public void ValidateDnaProteinTranslation()
{
// Get Node values from XML.
string alphabetName = utilityObj.xmlUtil.GetTextValue(
Constants.SimpleDnaAlphabetNode, Constants.AlphabetNameNode);
string expectedSeq = utilityObj.xmlUtil.GetTextValue(
Constants.TranscribeNode, Constants.DnaSequence);
string expectedProtein = utilityObj.xmlUtil.GetTextValue(
Constants.TranslationNode, Constants.AminoAcidForSixCharsV2);
ISequence transcribe = null;
var seq = new Sequence(Utility.GetAlphabet(alphabetName), expectedSeq);
// Transcription of DNA Sequence.
transcribe = Transcription.Transcribe(seq);
// Protein Translation.
ISequence proteinTranslation = new Sequence(Alphabets.RNA,
new string(transcribe.Select(a => (char)a).ToArray()));
ISequence protein = ProteinTranslation.Translate(proteinTranslation);
// Validate Protein Translation.
Assert.AreEqual(expectedProtein, new string(protein.Select(a => (char)a).ToArray()));
ApplicationLog.WriteLine(
"Translation P1: Protein translation validation is completed successfully.");
}
public void ValidateDnaProteinTranslationWithOffset()
{
// Get Node values from XML.
string alphabetName = _utilityObj._xmlUtil.GetTextValue(Constants.SimpleDnaAlphabetNode,
Constants.AlphabetNameNode);
string expectedSeq = _utilityObj._xmlUtil.GetTextValue(Constants.TranscribeNode,
Constants.DnaSequence);
string expectedProtein = _utilityObj._xmlUtil.GetTextValue(Constants.TranslationNode,
Constants.AminoAcidForOffsetTwelve);
string expectedOffset = _utilityObj._xmlUtil.GetTextValue(Constants.CodonsNode,
Constants.OffsetVaule1);
ISequence seq = new Sequence(Utility.GetAlphabet(alphabetName), expectedSeq);
// Transcription of DNA Sequence.
ISequence transcribe = Transcription.Transcribe(seq);
// Protein Translation by passing offset value.
ISequence proteinTranslation = new Sequence(Alphabets.RNA, transcribe.ToString());
ISequence protein = ProteinTranslation.Translate(proteinTranslation,
Convert.ToInt32(expectedOffset, null));
// Validate Protein Translation.
Assert.AreEqual(protein.ToString(), expectedProtein);
ApplicationLog.WriteLine(
"Translation P1: Protein translation validation is completed successfully.");
}
/// <summary>
/// Translate the coding sequence of a transcript
/// </summary>
/// <param name="transcript"></param>
/// <returns></returns>
public static ISequence OneFrameTranslation(ISequence dnaSequence, bool mitochondrial)
{
ISequence rnaSequence = Transcription.Transcribe(dnaSequence);
ISequence proteinSequence;
if (!mitochondrial)
{
proteinSequence = ProteinTranslation.Translate(rnaSequence);
}
else
{
List <byte> aminoAcidSequence = new List <byte>();
for (int codonNum = 0; codonNum < (int)(rnaSequence.Count / 3); codonNum++)
{
// Check for start codon, and add 'M' if so
if (aminoAcidSequence.Count == 0 &&
CodonsVertebrateMitochondrial.START_CODONS.Contains(
new string(dnaSequence.GetSubSequence(codonNum * 3, GeneModel.CODON_SIZE).Select(bp => (char)bp).ToArray())))
{
aminoAcidSequence.Add((byte)CodonsVertebrateMitochondrial.DEFAULT_START_AA);
continue;
}
aminoAcidSequence.Add(CodonsVertebrateMitochondrial.TryLookup(rnaSequence, codonNum * 3, out byte aa) ? aa : (byte)'X');
}
proteinSequence = new Sequence(Alphabets.AmbiguousProtein, aminoAcidSequence.ToArray());
}
return(proteinSequence);
}
/// <summary>
/// This method is called when the Transcribe button is clicked.
/// </summary>
/// <param name="sender"></param>
/// <param name="e"></param>
private void button1_Click(object sender, EventArgs e)
{
// If we have an active sequence
if (cbSequences.SelectedIndex >= 0)
{
ISequence seq = _sequences[cbSequences.SelectedIndex];
// Determine the sequence type (DNA vs. RNA)
ISequence result = null, proteinResult = null;
if (seq.Alphabet == Alphabets.DNA)
{
result = Transcription.Transcribe(seq);
proteinResult = ProteinTranslation.Translate(result);
}
else if (seq.Alphabet == Alphabets.RNA)
{
result = Transcription.ReverseTranscribe(seq);
}
// Set the result.
targetSequenceText.Text = (result != null)
? GetString(result)
: string.Empty;
// Translate the protein result
proteinTextBox.Text = (proteinResult != null)
? GetString(proteinResult)
: string.Empty;
}
else
{
// Reset the fields.
targetSequenceText.Text = string.Empty;
}
}
private void JaredTest_Click(object sender, RoutedEventArgs e)
{
Sequence rna = new Sequence(Alphabets.RNA, "AUGGCGCCGAUAAUGACGGUCCUUCCUUGA");
ISequence protein = ProteinTranslation.Translate(rna);
string rnaStr = rna.ToString();
StringBuilder buff = new StringBuilder();
foreach (byte aa in protein)
{
buff.Append((char)aa);
buff.Append(' ');
}
string aaStr = buff.ToString();
}
/// <summary>
/// Not used or tested right now...
/// </summary>
/// <param name="exons"></param>
/// <param name="proteinID"></param>
/// <returns></returns>
public static Protein ThreeFrameTranslation(List <Exon> exons, string proteinID)
{
string seq = String.Join("", exons.Select(x => SequenceExtensions.ConvertToString(x.Sequence)));
if (seq.Contains('N'))
{
return(null);
}
ISequence dna_seq = new Sequence(Alphabets.DNA, seq);
ISequence rna_seq = Transcription.Transcribe(exons[0].IsStrandPlus() ? dna_seq : dna_seq.GetReverseComplementedSequence());
ISequence[] prot_seq = Enumerable.Range(0, 3).Select(i => ProteinTranslation.Translate(rna_seq, i)).ToArray();
//return the protein sequence corresponding to the longest ORF
return(new Protein(prot_seq.SelectMany(s => SequenceExtensions.ConvertToString(s).Split('*')).OrderByDescending(s => s.Length).FirstOrDefault(), proteinID));
}
public void ValidateSingleSymbolTranslation()
{
// Get Node values from XML.
string expectedSeq = _utilityObj._xmlUtil.GetTextValue(
Constants.TranscribeNode, Constants.DnaSymbol);
// Translate Single char RNA to protein.
ISequence proteinTranslation = new Sequence(Alphabets.RNA, expectedSeq);
ISequence protein = ProteinTranslation.Translate(proteinTranslation);
// Validate Protein Translation.
Assert.AreEqual(protein.ToString(), string.Empty);
ApplicationLog.WriteLine(
"Translation P1: Amino Acid validation for a given sequence was completed successfully.");
}
public void ValidateMoreThanTwelveCharsProteinTranslation()
{
// Get Node values from XML.
string expectedSeq = _utilityObj._xmlUtil.GetTextValue(
Constants.TranslationNode, Constants.RnaSequenceWithMoreThanTwelveChars);
string expectedProtein = _utilityObj._xmlUtil.GetTextValue(
Constants.TranslationNode, Constants.AminoAcidForMoreThanTwelveChars);
// Translate more than twelve characters RNA to protein.
ISequence proteinTranslation = new Sequence(Alphabets.RNA, expectedSeq);
ISequence protein = ProteinTranslation.Translate(proteinTranslation);
// Validate Protein Translation.
Assert.AreEqual(protein.ToString(), expectedProtein);
ApplicationLog.WriteLine(
"Translation P1: Protein translation validation is completed successfully.");
}
public void ValidateTwelveCharsProteinTranslationWithOffsetTwelve()
{
// Get Node values from XML.
string expectedSeq = _utilityObj._xmlUtil.GetTextValue(
Constants.TranslationNode, Constants.RnaSequenceWithTwelveChars);
string expectedOffset = _utilityObj._xmlUtil.GetTextValue(
Constants.CodonsNode, Constants.OffsetVaule3);
// Translate twelve characters RNA to protein with offset value "12".
ISequence proteinTranslation = new Sequence(Alphabets.RNA, expectedSeq);
ISequence protein = ProteinTranslation.Translate(proteinTranslation,
Convert.ToInt32(expectedOffset, null));
// Validate Protein Translation.
Assert.AreEqual(protein.ToString(), string.Empty);
ApplicationLog.WriteLine(
"Translation P1: Protein translation validation is completed successfully.");
}
public void ValidateTranslationForNull()
{
bool Exthrown = false;
// Translation by passing null Sequence.
try
{
ProteinTranslation.Translate(null);
}
catch (NullReferenceException)
{
Exthrown = true;
}
// Validate if Translate method is throwing an exception.
Assert.IsTrue(Exthrown);
ApplicationLog.WriteLine(
"Translation P2: Translate method was throwing an expection for null value.");
}
public void TestProteinTranslation()
{
Sequence rnaSeq = new Sequence(Alphabets.RNA, "AUGCGCCCG");
ISequence phase1 = ProteinTranslation.Translate(rnaSeq);
Assert.IsTrue(CompareSequenceToString("MRP", phase1));
Assert.AreEqual(Alphabets.Protein, phase1.Alphabet);
rnaSeq = new Sequence(Alphabets.RNA, "AUGCGCCCG");
phase1 = ProteinTranslation.Translate(rnaSeq, 0);
Assert.IsTrue(CompareSequenceToString("MRP", phase1));
Assert.AreEqual(Alphabets.Protein, phase1.Alphabet);
rnaSeq = new Sequence(Alphabets.RNA, "AUGCGCCCG");
phase1 = ProteinTranslation.Translate(rnaSeq, 1);
Assert.IsTrue(CompareSequenceToString("CA", phase1));
Assert.AreEqual(Alphabets.Protein, phase1.Alphabet);
}
public string Translate(string seq)
{
try {
var parser = new FastAParser();
var byteArray = Encoding.UTF8.GetBytes(seq);
Bio.Sequence result;
using (var stream = new MemoryStream(byteArray)) {
result = parser.Parse(stream).First() as Bio.Sequence;
}
var transcribed = Transcription.Transcribe(result);
return(ProteinTranslation.Translate(transcribed) is Bio.Sequence translated ? translated.ConvertToString() : "Couldn't translate to protein.");
}
catch {
return("Invalid operation. Check your sequence. Check your format (must be FASTA).");
}
}
public void ValidateTwelveCharsProteinTranslation()
{
// Get Node values from XML.
string expectedSeq = utilityObj.xmlUtil.GetTextValue(
Constants.TranslationNode, Constants.RnaSequenceWithTwelveChars);
string expectedProtein = utilityObj.xmlUtil.GetTextValue(
Constants.TranslationNode, Constants.AminoAcidForTwelveChars);
ISequence protein = null;
// Translate twelve characters RNA to protein.
var proteinTranslation = new Sequence(Alphabets.RNA, expectedSeq);
protein = ProteinTranslation.Translate(proteinTranslation);
// Validate Protein Translation.
Assert.AreEqual(new string(protein.Select(a => (char)a).ToArray()), expectedProtein);
ApplicationLog.WriteLine(
"Translation P1: Protein translation validation is completed successfully.");
}
public void ValidateTranslationForInvalidOffset()
{
// Get Node values from XML.
bool Exthrown = false;
// Translation by passing null Sequence.
try
{
ProteinTranslation.Translate(null, 10);
}
catch (ArgumentNullException)
{
Exthrown = true;
}
// Validate if Translate method is throwing an exception.
Assert.IsTrue(Exthrown);
ApplicationLog.WriteLine(
"Translation P2: Translate method was throwing an expection for null value.");
}
public void ValidateProteinTranslationForAmbiguousRna()
{
// Get Node values from XML.
string expectedSeq = utilityObj.xmlUtil.GetTextValue(
Constants.TranslationNode, Constants.AmbiguousRnaSequence);
string expectedProtein = utilityObj.xmlUtil.GetTextValue(
Constants.TranslationNode, Constants.AmbiguousProteinSequence);
ISequence protein = null;
// Translate 15 characters ambiguous RNA to protein.
var proteinTranslation = new Sequence(Alphabets.AmbiguousRNA, expectedSeq);
protein = ProteinTranslation.Translate(proteinTranslation);
// Validate Protein Translation.
Assert.AreEqual(expectedProtein, new string(protein.Select(a => (char)a).ToArray()));
ApplicationLog.WriteLine(
"Translation P1: Protein translation validation is completed successfully.");
}
public void ValidateProteinTranslationWithOffset()
{
// Get Node values from XML.
string expectedSeq = Utility._xmlUtil.GetTextValue(
Constants.TranslationNode, Constants.ExpectedSequence);
string expectedAminoAcid = Utility._xmlUtil.GetTextValue(
Constants.TranslationNode, Constants.AminoAcid);
ISequence proteinTranslation = new Sequence(Alphabets.RNA, expectedSeq);
ISequence protein = ProteinTranslation.Translate(proteinTranslation, 0);
// Validate Protein Translation.
Assert.AreEqual(protein.Alphabet, Alphabets.Protein);
Assert.AreEqual(protein.ToString(), expectedAminoAcid);
ApplicationLog.WriteLine(string.Format(null,
"Translation BVT: Amino Acid {0} is expected.", protein));
ApplicationLog.WriteLine(
"Translation BVT: Amino Acid validation for a given sequence was completed successfully.");
}
public void ValidateSixCharsProteinTranslation()
{
// Get Node values from XML.
string expectedSeq = _utilityObj._xmlUtil.GetTextValue(
Constants.TranslationNode, Constants.RnaSequence);
string expectedProtein = _utilityObj._xmlUtil.GetTextValue(
Constants.TranslationNode, Constants.AminoAcidForSixChars);
string expectedOffset = _utilityObj._xmlUtil.GetTextValue(
Constants.CodonsNode, Constants.OffsetVaule);
// Translate Six characters RNA to protein.
ISequence proteinTranslation = new Sequence(Alphabets.RNA, expectedSeq);
ISequence protein = ProteinTranslation.Translate(proteinTranslation,
Convert.ToInt32(expectedOffset, null));
// Validate Protein Translation.
Assert.AreEqual(protein.ToString(), expectedProtein);
ApplicationLog.WriteLine(
"Translation P1: Protein translation validation is completed successfully.");
}
public void ValidateProteinTranslation()
{
// Get Node values from XML.
string expectedSeq = utilityObj.xmlUtil.GetTextValue(
Constants.TranslationNode, Constants.ExpectedSequence);
string expectedAminoAcid = utilityObj.xmlUtil.GetTextValue(
Constants.TranslationNode, Constants.AminoAcid);
ISequence protein = null;
Sequence proteinTranslation = new Sequence(Alphabets.RNA, expectedSeq);
protein = ProteinTranslation.Translate(proteinTranslation);
// Validate Protein Translation.
Assert.AreEqual(protein.Alphabet, Alphabets.Protein);
Assert.AreEqual(new string(protein.Select(a => (char)a).ToArray()), expectedAminoAcid);
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Translation BVT: Amino Acid {0} is expected.", protein));
ApplicationLog.WriteLine(
"Translation BVT: Amino Acid validation for a given sequence was completed successfully.");
}
public void TestProteinTranslationInvalid()
{
try
{
Sequence rnaSeq = new Sequence(Alphabets.RNA, "AUGCGCCCG");
ISequence phase1 = ProteinTranslation.Translate(rnaSeq, 100);
Assert.Fail();
}
catch (ArgumentException)
{
}
try
{
Sequence dnaSeq = new Sequence(Alphabets.DNA, "ATGC");
ISequence phase1 = ProteinTranslation.Translate(dnaSeq);
Assert.Fail();
}
catch (InvalidOperationException)
{
}
}
public void ValidateMoreThanTwelveCharsProteinTranslationWithOffsetTwelve()
{
// Get Node values from XML.
string expectedSeq = utilityObj.xmlUtil.GetTextValue(
Constants.TranslationNode, Constants.RnaSequenceWithMoreThanTwelveChars);
string expectedProtein = utilityObj.xmlUtil.GetTextValue(
Constants.TranslationNode, Constants.AminoAcidForOffsetTwelve);
string expectedOffset = utilityObj.xmlUtil.GetTextValue(
Constants.CodonsNode, Constants.OffsetVaule3);
ISequence protein = null;
// Translate twelve characters RNA to protein with offset value "12".
var proteinTranslation = new Sequence(Alphabets.RNA, expectedSeq);
protein = ProteinTranslation.Translate(proteinTranslation,
Convert.ToInt32(expectedOffset, null));
// Validate Protein Translation.
Assert.AreEqual(new string(protein.Select(a => (char)a).ToArray()), expectedProtein);
ApplicationLog.WriteLine(
"Translation P1: Protein translation validation is completed successfully.");
}
public void TestProteinTranslation()
{
Sequence rnaSeq = new Sequence(Alphabets.RNA, "AUGCGCCCG");
ISequence phase1 = ProteinTranslation.Translate(rnaSeq);
Assert.IsTrue(CompareSequenceToString("MRP", phase1));
Assert.AreEqual(Alphabets.Protein, phase1.Alphabet);
rnaSeq = new Sequence(Alphabets.RNA, "AUGCGCCCG");
phase1 = ProteinTranslation.Translate(rnaSeq, 0);
Assert.IsTrue(CompareSequenceToString("MRP", phase1));
Assert.AreEqual(Alphabets.Protein, phase1.Alphabet);
rnaSeq = new Sequence(Alphabets.RNA, "AUGCGCCCG");
phase1 = ProteinTranslation.Translate(rnaSeq, 1);
Assert.IsTrue(CompareSequenceToString("CA", phase1));
Assert.AreEqual(Alphabets.Protein, phase1.Alphabet);
rnaSeq = new Sequence(Alphabets.AmbiguousRNA, "NCUCCAUCUUNUUGGAACAAA");
phase1 = ProteinTranslation.Translate(rnaSeq, 0);
Assert.IsTrue(CompareSequenceToString("XPSXWNK", phase1));
Assert.AreEqual(Alphabets.AmbiguousProtein, phase1.Alphabet);
}
/// <summary>
/// This is called to transform sequences
/// </summary>
private void OnTransformSequences()
{
TranslatedSequences.Clear();
foreach (var sequence in SelectedSequences)
{
ISequence result = null;
try
{
if (sequence.Alphabet == Alphabets.DNA)
{
result = Transcription.Transcribe(sequence);
result.Metadata["Documentation"] = "Transcribed RNA from DNA sequence " + sequence.ID;
}
else if (sequence.Alphabet == Alphabets.RNA)
{
var alphabet = sequence.Alphabet;
var noGapSequence = new Sequence(alphabet, sequence.Where(b => !alphabet.CheckIsGap(b)).ToArray());
result = ProteinTranslation.Translate(noGapSequence);
result.Metadata["Documentation"] = "Translated Protein from RNA sequence " + sequence.ID;
}
}
catch (Exception ex)
{
ShowError("Translation Failed",
"Unable to transcribe/translate sequence", ex);
}
if (result != null)
{
TranslatedSequences.Add(result);
}
}
}
public void ValidateTranslationOfAmbiguousRnaUsingRnaAlphabet()
{
// Get Node values from XML.
string rnaSequenceStr = utilityObj.xmlUtil.GetTextValue(Constants.TranslationNode,
Constants.AmbiguousRnaSequence);
bool Exthrown = false;
// Build ambiguous RNA sequence using an RNA alphabet.
ISequence rnaSequence = new Sequence(Alphabets.RNA, rnaSequenceStr, false);
// Call a translate method by passing negative offset value.
try
{
ProteinTranslation.Translate(rnaSequence);
}
catch (InvalidOperationException)
{
Exthrown = true;
}
// Validate if Translate method is throwing an exception.
Assert.IsTrue(Exthrown);
ApplicationLog.WriteLine(
"Translation P2: Translate method was throwing an expection for ambiguous RNA.");
}
public void ValidateTranslationForNegativeOffset()
{
// Get Node values from XML.
string expectedSeq = _utilityObj._xmlUtil.GetTextValue(Constants.TranslationNode,
Constants.RnaSequence);
bool Exthrown = false;
// Translate Six characters RNA to protein.
ISequence proteinTranslation = new Sequence(Alphabets.RNA, expectedSeq);
// Call a translate method by passing negative offset value.
try
{
ProteinTranslation.Translate(proteinTranslation, -10);
}
catch (ArgumentOutOfRangeException)
{
Exthrown = true;
}
// Validate if Translate method is throwing an exception.
Assert.IsTrue(Exthrown);
ApplicationLog.WriteLine(
"Translation P2: Translate method was throwing an expection for null value.");
}
/// <summary>
/// The execution method for the activity.
/// </summary>
/// <param name="executionContext">The execution context.</param>
/// <returns>The execution status.</returns>
protected override ActivityExecutionStatus Execute(ActivityExecutionContext executionContext)
{
Protein = ProteinTranslation.Translate(RnaSequence, initialSequenceOffset);
return(ActivityExecutionStatus.Closed);
}
public void Stops_translation_if_stop_codon_present()
{
Assert.Equal(new[] { "Methionine", "Phenylalanine" }, ProteinTranslation.Translate("AUGUUUUAA"));
}
public void Identifies_methionine_codons(string codon)
{
Assert.Equal(new[] { "Methionine" }, ProteinTranslation.Translate(codon));
}
public void Stops_translation_of_longer_strand()
{
Assert.Equal(new[] { "Tryptophan", "Cysteine", "Tyrosine" }, ProteinTranslation.Translate("UGGUGUUAUUAAUGGUUU"));
}
public void Throws_for_invalid_codons()
{
Assert.Throws <Exception>(() => ProteinTranslation.Translate("CARROT"));
}
public ISequence Translate(SequenceModel sequenceData)
{
var sequence = _provider.Provide(sequenceData?.FileName, sequenceData?.Content)?.First();
return(ProteinTranslation.Translate(sequence));
}