obo_parser 0.4.0 → 0.4.1

checksums.yaml

@@ -1,7 +1,7 @@
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data/.gitignore

@@ -22,3 +22,6 @@ rdoc
 pkg
 
 ## PROJECT::SPECIFIC
+
+*.gem
+

data/.travis

@@ -0,0 +1,3 @@
+language: ruby
+rvm:
+  - 2.1.4

data/Gemfile.lock

@@ -1,14 +1,13 @@
 PATH
   remote: .
   specs:
-    obo_parser (0.4.0)
-      rake (~> 11.1.2)
+    obo_parser (0.4.1)
+      rake (~> 12.0)
 
 GEM
   remote: https://rubygems.org/
   specs:
-    awesome_print (1.7.0)
-    byebug (9.0.6)
+    awesome_print (1.8.0)
     coderay (1.1.1)
     diff-lcs (1.3)
     ffi (1.9.18)
@@ -31,7 +30,8 @@ GEM
       rb-fsevent (~> 0.9, >= 0.9.4)
       rb-inotify (~> 0.9, >= 0.9.7)
       ruby_dep (~> 1.2)
-    lumberjack (1.0.11)
+    logger (1.2.8)
+    lumberjack (1.0.12)
     method_source (0.8.2)
     nenv (0.3.0)
     notiffany (0.1.1)
@@ -41,38 +41,39 @@ GEM
       coderay (~> 1.1.0)
       method_source (~> 0.8.1)
       slop (~> 3.4)
-    rake (11.1.2)
-    rb-fsevent (0.9.8)
-    rb-inotify (0.9.8)
-      ffi (>= 0.5.0)
-    rspec (3.5.0)
-      rspec-core (~> 3.5.0)
-      rspec-expectations (~> 3.5.0)
-      rspec-mocks (~> 3.5.0)
-    rspec-core (3.5.4)
-      rspec-support (~> 3.5.0)
-    rspec-expectations (3.5.0)
+    rake (12.0.0)
+    rb-fsevent (0.10.2)
+    rb-inotify (0.9.10)
+      ffi (>= 0.5.0, < 2)
+    rspec (3.6.0)
+      rspec-core (~> 3.6.0)
+      rspec-expectations (~> 3.6.0)
+      rspec-mocks (~> 3.6.0)
+    rspec-core (3.6.0)
+      rspec-support (~> 3.6.0)
+    rspec-expectations (3.6.0)
       diff-lcs (>= 1.2.0, < 2.0)
-      rspec-support (~> 3.5.0)
-    rspec-mocks (3.5.0)
+      rspec-support (~> 3.6.0)
+    rspec-mocks (3.6.0)
       diff-lcs (>= 1.2.0, < 2.0)
-      rspec-support (~> 3.5.0)
-    rspec-support (3.5.0)
+      rspec-support (~> 3.6.0)
+    rspec-support (3.6.0)
     ruby_dep (1.5.0)
     shellany (0.0.1)
     slop (3.6.0)
-    thor (0.19.4)
+    thor (0.20.0)
 
 PLATFORMS
   ruby
 
 DEPENDENCIES
-  awesome_print (~> 1.6)
+  awesome_print (~> 1.8)
   bundler (~> 1.5)
-  byebug
-  guard-rspec
+  guard-rspec (~> 4.7.3)
+  logger (~> 1.2.8)
   obo_parser!
-  rspec (~> 3.4)
+  pry (~> 0.10.4)
+  rspec (~> 3.6)
 
 BUNDLED WITH
-   1.14.3
+   1.15.4

data/README.md

@@ -1,10 +1,13 @@
+[![Build Status](https://travis-ci.org/mjy/obo_parser.svg?branch=master)](https://travis-ci.org/mjy/obo_parser)
+[![Dependency Status](https://gemnasium.com/badges/github.com/mjy/obo_parser.svg)](https://gemnasium.com/github.com/mjy/obo_parser)
+
 # obo_parser
 
 A simple Ruby gem for parsing OBO 1.2 (?4) formatted ontology files.  Useful for reporting, comparing, and mapping data to other databases.  There is presently no functionality for logical inference across the ontology.
 
 ## Installation
 
-  gem install obo_parser
+    gem install obo_parser
 
 ## Use
 
@@ -12,8 +15,8 @@ A simple Ruby gem for parsing OBO 1.2 (?4) formatted ontology files.  Useful for
 
     require 'rubygems'
     require 'obo_parser'
-    foo = parse_obo_file(File.read('my_ontology.obo'))  # => An OboParser instance  
-    first_term = foo.terms.first                        # => An OboParser#Term instance 
+    o = parse_obo_file(File.read('my_ontology.obo'))  # => An OboParser instance  
+    first_term = o.terms.first                        # => An OboParser#Term instance 
    
     first_term.id.value                                 # => 'HAO:1234'
  
@@ -30,20 +33,20 @@ A simple Ruby gem for parsing OBO 1.2 (?4) formatted ontology files.  Useful for
     o = first_term.other_tags                           # => [OboParser#Tag, ... ] An array of tags that are not specially referenced in an OboParser::Stanza
     o.first                                             # => An OboParser#Tag instance    
 
-    first_typedef = foo.typdefs.first                   # => An OboParser#Typdef instance 
+    first_typedef = o.typdefs.first                   # => An OboParser#Typdef instance 
     first_typdef.id.value                               # => 'Some typedef id'
     first_typdef.name.value                             # => 'Some typedef name'
 
-    foo.terms.first.tags_named('synonym')               # => [OboParser#Tag, ... ]
-    foo.terms.first.tags_named('synonym').first.tag     # => 'synonym'
-    foo.terms.first.tags_named('synonym').first.value   # => 'Some label'
+    o.terms.first.tags_named('synonym')               # => [OboParser#Tag, ... ]
+    o.terms.first.tags_named('synonym').first.tag     # => 'synonym'
+    o.terms.first.tags_named('synonym').first.value   # => 'Some label'
 
-    foo.terms.first.relationships                       # => [['relationship', 'FOO:123'], ['other_relationship', 'FOO:456'] ...] An array of [relation, related term id], includes 'is_a', 'disjoint_from' and Typedefs
+    o.terms.first.relationships                       # => [['relationship', 'FOO:123'], ['other_relationship', 'FOO:456'] ...] An array of [relation, related term id], includes 'is_a', 'disjoint_from' and Typedefs
 
 ### Convenience methods  
     
-    foo.term_hash                                       # => { term (String) => id (String), ... for each [Term] in the file. } !! Assumes names terms are unique, they might not be, in which case you get key collisions. 
-    foo.id_hash                                         # => { id (String) => term (String), ... for each [Term] in the file. } 
+    o.term_hash                                       # => { term (String) => id (String), ... for each [Term] in the file. } !! Assumes names terms are unique, they might not be, in which case you get key collisions. 
+    o.id_hash                                         # => { id (String) => term (String), ... for each [Term] in the file. } 
 
 See also /test/test_obo_parser.rb
 
@@ -51,10 +54,18 @@ See also /test/test_obo_parser.rb
 
 A small set of methods (e.g. comparing OBO ontologies) utilizing the gem are included in /lib/utilities.rb.  For example: 1) shared labels across sets of ontologies can be found and returned, 2) ontologies can be dumped into a simple Cytoscape node/edge format; 3) given a set of correspondances between two ontologies various reports can be made. 
 
+### Viz
+   
+    OboParser::Utilities::Viz.mock_coordinate_space(o, size: 100) # => STDOUT tab delimited table with x, y, z, identifier, label 
+
 ## Documentation
 
 Code documentation is slowly being formalized using Yard.
 
+## Contributing
+
+Fork, test, code, test, pull request.
+
 ## Copyright
 
 Copyright (c) 2010-2017 Matt Yoder. See LICENSE for details.

data/Rakefile

@@ -1,9 +1,8 @@
-#!/usr/bin/env rake
-require "bundler/gem_tasks"
-
-require 'rspec/core/rake_task'
-
-RSpec::Core::RakeTask.new('spec')
-
-task :default => :rspec
+begin 
+  require 'rspec/core/rake_task'
+  require "bundler/gem_tasks"
+  RSpec::Core::RakeTask.new(:spec)
+  task :default => :spec
+rescue LoadError
+end
 

data/lib/obo_parser.rb

@@ -1,16 +1,16 @@
-# uses the PhyloTree parser/lexer engine by Krishna Dole which in turn was based on
+# Uses the PhyloTree parser/lexer engine by Krishna Dole which in turn was based on
 # Thomas Mailund's <mailund@birc.dk> 'newick-1.0.5' Python library
-
-#== Outstanding issues:
-# * Better documentation
-# * More tests
-
+#
+# A basic OBO file handling utility.
+#
 module OboParser
 
-  require File.expand_path(File.join(File.dirname(__FILE__), 'tokens'))
-  require File.expand_path(File.join(File.dirname(__FILE__), 'parser'))
-  require File.expand_path(File.join(File.dirname(__FILE__), 'lexer'))
-  require File.expand_path(File.join(File.dirname(__FILE__), 'utilities'))
+  require File.expand_path(File.join(File.dirname(__FILE__), 'obo_parser/tokens'))
+  require File.expand_path(File.join(File.dirname(__FILE__), 'obo_parser/parser'))
+  require File.expand_path(File.join(File.dirname(__FILE__), 'obo_parser/lexer'))
+  require File.expand_path(File.join(File.dirname(__FILE__), 'obo_parser/utilities'))
+  require File.expand_path(File.join(File.dirname(__FILE__), 'obo_parser/utilities/viz'))
+  require File.expand_path(File.join(File.dirname(__FILE__), 'obo_parser/utilities/helpers'))
 
   class OboParser 
     attr_accessor :terms, :typedefs
@@ -27,7 +27,9 @@ module OboParser
 
     # Warning! This assumes terms are unique, they are NOT required to be so in an OBO file.
     # Ignores hash colisions!!
-    def term_hash # :yields: Hash (String => String) (name => id)
+    # @return [Hash]
+    #  (String => String) (name => id)
+    def term_hash
       @terms.inject({}) {|sum, t| sum.update(t.name.value => t.id.value)}
     end
 

data/lib/{lexer.rb → obo_parser/lexer.rb}

@@ -4,15 +4,14 @@ class OboParser::Lexer
     @input = input
     @next_token = nil
   end
-  
+
   # checks whether the next token is of the specified class. 
   def peek(token_class)
     token = read_next_token(token_class)
     return token.class == token_class
   end
 
-  # return (and delete) the next token from the input stream, or raise an exception
-  # if the next token is not of the given class.
+  # return (and delete) the next token from the input stream, or raise an exception # if the next token is not of the given class.
   def pop(token_class)
     token = read_next_token(token_class)
     @next_token = nil
@@ -22,13 +21,13 @@ class OboParser::Lexer
       return token
     end
   end
-  
+
   private
-   # read (and store) the next token from the input, if it has not already been read.
-   def read_next_token(token_class)
-      if @next_token
-        return @next_token
-      else
+  # read (and store) the next token from the input, if it has not already been read.
+  def read_next_token(token_class)
+    if @next_token
+      return @next_token
+    else
       # check for a match on the specified class first
       if match(token_class)
         return @next_token
@@ -38,19 +37,19 @@ class OboParser::Lexer
           return @next_token if match(t)
         }
       end
-       # no match, either end of string or lex-error
-       if @input != ''
-           raise(OboParser::ParseError, "Lex Error, unknown token at #{@input[0..10]}...", caller)
-       else
+      # no match, either end of string or lex-error
+      if @input != ''
+        raise(OboParser::ParseError, "Lex Error, unknown token at #{@input[0..10]}...", caller)
+      else
         return nil
       end
     end
   end
-  
+
   def match(token_class)
     if (m = token_class.regexp.match(@input))
       @next_token = token_class.new(m[1])
-       @input = @input[m.end(0)..-1]
+      @input = @input[m.end(0)..-1]
       return true
     else
       return false

data/lib/{tokens.rb → obo_parser/tokens.rb}

@@ -66,11 +66,13 @@ module OboParser::Tokens
         qq = 0 # some failsafes
         while xref_list.length > 0
           qq += 1
-          debugger if qq == 499
-          raise "#{xref_list}" if qq > 500
+          raise "#{xref_list} is seemingly infinite" if qq > 500
           xref_list.gsub!(/\A\s*,\s*/, '')
 
-          xref_list =~ /\A(.+?:[^\"|\{|\,]+)/i 
+          xref_list =~ /\A(.+?:[^\"\{\,]+)/i 
+
+          # xref_list =~ /\A(.+?:[^\"|\{|\,]+)/i 
+
           v = $1
 
           if !(v == "") && !v.nil? 
@@ -79,7 +81,7 @@ module OboParser::Tokens
             xref_list.gsub!(/\A#{r}\s*/, '')
             @xrefs.push(v) if !v.nil?
           end
-         
+
           xref_list.strip!
 
           # A description
@@ -111,7 +113,7 @@ module OboParser::Tokens
       else
         @value = value.strip
       end
-      
+
       @value = @value[1..-2].strip if @value[0..0] == "\"" 
       @tag = tag.strip
       @value.strip!
@@ -137,7 +139,7 @@ module OboParser::Tokens
       @tag = 'relationship'
       @xrefs = [] 
       @relation, @related_term = str.split(/\s/,3)
-      
+
       str =~ /\s+!\s+(.*)\s*\n*/i
       @comment = $1
 
@@ -195,9 +197,22 @@ module OboParser::Tokens
     end
   end
 
+  # returns key => value hash for tokens like 'foo=bar' or foo = 'b a ar'
   # note we grab EOL and ; here 
   class ValuePair < Token
-    @regexp = Regexp.new(/\A\s*([\w\d\_\&]+\s*=\s*((\'[^\']+\')|(\(.*\))|(\"[^\"]+\")|([^\s\n\t;]+)))[\s\n\t;]+/i) #  returns key => value hash for tokens like 'foo=bar' or foo = 'b a ar'
+    @regexp = Regexp.new(
+      /\A\s*
+      ([\w\&]+\s*=\s*
+       (
+         (\'[^\']+\')|
+         (\(.*\))|
+         (\"[^\"]+\")|
+         ([^\s;]+)
+      )
+      )[\s;]+
+      /ix
+    ) 
+
     def initialize(str)
       str.strip!
       str = str.split(/=/)
@@ -221,35 +236,35 @@ module OboParser::Tokens
   #class LParen < Token
   #  @regexp = Regexp.new('\A\s*(\()\s*')
   #end
-  
+
   #class RBracket < Token
   #  @regexp = Regexp.new('\A\s*(\])\s*')
   #end
-  
+
   #class RParen < Token
   #  @regexp = Regexp.new('\A\s*(\))\s*')
   #end
-  
+
   #class Equals < Token
   #  @regexp = Regexp.new('\A\s*(=)\s*')
   #end
-  
+
   #class BckSlash < Token
   #  @regexp = Regexp.new('\A\s*(\/)\s*')
   #end
-  
+
   #class Colon < Token
   #  @regexp = Regexp.new('\A\s*(:)\s*')
   #end
-  
+
   #class SemiColon < Token
   #  @regexp = Regexp.new('\A\s*(;)\s*')
   #end
-  
+
   #class Comma < Token
   #  @regexp = Regexp.new('\A\s*(\,)\s*')
   #end
- 
+
   #class Number < Token
   #  @regexp = Regexp.new('\A\s*(-?\d+(\.\d+)?([eE][+-]?\d+)?)\s*')
   #  def initialize(str)

data/lib/{utilities.rb → obo_parser/utilities.rb}

@@ -1,6 +1,4 @@
-require 'rubygems'
-require 'byebug'
-require File.expand_path(File.join(File.dirname(__FILE__), 'obo_parser')) 
+require File.expand_path(File.join(File.dirname(__FILE__), '../obo_parser')) 
 
 module OboParser::Utilities
 

data/lib/obo_parser/utilities/helpers.rb

@@ -0,0 +1,23 @@
+module OboParser
+  module Utilities
+
+    # Methods to aid in visualization
+    module Helpers 
+
+      # @return [Array]
+      #   rows of data from ontology, just ID, name
+      def self.simple_data(ontology)
+        data = []
+
+        ontology.terms.each do |t|
+          row = []
+          row.push(t.id.value)
+          row.push(t.name.value)
+          data.push row
+        end
+        data 
+      end
+
+    end
+  end
+end

data/lib/obo_parser/utilities/viz.rb

@@ -0,0 +1,49 @@
+module OboParser
+  module Utilities
+
+    # Methods to aid in visualization
+    module Viz
+
+      # @params [ontology]
+      #   the result of a parse_obo_file
+      def self.mock_coordinate_space(ontology, size: 20, cutoff: nil)
+        data = ::OboParser::Utilities::Helpers.simple_data(ontology)
+
+        x,y,z = 1,1,1
+        center_distance = ( size / 2) 
+        edge_length = (size / 2) - (size * 0.2)
+        total_terms = ontology.terms.size
+        grid_length = Math.cbrt(total_terms).ceil.to_i
+        cutoff ||= size + 1
+
+        data.each_with_index do |row, i|
+          break if i > cutoff
+          print x * center_distance
+          print "\t"
+          print y * center_distance
+          print "\t"
+          print z * center_distance
+          print "\t"
+          print row[0]
+          print "\t"
+          print row[1]
+          print "\n"
+
+          x = x + 1
+          if (x % grid_length) == 0
+            x = 1
+            y = y + 1
+          end
+
+          if (y % grid_length) == 0
+            y = 1
+            x = 1
+            z = z + 1
+          end
+        end
+        true
+      end
+      
+    end
+  end
+end

data/lib/obo_parser/version.rb

@@ -1,3 +1,3 @@
 module OboParser 
-  VERSION = "0.4.0"
+  VERSION = "0.4.1"
 end

data/obo_parser.gemspec

@@ -5,7 +5,7 @@ require 'obo_parser/version'
 
 Gem::Specification.new do |spec|
   spec.name = 'obo_parser'
-  spec.version = OboParser::VERSION # "0.3.8"
+  spec.version = OboParser::VERSION 
 
   spec.authors = ["Matt Yoder"]
   spec.email = ["diapriid@gmail.com"]
@@ -17,12 +17,13 @@ Gem::Specification.new do |spec|
   spec.files = `git ls-files -z`.split("\x0")
   spec.require_paths = ["lib"]
 
-  spec.add_dependency 'rake', '~> 11.1.2'
-  spec.add_development_dependency 'rspec', '~> 3.4'
+  spec.add_dependency 'rake', '~> 12.0'
+  spec.add_development_dependency 'rspec', '~> 3.6'
   spec.add_development_dependency 'bundler', '~> 1.5'
-  spec.add_development_dependency 'guard-rspec'
-  spec.add_development_dependency 'byebug'
-  spec.add_development_dependency 'awesome_print', '~> 1.6'
+  spec.add_development_dependency 'guard-rspec', '~> 4.7.3'
+  spec.add_development_dependency 'pry', '~> 0.10.4'
+  spec.add_development_dependency 'awesome_print', '~> 1.8'
+  spec.add_development_dependency 'logger', '~> 1.2.8'
 
 end
 

data/spec/lib/obo_parser_spec.rb

@@ -242,7 +242,7 @@ describe OboParser do
 
   specify 'complex_file_parsing_3' do
     expect(of = File.read(File.expand_path(File.join(File.dirname(__FILE__), '../files/tgma.obo')) ) ).to be_truthy
-    expect(foo = parse_obo_file(of)).to be_truthy
+    expect(parse_obo_file(of)).to be_truthy
 
     # assert_equal 'anatomical entity', foo.terms.first.name.value
     # assert_equal 'ventral mesofurco-profurcal muscle', foo.terms[1].name.value
@@ -266,7 +266,7 @@ describe OboParser do
 
   specify 'file_completes_without_typedefs' do
     expect(of2 = File.read(File.expand_path(File.join(File.dirname(__FILE__), '../files/obo_1.0_test_wo_typedefs.txt')) )).to be_truthy
-    expect(foo = parse_obo_file(of2)).to be_truthy
+    expect(parse_obo_file(of2)).to be_truthy
   end
 
 end

data/spec/lib/utilities/viz_spec.rb

@@ -0,0 +1,13 @@
+require 'spec_helper'
+
+describe OboParser::Utilities::Viz do
+  let(:o) { parse_obo_file( 
+                           File.read(File.expand_path(File.join(File.dirname(__FILE__), '../../files/hao.obo')) )
+                          ) }
+
+  specify '#mock_coordinate_space' do
+    capture_stderr do 
+      expect(OboParser::Utilities::Viz.mock_coordinate_space(o, size: 50, cutoff: 10)).to be_truthy
+    end
+  end
+end

data/spec/spec_helper.rb

@@ -3,9 +3,10 @@ require 'bundler/setup'
 Bundler.setup
 
 require 'obo_parser'
-require 'byebug'
+require 'pry'
 require 'awesome_print'
 require 'fileutils'
+require "stringio"
 
 # FileUtils::mkdir_p 'tmp'
 
@@ -29,4 +30,13 @@ end
 #   return (value <= midpoint*(1.0 + percentage)) & (value >= midpoint*(1.0 - percentage))
 # end
 
+# https://stackoverflow.com/questions/4459330/how-do-i-temporarily-redirect-stderr-in-ruby
+def capture_stderr
+  previous_stdout, $stdout = $stdout, StringIO.new
+  yield
+  $stdout.string
+ensure
+  $stdout = previous_stdout
+end
+
 

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: obo_parser
 version: !ruby/object:Gem::Version
-  version: 0.4.0
+  version: 0.4.1
 platform: ruby
 authors:
 - Matt Yoder
@@ -16,28 +16,28 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 11.1.2
+        version: '12.0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 11.1.2
+        version: '12.0'
 - !ruby/object:Gem::Dependency
   name: rspec
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '3.4'
+        version: '3.6'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '3.4'
+        version: '3.6'
 - !ruby/object:Gem::Dependency
   name: bundler
   requirement: !ruby/object:Gem::Requirement
@@ -56,44 +56,58 @@ dependencies:
   name: guard-rspec
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '0'
+        version: 4.7.3
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '0'
+        version: 4.7.3
 - !ruby/object:Gem::Dependency
-  name: byebug
+  name: pry
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '0'
+        version: 0.10.4
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ">="
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '0'
+        version: 0.10.4
 - !ruby/object:Gem::Dependency
   name: awesome_print
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.6'
+        version: '1.8'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.8'
+- !ruby/object:Gem::Dependency
+  name: logger
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 1.2.8
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.6'
+        version: 1.2.8
 description: 'Provides all-in-one object containing the contents of an OBO formatted
   file.  OBO version 1.2 is targeted, though this should work for 1.0. '
 email:
@@ -104,21 +118,21 @@ extra_rdoc_files: []
 files:
 - ".document"
 - ".gitignore"
+- ".travis"
 - Gemfile
 - Gemfile.lock
 - Guardfile
 - LICENSE
 - README.md
 - Rakefile
-- VERSION
-- init.rb
-- install.rb
-- lib/lexer.rb
 - lib/obo_parser.rb
+- lib/obo_parser/lexer.rb
+- lib/obo_parser/parser.rb
+- lib/obo_parser/tokens.rb
+- lib/obo_parser/utilities.rb
+- lib/obo_parser/utilities/helpers.rb
+- lib/obo_parser/utilities/viz.rb
 - lib/obo_parser/version.rb
-- lib/parser.rb
-- lib/tokens.rb
-- lib/utilities.rb
 - obo_parser.gemspec
 - obo_parser/version.rb
 - spec/files/cell.obo
@@ -128,6 +142,7 @@ files:
 - spec/files/obo_1.0_test_wo_typedefs.txt
 - spec/files/tgma.obo
 - spec/lib/obo_parser_spec.rb
+- spec/lib/utilities/viz_spec.rb
 - spec/spec_helper.rb
 - tasks/obo_parser_tasks.rake
 - test/cell.obo
@@ -136,7 +151,6 @@ files:
 - test/obo_1.0_test.txt
 - test/obo_1.0_test_wo_typedefs.txt
 - test/tgma.obo
-- uninstall.rb
 homepage: http://github.com/mjy/obo_parser
 licenses:
 - MIT
@@ -157,7 +171,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.6.4
+rubygems_version: 2.6.12
 signing_key: 
 specification_version: 4
 summary: Ruby parsering for OBO files.

data/VERSION

@@ -1 +0,0 @@
-0.3.7

data/init.rb

@@ -1 +0,0 @@
-# Include hook code here

data/install.rb

@@ -1 +0,0 @@
-# Install hook code here

data/uninstall.rb

@@ -1 +0,0 @@
-# Uninstall hook code here