/// <summary>
/// Validate Add library information in existing libraries.
/// </summary>
/// <param name="nodeName">xml node name used for different testcases</param>
/// <param name="IsLibraryInfo">Is library info?</param>
internal void AddLibraryInformation(string nodeName, bool IsLibraryInfo)
{
string filePath = utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.FilePathNode);
string expectedPairedReadsCount = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.PairedReadsCountNode);
string[] backwardReadsNode = utilityObj.xmlUtil.GetTextValues(nodeName,
Constants.BackwardReadsNode);
string[] forwardReadsNode = utilityObj.xmlUtil.GetTextValues(nodeName,
Constants.ForwardReadsNode);
string expectedLibraray = utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.LibraryName);
string expectedStdDeviation = utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.StdDeviation);
string mean = utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.Mean);
IList<ISequence> sequenceReads = new List<ISequence>();
IList<MatePair> pairedreads = new List<MatePair>();
// Get the input reads
IEnumerable<ISequence> sequences = null;
using (FastAParser parser = new FastAParser(filePath))
{
sequences = parser.Parse();
foreach (ISequence seq in sequences)
{
sequenceReads.Add(seq);
}
// Add a new library infomration.
if (IsLibraryInfo)
{
CloneLibraryInformation libraryInfo =
new CloneLibraryInformation();
libraryInfo.LibraryName = expectedLibraray;
libraryInfo.MeanLengthOfInsert = float.Parse(mean, (IFormatProvider)null);
libraryInfo.StandardDeviationOfInsert = float.Parse(expectedStdDeviation, (IFormatProvider)null);
CloneLibrary.Instance.AddLibrary(libraryInfo);
}
else
{
CloneLibrary.Instance.AddLibrary(expectedLibraray,
float.Parse(mean, (IFormatProvider)null), float.Parse(expectedStdDeviation, (IFormatProvider)null));
}
// Convert reads to map paired reads.
MatePairMapper pair = new MatePairMapper();
pairedreads = pair.Map(sequenceReads);
// Validate Map paired reads.
Assert.AreEqual(expectedPairedReadsCount, pairedreads.Count.ToString((IFormatProvider)null));
for (int index = 0; index < pairedreads.Count; index++)
{
Assert.IsTrue(forwardReadsNode.Contains(new string(pairedreads[index].GetForwardRead(sequenceReads).Select(a => (char)a).ToArray())));
Assert.IsTrue(backwardReadsNode.Contains(new string(pairedreads[index].GetReverseRead(sequenceReads).Select(a => (char)a).ToArray())));
Assert.AreEqual(expectedStdDeviation,
pairedreads[index].StandardDeviationOfLibrary.ToString((IFormatProvider)null));
Assert.AreEqual(expectedLibraray, pairedreads[index].Library.ToString((IFormatProvider)null));
Assert.AreEqual(mean, pairedreads[index].MeanLengthOfLibrary.ToString((IFormatProvider)null));
}
}
ApplicationLog.WriteLine(@"Padena P1 : Map paired reads has been verified successfully");
}
/// <summary>
/// Validate Map paired reads for a sequence reads.
/// </summary>
/// <param name="nodeName">xml node name used for different testcases</param>
internal void ValidatePairedReads(string nodeName)
{
string filePath = utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.FilePathNode);
string expectedPairedReadsCount = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.PairedReadsCountNode);
string[] backwardReadsNode = utilityObj.xmlUtil.GetTextValues(nodeName,
Constants.BackwardReadsNode);
string[] forwardReadsNode = utilityObj.xmlUtil.GetTextValues(nodeName,
Constants.ForwardReadsNode);
string[] expectedLibrary = utilityObj.xmlUtil.GetTextValues(nodeName,
Constants.LibraryNode);
string[] expectedMean = utilityObj.xmlUtil.GetTextValues(nodeName,
Constants.MeanLengthNode);
string[] deviationNode = utilityObj.xmlUtil.GetTextValues(nodeName,
Constants.DeviationNode);
IList<ISequence> sequenceReads = new List<ISequence>();
IList<MatePair> pairedreads = new List<MatePair>();
// Get the input reads
IEnumerable<ISequence> sequences = null;
using (FastAParser parser = new FastAParser(filePath))
{
sequences = parser.Parse();
foreach (ISequence seq in sequences)
{
sequenceReads.Add(seq);
}
// Convert reads to map paired reads.
MatePairMapper pair = new MatePairMapper();
pairedreads = pair.Map(sequenceReads);
// Validate Map paired reads.
Assert.AreEqual(expectedPairedReadsCount,
pairedreads.Count.ToString((IFormatProvider)null));
for (int index = 0; index < pairedreads.Count; index++)
{
Assert.IsTrue(forwardReadsNode.Contains(new string(pairedreads[index].GetForwardRead(sequenceReads).Select(a => (char)a).ToArray())));
Assert.IsTrue(backwardReadsNode.Contains(new string(pairedreads[index].GetReverseRead(sequenceReads).Select(a => (char)a).ToArray())));
Assert.IsTrue(deviationNode.Contains(pairedreads[index].StandardDeviationOfLibrary.ToString((IFormatProvider)null)));
Assert.IsTrue(expectedMean.Contains(pairedreads[index].MeanLengthOfLibrary.ToString((IFormatProvider)null)));
Assert.IsTrue(expectedLibrary.Contains(pairedreads[index].Library.ToString((IFormatProvider)null)));
}
}
ApplicationLog.WriteLine(@"Padena P1 : Map paired reads has been verified successfully");
}
/// <summary>
/// Validate library information
/// </summary>
/// <param name="nodeName">xml node name used for different testcases</param>
internal void GetLibraryInformation(string nodeName)
{
string filePath = utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.FilePathNode);
string expectedPairedReadsCount = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.PairedReadsCountNode);
string expectedLibraray = utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.LibraryName);
string expectedStdDeviation = utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.StdDeviation);
string mean = utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.Mean);
IList<MatePair> pairedreads = new List<MatePair>();
// Get the input reads
IEnumerable<ISequence> sequences = null;
using (FastAParser parser = new FastAParser(filePath))
{
sequences = parser.Parse();
// Convert reads to map paired reads.
MatePairMapper pair = new MatePairMapper();
pairedreads = pair.Map(new List<ISequence>(sequences));
// Validate Map paired reads.
Assert.AreEqual(expectedPairedReadsCount,
pairedreads.Count.ToString((IFormatProvider)null));
// Get library infomration and validate
CloneLibraryInformation libraryInfo =
CloneLibrary.Instance.GetLibraryInformation
(pairedreads[0].Library);
Assert.AreEqual(expectedStdDeviation, libraryInfo.StandardDeviationOfInsert.ToString((IFormatProvider)null));
Assert.AreEqual(expectedLibraray, libraryInfo.LibraryName.ToString((IFormatProvider)null));
Assert.AreEqual(mean, libraryInfo.MeanLengthOfInsert.ToString((IFormatProvider)null));
}
ApplicationLog.WriteLine(@"Padena P1 : Map paired reads has been verified successfully");
}
/// <summary>
/// Validate Add library information to existing libraries.
/// </summary>
/// <param name="nodeName">xml node name used for different testcases</param>
internal void AddLibraryInformation(string nodeName)
{
string filePath = utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.FilePathNode);
string expectedPairedReadsCount = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.PairedReadsCountNode);
string[] backwardReadsNode = utilityObj.xmlUtil.GetTextValues(nodeName,
Constants.BackwardReadsNode);
string[] forwardReadsNode = utilityObj.xmlUtil.GetTextValues(nodeName,
Constants.ForwardReadsNode);
string[] expectedLibrary = utilityObj.xmlUtil.GetTextValues(nodeName,
Constants.LibraryNode);
string[] expectedMean = utilityObj.xmlUtil.GetTextValues(nodeName,
Constants.MeanLengthNode);
string[] deviationNode = utilityObj.xmlUtil.GetTextValues(nodeName,
Constants.DeviationNode);
string libraray = utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.LibraryName);
string StdDeviation = utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.StdDeviation);
string mean = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.Mean);
IList<MatePair> pairedreads = new List<MatePair>();
// Get the input reads
IEnumerable<ISequence> sequences = null;
FastAParser parser = new FastAParser();
parser.Open( filePath.Replace("\\", System.IO.Path.DirectorySeparatorChar.ToString()));
sequences = parser.Parse().ToList();
parser.Close ();
IList<ISequence> sequenceReads =
new List<ISequence>(sequences);
// Add a new library infomration.
CloneLibrary.Instance.AddLibrary(libraray,
float.Parse(mean, (IFormatProvider)null), float.Parse(StdDeviation, (IFormatProvider)null));
// Convert reads to map paired reads.
MatePairMapper pair = new MatePairMapper();
pairedreads = pair.Map(sequenceReads);
// Validate Map paired reads.
Assert.AreEqual(expectedPairedReadsCount, pairedreads.Count.ToString((IFormatProvider)null));
for (int index = 0; index < pairedreads.Count; index++)
{
Assert.IsTrue(forwardReadsNode.Contains(
new string(pairedreads[index].GetForwardRead(sequenceReads).Select(a => (char)a).ToArray())));
Assert.IsTrue(backwardReadsNode.Contains(
new string(pairedreads[index].GetReverseRead(sequenceReads).Select(a => (char)a).ToArray())));
Assert.IsTrue(deviationNode.Contains(pairedreads[index].StandardDeviationOfLibrary.ToString((IFormatProvider)null)));
Assert.IsTrue(expectedLibrary.Contains(pairedreads[index].Library.ToString((IFormatProvider)null)));
Assert.IsTrue(expectedMean.Contains(pairedreads[index].MeanLengthOfLibrary.ToString((IFormatProvider)null)));
}
ApplicationLog.WriteLine(@"Padena BVT : Map paired reads has been verified successfully");
}