scbi_testcode 0.0.1

data/History.txt

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+=== 0.0.1 2012-07-02
+
+* Initial release

data/Manifest.txt

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+History.txt
+Manifest.txt
+PostInstall.txt
+README.rdoc
+Rakefile
+lib/scbi_testcode.rb
+lib/scbi_testcode/testcode.rb
+script/console
+script/destroy
+script/generate
+test/test_helper.rb
+test/test_scbi_testcode.rb

data/PostInstall.txt

@@ -0,0 +1,7 @@
+
+For more information on scbi_testcode, see http://scbi_testcode.rubyforge.org
+
+NOTE: Change this information in PostInstall.txt 
+You can also delete it if you don't want it.
+
+

data/README.rdoc

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+= scbi_testcode
+
+* http://www.scbi.uma.es/downloads
+
+== DESCRIPTION:
+
+scbi_testcode is a ruby gem that checks if a genetic sequence is coding or not based on the testcode algorithm.
+
+== FEATURES/PROBLEMS:
+
+Returns:
+
+* Testcode algorithm value
+* Coding conclusion (:coding, :non_coding, :unknown)
+
+
+== SYNOPSIS:
+
+Usage:
+
+s='gcagcccagccaagcactgtacaggaatcctgtgaagcagctccagctatgtgtgaagaagaggacagcactgccttggtgtgtgacaatggctctgggctctgtaaggccggctttgctggggacgatgctcccagggctgttttcccatccattgtgggacgtcccagacatcagggggtgatggtgggaatgggacaaaaagacagctacgtgggtgacgaagcacagagcaaaagaggaatcctgaccctgaagtacccgatagaacatggcatcatcaccaactgggacgacatggaaaagatctggcaccactctttctacaatgagcttcgtgttgcccctgaagagcatcccaccctgctcacggaggcacccctgaaccccaaggccaaccgggagaaaatgactcaaattatgtttgagactttcaatgtcccagccatgtatgtggctatccaggcggtgctgtctctctatgcctctggacgcacaactggcatcgtgctggactctggagatggtgtcacccacaatgtccccatctatgagggctatgccttgccccatgccatcatgcgtctggatctggctggccgagatctcactgactacctcatgaagatcctgactgagcgtggctattccttcgttactactgctgagcgtgagattgtccgggacatcaaggagaaactgtgttatgtagctctggactttgaaaatgagatggccactgccgcatggtcatcctcccttgagaagagttacgagttgcctgatgggcaagtgatcaccatcggaaatgaacgtttccgctgcccagagaccctgttccagccatccttcatcgggatggagtctgctggcatccatgaaaccacctacaacagcatcatgaagtgtgatattgacatcaggaaggacctctatgctaacaatgtcctatcagggggcaccactatgtaccctggcattgccgaccgaatgcagaaggagatcacggccctagcacccagcaccatgaagatcaagatcattgcccctccggagcgcaaatactctgtctggatcggtggctccatcctggcctctctgtccaccttccagcagatgtggatcagcaaacaggaatacgatgaagccgggccttccattgtccaccgcaaatgcttctaaaacactttcctgctcctctctgtctcatgcacacaactgtgaatgtcctgtggaattatgccttcagttcttttccaaatcattcctagccaaagctctgactcgttacctatgtgttttttaataaatctgaaataggctactggt'
+
+require 'scbi_testcode'
+
+tc=Testcode.new(s)
+
+puts tc.testcode_value
+puts tc.coding_conclusion
+
+
+== REQUIREMENTS:
+
+None
+
+== INSTALL:
+
+  gem install scbi_testcode
+
+== LICENSE:
+
+(The MIT License)
+
+Copyright (c) 2011 Dario Guerrero
+
+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/Rakefile

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+require 'rubygems'
+gem 'hoe', '>= 2.1.0'
+require 'hoe'
+require 'fileutils'
+require './lib/scbi_testcode'
+
+Hoe.plugin :newgem
+# Hoe.plugin :website
+# Hoe.plugin :cucumberfeatures
+
+# Generate all the Rake tasks
+# Run 'rake -T' to see list of generated tasks (from gem root directory)
+$hoe = Hoe.spec 'scbi_testcode' do
+  self.developer 'Dario Guerrero', 'dariogf@gmail.com'
+  # self.post_install_message = 'PostInstall.txt' # TODO remove if post-install message not required
+  self.rubyforge_name       = self.name # TODO this is default value
+  # self.extra_deps         = [['activesupport','>= 2.0.2']]
+
+end
+
+require 'newgem/tasks'
+Dir['tasks/**/*.rake'].each { |t| load t }
+
+# TODO - want other tests/tasks run by default? Add them to the list
+# remove_task :default
+# task :default => [:spec, :features]

data/lib/scbi_testcode.rb

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+$:.unshift(File.dirname(__FILE__)) unless
+  $:.include?(File.dirname(__FILE__)) || $:.include?(File.expand_path(File.dirname(__FILE__)))
+
+require 'scbi_testcode/testcode'
+
+module ScbiTestcode
+  VERSION = '0.0.1'
+end

data/lib/scbi_testcode/testcode.rb

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+#!/usr/bin/env ruby
+
+class Testcode
+
+
+  attr_accessor :testcode_value,:coding_conclusion
+  
+  def initialize(sequence)
+
+    @testcode_value=testcode_calculation(sequence)
+    @coding_conclusion=getConclusion(@testcode_value)
+  end
+  
+  def testcode_calculation(sequence)
+    sequence.downcase!
+    basesOne = [0,0,0,0];
+    basesTwo = [0,0,0,0];
+    basesThree = [0,0,0,0];
+
+    #for (j = 0; j < sequence.length; j = j + 3)
+    0.step(sequence.length-1,3) do |j|
+      if (sequence[j].chr == "g")
+        basesOne[0] = basesOne[0] + 1;
+      elsif (sequence[j].chr == "a")
+        basesOne[1] = basesOne[1] + 1;
+      elsif (sequence[j].chr == "t")
+        basesOne[2] = basesOne[2] + 1;
+      elsif (sequence[j].chr == "c")
+        basesOne[3] = basesOne[3] + 1;
+      else
+      end
+    end
+
+    #for (j = 1; j < sequence.length; j = j + 3)
+    1.step(sequence.length-1,3) do |j|
+      if (sequence[j].chr == "g")
+        basesTwo[0] = basesTwo[0] + 1;
+      elsif (sequence[j].chr == "a")
+        basesTwo[1] = basesTwo[1] + 1;
+      elsif (sequence[j].chr == "t")
+        basesTwo[2] = basesTwo[2] + 1;
+      elsif (sequence[j].chr == "c")
+        basesTwo[3] = basesTwo[3] + 1;
+      else
+      end
+    end
+
+
+    #for (j = 2; j < sequence.length; j = j + 3)
+    2.step(sequence.length-1,3) do |j|
+      if (sequence[j].chr == "g")
+        basesThree[0] = basesThree[0] + 1;
+      elsif (sequence[j].chr == "a")
+        basesThree[1] = basesThree[1] + 1;
+      elsif (sequence[j].chr == "t")
+        basesThree[2] = basesThree[2] + 1;
+      elsif (sequence[j].chr == "c")
+        basesThree[3] = basesThree[3] + 1;
+      else
+      end
+    end
+
+    paramG = calcParam(basesOne[0],basesTwo[0],basesThree[0]);
+    contentG = countBases(basesOne[0],basesTwo[0],basesThree[0]) / sequence.length.to_f;
+    posProbG = usePosParam(paramG,"g");
+    contProbG = useContParam(contentG,"g");
+    paramA = calcParam(basesOne[1],basesTwo[1],basesThree[1]);
+    contentA = countBases(basesOne[1],basesTwo[1],basesThree[1]) / sequence.length.to_f;
+    posProbA = usePosParam(paramA,"a");
+    contProbA = useContParam(contentA,"a");
+    paramT = calcParam(basesOne[2],basesTwo[2],basesThree[2]);
+    contentT = countBases(basesOne[2],basesTwo[2],basesThree[2]) / sequence.length.to_f;
+    posProbT = usePosParam(paramT,"t");
+    contProbT = useContParam(contentT,"t");
+    paramC = calcParam(basesOne[3],basesTwo[3],basesThree[3]);
+    contentC = countBases(basesOne[3],basesTwo[3],basesThree[3]) / sequence.length.to_f;
+    posProbC = usePosParam(paramC,"c");
+    contProbC = useContParam(contentC,"c");
+    valueY = posProbG * 0.31 + contProbG * 0.15 + posProbA * 0.26 + contProbA * 0.11 + posProbT * 0.33 + contProbT * 0.14 + posProbC * 0.18 + contProbC * 0.12;
+    valueY = ((valueY*1000.0).round/1000.0);
+    # return 'The TestCode value is <b>' + valueY.to_s + '</b>, which indicates that the sequence ' + getConclusion(valueY) + '.';
+    return valueY
+  end
+
+
+  def calcParam (valueOne,valueTwo,valueThree)
+    paramArray = [valueOne,valueTwo,valueThree];
+    paramArray = paramArray.sort#{|a,b| return a-b}#(compareNumbers);
+    paramValue = paramArray[2] / (paramArray[0] + 1.0);
+    #puts paramArray.to_json
+    return paramValue;
+  end
+
+  def countBases (valueOne,valueTwo,valueThree)
+    return valueOne + valueTwo + valueThree;
+  end
+
+  def usePosParam (paramValue,base)
+    arrayOfCodingProb = [];
+    codeProb = 0;
+    if (base == "g")
+      arrayOfCodingProb = [0.08,0.08,0.16,0.27,0.48,0.53,0.64,0.74,0.88,0.90]
+    elsif (base == "a")
+      arrayOfCodingProb = [0.22,0.20,0.34,0.45,0.68,0.58,0.93,0.84,0.68,0.94]
+    elsif (base == "t")
+      arrayOfCodingProb = [0.09,0.09,0.20,0.54,0.44,0.69,0.68,0.91,0.97,0.97]
+    elsif (base == "c")
+      arrayOfCodingProb = [0.23,0.30,0.33,0.51,0.48,0.66,0.81,0.70,0.70,0.80]
+    end
+
+
+    if (paramValue >= 0 and paramValue < 1.1)
+      codeProb = arrayOfCodingProb[0];
+    elsif (paramValue >=1.1 and paramValue < 1.2)
+      codeProb = arrayOfCodingProb[1];
+    elsif (paramValue >=1.2 and paramValue < 1.3)
+      codeProb = arrayOfCodingProb[2];
+    elsif (paramValue >=1.3 and paramValue < 1.4)
+      codeProb = arrayOfCodingProb[3];
+    elsif (paramValue >=1.4 and paramValue < 1.5)
+      codeProb = arrayOfCodingProb[4];
+    elsif (paramValue >=1.5 and paramValue < 1.6)
+      codeProb = arrayOfCodingProb[5];
+    elsif (paramValue >=1.6 and paramValue < 1.7)
+      codeProb = arrayOfCodingProb[6];
+    elsif (paramValue >=1.7 and paramValue < 1.8)
+      codeProb = arrayOfCodingProb[7];
+    elsif (paramValue >=1.8 and paramValue < 1.9)
+      codeProb = arrayOfCodingProb[8];
+    elsif (paramValue >=1.9)
+      codeProb = arrayOfCodingProb[9];
+    end
+
+    return codeProb;
+  end
+  def useContParam (paramValue,base)
+    arrayOfCodingProb = [];
+    codeProb = 0;
+    if (base == "g")
+      arrayOfCodingProb = [0.29,0.33,0.41,0.41,0.73,0.64,0.64,0.47,0.54,0.40]
+    elsif (base == "a")
+      arrayOfCodingProb = [0.21,0.81,0.65,0.67,0.49,0.62,0.55,0.44,0.49,0.28]
+    elsif (base == "t")
+      arrayOfCodingProb = [0.58,0.51,0.69,0.56,0.75,0.55,0.40,0.39,0.24,0.28]
+    elsif (base == "c")
+      arrayOfCodingProb = [0.31,0.39,0.44,0.43,0.59,0.59,0.64,0.51,0.64,0.82]
+    end
+
+    if (paramValue >= 0 and paramValue < 0.17)
+      codeProb = arrayOfCodingProb[0];
+    elsif (paramValue >=0.17 and paramValue < 0.19)
+      codeProb = arrayOfCodingProb[1];
+    elsif (paramValue >=0.19 and paramValue < 0.21)
+      codeProb = arrayOfCodingProb[2];
+    elsif (paramValue >=0.21 and paramValue < 0.23)
+      codeProb = arrayOfCodingProb[3];
+    elsif (paramValue >=0.23 and paramValue < 0.25)
+      codeProb = arrayOfCodingProb[4];
+    elsif (paramValue >=0.25 and paramValue < 0.27)
+      codeProb = arrayOfCodingProb[5];
+    elsif (paramValue >=0.27 and paramValue < 0.29)
+      codeProb = arrayOfCodingProb[6];
+    elsif (paramValue >=0.29 and paramValue < 0.31)
+      codeProb = arrayOfCodingProb[7];
+    elsif (paramValue >=0.31 and paramValue < 0.33)
+      codeProb = arrayOfCodingProb[8];
+    elsif (paramValue >=0.33)
+      codeProb = arrayOfCodingProb[9];
+    end
+
+    return codeProb;
+  end
+
+
+  def getConclusion (testCode)
+    codeProb = :non_coding;
+    if (testCode < 0.74)
+      codeProb = :non_coding;
+    elsif (testCode >=0.74 and testCode < 0.95)
+      codeProb = :unknown;
+    elsif (testCode >=0.95)
+      codeProb = :coding;
+    end
+
+    return codeProb;
+  end
+  
+  
+end
+
+#The Sequence Manipulation Suite: TestCode
+#Results for 1329 residue sequence "sample sequence" starting "gcagcccagc".
+#The TestCode value is 1.236, which indicates that the sequence is coding.

data/script/console

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+#!/usr/bin/env ruby
+# File: script/console
+irb = RUBY_PLATFORM =~ /(:?mswin|mingw)/ ? 'irb.bat' : 'irb'
+
+libs =  " -r irb/completion"
+# Perhaps use a console_lib to store any extra methods I may want available in the cosole
+# libs << " -r #{File.dirname(__FILE__) + '/../lib/console_lib/console_logger.rb'}"
+libs <<  " -r #{File.dirname(__FILE__) + '/../lib/scbi_testcode.rb'}"
+puts "Loading scbi_testcode gem"
+exec "#{irb} #{libs} --simple-prompt"

data/script/destroy

@@ -0,0 +1,14 @@
+#!/usr/bin/env ruby
+APP_ROOT = File.expand_path(File.join(File.dirname(__FILE__), '..'))
+
+begin
+  require 'rubigen'
+rescue LoadError
+  require 'rubygems'
+  require 'rubigen'
+end
+require 'rubigen/scripts/destroy'
+
+ARGV.shift if ['--help', '-h'].include?(ARGV[0])
+RubiGen::Base.use_component_sources! [:rubygems, :newgem, :newgem_theme, :test_unit]
+RubiGen::Scripts::Destroy.new.run(ARGV)

data/script/generate

@@ -0,0 +1,14 @@
+#!/usr/bin/env ruby
+APP_ROOT = File.expand_path(File.join(File.dirname(__FILE__), '..'))
+
+begin
+  require 'rubigen'
+rescue LoadError
+  require 'rubygems'
+  require 'rubigen'
+end
+require 'rubigen/scripts/generate'
+
+ARGV.shift if ['--help', '-h'].include?(ARGV[0])
+RubiGen::Base.use_component_sources! [:rubygems, :newgem, :newgem_theme, :test_unit]
+RubiGen::Scripts::Generate.new.run(ARGV)

data/test/test_helper.rb

@@ -0,0 +1,3 @@
+require 'stringio'
+require 'test/unit'
+require File.dirname(__FILE__) + '/../lib/scbi_testcode'

data/test/test_scbi_testcode.rb

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+require File.dirname(__FILE__) + '/test_helper.rb'
+
+class TestScbiTestcode < Test::Unit::TestCase
+
+  def setup
+  end
+  
+  def test_coding
+    s='gcagcccagccaagcactgtacaggaatcctgtgaagcagctccagctatgtgtgaagaagaggacagcactgccttggtgtgtgacaatggctctgggctctgtaaggccggctttgctggggacgatgctcccagggctgttttcccatccattgtgggacgtcccagacatcagggggtgatggtgggaatgggacaaaaagacagctacgtgggtgacgaagcacagagcaaaagaggaatcctgaccctgaagtacccgatagaacatggcatcatcaccaactgggacgacatggaaaagatctggcaccactctttctacaatgagcttcgtgttgcccctgaagagcatcccaccctgctcacggaggcacccctgaaccccaaggccaaccgggagaaaatgactcaaattatgtttgagactttcaatgtcccagccatgtatgtggctatccaggcggtgctgtctctctatgcctctggacgcacaactggcatcgtgctggactctggagatggtgtcacccacaatgtccccatctatgagggctatgccttgccccatgccatcatgcgtctggatctggctggccgagatctcactgactacctcatgaagatcctgactgagcgtggctattccttcgttactactgctgagcgtgagattgtccgggacatcaaggagaaactgtgttatgtagctctggactttgaaaatgagatggccactgccgcatggtcatcctcccttgagaagagttacgagttgcctgatgggcaagtgatcaccatcggaaatgaacgtttccgctgcccagagaccctgttccagccatccttcatcgggatggagtctgctggcatccatgaaaccacctacaacagcatcatgaagtgtgatattgacatcaggaaggacctctatgctaacaatgtcctatcagggggcaccactatgtaccctggcattgccgaccgaatgcagaaggagatcacggccctagcacccagcaccatgaagatcaagatcattgcccctccggagcgcaaatactctgtctggatcggtggctccatcctggcctctctgtccaccttccagcagatgtggatcagcaaacaggaatacgatgaagccgggccttccattgtccaccgcaaatgcttctaaaacactttcctgctcctctctgtctcatgcacacaactgtgaatgtcctgtggaattatgccttcagttcttttccaaatcattcctagccaaagctctgactcgttacctatgtgttttttaataaatctgaaataggctactggt'
+
+    tc=Testcode.new(s)
+
+    assert_equal(tc.testcode_value,1.236)
+    assert_equal(tc.coding_conclusion,:coding)
+    
+    puts tc.testcode_value
+    puts tc.coding_conclusion
+    
+    
+  end
+  
+  def test_non_coding
+    
+    s='aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaacccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc'
+
+    tc=Testcode.new(s)
+
+    assert_equal(tc.testcode_value,0.448)
+    assert_equal(tc.coding_conclusion,:non_coding)
+    
+    puts tc.testcode_value
+    puts tc.coding_conclusion
+        
+  end
+  
+  def test_unknown
+     s='AAAAATATATATTATATATATATATTATACGCTCTCTCTCTCTCTCTCTCTCTCTTCTCTCTCTCTCCCCCCCCCCCCCCCCCCCCCCCTTTTTTTTTTTTTTTTTTTTTTTTTTAAAAAAAAAAAAAAAAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccaccctgctcacggaggcacccctgaaccccaaggccaaccgggagaaaatgactcaaattatgtttgagactttcaatgtcccagccatgtatgtggctatccaggcggtgctgtctctctatgcctctggacgcacaactggcatcgtgctggactctggagatggtgtcacccacaatgtccccatctatgagggctatgccttgccccatgccatcatgcgtctggatctggctggccgagatctcactgactacctcatgaagatcctgactgagcgtggctattccttcgttactactgctgagcgtgagattgtccgggacatcaaggagaaactgtgttatgtagctctggactttgaaaatgagatggccactgccgcatggtcatcctcccttgagaagagttacgagttgcctgatgggcaagtgatcaccatcGACCGTTACACTTACGGTATCAGTATGACGTACTACGTACTACTCAGTACGTCAGTAGCTACGGTACGTACGTAGCTACGTACGTACGTAGCGTACGTATAGCGTACGTACATTC'
+
+      tc=Testcode.new(s)
+
+      assert_equal(tc.testcode_value,0.926)
+      assert_equal(tc.coding_conclusion,:unknown)
+
+      puts tc.testcode_value
+      puts tc.coding_conclusion
+    
+    
+  end
+end

metadata

@@ -0,0 +1,80 @@
+--- !ruby/object:Gem::Specification 
+name: scbi_testcode
+version: !ruby/object:Gem::Version 
+  prerelease: 
+  version: 0.0.1
+platform: ruby
+authors: 
+- Dario Guerrero
+autorequire: 
+bindir: bin
+cert_chain: []
+
+date: 2012-07-02 00:00:00 Z
+dependencies: 
+- !ruby/object:Gem::Dependency 
+  name: hoe
+  prerelease: false
+  requirement: &id001 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: 2.8.0
+  type: :development
+  version_requirements: *id001
+description: scbi_testcode is a ruby gem that checks if a genetic sequence is coding or not based on the testcode algorithm.
+email: 
+- dariogf@gmail.com
+executables: []
+
+extensions: []
+
+extra_rdoc_files: 
+- History.txt
+- Manifest.txt
+- PostInstall.txt
+files: 
+- History.txt
+- Manifest.txt
+- PostInstall.txt
+- README.rdoc
+- Rakefile
+- lib/scbi_testcode.rb
+- lib/scbi_testcode/testcode.rb
+- script/console
+- script/destroy
+- script/generate
+- test/test_helper.rb
+- test/test_scbi_testcode.rb
+homepage: http://www.scbi.uma.es/downloads
+licenses: []
+
+post_install_message: 
+rdoc_options: 
+- --main
+- README.rdoc
+require_paths: 
+- lib
+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: scbi_testcode
+rubygems_version: 1.8.24
+signing_key: 
+specification_version: 3
+summary: scbi_testcode is a ruby gem that checks if a genetic sequence is coding or not based on the testcode algorithm.
+test_files: 
+- test/test_helper.rb
+- test/test_scbi_testcode.rb