public void XsvSparseParseContig()
{
// Gets the expected file from the Xml
string filePathObj = utilityObj.xmlUtil.GetTextValue(
Constants.SimpleXsvSparseNodeName,
Constants.FilePathNode);
Assert.IsTrue(File.Exists(filePathObj));
// Logs information to the log file
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"XsvSparse Formatter BVT: File Exists in the Path '{0}'.",
filePathObj));
using (XsvContigParser parserObj = new XsvContigParser(filePathObj,
Alphabets.DNA, ',', '#'))
{
parserObj.Parse();
Contig contig = parserObj.ParseContig();
// Validate parsed temp file with original Xsv file.
Assert.AreEqual(26048682, contig.Length);
Assert.AreEqual(26048682, contig.Consensus.Count);
Assert.AreEqual("Chr22+Chr22+Chr22+Chr22", contig.Consensus.ID);
Assert.AreEqual(56, contig.Sequences.Count);
}
// Log to GUI.
Console.WriteLine("Successfully validated the ParseConting() method with Xsv file");
ApplicationLog.WriteLine("Successfully validated the ParseConting() method with Xsv file");
}
public void XsvSparseContigFormatterWrite()
{
// Gets the expected sequence from the Xml
string filePathObj = utilityObj.xmlUtil.GetTextValue(
Constants.SimpleXsvSparseNodeName,
Constants.FilePathNode);
Assert.IsTrue(File.Exists(filePathObj));
// Logs information to the log file
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Xsv Contig Formatter BVT: File Exists in the Path '{0}'.",
filePathObj));
Contig contig, expectedContig;
using (XsvContigParser parserObj = new XsvContigParser(filePathObj, Alphabets.DNA,
',', '#'))
{
contig = parserObj.ParseContig();
}
string seqId = string.Empty;
foreach (Contig.AssembledSequence seq in contig.Sequences)
{
seqId += seq.Sequence.ID + ",";
}
// Write Xsv file.
using (XsvContigFormatter formatObj = new XsvContigFormatter(Constants.XsvTempFileName, ',', '#'))
{
formatObj.Write(contig);
}
using (XsvContigParser parserObjNew = new XsvContigParser(Constants.XsvTempFileName, Alphabets.DNA,
',', '#'))
{
expectedContig = parserObjNew.ParseContig();
}
string expectedseqId = string.Empty;
foreach (Contig.AssembledSequence seq in expectedContig.Sequences)
{
expectedseqId += seq.Sequence.ID + ",";
}
// Validate parsed temp file with original Xsv file.
Assert.AreEqual(contig.Length, expectedContig.Length);
Assert.AreEqual(contig.Consensus.Count, expectedContig.Consensus.Count);
Assert.AreEqual(contig.Consensus.ID, expectedContig.Consensus.ID);
Assert.AreEqual(contig.Sequences.Count, expectedContig.Sequences.Count);
Assert.AreEqual(seqId.Length, expectedseqId.Length);
Assert.AreEqual(seqId, expectedseqId);
// Log to VSTest GUI.
Console.WriteLine("Successfully validated the Write Xsv file");
ApplicationLog.WriteLine("Successfully validated the Write Xsv file");
}
public void XsvContigFormatter()
{
// Gets the expected sequence from the Xml
string filePathObj = Directory.GetCurrentDirectory() + XsvFilename;
string XsvTempFileName = Path.GetTempFileName();
Assert.IsTrue(File.Exists(filePathObj));
XsvContigParser parserObj = new XsvContigParser(filePathObj, Alphabets.DNA, ',', '#');
Contig contig, expectedContig;
contig = parserObj.ParseContig();
string seqId = string.Empty;
foreach (Contig.AssembledSequence seq in contig.Sequences)
{
seqId += seq.Sequence.ID + ",";
}
// Format Xsv file.
XsvContigFormatter formatObj = new XsvContigFormatter(XsvTempFileName, ',', '#');
formatObj.Write(contig);
formatObj.Close();
formatObj.Dispose();
XsvContigParser parserObj1 = new XsvContigParser(XsvTempFileName, Alphabets.DNA, ',', '#');
expectedContig = parserObj1.ParseContig();
string expectedseqId = string.Empty;
foreach (Contig.AssembledSequence seq in expectedContig.Sequences)
{
expectedseqId += seq.Sequence.ID + ",";
}
// Validate parsed temp file with original Xsv file.
Assert.AreEqual(contig.Length, expectedContig.Length);
Assert.AreEqual(contig.Consensus.Count, expectedContig.Consensus.Count);
Assert.AreEqual(contig.Consensus.ID, expectedContig.Consensus.ID);
Assert.AreEqual(contig.Sequences.Count, expectedContig.Sequences.Count);
Assert.AreEqual(seqId.Length, expectedseqId.Length);
Assert.AreEqual(seqId, expectedseqId);
}
public void XsvSparseContigFormatterWrite()
{
// Gets the expected sequence from the Xml
string filePathObj = this.utilityObj.xmlUtil.GetTextValue(
Constants.SimpleXsvSparseNodeName,
Constants.FilePathNode).TestDir();
Assert.IsTrue(File.Exists(filePathObj));
// Logs information to the log file
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Xsv Contig Formatter BVT: File Exists in the Path '{0}'.",
filePathObj));
Contig expectedContig;
XsvContigParser parserObj = new XsvContigParser(Alphabets.DNA, ',', '#');
Contig contig = parserObj.ParseContig(filePathObj);
string seqId = contig.Sequences.Aggregate(string.Empty, (current, seq) => current + (seq.Sequence.ID + ","));
// Write Xsv file.
XsvContigFormatter formatObj = new XsvContigFormatter(',', '#');
formatObj.Format(contig, Constants.XsvTempFileName);
XsvContigParser parserObjNew = new XsvContigParser(Alphabets.DNA, ',', '#');
expectedContig = parserObjNew.ParseContig(Constants.XsvTempFileName);
string expectedseqId = expectedContig.Sequences.Aggregate(string.Empty, (current, seq) => current + (seq.Sequence.ID + ","));
// Validate parsed temp file with original Xsv file.
Assert.AreEqual(contig.Length, expectedContig.Length);
Assert.AreEqual(contig.Consensus.Count, expectedContig.Consensus.Count);
Assert.AreEqual(contig.Consensus.ID, expectedContig.Consensus.ID);
Assert.AreEqual(contig.Sequences.Count, expectedContig.Sequences.Count);
Assert.AreEqual(seqId.Length, expectedseqId.Length);
Assert.AreEqual(seqId, expectedseqId);
File.Delete(Constants.XsvTempFileName);
ApplicationLog.WriteLine("Successfully validated the Write Xsv file");
}
public void XsvSparseContigFormatterFormat()
{
// Gets the expected sequence from the Xml
string filePathObj = Utility._xmlUtil.GetTextValue(
Constants.SimpleXsvSparseNodeName,
Constants.FilePathNode);
Assert.IsTrue(File.Exists(filePathObj));
// Logs information to the log file
ApplicationLog.WriteLine(string.Format(null,
"XsvSparse Formatter BVT: File Exists in the Path '{0}'.",
filePathObj));
IEncoding encode = Encodings.IupacNA;
XsvContigParser parserObj = new XsvContigParser(encode,
Alphabets.DNA, ',', '#');
Contig contig, expectedContig;
// Parse a file.
using (TextReader tr = new StreamReader(File.OpenRead(filePathObj)))
{
contig = parserObj.ParseContig(tr, false);
}
string seqId = string.Empty;
foreach (Contig.AssembledSequence seq in contig.Sequences)
{
seqId += seq.Sequence.ID + ",";
}
// Format Xsv file.
XsvContigFormatter formatObj = new XsvContigFormatter(',', '#');
using (TextWriter tw = new StreamWriter(File.OpenWrite(
Constants.XsvTempFileName)))
{
formatObj.Format(contig, tw);
}
// Parse formatted TempFile.
using (TextReader tr = new StreamReader(
File.OpenRead(Constants.XsvTempFileName)))
{
expectedContig = parserObj.ParseContig(tr, false);
}
string expectedseqId = string.Empty;
foreach (Contig.AssembledSequence seq in expectedContig.Sequences)
{
expectedseqId += seq.Sequence.ID + ",";
}
// Validate parsed temp file with original Xsv file.
Assert.AreEqual(contig.Length, expectedContig.Length);
Assert.AreEqual(contig.Consensus.Count, expectedContig.Consensus.Count);
Assert.AreEqual(contig.Consensus.DisplayID, expectedContig.Consensus.DisplayID);
Assert.AreEqual(contig.Consensus.ID, expectedContig.Consensus.ID);
Assert.AreEqual(contig.Sequences.Count, expectedContig.Sequences.Count);
Assert.AreEqual(seqId.Length, expectedseqId.Length);
Assert.AreEqual(seqId, expectedseqId);
// Log to Nunit GUI.
Console.WriteLine("Successfully validated the format Xsv file");
ApplicationLog.WriteLine("Successfully validated the format Xsv file");
}