/// <summary>
/// Get Amino Acids Using Ambiguous RNA Codons.
/// </summary>
/// <param name="firstPos">First position.</param>
/// <param name="secondPos">Second position.</param>
/// <param name="thirdPos">Third position.</param>
/// <returns>Returns list of bytes.</returns>
private static IList <byte> GetAminoAcidsUsingAmbigiousRNACodons(byte firstPos, byte secondPos, byte thirdPos)
{
IList <byte> aminoAcids = new List <byte>();
HashSet <byte> firstBasicSymbols;
RnaAlphabet.Instance.TryGetBasicSymbols(firstPos, out firstBasicSymbols);
HashSet <byte> secondBasicSymbols;
RnaAlphabet.Instance.TryGetBasicSymbols(secondPos, out secondBasicSymbols);
HashSet <byte> thirdBasicSymbols;
RnaAlphabet.Instance.TryGetBasicSymbols(thirdPos, out thirdBasicSymbols);
foreach (byte firstPosAlphabet in firstBasicSymbols)
{
foreach (byte secondPosAlphabet in secondBasicSymbols)
{
foreach (byte thirdPosAlphabet in thirdBasicSymbols)
{
aminoAcids.Add(Codons.Lookup(firstPosAlphabet, secondPosAlphabet, thirdPosAlphabet));
}
}
}
return(aminoAcids);
}
/// <summary>
/// Get Amino Acids Using Ambiguous DNA Codons.
/// </summary>
/// <param name="firstPos">First position.</param>
/// <param name="secondPos">Second position.</param>
/// <param name="thirdPos">Third position.</param>
/// <returns>Returns list of bytes.</returns>
private static IList <byte> GetAminoAcidsUsingAmbigiousDNACodons(byte firstPos, byte secondPos, byte thirdPos)
{
IList <byte> aminoAcids = new List <byte>();
HashSet <byte> firstBasicSymbols;
DnaAlphabet.Instance.TryGetBasicSymbols(firstPos, out firstBasicSymbols);
HashSet <byte> secondBasicSymbols;
DnaAlphabet.Instance.TryGetBasicSymbols(secondPos, out secondBasicSymbols);
HashSet <byte> thirdBasicSymbols;
DnaAlphabet.Instance.TryGetBasicSymbols(thirdPos, out thirdBasicSymbols);
foreach (byte firstPosAlphabet in firstBasicSymbols)
{
byte firstPosNucleotide = Transcription.GetRnaComplement(firstPosAlphabet);
foreach (byte secondPosAlphabet in secondBasicSymbols)
{
byte secondPosNucleotide = Transcription.GetRnaComplement(secondPosAlphabet);
foreach (byte thirdPosAlphabet in thirdBasicSymbols)
{
aminoAcids.Add(Codons.Lookup(firstPosNucleotide, secondPosNucleotide, Transcription.GetRnaComplement(thirdPosAlphabet)));
}
}
}
return(aminoAcids);
}
public void ValidateLookupWithDnaSequence()
{
string alphabetName = _utilityObj._xmlUtil.GetTextValue(
Constants.SimpleDnaAlphabetNode, Constants.AlphabetNameNode);
string expectedSeq = _utilityObj._xmlUtil.GetTextValue(
Constants.TranscribeNode, Constants.DnaSequence);
string expectedAminoAcid = _utilityObj._xmlUtil.GetTextValue(
Constants.CodonsNode, Constants.DnaSeqAminoAcid);
string expectedOffset = _utilityObj._xmlUtil.GetTextValue(
Constants.CodonsNode, Constants.OffsetVaule);
ISequence seq = new Sequence(Utility.GetAlphabet(alphabetName), expectedSeq);
// Transcribe DNA to RNA.
ISequence transcribe = Transcription.Transcribe(seq);
// Validate Codons lookup method.
AminoAcid aminoAcid = Codons.Lookup(transcribe, Convert.ToInt32(expectedOffset, null));
// Validate amino acids for a given sequence.
Assert.AreEqual(aminoAcid.Name.ToString((IFormatProvider)null), expectedAminoAcid);
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Translation P1: Amino Acid {0} is expected.", aminoAcid));
ApplicationLog.WriteLine(
"Translation P1: Amino Acid validation for a given sequence was completed successfully.");
}
public void ValidateAminoAcidForSequence()
{
// Get Node values from XML.
string alphabetName = utilityObj.xmlUtil.GetTextValue(Constants.SimpleRnaAlphabetNode,
Constants.AlphabetNameNode);
string expectedSeq = utilityObj.xmlUtil.GetTextValue(Constants.CodonsNode,
Constants.ExpectedNormalString);
string expectedAminoAcid = utilityObj.xmlUtil.GetTextValue(Constants.CodonsNode,
Constants.SeqAminoAcidV2);
string expectedOffset = utilityObj.xmlUtil.GetTextValue(Constants.CodonsNode,
Constants.OffsetVaule1);
string aminoAcid = null;
Sequence seq = new Sequence(Utility.GetAlphabet(alphabetName), expectedSeq);
// Validate Codons lookup method.
aminoAcid = Codons.Lookup(seq, Convert.ToInt32(expectedOffset, null)).ToString();
// Validate amino acids for each triplet.
Assert.AreEqual(expectedAminoAcid, aminoAcid);
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Translation BVT: Amino Acid {0} is expected.", aminoAcid));
ApplicationLog.WriteLine(
"Translation BVT: Amino Acid validation for a given sequence was completed successfully.");
}
public void ValidateLookupWithZeroOffset()
{
string alphabetName = utilityObj.xmlUtil.GetTextValue(Constants.SimpleRnaAlphabetNode,
Constants.AlphabetNameNode);
string expectedSeq = utilityObj.xmlUtil.GetTextValue(Constants.CodonsNode,
Constants.SequenceWithmoreThanTweleveChars);
string expectedAminoAcid = utilityObj.xmlUtil.GetTextValue(Constants.CodonsNode,
Constants.OffsetOneMoreThanTwelveCharsAminoAcidV2);
string expectedOffset = utilityObj.xmlUtil.GetTextValue(Constants.CodonsNode,
Constants.OffsetVaule4);
string aminoAcid = null;
Sequence seq = new Sequence(Utility.GetAlphabet(alphabetName), expectedSeq);
// Validate Codons lookup method.
aminoAcid = Codons.Lookup(seq, Convert.ToInt32(expectedOffset, null)).ToString();
// Validate amino acids for a given sequence.
Assert.AreEqual(expectedAminoAcid, aminoAcid);
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Translation P2: Amino Acid {0} is expected.", aminoAcid));
ApplicationLog.WriteLine(
"Translation P2: Amino Acid validation for a given sequence was completed successfully.");
}
/// <summary>
/// Translates the RNA sequence passed in as a source into a Protein
/// sequence of amino acids. Allows the setting of a particular index
/// into the source sequence for the start of translation.
///
/// For instance if you wanted to translate all the phases of an RNA
/// sequence you could perform the following:
///
/// Sequence rnaSeq = new Sequence(Alphabets.RNA), "AUGCGCCCG");
/// Sequence phase1 = ProteinTranslation.Translate(rnaSeq, 0);
/// Sequence phase2 = ProteinTranslation.Translate(rnaSeq, 1);
/// Sequence phase3 = ProteinTranslation.Translate(rnaSeq, 2);
/// </summary>
/// <param name="source">The source RNA sequence to translate from</param>
/// <param name="nucleotideOffset">
/// An offset into the source sequence from which to begin translation.
/// Note that this offset begins counting from 0. Set this parameter to
/// 0 to translate the entire source sequence. Set it to 1 to ignore the
/// first nucleotide in the source sequence, etc.
/// </param>
/// <returns></returns>
public static ISequence Translate(ISequence source, int nucleotideOffset)
{
Sequence result = new Sequence(Alphabets.Protein);
result.IsReadOnly = false;
result.ID = "AA: " + source.ID;
result.DisplayID = "Amino Acids translated from: " + source.DisplayID;
for (int i = nucleotideOffset; i < source.Count - 2; i += 3)
{
result.Add(Codons.Lookup(source, i));
}
return(result);
}
/// <summary>
/// Passes a valid RNA sequence with offset value and validates if
/// Lookup(sequence) method is returning corresponding amino acid.
/// </summary>
/// <param name="sequenceNode">Sequence xml node.</param>
/// <param name="offsetNode">Offset node with value.</param>
/// <param name="aminoAcidNode">Expected amino acid value.</param>
void ValidateCodonsTranslationWithOffset(string sequenceNode,
string offsetNode, string aminoAcidNode)
{
// Get Node values from XML.
string expectedSeq = _utilityObj._xmlUtil.GetTextValue(Constants.TranslationNode,
sequenceNode);
string expectedAminoAcid = _utilityObj._xmlUtil.GetTextValue(Constants.TranslationNode,
aminoAcidNode);
string expectedOffset = _utilityObj._xmlUtil.GetTextValue(Constants.CodonsNode, offsetNode);
// Translate Rna to corresponding amino acid.
ISequence codonsTranslation = new Sequence(Alphabets.RNA, expectedSeq);
AminoAcid aminoAcid = Codons.Lookup(codonsTranslation, int.Parse(expectedOffset, null));
// Validate Codon Translation.
Assert.AreEqual(expectedAminoAcid.ToString((IFormatProvider)null), aminoAcid.Symbol.ToString((IFormatProvider)null));
ApplicationLog.WriteLine(
"Translation P1: Codon translation with offset validation is completed successfully.");
}
public void ValidateLookupWithOffsetValueSix()
{
string alphabetName = utilityObj.xmlUtil.GetTextValue(
Constants.SimpleRnaAlphabetNode, Constants.AlphabetNameNode);
string expectedSeq = utilityObj.xmlUtil.GetTextValue(
Constants.CodonsNode, Constants.ExpectedNormalString);
string expectedAminoAcid = utilityObj.xmlUtil.GetTextValue(
Constants.CodonsNode, Constants.OffsetZeroSixCharsAminoAcidV2);
string expectedOffset = utilityObj.xmlUtil.GetTextValue(
Constants.CodonsNode, Constants.OffsetVaule2);
var seq = new Sequence(Utility.GetAlphabet(alphabetName), expectedSeq);
// Validate Codons lookup method.
string aminoAcid = Codons.Lookup(seq, Convert.ToInt32(expectedOffset, null)).ToString();
// Validate amino acids for a given sequence.
Assert.AreEqual(expectedAminoAcid, aminoAcid);
ApplicationLog.WriteLine(string.Format(null,
"Translation P1: Amino Acid {0} is expected.", aminoAcid));
ApplicationLog.WriteLine(
"Translation P1: Amino Acid validation for a given sequence was completed successfully.");
}
public void ValidateAminoAcid()
{
// Get Node values from XML.
string expectedNucleo = Utility._xmlUtil.GetTextValue(
Constants.CodonsNode, Constants.Nucleotide);
string expectedAminoAcid = Utility._xmlUtil.GetTextValue(
Constants.CodonsNode, Constants.AminoAcid);
// Create Nucleotide objects.
Nucleotide firstNucleo1 = new Nucleotide(expectedNucleo[0], "Uracil");
Nucleotide firstNucleo2 = new Nucleotide(expectedNucleo[1], "Uracil");
Nucleotide firstNucleo3 = new Nucleotide(expectedNucleo[2], "Uracil");
// Validate Codons lookup method.
AminoAcid aminoAcid = Codons.Lookup(firstNucleo1, firstNucleo2, firstNucleo3);
// Validate amino acids for each triplet.
Assert.AreEqual(aminoAcid.Name.ToString(), expectedAminoAcid);
ApplicationLog.WriteLine(string.Format(null,
"Translation BVT: Amino Acid {0} is expected.", aminoAcid));
ApplicationLog.WriteLine(
"Translation BVT: Amino Acid validation for a given triplets of nucleotide was completed successfully.");
}
