ProteinTranslate 0.0.1

checksums.yaml

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+---
+SHA1:
+  metadata.gz: de1765ceecea78bbf9b6aaf67acffefee9e3c071
+  data.tar.gz: 299f7d7b43c484beaf56045948bea1b1ab907271
+SHA512:
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data/.coveralls.yml

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+service_name: travis-ci

data/.gitignore

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

data/.rspec

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+--color
+--require spec_helper

data/.travis.yml

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+language: ruby
+rvm:
+- 2.2.0
+- rbx-19mode

data/Gemfile

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

data/LICENSE.txt

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+Copyright (c) 2016 marrero-
+
+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/ProteinTranslate.gemspec

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+# coding: utf-8
+lib = File.expand_path('../lib', __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require 'ProteinTranslate/version'
+
+Gem::Specification.new do |spec|
+  spec.name          = "ProteinTranslate"
+  spec.version       = ProteinTranslate::VERSION
+  spec.authors       = ["marrero-"]
+  spec.email         = ["alexmd54@gmail.com"]
+  spec.summary       = %q{Gem.}
+  spec.description   = %q{Ruby Gem which translate RNA to Protein}
+  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.add_development_dependency "bundler", "~> 1.7"
+  spec.add_development_dependency "rake", "~> 10.0"
+  spec.add_development_dependency "rspec"
+  spec.add_development_dependency "coveralls"
+end

data/README.md

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+# ProteinTranslate
+
+For documentation:
+https://marrero-.github.io/ProteinTranslate
+
+## Installation
+
+Add this line to your application's Gemfile:
+
+```ruby
+gem 'ProteinTranslate'
+```
+
+And then execute:
+
+    $ bundle
+
+Or install it yourself as:
+
+    $ gem install ProteinTranslate
+
+## Usage
+
+Install the Gem and then you can translate a ARN string to the protein equivalence:
+```ruby
+    
+    translateString("AUGUUUUCUUAG") 
+    #=> "Methionine","Phenylalanine", "Serine"
+
+```
+
+## Contributing
+
+1. Fork it ( https://github.com/marrero-/ProteinTranslate/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"
+
+
+task :default => :spec
+
+desc "Expectativas Básicas"
+task :spec do 
+	sh "rspec -I. spec/spec_protein.rb"
+end

data/lib/ProteinTranslate.rb

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+require "ProteinTranslate/version"
+require "ProteinTranslate/protein"
+module ProteinTranslate
+  # Your code goes here...
+end

data/lib/ProteinTranslate/protein.rb

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+
+
+module ProteinTranslate
+
+	#Clase para traduciar una cadena en ARN
+	#a los codones y proteinas correspondientes
+	class ProteinTranslate
+		
+		attr_reader :equivalence, :stop
+
+		def initialize
+
+			#Hash que contiene las equivalencias entre
+			#codones y las respectivas proteínas
+			@equivalence = {
+				"AUG" => "Methionine",
+				"UUU" => "Phenylalanine",
+				"UUC" => "Phenylalanine",
+				"UUA" => "Leucine",
+				"UUG" => "Leucine",
+				"UCU" => "Serine",
+				"UCC" => "Serine",
+				"UCA" => "Serine",
+				"UCG" => "Serine",
+				"UAU" => "Tyrosine",
+				"UAC" => "Tyrosine",
+				"UGU" => "Cysteine",
+				"UGC" => "Cysteine",
+				"UGG"=> "Tryptophan"
+			}
+
+			#Array que contiene los valores que si son detectados
+			#en la cadena indican que se pueden terminar la traduccion
+			@stop = ["UAA", "UAG", "UGA"]
+		end
+
+		#Metodo que recibe una cadena y devuelve
+		#un array de codons que la conforman
+		def divideStringInCondons(cadena)
+			array = Array.new
+			i = 0
+			while i <= cadena.length-3
+				if (@stop.include?("#{cadena[i,3]}"))
+					break
+				end
+				array << cadena[i,3]
+				i += 3
+			end
+			array
+		end
+
+		#Metodo que recibe una cadena y devuelve un array con las
+		#proteinas que la conforman
+		#Previamente se convierten en codones
+		def translateString(cadena)
+			array = divideStringInCondons(cadena)
+			proteina = Array.new
+			i = 0
+				array.each do |value|
+					if(@equivalence.has_key?("#{value}"))
+						proteina[i] = @equivalence["#{value}"]
+						i += 1
+					end
+				end
+			proteina
+		end
+
+	end
+
+end

data/lib/ProteinTranslate/version.rb

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+module ProteinTranslate
+  VERSION = "0.0.1"
+end

data/spec/spec_helper.rb

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+# This file was generated by the `rspec --init` command. Conventionally, all
+# specs live under a `spec` directory, which RSpec adds to the `$LOAD_PATH`.
+# The generated `.rspec` file contains `--require spec_helper` which will cause
+# this file to always be loaded, without a need to explicitly require it in any
+# files.
+#
+# Given that it is always loaded, you are encouraged to keep this file as
+# light-weight as possible. Requiring heavyweight dependencies from this file
+# will add to the boot time of your test suite on EVERY test run, even for an
+# individual file that may not need all of that loaded. Instead, consider making
+# a separate helper file that requires the additional dependencies and performs
+# the additional setup, and require it from the spec files that actually need
+# it.
+#
+# The `.rspec` file also contains a few flags that are not defaults but that
+# users commonly want.
+#
+require 'coveralls'
+Coveralls.wear!
+# See http://rubydoc.info/gems/rspec-core/RSpec/Core/Configuration
+RSpec.configure do |config|
+  # rspec-expectations config goes here. You can use an alternate
+  # assertion/expectation library such as wrong or the stdlib/minitest
+  # assertions if you prefer.
+  config.expect_with :rspec do |expectations|
+    # This option will default to `true` in RSpec 4. It makes the `description`
+    # and `failure_message` of custom matchers include text for helper methods
+    # defined using `chain`, e.g.:
+    #     be_bigger_than(2).and_smaller_than(4).description
+    #     # => "be bigger than 2 and smaller than 4"
+    # ...rather than:
+    #     # => "be bigger than 2"
+    expectations.include_chain_clauses_in_custom_matcher_descriptions = true
+  end
+
+  # rspec-mocks config goes here. You can use an alternate test double
+  # library (such as bogus or mocha) by changing the `mock_with` option here.
+  config.mock_with :rspec do |mocks|
+    # Prevents you from mocking or stubbing a method that does not exist on
+    # a real object. This is generally recommended, and will default to
+    # `true` in RSpec 4.
+    mocks.verify_partial_doubles = true
+  end
+
+# The settings below are suggested to provide a good initial experience
+# with RSpec, but feel free to customize to your heart's content.
+=begin
+  # These two settings work together to allow you to limit a spec run
+  # to individual examples or groups you care about by tagging them with
+  # `:focus` metadata. When nothing is tagged with `:focus`, all examples
+  # get run.
+  config.filter_run :focus
+  config.run_all_when_everything_filtered = true
+
+  # Allows RSpec to persist some state between runs in order to support
+  # the `--only-failures` and `--next-failure` CLI options. We recommend
+  # you configure your source control system to ignore this file.
+  config.example_status_persistence_file_path = "spec/examples.txt"
+
+  # Limits the available syntax to the non-monkey patched syntax that is
+  # recommended. For more details, see:
+  #   - http://rspec.info/blog/2012/06/rspecs-new-expectation-syntax/
+  #   - http://www.teaisaweso.me/blog/2013/05/27/rspecs-new-message-expectation-syntax/
+  #   - http://rspec.info/blog/2014/05/notable-changes-in-rspec-3/#zero-monkey-patching-mode
+  config.disable_monkey_patching!
+
+  # This setting enables warnings. It's recommended, but in some cases may
+  # be too noisy due to issues in dependencies.
+  config.warnings = true
+
+  # Many RSpec users commonly either run the entire suite or an individual
+  # file, and it's useful to allow more verbose output when running an
+  # individual spec file.
+  if config.files_to_run.one?
+    # Use the documentation formatter for detailed output,
+    # unless a formatter has already been configured
+    # (e.g. via a command-line flag).
+    config.default_formatter = 'doc'
+  end
+
+  # Print the 10 slowest examples and example groups at the
+  # end of the spec run, to help surface which specs are running
+  # particularly slow.
+  config.profile_examples = 10
+
+  # Run specs in random order to surface order dependencies. If you find an
+  # order dependency and want to debug it, you can fix the order by providing
+  # the seed, which is printed after each run.
+  #     --seed 1234
+  config.order = :random
+
+  # Seed global randomization in this process using the `--seed` CLI option.
+  # Setting this allows you to use `--seed` to deterministically reproduce
+  # test failures related to randomization by passing the same `--seed` value
+  # as the one that triggered the failure.
+  Kernel.srand config.seed
+=end
+end

data/spec/spec_protein.rb

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+
+
+require 'ProteinTranslate/protein'
+
+describe ProteinTranslate::ProteinTranslate do
+	before :each do
+		@protein = ProteinTranslate::ProteinTranslate.new
+	end
+
+	context "#Basic"do
+
+		it "Debe exisistir un objeto de la clase ProteinTranslate::ProteinTranslate"do
+			expect(@protein).not_to eq(nil)
+		end
+
+		it "Debe existir un hash que contenga las equivalencias"do
+			expect(@protein.equivalence).not_to eq(nil)
+		end
+
+	end
+
+	context "#Methionine" do
+		it "Debe tener la equivalencia para AUG"do
+			expect(@protein.equivalence["AUG"]).to eq("Methionine")
+		end
+	end
+
+	context "#Phenylalanine" do
+
+		it "Debe tener la equivalencia para UUU" do
+			expect(@protein.equivalence["UUU"]).to eq("Phenylalanine")
+		end
+		it "Debe tener la otra equivalencia para Phenylalanine"do
+			expect(@protein.equivalence["UUC"]).to eq("Phenylalanine")
+		end
+	end
+
+	context "#Leucine"do
+		it "Debe tener una de las equivalencias a Leucine" do
+			expect(@protein.equivalence["UUA"]).to eq("Leucine")
+		end
+		it "UUG tambien es una equivalencia para Leucina"do
+			expect(@protein.equivalence["UUG"]).to eq("Leucine")
+		end
+	end
+
+	context "#Serine" do
+
+		it "UCU => Serine" do
+			expect(@protein.equivalence["UCU"]).to eq("Serine")
+		end
+
+		it "UCC => Serine" do
+			expect(@protein.equivalence["UCC"]).to eq("Serine")
+		end
+
+		it "UCA => Serine" do
+			expect(@protein.equivalence["UCA"]).to eq("Serine")
+		end
+
+		it "UCG => Serine" do
+			expect(@protein.equivalence["UCG"]).to eq("Serine")
+		end
+	end
+
+	context "#Tyrosine" do
+
+		it "UAU  => Tyrosine" do
+			expect(@protein.equivalence["UAU"]).to eq("Tyrosine")
+		end
+
+		it "UAC => Tyrosine" do
+			expect(@protein.equivalence["UAC"]).to eq("Tyrosine")
+		end
+	end
+
+	context "#Cysteine" do
+
+		it "UGU => Cysteine" do
+			expect(@protein.equivalence["UGU"]).to eq("Cysteine")
+		end
+
+		it "UGC => Cysteine" do
+			expect(@protein.equivalence["UGC"]).to eq("Cysteine")
+		end
+	end
+
+	context "#Tryptophan"do
+		it "UGG => Tryptophan" do
+			expect(@protein.equivalence["UGG"]).to eq("Tryptophan")
+		end
+	end
+
+	context "#Funcionamiento" do
+		it "Existe un metodo que dada una cadena te devuelve un array con los 'condon'" do
+			expect(@protein.respond_to?:divideStringInCondons).to eq(true)
+		end
+		it "El metodo tiene que funcionar correctamente " do
+			expect(@protein.divideStringInCondons("AUGUUUUCUUAG")).to eq(["AUG", "UUU", "UCU"])
+		end
+		it "EL metodo de Translate devuelve las proteínas"do
+			expect(@protein.translateString("AUGUUUUCUUAG")).to eq(["Methionine","Phenylalanine", "Serine"])
+		end
+	end
+
+	context "#STOP" do
+		it "Debe tener un array para parar la traduccion" do
+			expect(@protein.stop).not_to eq(nil)
+		end
+		it "Debe contener el valor UAA" do
+			expect(@protein.stop.include?("UAA")).to eq(true)
+		end
+		it "Debe incluir el valor UAG"do
+			expect(@protein.stop.include?("UAG")).to eq(true)
+		end
+		it "Debe incluir el valor UGA" do
+			expect(@protein.stop.include?("UGA")).to eq(true)
+		end
+	end
+end
+
+=begin
+UAU, UAC |Tyrosine
+
+UGU, UGC |Cysteine
+
+UGG |Tryptophan
+
+UAA, UAG, UGA |STOP
+=end

metadata

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+--- !ruby/object:Gem::Specification
+name: ProteinTranslate
+version: !ruby/object:Gem::Version
+  version: 0.0.1
+platform: ruby
+authors:
+- marrero-
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2016-01-27 00:00:00.000000000 Z
+dependencies:
+- !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: rake
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '10.0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '10.0'
+- !ruby/object:Gem::Dependency
+  name: rspec
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: coveralls
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+description: Ruby Gem which translate RNA to Protein
+email:
+- alexmd54@gmail.com
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- ".coveralls.yml"
+- ".gitignore"
+- ".rspec"
+- ".travis.yml"
+- Gemfile
+- LICENSE.txt
+- ProteinTranslate.gemspec
+- README.md
+- Rakefile
+- lib/ProteinTranslate.rb
+- lib/ProteinTranslate/protein.rb
+- lib/ProteinTranslate/version.rb
+- spec/spec_helper.rb
+- spec/spec_protein.rb
+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: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 2.4.6
+signing_key: 
+specification_version: 4
+summary: Gem.
+test_files:
+- spec/spec_helper.rb
+- spec/spec_protein.rb