/// <summary>
/// Writes the specified QualitativeSequence in FastQ format to the file.
/// </summary>
/// <param name="qualitativeSequence">QualitativeSequence to write.</param>
public void Write(QualitativeSequence qualitativeSequence)
{
if (qualitativeSequence == null)
{
throw new ArgumentNullException("qualitativeSequence");
}
if (this.streamWriter == null)
{
throw new InvalidOperationException(Properties.Resource.FileNotOpened);
}
string header = qualitativeSequence.ID;
string lengthStr = " length=";
if (qualitativeSequence.ID.Contains(lengthStr))
{
int startIndex = qualitativeSequence.ID.LastIndexOf(lengthStr, StringComparison.OrdinalIgnoreCase);
header = header.Substring(0, startIndex + 8) + qualitativeSequence.Count;
}
// Write to stream.
this.streamWriter.WriteLine("@" + header);
byte[] sequenceBytes = qualitativeSequence.ToArray();
this.streamWriter.WriteLine(UTF8Encoding.UTF8.GetString(sequenceBytes, 0, sequenceBytes.Length));
this.streamWriter.WriteLine("+" + header);
byte[] qualityValues = QualitativeSequence.ConvertEncodedQualityScore(qualitativeSequence.FormatType, this.FormatType, qualitativeSequence.GetEncodedQualityScores());
this.streamWriter.WriteLine(UTF8Encoding.UTF8.GetString(qualityValues, 0, qualityValues.Length));
if (this.AutoFlush)
{
this.streamWriter.Flush();
}
}
public void ConvertIlluminaToSangerAndSolexa()
{
// Gets the actual sequence and the Qual score from the Xml
string illuminaSequence = utilityObj.xmlUtil.GetTextValue(
Constants.IlluminaToSangerAndSolexaNode, Constants.IlluminaSequence);
string illuminaQualScore = utilityObj.xmlUtil.GetTextValue(
Constants.IlluminaToSangerAndSolexaNode, Constants.IlluminaQualScore);
string expectedSangerQualScore = utilityObj.xmlUtil.GetTextValue(
Constants.IlluminaToSangerAndSolexaNode, Constants.SangerQualScore);
string expectedSolexaQualScore = utilityObj.xmlUtil.GetTextValue(
Constants.IlluminaToSangerAndSolexaNode, Constants.SolexaQualScore);
byte[] illuminaSequenceinBytes = Encoding.UTF8.GetBytes(illuminaSequence);
byte[] illuminaQualScoreinBytes = Encoding.UTF8.GetBytes(illuminaQualScore);
byte[] sangerQualScore = QualitativeSequence.ConvertEncodedQualityScore(FastQFormatType.Illumina_v1_3, FastQFormatType.Sanger, illuminaQualScoreinBytes);
string qualSequenceSanger = new string(Encoding.UTF8.GetChars(sangerQualScore));
// Validate converted sanger score.
Assert.AreEqual(expectedSangerQualScore, qualSequenceSanger);
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Qualitative Sequence BVT:Qualitative Sanger score type {0} is as expected.",
sangerQualScore));
byte[] solexaQualScore = QualitativeSequence.ConvertEncodedQualityScore(FastQFormatType.Illumina_v1_3, FastQFormatType.Solexa_Illumina_v1_0, illuminaQualScoreinBytes);
string qualSequenceSolexa = new string(Encoding.UTF8.GetChars(solexaQualScore));
// Validate converted illumina score.
Assert.AreEqual(expectedSolexaQualScore, qualSequenceSolexa);
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Qualitative Sequence BVT:Qualitative Solexa format type {0} is as expected.",
illuminaQualScore));
}
public void TestConvertFromSolexa_Illumina_v1_0ToSanger()
{
byte[] sangerScores;
byte[] solexaScores = new byte[1];
solexaScores[0] = (byte)59;
sangerScores = QualitativeSequence.ConvertEncodedQualityScore(FastQFormatType.Solexa_Illumina_v1_0, FastQFormatType.Sanger, solexaScores);
Assert.IsNotNull((object)sangerScores);
Assert.AreEqual(1, sangerScores.Length);
Assert.AreEqual((byte)33, sangerScores[0]);
}
public void TestConvertFromIllumina_v1_3ToSanger()
{
byte[] sangerScores;
byte[] illuminaScores = new byte[2];
illuminaScores[0] = (byte)64;
illuminaScores[1] = (byte)64;
sangerScores = QualitativeSequence.ConvertEncodedQualityScore(FastQFormatType.Illumina_v1_3, FastQFormatType.Sanger, illuminaScores);
Assert.IsNotNull((object)sangerScores);
Assert.AreEqual(2, sangerScores.Length);
Assert.AreEqual((byte)33, sangerScores[0]);
Assert.AreEqual((byte)33, sangerScores[1]);
}
public void TestConvertFromIllumina_v1_3ToSolexa_Illumina_v1_0()
{
byte[] solexaScores;
byte[] illuminaScores = new byte[2];
illuminaScores[0] = (byte)65;
illuminaScores[1] = (byte)65;
solexaScores = QualitativeSequence.ConvertEncodedQualityScore(FastQFormatType.Illumina_v1_3, FastQFormatType.Solexa_Illumina_v1_0, illuminaScores);
Assert.IsNotNull((object)solexaScores);
Assert.AreEqual(2, solexaScores.Length);
Assert.AreEqual((byte)59, solexaScores[0]);
Assert.AreEqual((byte)59, solexaScores[1]);
}
public void TestConvertFromSangerToIllumina_v1_3()
{
byte[] illuminaScores;
byte[] sangerScores = new byte[2];
sangerScores[0] = (byte)33;
sangerScores[1] = (byte)33;
illuminaScores = QualitativeSequence.ConvertEncodedQualityScore(FastQFormatType.Sanger, FastQFormatType.Illumina_v1_3, sangerScores);
Assert.IsNotNull((object)illuminaScores);
Assert.AreEqual <int>(2, illuminaScores.Length);
Assert.AreEqual <byte>((byte)64, illuminaScores[0]);
Assert.AreEqual <byte>((byte)64, illuminaScores[1]);
}
public void TestConvertFromSangerToSolexa_Illumina_v1_0()
{
byte[] solexaScores;
byte[] sangerScores = new byte[2];
sangerScores[0] = (byte)34;
sangerScores[1] = (byte)34;
solexaScores = QualitativeSequence.ConvertEncodedQualityScore(FastQFormatType.Sanger, FastQFormatType.Solexa_Illumina_v1_0, sangerScores);
Assert.IsNotNull((object)solexaScores);
Assert.AreEqual <int>(2, solexaScores.Length);
Assert.AreEqual <byte>((byte)59, solexaScores[0]);
Assert.AreEqual <byte>((byte)59, solexaScores[1]);
}
/// <summary>
/// Write out a sequence to the given stream writer.
/// </summary>
/// <param name="writer"></param>
/// <param name="qualitativeSequence"></param>
private void Format(StreamWriter writer, IQualitativeSequence qualitativeSequence)
{
string header = qualitativeSequence.ID;
const string LengthStr = " length=";
if (qualitativeSequence.ID.Contains(LengthStr))
{
int startIndex = qualitativeSequence.ID.LastIndexOf(LengthStr, StringComparison.OrdinalIgnoreCase);
header = header.Substring(0, startIndex + 8) + qualitativeSequence.Count;
}
// Write to stream.
writer.WriteLine("@" + header);
byte[] sequenceBytes = qualitativeSequence.ToArray();
writer.WriteLine(Encoding.UTF8.GetString(sequenceBytes, 0, sequenceBytes.Length));
writer.WriteLine("+" + header);
byte[] qualityValues = QualitativeSequence.ConvertEncodedQualityScore(qualitativeSequence.FormatType, this.FormatType, qualitativeSequence.GetEncodedQualityScores());
writer.WriteLine(Encoding.UTF8.GetString(qualityValues, 0, qualityValues.Length));
if (this.AutoFlush)
{
writer.Flush();
}
}
/// <summary>
/// Writes SAMAlignedSequence to specified text writer.
/// </summary>
/// <param name="alignedSequence">SAM aligned sequence to write</param>
/// <param name="writer">Text writer.</param>
public static void WriteSAMAlignedSequence(IAlignedSequence alignedSequence, TextWriter writer)
{
if (writer == null)
{
throw new ArgumentNullException("writer");
}
if (alignedSequence == null)
{
throw new ArgumentNullException("alignedSequence");
}
SAMAlignedSequenceHeader alignedHeader = alignedSequence.Metadata[Helper.SAMAlignedSequenceHeaderKey] as SAMAlignedSequenceHeader;
if (alignedHeader == null)
{
throw new ArgumentException(Properties.Resource.SAM_AlignedSequenceHeaderMissing);
}
ISequence sequence = alignedSequence.Sequences[0];
if (!(sequence.Alphabet is DnaAlphabet))
{
throw new ArgumentException(Properties.Resource.SAMFormatterSupportsDNAOnly);
}
string seq = "*";
if (sequence.Count > 0)
{
char[] symbols = new char[sequence.Count];
for (int i = 0; i < sequence.Count; i++)
{
symbols[i] = (char)sequence[i];
}
seq = new string(symbols);
}
string qualValues = "*";
QualitativeSequence qualSeq = sequence as QualitativeSequence;
if (qualSeq != null)
{
byte[] bytes = qualSeq.GetEncodedQualityScores();
// if FormatType is not sanger then convert the quality scores to sanger.
if (qualSeq.FormatType != FastQFormatType.Sanger)
{
bytes = QualitativeSequence.ConvertEncodedQualityScore(qualSeq.FormatType, FastQFormatType.Sanger, bytes);
}
qualValues = System.Text.ASCIIEncoding.ASCII.GetString(bytes);
}
writer.Write(AlignedSequenceFormat,
alignedHeader.QName, (int)alignedHeader.Flag, alignedHeader.RName,
alignedHeader.Pos, alignedHeader.MapQ, alignedHeader.CIGAR,
alignedHeader.MRNM.Equals(alignedHeader.RName) ? "=" : alignedHeader.MRNM,
alignedHeader.MPos, alignedHeader.ISize, seq, qualValues);
foreach (var j in alignedHeader.OptionalFields)
{
writer.Write(OptionalFieldFormat, j.Tag,
j.VType, j.Value);
}
writer.WriteLine();
}
public void ConvertSangerToSolexaAndIllumina()
{
// Gets the actual sequence and the Qual score from the Xml
string sangerSequence = utilityObj.xmlUtil.GetTextValue(
Constants.SangerToSolexaAndIlluminaNode, Constants.SangerSequence);
string expectedSolexaSequence = utilityObj.xmlUtil.GetTextValue(
Constants.SangerToSolexaAndIlluminaNode, Constants.SolexaSequence);
string expectedIlluminaSequence = utilityObj.xmlUtil.GetTextValue(
Constants.SangerToSolexaAndIlluminaNode, Constants.IlluminaSequence);
string sangerQualScore = utilityObj.xmlUtil.GetTextValue(
Constants.SangerToSolexaAndIlluminaNode, Constants.SangerQualScore);
string expectedSolexaQualScore = utilityObj.xmlUtil.GetTextValue(
Constants.SangerToSolexaAndIlluminaNode, Constants.SolexaQualScore);
string expectedIlluminaQualScore = utilityObj.xmlUtil.GetTextValue(
Constants.SangerToSolexaAndIlluminaNode, Constants.IlluminaQualScore);
string solexaQualScore = null;
string illuminaQualScore = null;
byte[] scoreValue = Encoding.UTF8.GetBytes(sangerQualScore);
// Create a Sanger qualitative sequence.
QualitativeSequence sangerQualSequence = new QualitativeSequence(Alphabets.DNA,
FastQFormatType.Sanger, sangerSequence, sangerQualScore);
// Convert Sanger to Solexa.
QualitativeSequence solexaQualSequence = sangerQualSequence.ConvertTo(
FastQFormatType.Solexa_Illumina_v1_0);
byte[] sangerToSolexa = QualitativeSequence.ConvertEncodedQualityScore(FastQFormatType.Sanger, FastQFormatType.Solexa_Illumina_v1_0, scoreValue);
var scores = solexaQualSequence.GetEncodedQualityScores();
solexaQualScore = Encoding.UTF8.GetString(scores, 0, scores.Length);
// Validate converted solexa score.
string qualSequence = new string(Encoding.UTF8.GetChars(sangerToSolexa));
Assert.AreEqual(expectedSolexaQualScore, qualSequence);
Assert.AreEqual(solexaQualScore, expectedSolexaQualScore);
string solexaQualString = new string(solexaQualSequence.Select(a => (char)a).ToArray());
Assert.AreEqual(solexaQualString, expectedSolexaSequence);
ApplicationLog.WriteLine(string.Format(null,
"Qualitative Sequence BVT:Qualitative Solexa score type {0} is as expected.",
solexaQualScore));
// Convert Sanger to Illumina.
QualitativeSequence illuminaQualSequence = sangerQualSequence.ConvertTo(
FastQFormatType.Illumina_v1_3);
scores = illuminaQualSequence.GetEncodedQualityScores();
illuminaQualScore = Encoding.UTF8.GetString(scores, 0, scores.Length);
byte[] sangerToIllumina = QualitativeSequence.ConvertEncodedQualityScore(FastQFormatType.Sanger, FastQFormatType.Illumina_v1_3, scoreValue);
string illuminaQualSeq = new string(illuminaQualSequence.Select(a => (char)a).ToArray());
//// Validate converted illumina score.
Assert.AreEqual(illuminaQualScore, expectedIlluminaQualScore);
Assert.AreEqual(illuminaQualSeq, expectedIlluminaSequence);
string sangerToIlluminaString = new string(Encoding.UTF8.GetChars(sangerToIllumina));
Assert.AreEqual(expectedIlluminaQualScore, sangerToIlluminaString);
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Qualitative Sequence BVT:Qualitative Illumina score type {0} is as expected.",
illuminaQualScore));
}
