Class: Testcode

Inherits:
Object
  • Object
show all
Defined in:
lib/scbi_testcode/testcode.rb

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(sequence) ⇒ Testcode

Returns a new instance of Testcode.



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# File 'lib/scbi_testcode/testcode.rb', line 8

def initialize(sequence)

  @testcode_value=testcode_calculation(sequence)
  @coding_conclusion=getConclusion(@testcode_value)
end

Instance Attribute Details

#coding_conclusion ⇒ Object

Returns the value of attribute coding_conclusion.



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# File 'lib/scbi_testcode/testcode.rb', line 6

def coding_conclusion
  @coding_conclusion
end

#testcode_value ⇒ Object

Returns the value of attribute testcode_value.



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# File 'lib/scbi_testcode/testcode.rb', line 6

def testcode_value
  @testcode_value
end

Instance Method Details

#calcParam(valueOne, valueTwo, valueThree) ⇒ Object 



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# File 'lib/scbi_testcode/testcode.rb', line 86

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

#countBases(valueOne, valueTwo, valueThree) ⇒ Object 



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# File 'lib/scbi_testcode/testcode.rb', line 94

def countBases (valueOne,valueTwo,valueThree)
  return valueOne + valueTwo + valueThree;
end

#getConclusion(testCode) ⇒ Object 



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# File 'lib/scbi_testcode/testcode.rb', line 175

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

#testcode_calculation(sequence) ⇒ Object 



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# File 'lib/scbi_testcode/testcode.rb', line 14

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

#useContParam(paramValue, base) ⇒ Object 



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# File 'lib/scbi_testcode/testcode.rb', line 136

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

#usePosParam(paramValue, base) ⇒ Object 



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# File 'lib/scbi_testcode/testcode.rb', line 98

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