public void FastQFormatter()
{
const string FilepathOriginal = @"TestUtils\FASTQ\SRR002012_5.fastq";
Assert.IsTrue(File.Exists(FilepathOriginal));
IList <IQualitativeSequence> seqsOriginal;
string filepathTmp = Path.GetTempFileName();
FastQParser parser = new FastQParser();
using (parser.Open(FilepathOriginal))
{
// Read the original file
seqsOriginal = parser.Parse().ToList();
Assert.IsNotNull(seqsOriginal);
// Use the formatter to write the original sequences to a temp file
new FastQFormatter()
.Format(seqsOriginal, filepathTmp);
}
// Read the new file, then compare the sequences
using (parser.Open(filepathTmp))
{
IList <IQualitativeSequence> seqsNew = parser.Parse().ToList();
Assert.IsNotNull(seqsNew);
// Now compare the sequences.
int countOriginal = seqsOriginal.Count();
int countNew = seqsNew.Count();
Assert.AreEqual(countOriginal, countNew);
int i;
for (i = 0; i < countOriginal; i++)
{
var orgSequence = seqsOriginal[i];
var sequence = seqsNew[i];
Assert.AreEqual(seqsOriginal[i].ID, sequence.ID);
string orgSeq = Encoding.ASCII.GetString(orgSequence.ToArray());
string newSeq = Encoding.ASCII.GetString(sequence.ToArray());
string orgscores = Encoding.ASCII.GetString(orgSequence.GetEncodedQualityScores());
string newscores = Encoding.ASCII.GetString(sequence.GetEncodedQualityScores());
Assert.AreEqual(orgSeq, newSeq);
Assert.AreEqual(orgscores, newscores);
}
}
// Passed all the tests, delete the tmp file. If we failed an Assert,
// the tmp file will still be there in case we need it for debugging.
File.Delete(filepathTmp);
}
public void FastQFormatter()
{
const string FilepathOriginal = @"TestUtils\FASTQ\SRR002012_5.fastq";
Assert.IsTrue(File.Exists(FilepathOriginal));
IList<IQualitativeSequence> seqsOriginal;
string filepathTmp = Path.GetTempFileName();
FastQParser parser = new FastQParser();
using (parser.Open(FilepathOriginal))
{
// Read the original file
seqsOriginal = parser.Parse().ToList();
Assert.IsNotNull(seqsOriginal);
// Use the formatter to write the original sequences to a temp file
new FastQFormatter()
.Format(seqsOriginal, filepathTmp);
}
// Read the new file, then compare the sequences
using (parser.Open(filepathTmp))
{
IList<IQualitativeSequence> seqsNew = parser.Parse().ToList();
Assert.IsNotNull(seqsNew);
// Now compare the sequences.
int countOriginal = seqsOriginal.Count();
int countNew = seqsNew.Count();
Assert.AreEqual(countOriginal, countNew);
int i;
for (i = 0; i < countOriginal; i++)
{
var orgSequence = seqsOriginal[i];
var sequence = seqsNew[i];
Assert.AreEqual(seqsOriginal[i].ID, sequence.ID);
string orgSeq = Encoding.ASCII.GetString(orgSequence.ToArray());
string newSeq = Encoding.ASCII.GetString(sequence.ToArray());
string orgscores = Encoding.ASCII.GetString(orgSequence.GetEncodedQualityScores());
string newscores = Encoding.ASCII.GetString(sequence.GetEncodedQualityScores());
Assert.AreEqual(orgSeq, newSeq);
Assert.AreEqual(orgscores, newscores);
}
}
// Passed all the tests, delete the tmp file. If we failed an Assert,
// the tmp file will still be there in case we need it for debugging.
File.Delete(filepathTmp);
}
/// <summary>
/// General method to validate FastQ Parser.
/// <param name="nodeName">xml node name.</param>
/// </summary>
private void ValidateFastQParser(string nodeName)
{
// Gets the expected sequence from the Xml
string filePath = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.FilePathNode);
string expectedQualitativeSequence = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ExpectedSequenceNode);
string expectedSequenceId = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.SequenceIdNode);
int expectedSeqCount = int.Parse(utilityObj.xmlUtil.GetTextValue(nodeName, Constants.SeqsCount));
// Parse a FastQ file.
var fastQParserObj = new FastQParser();
using (fastQParserObj.Open(filePath))
{
IList <IQualitativeSequence> qualSequenceList = fastQParserObj.Parse().ToList();
// Validate qualitative Sequence upon parsing FastQ file.
Assert.AreEqual(expectedSeqCount, qualSequenceList.Count);
Assert.AreEqual(expectedQualitativeSequence, qualSequenceList[0].ConvertToString());
Assert.AreEqual(expectedSequenceId, qualSequenceList[0].ID);
ApplicationLog.WriteLine(string.Format("FastQ Parser BVT: The FASTQ sequence '{0}' validation after Parse() is found to be as expected.",
qualSequenceList[0].ConvertToString()));
ApplicationLog.WriteLine(string.Format("FastQ Parser BVT: The FASTQ sequence ID '{0}' validation after Parse() is found to be as expected.",
qualSequenceList[0].ID));
}
}
private void InValidateFastQFormatter(FastQFormatParameters param)
{
// Gets the expected sequence from the Xml
string filepath = utilityObj.xmlUtil.GetTextValue(
Constants.MultiSeqSangerRnaProNode, Constants.FilePathNode);
// Parse a FastQ file.
var fastQParser = new FastQParser();
using (fastQParser.Open(filepath))
{
FastQFormatter fastQFormatter = null;
switch (param)
{
case FastQFormatParameters.Sequence:
try
{
fastQFormatter = new FastQFormatter();
fastQFormatter.Format(null as ISequence, filepath);
Assert.Fail();
}
catch (ArgumentNullException)
{
fastQFormatter.Close();
ApplicationLog.WriteLine(
"FastQ Parser P2 : Successfully validated the exception");
}
break;
default:
try
{
IEnumerable <IQualitativeSequence> sequence = fastQParser.Parse();
fastQFormatter = new FastQFormatter();
fastQFormatter.Format(sequence, null);
Assert.Fail();
}
catch (ArgumentNullException)
{
ApplicationLog.WriteLine("FastQ Parser P2 : Successfully validated the exception");
}
break;
}
}
}
/// <summary>
/// General method to validate FastQ Formatter.
/// <param name="nodeName">xml node name.</param>
/// <param name="fileExtension">Different temporary file extensions</param>
/// </summary>
private void ValidateFastQFormatter(string nodeName, FastQFileParameters fileExtension)
{
// Gets the expected sequence from the Xml
string filePath = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.FilePathNode);
string expectedQualitativeSequence = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.ExpectedSequenceNode);
string expectedSequenceId = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.SequenceIdNode);
string tempFileName = Path.GetTempFileName();
// Parse a FastQ file using parseOne method.
var fastQParserObj = new FastQParser();
using (fastQParserObj.Open(filePath))
{
IQualitativeSequence oneSequence = fastQParserObj.ParseOne();
// Format Parsed Sequence to temp file with different extension.
var fastQFormatter = new FastQFormatter();
using (fastQFormatter.Open(tempFileName))
{
fastQFormatter.Format(oneSequence);
}
string parsedValue;
string parsedId;
var fastQParserObjTemp = new FastQParser();
using (fastQParserObjTemp.Open(tempFileName))
{
oneSequence = fastQParserObjTemp.Parse().First();
parsedValue = oneSequence.ConvertToString();
parsedId = oneSequence.ID;
}
// Validate qualitative parsing temporary file.
Assert.AreEqual(expectedQualitativeSequence, parsedValue);
Assert.AreEqual(expectedSequenceId, parsedId);
ApplicationLog.WriteLine(string.Format("FastQ Formatter BVT: The FASTQ sequence '{0}' validation after Write() and Parse() is found to be as expected.",
parsedValue));
ApplicationLog.WriteLine(string.Format("FastQ Formatter BVT: The FASTQ sequence '{0}' validation after Write() and Parse() is found to be as expected.",
parsedId));
File.Delete(tempFileName);
}
}
public void TestFastQWhenParsingOneOfMany()
{
string filepath = @"TestUtils\FASTQ\SRR002012_5.fastq";
// Parse
ISequence seq = new FastQParser().ParseOne(filepath);
Assert.IsNotNull(seq);
FastQParser fqParser = new FastQParser
{
FormatType = FastQFormatType.Sanger,
Alphabet = Alphabets.DNA
};
using (fqParser.Open(filepath))
{
var qualSeq = fqParser.Parse().First() as QualitativeSequence;
Assert.IsNotNull(qualSeq);
}
}
public void TestFastQWhenParsingOneOfMany()
{
string filepath = @"TestUtils\FASTQ\SRR002012_5.fastq";
// Parse
ISequence seq = new FastQParser().ParseOne(filepath);
Assert.IsNotNull(seq);
FastQParser fqParser = new FastQParser
{
FormatType = FastQFormatType.Sanger,
Alphabet = Alphabets.DNA
};
using (fqParser.Open(filepath))
{
var qualSeq = fqParser.Parse().First() as QualitativeSequence;
Assert.IsNotNull(qualSeq);
}
}
private void InValidateFastQFormatter(FastQFormatParameters param)
{
// Gets the expected sequence from the Xml
string filepath = utilityObj.xmlUtil.GetTextValue(
Constants.MultiSeqSangerRnaProNode, Constants.FilePathNode);
// Parse a FastQ file.
var fastQParser = new FastQParser();
using (fastQParser.Open(filepath))
{
FastQFormatter fastQFormatter = null;
switch (param)
{
case FastQFormatParameters.Sequence:
try
{
fastQFormatter = new FastQFormatter();
fastQFormatter.Format(null as ISequence, filepath);
Assert.Fail();
}
catch (ArgumentNullException)
{
fastQFormatter.Close();
ApplicationLog.WriteLine(
"FastQ Parser P2 : Successfully validated the exception");
}
break;
default:
try
{
IEnumerable<IQualitativeSequence> sequence = fastQParser.Parse();
fastQFormatter = new FastQFormatter();
fastQFormatter.Format(sequence, null);
Assert.Fail();
}
catch (ArgumentNullException)
{
ApplicationLog.WriteLine("FastQ Parser P2 : Successfully validated the exception");
}
break;
}
}
}
public void FastQFormatterUsingInterface()
{
string filepathOriginal = @"TestUtils\FASTQ\SRR002012_5.fastq";
Assert.IsTrue(File.Exists(filepathOriginal));
IList <QualitativeSequence> seqsOriginal = null;
string filepathTmp = Path.GetTempFileName();
using (FastQParser parser = new FastQParser())
{
parser.Open(filepathOriginal);
// Read the original file
seqsOriginal = parser.Parse().ToList();
Assert.IsNotNull(seqsOriginal);
// Use the formatter to write the original sequences to a temp file
ISequenceFormatter formatter = null;
try
{
formatter = new FastQFormatter();
formatter.Open(filepathTmp);
foreach (ISequence s in seqsOriginal)
{
formatter.Write(s);
}
formatter.Close();
}
finally
{
if (formatter != null)
{
((FastQFormatter)formatter).Dispose();
}
}
}
// Read the new file, then compare the sequences
IList <QualitativeSequence> seqsNew = null;
using (FastQParser parser = new FastQParser(filepathTmp))
{
seqsNew = parser.Parse().ToList();
Assert.IsNotNull(seqsNew);
// Now compare the sequences.
int countOriginal = seqsOriginal.Count();
int countNew = seqsNew.Count();
Assert.AreEqual(countOriginal, countNew);
int i;
for (i = 0; i < countOriginal; i++)
{
Assert.AreEqual(seqsOriginal[i].ID, seqsNew[i].ID);
string orgSeq = ASCIIEncoding.ASCII.GetString(seqsOriginal[i].ToArray());
string newSeq = ASCIIEncoding.ASCII.GetString(seqsNew[i].ToArray());
string orgscores = ASCIIEncoding.ASCII.GetString(seqsOriginal[i].GetEncodedQualityScores());
string newscores = ASCIIEncoding.ASCII.GetString(seqsNew[i].GetEncodedQualityScores());
Assert.AreEqual(orgSeq, newSeq);
Assert.AreEqual(orgscores, newscores);
}
// Passed all the tests, delete the tmp file. If we failed an Assert,
// the tmp file will still be there in case we need it for debugging.
File.Delete(filepathTmp);
}
}
/// <summary>
/// General method to validate multi sequence FastQ Format.
/// </summary>
/// <param name="nodeName">xml node name.</param>
private void ValidateMultiSeqFastQFormatter(string nodeName)
{
// Gets the expected sequence from the Xml
string filePath = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.FilePathNode);
string expectedQualitativeSequence = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.ExpectedSequenceNode);
string expectedSequenceId = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.SequenceIdNode);
string expectedSecondQualitativeSequence = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.ExpectedSequence2Node);
string expectedSecondSeqID = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.ExpectedSequenceId1Node);
// Parse a FastQ file.
var fastQParserObj = new FastQParser();
using (fastQParserObj.Open(filePath))
{
var qualSequenceList = fastQParserObj.Parse().ToList();
// Format a first Qualitative sequence
new FastQFormatter().Format(qualSequenceList[0], Constants.FastQTempFileName);
// Read it back
var seqsNew = new FastQParser().Parse(Constants.FastQTempFileName).ToList();
// Format a Second Qualitative sequence
new FastQFormatter().Format(qualSequenceList[1], Constants.StreamWriterFastQTempFileName);
var secondSeqsNew = new FastQParser().Parse(Constants.StreamWriterFastQTempFileName).ToList();
// Validate Second qualitative Sequence upon parsing FastQ file.
Assert.AreEqual(expectedSecondQualitativeSequence, secondSeqsNew[0].ConvertToString());
Assert.AreEqual(expectedSecondSeqID, secondSeqsNew[0].ID);
// Validate first qualitative Sequence upon parsing FastQ file.
Assert.AreEqual(expectedQualitativeSequence, seqsNew[0].ConvertToString());
Assert.AreEqual(expectedSequenceId, seqsNew[0].ID);
ApplicationLog.WriteLine(string.Format("FastQ Parser P1: The FASTQ sequence '{0}' validation after Parse() is found to be as expected.", seqsNew[0]));
File.Delete(Constants.FastQTempFileName);
File.Delete(Constants.StreamWriterFastQTempFileName);
}
}
private void ValidateFastQFormatter(string nodeName, bool writeMultipleSequences)
{
// Gets the expected sequence from the Xml
string filePath = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.FilePathNode);
string expectedQualitativeSequence = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.ExpectedSequenceNode);
string expectedSequenceId = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.SequenceIdNode);
string tempFileName = Path.GetTempFileName();
// Parse a FastQ file.
var fastQParserObj = new FastQParser();
using (fastQParserObj.Open(filePath))
{
IEnumerable<IQualitativeSequence> qualSequenceList = fastQParserObj.Parse();
var fastQFormatter = new FastQFormatter();
using (fastQFormatter.Open(tempFileName))
{
if (writeMultipleSequences)
{
foreach (IQualitativeSequence newQualSeq in qualSequenceList)
{
fastQFormatter.Format(newQualSeq);
}
}
else
{
fastQFormatter.Format(qualSequenceList.First());
}
} // temp file is closed.
// Read the new file and validate the first Sequence.
FastQParser fastQParserObjNew = new FastQParser();
IQualitativeSequence firstSequence = fastQParserObjNew.ParseOne(tempFileName);
// Validate qualitative Sequence upon parsing FastQ file.
Assert.AreEqual(expectedQualitativeSequence, firstSequence.ConvertToString());
Assert.AreEqual(expectedSequenceId, firstSequence.ID);
ApplicationLog.WriteLine(string.Format("FastQ Parser P1: The FASTQ sequence '{0}' validation after Parse() is found to be as expected.", firstSequence));
File.Delete(tempFileName);
}
}
/// <summary>
/// General method to validate FastQ formatting
/// Qualitative Sequence by passing TextWriter as a parameter
/// <param name="nodeName">xml node name.</param>
/// </summary>
private void ValidateFastQFormatByFormattingQualSeqeunce(string nodeName)
{
// Gets the actual sequence and the alphabet from the Xml
IAlphabet alphabet = Utility.GetAlphabet(utilityObj.xmlUtil.GetTextValue(nodeName, Constants.AlphabetNameNodeV2));
FastQFormatType expectedFormatType = Utility.GetFastQFormatType(utilityObj.xmlUtil.GetTextValue(nodeName, Constants.FastQFormatType));
string qualSequence = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.ExpectedSequenceNode);
string expectedQualitativeSequence = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.ExpectedSequenceNode);
string qualityScores = "";
int i;
for (i = 0; i < qualSequence.Length; i++)
qualityScores = qualityScores + "}";
byte[] seq = Encoding.UTF8.GetBytes(qualSequence);
byte[] qScore = Encoding.UTF8.GetBytes(qualityScores);
string tempFileName = Path.GetTempFileName();
// Create a Qualitative Sequence.
var qualSeq = new QualitativeSequence(alphabet, expectedFormatType, seq, qScore);
var formatter = new FastQFormatter();
using (formatter.Open(tempFileName))
{
formatter.Format(qualSeq);
formatter.Close();
var fastQParserObj = new FastQParser();
using (fastQParserObj.Open(tempFileName))
{
// Read the new file and validate Sequences.
var seqsNew = fastQParserObj.Parse();
var firstSequence = seqsNew.First();
// Validate qualitative Sequence upon parsing FastQ file.
Assert.AreEqual(expectedQualitativeSequence, firstSequence.ConvertToString());
Assert.IsTrue(string.IsNullOrEmpty(firstSequence.ID));
ApplicationLog.WriteLine(string.Format("FastQ Parser P1: The FASTQ sequence '{0}' validation after Parse() is found to be as expected.", firstSequence));
}
File.Delete(tempFileName);
}
}
/// <summary>
/// General method to validate FastQ Parser for Multiple sequence with
/// different alphabets.
/// <param name="nodeName">xml node name.</param>
/// <param name="triSeq">Tri Sequence</param>
/// </summary>
private void ValidateMulitpleSequenceFastQParser(string nodeName, string triSeq)
{
// Gets the expected sequence from the Xml
string filePath = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.FilePathNode);
string expectedFirstQualitativeSequence = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.ExpectedSequence1Node);
string expectedSecondQualitativeSequence = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.ExpectedSequence2Node);
string expectedthirdQualitativeSequence = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.ExpectedSequence3Node);
string expectedSequenceId = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.SequenceIdNode);
int expectedSeqCount = int.Parse(utilityObj.xmlUtil.GetTextValue(nodeName, Constants.SeqsCount));
// Parse a multiple sequence FastQ file.
var fastQParserObj = new FastQParser();
using (fastQParserObj.Open(filePath))
{
IList<IQualitativeSequence> qualSequenceList = fastQParserObj.Parse().ToList();
// Validate first qualitative Sequence upon parsing FastQ file.
Assert.AreEqual(expectedSeqCount, qualSequenceList.Count);
Assert.AreEqual(expectedFirstQualitativeSequence, qualSequenceList[0].ConvertToString());
Assert.AreEqual(expectedSequenceId, qualSequenceList[0].ID);
// Validate second qualitative Sequence upon parsing FastQ file.
Assert.AreEqual(expectedSecondQualitativeSequence, qualSequenceList[1].ConvertToString());
Assert.AreEqual(expectedSequenceId, qualSequenceList[1].ID);
// Validate third sequence in FastQ file if it is tri sequence FastQ file.
if (0 == string.Compare(triSeq, "MultiSequenceFastQ", CultureInfo.CurrentCulture, CompareOptions.IgnoreCase))
{
// Validate second qualitative Sequence upon parsing FastQ file.
Assert.AreEqual(expectedthirdQualitativeSequence, qualSequenceList[2].ConvertToString());
Assert.AreEqual(expectedSequenceId, qualSequenceList[2].ID);
}
ApplicationLog.WriteLine(string.Format("FastQ Parser P1: The FASTQ sequence '{0}' validation after Parse() is found to be as expected.",
qualSequenceList[0]));
}
}
/// <summary>
/// General method to validate FastQ Formatter on a Stream.
/// <param name="nodeName">xml node name.</param>
/// </summary>
private void ValidateFastQFormatterOnAStream(string nodeName)
{
// Gets the expected sequence from the Xml
string filePath = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.FilePathNode);
string expectedQualitativeSequence = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.ExpectedSequenceNode);
string expectedSequenceId = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.SequenceIdNode);
string tempFileName1 = Path.GetTempFileName();
// Parse a FastQ file using parseOne method.
var fastQParserObj = new FastQParser();
using (fastQParserObj.Open(filePath))
{
var oneSequence = fastQParserObj.ParseOne();
// New Sequence after formatting file.
var fastQFormatter = new FastQFormatter();
using (fastQFormatter.Open(tempFileName1))
fastQFormatter.Format(oneSequence);
var fastQParserObjTemp = new FastQParser();
string parsedValue, parsedId;
using (fastQParserObjTemp.Open(tempFileName1))
{
oneSequence = fastQParserObjTemp.Parse().First();
parsedValue = oneSequence.ConvertToString();
parsedId = oneSequence.ID;
}
// Validate qualitative parsing temporary file.
Assert.AreEqual(expectedQualitativeSequence, parsedValue);
Assert.AreEqual(expectedSequenceId, parsedId);
ApplicationLog.WriteLine(string.Format("FastQ Formatter BVT: The FASTQ sequence '{0}' validation after Write() and Parse() is found to be as expected.", parsedValue));
ApplicationLog.WriteLine(string.Format("FastQ Formatter BVT: The FASTQ sequence '{0}' validation after Write() and Parse() is found to be as expected.", parsedId));
File.Delete(tempFileName1);
}
}
/// <summary>
/// General method to validate FastQ Parser.
/// <param name="nodeName">xml node name.</param>
/// </summary>
private void ValidateFastQParser(string nodeName)
{
// Gets the expected sequence from the Xml
string filePath = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.FilePathNode);
string expectedQualitativeSequence = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ExpectedSequenceNode);
string expectedSequenceId = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.SequenceIdNode);
int expectedSeqCount = int.Parse(utilityObj.xmlUtil.GetTextValue(nodeName, Constants.SeqsCount));
// Parse a FastQ file.
var fastQParserObj = new FastQParser();
using (fastQParserObj.Open(filePath))
{
IList<IQualitativeSequence> qualSequenceList = fastQParserObj.Parse().ToList();
// Validate qualitative Sequence upon parsing FastQ file.
Assert.AreEqual(expectedSeqCount, qualSequenceList.Count);
Assert.AreEqual(expectedQualitativeSequence, qualSequenceList[0].ConvertToString());
Assert.AreEqual(expectedSequenceId, qualSequenceList[0].ID);
ApplicationLog.WriteLine(string.Format("FastQ Parser BVT: The FASTQ sequence '{0}' validation after Parse() is found to be as expected.",
qualSequenceList[0].ConvertToString()));
ApplicationLog.WriteLine(string.Format("FastQ Parser BVT: The FASTQ sequence ID '{0}' validation after Parse() is found to be as expected.",
qualSequenceList[0].ID));
}
}
