{Parses gene ontology .obo files, links terms through `is_a` and provides methods to find levels and traverse the tree.}
+  spec.homepage      = "https://github.com/princelab/gene_ontology"
+  spec.license       = "MIT"
+
+  spec.files         = `git ls-files -z`.split("\x0").reject do |f|
+    f.match(%r{^(test|spec|features)/})
+  end
+  spec.bindir        = "exe"
+  spec.executables   = spec.files.grep(%r{^exe/}) { |f| File.basename(f) }
+  spec.require_paths = ["lib"]
+
+  spec.add_development_dependency "bundler", "~> 1.16"
+  spec.add_development_dependency "rake", "~> 10.0"
+  spec.add_development_dependency "minitest", "~> 5.0"
+end

data/lib/gene_ontology.rb

@@ -1,12 +1,30 @@
+require 'gene_ontology/version'
 
-# typical usage: 
-#     
-#     terms = GeneOntology.new.from_file(filename)
 class GeneOntology
 
+  EXPECTED_HEADER_FIELDS = %i(
+    format-version
+    date
+    saved-by
+    auto-generated-by
+    synonymtypedef
+    systematic_synonym
+    default-namespace
+    remark
+    ontology
+    subsetdefs
+    other
+  )
+
   attr_accessor :header
   attr_accessor :id_to_term
 
+  class << self
+    def from_file(filename)
+      new.from_file(filename)
+    end
+  end
+
   # returns self
   def from_file(filename)
     File.open(filename) do |io|
@@ -35,7 +53,7 @@ class GeneOntology
   # turns is_a links from strings to actual GeneOntology objects
   # returns id_to_term
   def self.link!(terms)
-    id_to_term = {} 
+    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] }
@@ -74,12 +92,36 @@ class GeneOntology
   # 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)
+
+    FIELDS = %i(
+      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
+      property_value
+    )
+
+    attr_accessor(*FIELDS)
 
     PLURAL = [:synonym, :xref, :consider, :is_a]
     def initialize
       PLURAL.each {|k| self.send("#{k}=", []) }
-      self
+      @level = nil
     end
 
     def inspect
@@ -89,7 +131,7 @@ class GeneOntology
     # starting with that term, traverses upwards in the tree
     def each(&block)
       block.call(self)
-      is_a.each do |term| 
+      is_a.each do |term|
         term.each(&block)
       end
     end
@@ -108,9 +150,10 @@ class GeneOntology
     # returns the number of levels below the top (top 3 categories [mf, bp,
     # cc] are at level 0)
     def find_level
-      if @level ; @level
+      if @level
+        @level
       else
-        @level = 
+        @level =
           if @is_a.size == 0 ; 0
           else
             @is_a.map {|term| term.find_level }.min + 1
@@ -121,7 +164,7 @@ class GeneOntology
 
   # 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) )
+  Header = Struct.new(*EXPECTED_HEADER_FIELDS)
   class Header
     def initialize(*args)
       super(*args)

data/lib/gene_ontology/version.rb

@@ -0,0 +1,3 @@
+class GeneOntology
+  VERSION = "0.1.1"
+end

metadata

@@ -1,110 +1,95 @@
---- !ruby/object:Gem::Specification 
+--- !ruby/object:Gem::Specification
 name: gene_ontology
-version: !ruby/object:Gem::Version 
-  prerelease: 
-  version: 0.0.1
+version: !ruby/object:Gem::Version
+  version: 0.1.1
 platform: ruby
-authors: 
+authors:
 - John T. Prince
 autorequire: 
-bindir: bin
+bindir: exe
 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 
+date: 2017-12-04 00:00:00.000000000 Z
+dependencies:
+- !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
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.16'
   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
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.16'
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '10.0'
   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"
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '10.0'
+- !ruby/object:Gem::Dependency
+  name: minitest
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '5.0'
   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
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '5.0'
+description: Parses gene ontology .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
+extra_rdoc_files: []
+files:
+- ".document"
+- ".gitignore"
 - LICENSE
-- README.rdoc
+- README.md
 - Rakefile
-- VERSION
+- gene_ontology.gemspec
 - lib/gene_ontology.rb
-- spec/gene_ontology_spec.rb
-- spec/spec_helper.rb
-has_rdoc: true
-homepage: http://github.com/princelab/gene_ontology
-licenses: 
+- lib/gene_ontology/version.rb
+homepage: https://github.com/princelab/gene_ontology
+licenses:
 - MIT
+metadata: {}
 post_install_message: 
 rdoc_options: []
-
-require_paths: 
+require_paths:
 - lib
-required_ruby_version: !ruby/object:Gem::Requirement 
-  none: false
-  requirements: 
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
   - - ">="
-    - !ruby/object:Gem::Version 
-      version: "0"
-required_rubygems_version: !ruby/object:Gem::Requirement 
-  none: false
-  requirements: 
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
   - - ">="
-    - !ruby/object:Gem::Version 
-      version: "0"
+    - !ruby/object:Gem::Version
+      version: '0'
 requirements: []
-
 rubyforge_project: 
-rubygems_version: 1.6.2
+rubygems_version: 2.6.11
 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
+specification_version: 4
+summary: Parses gene ontology .obo files
+test_files: []

data/README.rdoc

@@ -1,23 +0,0 @@
-= 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/VERSION

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

data/spec/gene_ontology_spec.rb

@@ -1,7 +0,0 @@
-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

@@ -1,8 +0,0 @@
-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