ProteinTranslate 0.0.1

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+ service_name: travis-ci
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+ /.bundle/
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+ /.yardoc
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+ /Gemfile.lock
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+ /_yardoc/
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+ /coverage/
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+ /doc/
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+ /pkg/
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+ /spec/reports/
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+ /tmp/
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+ *.bundle
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+ *.so
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+ *.o
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+ *.a
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+ mkmf.log
data/.rspec ADDED
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+ --color
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+ --require spec_helper
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+ language: ruby
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+ rvm:
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+ - 2.2.0
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+ - rbx-19mode
data/Gemfile ADDED
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+ source 'https://rubygems.org'
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+
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+ # Specify your gem's dependencies in ProteinTranslate.gemspec
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+ gemspec
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+ Copyright (c) 2016 marrero-
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+
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+ MIT License
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+
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+ Permission is hereby granted, free of charge, to any person obtaining
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+ a copy of this software and associated documentation files (the
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+ "Software"), to deal in the Software without restriction, including
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+ without limitation the rights to use, copy, modify, merge, publish,
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+ distribute, sublicense, and/or sell copies of the Software, and to
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+ permit persons to whom the Software is furnished to do so, subject to
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+ the following conditions:
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+
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+ The above copyright notice and this permission notice shall be
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+ included in all copies or substantial portions of the Software.
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+
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+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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+ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
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+ MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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+ NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
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+ LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
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+ OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
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+ WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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+ # coding: utf-8
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+ lib = File.expand_path('../lib', __FILE__)
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+ $LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
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+ require 'ProteinTranslate/version'
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+
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+ Gem::Specification.new do |spec|
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+ spec.name = "ProteinTranslate"
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+ spec.version = ProteinTranslate::VERSION
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+ spec.authors = ["marrero-"]
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+ spec.email = ["alexmd54@gmail.com"]
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+ spec.summary = %q{Gem.}
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+ spec.description = %q{Ruby Gem which translate RNA to Protein}
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+ spec.homepage = ""
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+ spec.license = "MIT"
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+
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+ spec.files = `git ls-files -z`.split("\x0")
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+ spec.executables = spec.files.grep(%r{^bin/}) { |f| File.basename(f) }
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+ spec.test_files = spec.files.grep(%r{^(test|spec|features)/})
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+ spec.require_paths = ["lib"]
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+
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+ spec.add_development_dependency "bundler", "~> 1.7"
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+ spec.add_development_dependency "rake", "~> 10.0"
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+ spec.add_development_dependency "rspec"
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+ spec.add_development_dependency "coveralls"
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+ end
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+ # ProteinTranslate
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+
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+ For documentation:
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+ https://marrero-.github.io/ProteinTranslate
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+
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+ ## Installation
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+
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+ Add this line to your application's Gemfile:
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+
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+ ```ruby
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+ gem 'ProteinTranslate'
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+ ```
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+
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+ And then execute:
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+
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+ $ bundle
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+
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+ Or install it yourself as:
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+
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+ $ gem install ProteinTranslate
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+
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+ ## Usage
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+
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+ Install the Gem and then you can translate a ARN string to the protein equivalence:
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+ ```ruby
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+
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+ translateString("AUGUUUUCUUAG")
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+ #=> "Methionine","Phenylalanine", "Serine"
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+
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+ ```
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+
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+ ## Contributing
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+
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+ 1. Fork it ( https://github.com/marrero-/ProteinTranslate/fork )
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+ 2. Create your feature branch (`git checkout -b my-new-feature`)
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+ 3. Commit your changes (`git commit -am 'Add some feature'`)
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+ 4. Push to the branch (`git push origin my-new-feature`)
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+ 5. Create a new Pull Request
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+ require "bundler/gem_tasks"
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+
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+
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+ task :default => :spec
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+
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+ desc "Expectativas Básicas"
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+ task :spec do
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+ sh "rspec -I. spec/spec_protein.rb"
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+ end
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+ require "ProteinTranslate/version"
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+ require "ProteinTranslate/protein"
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+ module ProteinTranslate
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+ # Your code goes here...
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+ end
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+
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+
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+ module ProteinTranslate
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+
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+ #Clase para traduciar una cadena en ARN
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+ #a los codones y proteinas correspondientes
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+ class ProteinTranslate
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+
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+ attr_reader :equivalence, :stop
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+
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+ def initialize
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+
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+ #Hash que contiene las equivalencias entre
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+ #codones y las respectivas proteínas
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+ @equivalence = {
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+ "AUG" => "Methionine",
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+ "UUU" => "Phenylalanine",
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+ "UUC" => "Phenylalanine",
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+ "UUA" => "Leucine",
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+ "UUG" => "Leucine",
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+ "UCU" => "Serine",
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+ "UCC" => "Serine",
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+ "UCA" => "Serine",
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+ "UCG" => "Serine",
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+ "UAU" => "Tyrosine",
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+ "UAC" => "Tyrosine",
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+ "UGU" => "Cysteine",
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+ "UGC" => "Cysteine",
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+ "UGG"=> "Tryptophan"
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+ }
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+
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+ #Array que contiene los valores que si son detectados
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+ #en la cadena indican que se pueden terminar la traduccion
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+ @stop = ["UAA", "UAG", "UGA"]
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+ end
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+
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+ #Metodo que recibe una cadena y devuelve
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+ #un array de codons que la conforman
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+ def divideStringInCondons(cadena)
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+ array = Array.new
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+ i = 0
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+ while i <= cadena.length-3
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+ if (@stop.include?("#{cadena[i,3]}"))
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+ break
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+ end
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+ array << cadena[i,3]
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+ i += 3
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+ end
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+ array
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+ end
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+
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+ #Metodo que recibe una cadena y devuelve un array con las
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+ #proteinas que la conforman
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+ #Previamente se convierten en codones
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+ def translateString(cadena)
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+ array = divideStringInCondons(cadena)
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+ proteina = Array.new
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+ i = 0
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+ array.each do |value|
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+ if(@equivalence.has_key?("#{value}"))
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+ proteina[i] = @equivalence["#{value}"]
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+ i += 1
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+ end
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+ end
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+ proteina
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+ end
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+
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+ end
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+
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+ end
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+ module ProteinTranslate
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+ VERSION = "0.0.1"
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+ end
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+ # This file was generated by the `rspec --init` command. Conventionally, all
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+ # specs live under a `spec` directory, which RSpec adds to the `$LOAD_PATH`.
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+ # The generated `.rspec` file contains `--require spec_helper` which will cause
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+ # this file to always be loaded, without a need to explicitly require it in any
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+ # files.
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+ #
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+ # Given that it is always loaded, you are encouraged to keep this file as
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+ # light-weight as possible. Requiring heavyweight dependencies from this file
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+ # will add to the boot time of your test suite on EVERY test run, even for an
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+ # individual file that may not need all of that loaded. Instead, consider making
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+ # a separate helper file that requires the additional dependencies and performs
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+ # the additional setup, and require it from the spec files that actually need
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+ # it.
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+ #
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+ # The `.rspec` file also contains a few flags that are not defaults but that
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+ # users commonly want.
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+ #
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+ require 'coveralls'
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+ Coveralls.wear!
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+ # See http://rubydoc.info/gems/rspec-core/RSpec/Core/Configuration
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+ RSpec.configure do |config|
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+ # rspec-expectations config goes here. You can use an alternate
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+ # assertion/expectation library such as wrong or the stdlib/minitest
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+ # assertions if you prefer.
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+ config.expect_with :rspec do |expectations|
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+ # This option will default to `true` in RSpec 4. It makes the `description`
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+ # and `failure_message` of custom matchers include text for helper methods
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+ # defined using `chain`, e.g.:
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+ # be_bigger_than(2).and_smaller_than(4).description
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+ # # => "be bigger than 2 and smaller than 4"
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+ # ...rather than:
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+ # # => "be bigger than 2"
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+ expectations.include_chain_clauses_in_custom_matcher_descriptions = true
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+ end
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+
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+ # rspec-mocks config goes here. You can use an alternate test double
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+ # library (such as bogus or mocha) by changing the `mock_with` option here.
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+ config.mock_with :rspec do |mocks|
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+ # Prevents you from mocking or stubbing a method that does not exist on
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+ # a real object. This is generally recommended, and will default to
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+ # `true` in RSpec 4.
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+ mocks.verify_partial_doubles = true
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+ end
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+
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+ # The settings below are suggested to provide a good initial experience
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+ # with RSpec, but feel free to customize to your heart's content.
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+ =begin
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+ # These two settings work together to allow you to limit a spec run
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+ # to individual examples or groups you care about by tagging them with
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+ # `:focus` metadata. When nothing is tagged with `:focus`, all examples
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+ # get run.
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+ config.filter_run :focus
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+ config.run_all_when_everything_filtered = true
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+
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+ # Allows RSpec to persist some state between runs in order to support
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+ # the `--only-failures` and `--next-failure` CLI options. We recommend
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+ # you configure your source control system to ignore this file.
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+ config.example_status_persistence_file_path = "spec/examples.txt"
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+
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+ # Limits the available syntax to the non-monkey patched syntax that is
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+ # recommended. For more details, see:
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+ # - http://rspec.info/blog/2012/06/rspecs-new-expectation-syntax/
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+ # - http://www.teaisaweso.me/blog/2013/05/27/rspecs-new-message-expectation-syntax/
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+ # - http://rspec.info/blog/2014/05/notable-changes-in-rspec-3/#zero-monkey-patching-mode
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+ config.disable_monkey_patching!
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+
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+ # This setting enables warnings. It's recommended, but in some cases may
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+ # be too noisy due to issues in dependencies.
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+ config.warnings = true
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+
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+ # Many RSpec users commonly either run the entire suite or an individual
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+ # file, and it's useful to allow more verbose output when running an
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+ # individual spec file.
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+ if config.files_to_run.one?
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+ # Use the documentation formatter for detailed output,
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+ # unless a formatter has already been configured
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+ # (e.g. via a command-line flag).
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+ config.default_formatter = 'doc'
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+ end
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+
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+ # Print the 10 slowest examples and example groups at the
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+ # end of the spec run, to help surface which specs are running
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+ # particularly slow.
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+ config.profile_examples = 10
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+
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+ # Run specs in random order to surface order dependencies. If you find an
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+ # order dependency and want to debug it, you can fix the order by providing
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+ # the seed, which is printed after each run.
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+ # --seed 1234
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+ config.order = :random
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+
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+ # Seed global randomization in this process using the `--seed` CLI option.
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+ # Setting this allows you to use `--seed` to deterministically reproduce
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+ # test failures related to randomization by passing the same `--seed` value
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+ # as the one that triggered the failure.
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+ Kernel.srand config.seed
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+ =end
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+ end
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+
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+
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+ require 'ProteinTranslate/protein'
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+
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+ describe ProteinTranslate::ProteinTranslate do
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+ before :each do
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+ @protein = ProteinTranslate::ProteinTranslate.new
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+ end
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+
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+ context "#Basic"do
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+
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+ it "Debe exisistir un objeto de la clase ProteinTranslate::ProteinTranslate"do
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+ expect(@protein).not_to eq(nil)
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+ end
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+
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+ it "Debe existir un hash que contenga las equivalencias"do
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+ expect(@protein.equivalence).not_to eq(nil)
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+ end
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+
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+ end
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+
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+ context "#Methionine" do
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+ it "Debe tener la equivalencia para AUG"do
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+ expect(@protein.equivalence["AUG"]).to eq("Methionine")
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+ end
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+ end
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+
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+ context "#Phenylalanine" do
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+
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+ it "Debe tener la equivalencia para UUU" do
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+ expect(@protein.equivalence["UUU"]).to eq("Phenylalanine")
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+ end
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+ it "Debe tener la otra equivalencia para Phenylalanine"do
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+ expect(@protein.equivalence["UUC"]).to eq("Phenylalanine")
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+ end
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+ end
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+
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+ context "#Leucine"do
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+ it "Debe tener una de las equivalencias a Leucine" do
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+ expect(@protein.equivalence["UUA"]).to eq("Leucine")
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+ end
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+ it "UUG tambien es una equivalencia para Leucina"do
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+ expect(@protein.equivalence["UUG"]).to eq("Leucine")
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+ end
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+ end
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+
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+ context "#Serine" do
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+
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+ it "UCU => Serine" do
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+ expect(@protein.equivalence["UCU"]).to eq("Serine")
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+ end
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+
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+ it "UCC => Serine" do
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+ expect(@protein.equivalence["UCC"]).to eq("Serine")
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+ end
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+
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+ it "UCA => Serine" do
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+ expect(@protein.equivalence["UCA"]).to eq("Serine")
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+ end
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+
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+ it "UCG => Serine" do
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+ expect(@protein.equivalence["UCG"]).to eq("Serine")
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+ end
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+ end
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+
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+ context "#Tyrosine" do
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+
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+ it "UAU => Tyrosine" do
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+ expect(@protein.equivalence["UAU"]).to eq("Tyrosine")
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+ end
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+
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+ it "UAC => Tyrosine" do
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+ expect(@protein.equivalence["UAC"]).to eq("Tyrosine")
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+ end
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+ end
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+
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+ context "#Cysteine" do
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+
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+ it "UGU => Cysteine" do
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+ expect(@protein.equivalence["UGU"]).to eq("Cysteine")
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+ end
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+
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+ it "UGC => Cysteine" do
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+ expect(@protein.equivalence["UGC"]).to eq("Cysteine")
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+ end
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+ end
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+
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+ context "#Tryptophan"do
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+ it "UGG => Tryptophan" do
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+ expect(@protein.equivalence["UGG"]).to eq("Tryptophan")
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+ end
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+ end
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+
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+ context "#Funcionamiento" do
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+ it "Existe un metodo que dada una cadena te devuelve un array con los 'condon'" do
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+ expect(@protein.respond_to?:divideStringInCondons).to eq(true)
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+ end
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+ it "El metodo tiene que funcionar correctamente " do
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+ expect(@protein.divideStringInCondons("AUGUUUUCUUAG")).to eq(["AUG", "UUU", "UCU"])
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+ end
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+ it "EL metodo de Translate devuelve las proteínas"do
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+ expect(@protein.translateString("AUGUUUUCUUAG")).to eq(["Methionine","Phenylalanine", "Serine"])
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+ end
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+ end
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+
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+ context "#STOP" do
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+ it "Debe tener un array para parar la traduccion" do
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+ expect(@protein.stop).not_to eq(nil)
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+ end
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+ it "Debe contener el valor UAA" do
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+ expect(@protein.stop.include?("UAA")).to eq(true)
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+ end
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+ it "Debe incluir el valor UAG"do
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+ expect(@protein.stop.include?("UAG")).to eq(true)
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+ end
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+ it "Debe incluir el valor UGA" do
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+ expect(@protein.stop.include?("UGA")).to eq(true)
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+ end
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+ end
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+ end
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+
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+ =begin
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+ UAU, UAC |Tyrosine
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+
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+ UGU, UGC |Cysteine
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+
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+ UGG |Tryptophan
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+
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+ UAA, UAG, UGA |STOP
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+ =end
metadata ADDED
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+ --- !ruby/object:Gem::Specification
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+ name: ProteinTranslate
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+ version: !ruby/object:Gem::Version
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+ version: 0.0.1
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+ platform: ruby
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+ authors:
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+ - marrero-
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+ autorequire:
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+ bindir: bin
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+ cert_chain: []
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+ date: 2016-01-27 00:00:00.000000000 Z
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+ dependencies:
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+ - !ruby/object:Gem::Dependency
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+ name: bundler
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+ requirement: !ruby/object:Gem::Requirement
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+ requirements:
17
+ - - "~>"
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+ - !ruby/object:Gem::Version
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+ version: '1.7'
20
+ type: :development
21
+ prerelease: false
22
+ version_requirements: !ruby/object:Gem::Requirement
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+ requirements:
24
+ - - "~>"
25
+ - !ruby/object:Gem::Version
26
+ version: '1.7'
27
+ - !ruby/object:Gem::Dependency
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+ name: rake
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+ requirement: !ruby/object:Gem::Requirement
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+ requirements:
31
+ - - "~>"
32
+ - !ruby/object:Gem::Version
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+ version: '10.0'
34
+ type: :development
35
+ prerelease: false
36
+ version_requirements: !ruby/object:Gem::Requirement
37
+ requirements:
38
+ - - "~>"
39
+ - !ruby/object:Gem::Version
40
+ version: '10.0'
41
+ - !ruby/object:Gem::Dependency
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+ name: rspec
43
+ requirement: !ruby/object:Gem::Requirement
44
+ requirements:
45
+ - - ">="
46
+ - !ruby/object:Gem::Version
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+ version: '0'
48
+ type: :development
49
+ prerelease: false
50
+ version_requirements: !ruby/object:Gem::Requirement
51
+ requirements:
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+ - - ">="
53
+ - !ruby/object:Gem::Version
54
+ version: '0'
55
+ - !ruby/object:Gem::Dependency
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+ name: coveralls
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+ requirement: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - ">="
60
+ - !ruby/object:Gem::Version
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+ version: '0'
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+ type: :development
63
+ prerelease: false
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+ version_requirements: !ruby/object:Gem::Requirement
65
+ requirements:
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+ - - ">="
67
+ - !ruby/object:Gem::Version
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+ version: '0'
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+ description: Ruby Gem which translate RNA to Protein
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+ email:
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+ - alexmd54@gmail.com
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+ executables: []
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+ extensions: []
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+ extra_rdoc_files: []
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+ files:
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+ - ".coveralls.yml"
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+ - ".gitignore"
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+ - ".rspec"
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+ - ".travis.yml"
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+ - Gemfile
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+ - LICENSE.txt
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+ - ProteinTranslate.gemspec
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+ - README.md
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+ - Rakefile
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+ - lib/ProteinTranslate.rb
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+ - lib/ProteinTranslate/protein.rb
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+ - lib/ProteinTranslate/version.rb
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+ - spec/spec_helper.rb
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+ - spec/spec_protein.rb
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+ homepage: ''
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+ licenses:
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+ - MIT
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+ metadata: {}
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+ post_install_message:
95
+ rdoc_options: []
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+ require_paths:
97
+ - lib
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+ required_ruby_version: !ruby/object:Gem::Requirement
99
+ requirements:
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+ - - ">="
101
+ - !ruby/object:Gem::Version
102
+ version: '0'
103
+ required_rubygems_version: !ruby/object:Gem::Requirement
104
+ requirements:
105
+ - - ">="
106
+ - !ruby/object:Gem::Version
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+ version: '0'
108
+ requirements: []
109
+ rubyforge_project:
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+ rubygems_version: 2.4.6
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+ signing_key:
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+ specification_version: 4
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+ summary: Gem.
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+ test_files:
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+ - spec/spec_helper.rb
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+ - spec/spec_protein.rb