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1 parent 3d8d684 commit df48931e881348e95b61f16334111b37e5f1bce6 @trevor committed Sep 10, 2011
Showing with 7,888 additions and 83 deletions.
  1. +0 −8 Gemfile
  2. +11 −17 LICENSE.txt
  3. +6 −15 README.rdoc
  4. +6 −7 Rakefile
  5. +1 −1 VERSION
  6. +53 −0 bio-data-restriction_enzyme.gemspec
  7. +0 −10 lib/bio-data-restriction_enzyme.rb
  8. +7,811 −0 lib/bio/data/enzymes.yaml
  9. +0 −18 test/helper.rb
  10. +0 −7 test/test_bio-data-restriction_enzyme.rb
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@@ -1,12 +1,4 @@
-source "http://rubygems.org"
-# Add dependencies required to use your gem here.
-# Example:
-# gem "activesupport", ">= 2.3.5"
-
-# Add dependencies to develop your gem here.
-# Include everything needed to run rake, tests, features, etc.
group :development do
- gem "shoulda", ">= 0"
gem "bundler", "~> 1.0.0"
gem "jeweler", "~> 1.6.4"
gem "rcov", ">= 0"
View
@@ -1,20 +1,14 @@
-Copyright (c) 2011 Trevor Wennblom
+Copyright (c) Dr. Richard J. Roberts, 2011. All rights reserved.
-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:
+Sir Richard J. Roberts
-The above copyright notice and this permission notice shall be
-included in all copies or substantial portions of the Software.
+Those seeking to distribute REBASE files with their software packages are welcome to do so, providing it is clear to your users that they are not being charged for the REBASE data. It should be transparent that REBASE is a free and independent resource, with the following bibliographical reference:
-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.
+LATEST REVIEW:
+PubMed 19846593
+Roberts, R.J., Vincze, T., Posfai, J., Macelis, D. (2010)
+REBASE--a database for DNA restriction and modification: enzymes, genes and genomes.
+Nucl. Acids Res. 38: D234-D236.
+
+OFFICIAL REBASE WEB SITE:
+http://rebase.neb.com
View
@@ -1,19 +1,10 @@
= bio-data-restriction_enzyme
-Description goes here.
+Restriction Enzyme Dataset from REBASE in yaml form
-== Contributing to bio-data-restriction_enzyme
-
-* Check out the latest master to make sure the feature hasn't been implemented or the bug hasn't been fixed yet
-* Check out the issue tracker to make sure someone already hasn't requested it and/or contributed it
-* Fork the project
-* Start a feature/bugfix branch
-* Commit and push until you are happy with your contribution
-* Make sure to add tests for it. This is important so I don't break it in a future version unintentionally.
-* Please try not to mess with the Rakefile, version, or history. If you want to have your own version, or is otherwise necessary, that is fine, but please isolate to its own commit so I can cherry-pick around it.
-
-== Copyright
-
-Copyright (c) 2011 Trevor Wennblom. See LICENSE.txt for
-further details.
+http://rebase.neb.com/rebase/link_emboss_e
+REBASE, The Restriction Enzyme Database http://rebase.neb.com
+Copyright (c) Dr. Richard J. Roberts, 2011. All rights reserved.
+Rich Roberts
+Aug 29 2011
View
@@ -14,13 +14,12 @@ 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 = "bio-data-restriction_enzyme"
- gem.homepage = "http://github.com/trevor/bioruby-data-restriction_enzyme"
- gem.license = "MIT"
- gem.summary = %Q{TODO: one-line summary of your gem}
- gem.description = %Q{TODO: longer description of your gem}
- gem.email = "trevor@well.com"
- gem.authors = ["Trevor Wennblom"]
+ gem.name = 'bio-data-restriction_enzyme'
+ gem.homepage = 'http://github.com/trevor/bioruby-data-restriction_enzyme'
+ gem.summary = %Q{Restriction Enzyme Dataset}
+ gem.description = %Q{Restriction Enzyme Dataset from REBASE in yaml form}
+ gem.email = 'trevor@well.com'
+ gem.authors = ['Sir Richard J. Roberts', 'Trevor Wennblom']
# dependencies defined in Gemfile
end
Jeweler::RubygemsDotOrgTasks.new
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@@ -1 +1 @@
-0.0.0
+1.109.0
@@ -0,0 +1,53 @@
+# Generated by jeweler
+# DO NOT EDIT THIS FILE DIRECTLY
+# Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
+# -*- encoding: utf-8 -*-
+
+Gem::Specification.new do |s|
+ s.name = "bio-data-restriction_enzyme"
+ s.version = "1.109.0"
+
+ s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
+ s.authors = ["Sir Richard J. Roberts", "Trevor Wennblom"]
+ s.date = "2011-09-10"
+ s.description = "Restriction Enzyme Dataset from REBASE in yaml form"
+ s.email = "trevor@well.com"
+ s.extra_rdoc_files = [
+ "LICENSE.txt",
+ "README.rdoc"
+ ]
+ s.files = [
+ ".document",
+ "Gemfile",
+ "LICENSE.txt",
+ "README.rdoc",
+ "Rakefile",
+ "VERSION"
+ ]
+ s.homepage = "http://github.com/trevor/bioruby-data-restriction_enzyme"
+ s.require_paths = ["lib"]
+ s.rubygems_version = "1.8.10"
+ s.summary = "Restriction Enzyme Dataset"
+
+ if s.respond_to? :specification_version then
+ s.specification_version = 3
+
+ if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
+ s.add_development_dependency(%q<bundler>, ["~> 1.0.0"])
+ s.add_development_dependency(%q<jeweler>, ["~> 1.6.4"])
+ s.add_development_dependency(%q<rcov>, [">= 0"])
+ s.add_development_dependency(%q<bio>, [">= 1.4.1"])
+ else
+ s.add_dependency(%q<bundler>, ["~> 1.0.0"])
+ s.add_dependency(%q<jeweler>, ["~> 1.6.4"])
+ s.add_dependency(%q<rcov>, [">= 0"])
+ s.add_dependency(%q<bio>, [">= 1.4.1"])
+ end
+ else
+ s.add_dependency(%q<bundler>, ["~> 1.0.0"])
+ s.add_dependency(%q<jeweler>, ["~> 1.6.4"])
+ s.add_dependency(%q<rcov>, [">= 0"])
+ s.add_dependency(%q<bio>, [">= 1.4.1"])
+ end
+end
+
@@ -1,10 +0,0 @@
-# Please require your code below, respecting the bioruby directory tree.
-# For instance, perhaps the only uncommented line in this file might
-# be something like this:
-#
-# require 'bio/sequence/awesome_sequence_plugin_thingy'
-#
-# and then create the ruby file 'lib/bio/sequence/awesome_sequence_thingy.rb'
-# and put your plugin's code there. It is bad practice to write other code
-# directly into this file, because doing so causes confusion if this biogem
-# was ever to get merged into the main bioruby tree.
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