rbfam_bridge 1.0.0

checksums.yaml

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+SHA1:
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data/.gitignore

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+/.bundle/
+/.yardoc
+/Gemfile.lock
+/_yardoc/
+/coverage/
+/doc/
+/pkg/
+/spec/reports/
+/tmp/
+*.bundle
+*.so
+*.o
+*.a
+mkmf.log

data/Gemfile

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+source 'https://rubygems.org'
+
+# Specify your gem's dependencies in rbfam_bridge.gemspec
+gemspec

data/LICENSE.txt

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+Copyright (c) 2014 Evan Senter
+
+MIT License
+
+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.md

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+# RbfamBridge
+
+TODO: Write a gem description
+
+## Installation
+
+Add this line to your application's Gemfile:
+
+```ruby
+gem 'rbfam_bridge'
+```
+
+And then execute:
+
+    $ bundle
+
+Or install it yourself as:
+
+    $ gem install rbfam_bridge
+
+## Usage
+
+TODO: Write usage instructions here
+
+## Contributing
+
+1. Fork it ( https://github.com/[my-github-username]/rbfam_bridge/fork )
+2. Create your feature branch (`git checkout -b my-new-feature`)
+3. Commit your changes (`git commit -am 'Add some feature'`)
+4. Push to the branch (`git push origin my-new-feature`)
+5. Create a new Pull Request

data/Rakefile

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+require "bundler/gem_tasks"
+

data/lib/rbfam_bridge.rb

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+require "wrnap"
+require "rbfam"
+require "rbfam_bridge/version"
+
+Rbfam::Family.class_eval do
+  def wrnap
+    Wrnap::Rna::Box.new(rnas.map(&:wrnap), name)
+  end
+end
+
+Rbfam::Rna.class_eval do
+  def wrnap
+    Wrnap::Rna::Context.init_from_string(*instance_eval { [seq, accession, from, to] })
+  end
+end

data/lib/rbfam_bridge/version.rb

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+module RbfamBridge
+  VERSION = "1.0.0"
+end

data/rbfam_bridge.gemspec

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+# coding: utf-8
+lib = File.expand_path('../lib', __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require 'rbfam_bridge/version'
+
+Gem::Specification.new do |spec|
+  spec.name          = "rbfam_bridge"
+  spec.version       = RbfamBridge::VERSION
+  spec.authors       = ["Evan Senter"]
+  spec.email         = ["evansenter@gmail.com"]
+  spec.summary       = %q{Rbfam (╯°□°）╯︵ ┻━┻ Wrnap}
+  spec.description   = %q{A bridge for the Rbfam gem that allows the sequences from Rbfam to be converted to Wrnap objects.}
+  spec.homepage      = ""
+  spec.license       = "MIT"
+
+  spec.files         = `git ls-files -z`.split("\x0")
+  spec.executables   = spec.files.grep(%r{^bin/}) { |f| File.basename(f) }
+  spec.test_files    = spec.files.grep(%r{^(test|spec|features)/})
+  spec.require_paths = ["lib"]
+  
+  spec.required_ruby_version = ">= 2.0"
+
+  spec.add_development_dependency "awesome_print", "~> 1.2"
+  spec.add_development_dependency "bundler",       "~> 1.7"
+  spec.add_development_dependency "gem-release",   "~> 0.7"
+  spec.add_development_dependency "rake",          "~> 10.4"
+    
+  spec.add_runtime_dependency "rbfam", "~> 12.0", ">= 12.0.0"
+  spec.add_runtime_dependency "wrnap", "~> 1.2", ">= 1.2.2"
+end

metadata

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+--- !ruby/object:Gem::Specification
+name: rbfam_bridge
+version: !ruby/object:Gem::Version
+  version: 1.0.0
+platform: ruby
+authors:
+- Evan Senter
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2015-01-03 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: awesome_print
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.2'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.2'
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.7'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.7'
+- !ruby/object:Gem::Dependency
+  name: gem-release
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.7'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.7'
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '10.4'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '10.4'
+- !ruby/object:Gem::Dependency
+  name: rbfam
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '12.0'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 12.0.0
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '12.0'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 12.0.0
+- !ruby/object:Gem::Dependency
+  name: wrnap
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.2'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.2.2
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.2'
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.2.2
+description: A bridge for the Rbfam gem that allows the sequences from Rbfam to be
+  converted to Wrnap objects.
+email:
+- evansenter@gmail.com
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- ".gitignore"
+- Gemfile
+- LICENSE.txt
+- README.md
+- Rakefile
+- lib/rbfam_bridge.rb
+- lib/rbfam_bridge/version.rb
+- rbfam_bridge.gemspec
+homepage: ''
+licenses:
+- MIT
+metadata: {}
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '2.0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 2.4.5
+signing_key: 
+specification_version: 4
+summary: Rbfam (╯°□°）╯︵ ┻━┻ Wrnap
+test_files: []