idclight 0.1.2 → 0.1.3

data/Gemfile

@@ -0,0 +1,7 @@
+source "http://rubygems.org"
+
+gem "hpricot", ">= 0.8"
+
+group :development do
+	gem "thoughtbot-shoulda"
+end

data/Gemfile.lock

@@ -0,0 +1,12 @@
+GEM
+  remote: http://rubygems.org/
+  specs:
+    hpricot (0.8.6)
+    thoughtbot-shoulda (2.11.1)
+
+PLATFORMS
+  ruby
+
+DEPENDENCIES
+  hpricot (>= 0.8)
+  thoughtbot-shoulda

data/Rakefile

@@ -8,10 +8,8 @@ begin
     gem.summary = %Q{Ruby programmnig interface to the IDCLight online database.}
     gem.description = %Q{A Ruby gem for accessing the freely available IDClight (IDConverter Light) web service, which convert between different types of gene IDs such as Hugo and Entrez. Queries are screen scraped from http://idclight.bioinfo.cnio.es.}
     gem.email = "conmotto@gmail.com"
-    gem.homepage = "http://github.com/preston/idclight"
+    gem.homepage = "http://github.com/tgen/idclight"
     gem.authors = ["Preston Lee"]
-    gem.add_development_dependency "thoughtbot-shoulda", ">= 0"
-    gem.add_dependency "hpricot", ">= 0.8"
     # gem is a Gem::Specification... see http://www.rubygems.org/read/chapter/20 for additional settings
   end
   Jeweler::GemcutterTasks.new
@@ -43,7 +41,7 @@ task :test => :check_dependencies
 
 task :default => :test
 
-require 'rake/rdoctask'
+require 'rdoc/task'
 Rake::RDocTask.new do |rdoc|
   version = File.exist?('VERSION') ? File.read('VERSION') : ""
 

data/VERSION

@@ -1 +1 @@
-0.1.2
+0.1.3

data/bin/{convert.rb → idclight_convert.rb}

@@ -28,6 +28,21 @@ if ARGV.length >= 2 and ARGV.length <= 3
 	end
 else
 	puts "\n\tUsage: #{__FILE__} <id_type> <id> [organism (defaults to human)]"
+	puts <<EOF
+	
+	From the website:
+	
+	idtype refers to the type of ID from which you want to obtain further information.
+	Current options are: ug (UniGene cluster), entrez (EntrezGene ID),
+	ensembl (Ensembl Gene), hugo (HUGO Gene Name), acc (GenBank accession),
+	clone (Clone ID), affy (Affymetrix ID), rsdna (RefSeq_RNA),
+	rspep (RefSeq_peptide), and swissp (SwissProt name). 
+	
+	id is the ID of the gene or clone for which more information is required. 
+	
+	org is the organism you are working with. Three different organisms are available
+	Hs (Human - Homo sapiens), Mm (Mouse - Mus musculus), and Rn (Rat - Rattus norvegicus).
+EOF
 end
 puts "\n"
 

data/idclight.gemspec

@@ -1,64 +1,59 @@
 # Generated by jeweler
 # DO NOT EDIT THIS FILE DIRECTLY
-# Instead, edit Jeweler::Tasks in Rakefile, and run the gemspec command
+# Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
 # -*- encoding: utf-8 -*-
 
 Gem::Specification.new do |s|
-  s.name = %q{idclight}
-  s.version = "0.1.2"
+  s.name = "idclight"
+  s.version = "0.1.3"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Preston Lee"]
-  s.date = %q{2010-05-11}
-  s.description = %q{A Ruby gem for accessing the freely available IDClight (IDConverter Light) web service, which convert between different types of gene IDs such as Hugo and Entrez. Queries are screen scraped from http://idclight.bioinfo.cnio.es.}
-  s.email = %q{conmotto@gmail.com}
-  s.executables = ["convert.rb", "ensembl_to_entrez.rb", "ensembl_to_hugo.rb", "hugo_to_ensembl.rb", "hugo_to_entrez.rb"]
+  s.date = "2012-04-12"
+  s.description = "A Ruby gem for accessing the freely available IDClight (IDConverter Light) web service, which convert between different types of gene IDs such as Hugo and Entrez. Queries are screen scraped from http://idclight.bioinfo.cnio.es."
+  s.email = "conmotto@gmail.com"
+  s.executables = ["ensembl_to_entrez.rb", "ensembl_to_hugo.rb", "hugo_to_ensembl.rb", "hugo_to_entrez.rb", "idclight_convert.rb"]
   s.extra_rdoc_files = [
     "LICENSE",
-     "README.rdoc"
+    "README.rdoc"
   ]
   s.files = [
     ".document",
-     ".gitignore",
-     ".project",
-     "LICENSE",
-     "README.rdoc",
-     "Rakefile",
-     "VERSION",
-     "bin/convert.rb",
-     "bin/ensembl_to_entrez.rb",
-     "bin/ensembl_to_hugo.rb",
-     "bin/hugo_to_ensembl.rb",
-     "bin/hugo_to_entrez.rb",
-     "idclight.gemspec",
-     "lib/idclight.rb",
-     "test/helper.rb",
-     "test/test_idclight.rb"
-  ]
-  s.homepage = %q{http://github.com/preston/idclight}
-  s.rdoc_options = ["--charset=UTF-8"]
-  s.require_paths = ["lib"]
-  s.rubygems_version = %q{1.3.6}
-  s.summary = %q{Ruby programmnig interface to the IDCLight online database.}
-  s.test_files = [
+    ".project",
+    "Gemfile",
+    "Gemfile.lock",
+    "LICENSE",
+    "README.rdoc",
+    "Rakefile",
+    "VERSION",
+    "bin/ensembl_to_entrez.rb",
+    "bin/ensembl_to_hugo.rb",
+    "bin/hugo_to_ensembl.rb",
+    "bin/hugo_to_entrez.rb",
+    "bin/idclight_convert.rb",
+    "idclight.gemspec",
+    "lib/idclight.rb",
     "test/helper.rb",
-     "test/test_idclight.rb"
+    "test/test_idclight.rb"
   ]
+  s.homepage = "http://github.com/tgen/idclight"
+  s.require_paths = ["lib"]
+  s.rubygems_version = "1.8.21"
+  s.summary = "Ruby programmnig interface to the IDCLight online database."
 
   if s.respond_to? :specification_version then
-    current_version = Gem::Specification::CURRENT_SPECIFICATION_VERSION
     s.specification_version = 3
 
-    if Gem::Version.new(Gem::RubyGemsVersion) >= Gem::Version.new('1.2.0') then
-      s.add_development_dependency(%q<thoughtbot-shoulda>, [">= 0"])
+    if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
       s.add_runtime_dependency(%q<hpricot>, [">= 0.8"])
+      s.add_development_dependency(%q<thoughtbot-shoulda>, [">= 0"])
     else
-      s.add_dependency(%q<thoughtbot-shoulda>, [">= 0"])
       s.add_dependency(%q<hpricot>, [">= 0.8"])
+      s.add_dependency(%q<thoughtbot-shoulda>, [">= 0"])
     end
   else
-    s.add_dependency(%q<thoughtbot-shoulda>, [">= 0"])
     s.add_dependency(%q<hpricot>, [">= 0.8"])
+    s.add_dependency(%q<thoughtbot-shoulda>, [">= 0"])
   end
 end
 

metadata

@@ -1,107 +1,102 @@
---- !ruby/object:Gem::Specification 
+--- !ruby/object:Gem::Specification
 name: idclight
-version: !ruby/object:Gem::Version 
-  prerelease: false
-  segments: 
-  - 0
-  - 1
-  - 2
-  version: 0.1.2
+version: !ruby/object:Gem::Version
+  version: 0.1.3
+  prerelease: 
 platform: ruby
-authors: 
+authors:
 - Preston Lee
 autorequire: 
 bindir: bin
 cert_chain: []
-
-date: 2010-05-11 00:00:00 -07:00
-default_executable: 
-dependencies: 
-- !ruby/object:Gem::Dependency 
-  name: thoughtbot-shoulda
+date: 2012-04-12 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: hpricot
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0.8'
+  type: :runtime
   prerelease: false
-  requirement: &id001 !ruby/object:Gem::Requirement 
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        segments: 
-        - 0
-        version: "0"
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0.8'
+- !ruby/object:Gem::Dependency
+  name: thoughtbot-shoulda
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
   type: :development
-  version_requirements: *id001
-- !ruby/object:Gem::Dependency 
-  name: hpricot
   prerelease: false
-  requirement: &id002 !ruby/object:Gem::Requirement 
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        segments: 
-        - 0
-        - 8
-        version: "0.8"
-  type: :runtime
-  version_requirements: *id002
-description: A Ruby gem for accessing the freely available IDClight (IDConverter Light) web service, which convert between different types of gene IDs such as Hugo and Entrez. Queries are screen scraped from http://idclight.bioinfo.cnio.es.
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+description: A Ruby gem for accessing the freely available IDClight (IDConverter Light)
+  web service, which convert between different types of gene IDs such as Hugo and
+  Entrez. Queries are screen scraped from http://idclight.bioinfo.cnio.es.
 email: conmotto@gmail.com
-executables: 
-- convert.rb
+executables:
 - ensembl_to_entrez.rb
 - ensembl_to_hugo.rb
 - hugo_to_ensembl.rb
 - hugo_to_entrez.rb
+- idclight_convert.rb
 extensions: []
-
-extra_rdoc_files: 
+extra_rdoc_files:
 - LICENSE
 - README.rdoc
-files: 
+files:
 - .document
-- .gitignore
 - .project
+- Gemfile
+- Gemfile.lock
 - LICENSE
 - README.rdoc
 - Rakefile
 - VERSION
-- bin/convert.rb
 - bin/ensembl_to_entrez.rb
 - bin/ensembl_to_hugo.rb
 - bin/hugo_to_ensembl.rb
 - bin/hugo_to_entrez.rb
+- bin/idclight_convert.rb
 - idclight.gemspec
 - lib/idclight.rb
 - test/helper.rb
 - test/test_idclight.rb
-has_rdoc: true
-homepage: http://github.com/preston/idclight
+homepage: http://github.com/tgen/idclight
 licenses: []
-
 post_install_message: 
-rdoc_options: 
-- --charset=UTF-8
-require_paths: 
+rdoc_options: []
+require_paths:
 - lib
-required_ruby_version: !ruby/object:Gem::Requirement 
-  requirements: 
-  - - ">="
-    - !ruby/object:Gem::Version 
-      segments: 
-      - 0
-      version: "0"
-required_rubygems_version: !ruby/object:Gem::Requirement 
-  requirements: 
-  - - ">="
-    - !ruby/object:Gem::Version 
-      segments: 
-      - 0
-      version: "0"
+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: 1.3.6
+rubygems_version: 1.8.21
 signing_key: 
 specification_version: 3
 summary: Ruby programmnig interface to the IDCLight online database.
-test_files: 
-- test/helper.rb
-- test/test_idclight.rb
+test_files: []

data/.gitignore

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