public void ValidateSeqParserProperties()
{
// Gets the expected sequence from the Xml
string fastaParserName = _utilityObj._xmlUtil.GetTextValue(Constants.FastAFileParserNode,
Constants.ParserNameNode);
string genBankParserName = _utilityObj._xmlUtil.GetTextValue(Constants.GenBankFileParserNode,
Constants.ParserNameNode);
string gffParserName = _utilityObj._xmlUtil.GetTextValue(Constants.GffFileParserNode,
Constants.ParserNameNode);
string fastQParserName = _utilityObj._xmlUtil.GetTextValue(Constants.FastQFileParserNode,
Constants.ParserNameNode);
// Get SequenceParser class properties.
FastaParser actualFastAParser = SequenceParsers.Fasta;
IList <ISequenceParser> allParser = SequenceParsers.All;
GenBankParser actualgenBankParserName = SequenceParsers.GenBank;
FastQParser actualFastQParserName = SequenceParsers.FastQ;
GffParser actualGffParserName = SequenceParsers.Gff;
// Validate Sequence parsers
Assert.AreEqual(fastaParserName, actualFastAParser.Name);
Assert.AreEqual(genBankParserName, actualgenBankParserName.Name);
Assert.AreEqual(gffParserName, actualGffParserName.Name);
Assert.AreEqual(fastQParserName, actualFastQParserName.Name);
Assert.IsNotNull(allParser);
Console.WriteLine(string.Format((IFormatProvider)null,
"SequenceParser : Type of the parser is validated successfully"));
ApplicationLog.WriteLine("Type of the parser is validated successfully");
}
/// <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).TestDir();
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));
}
}
public void TestFastQWhenParsingOneOfMany()
{
string filepath = @"TestUtils\FASTQ\SRR002012_5.fastq";
// parse
ISequenceParser parser = new FastQParser(filepath);
try
{
ISequence seq = parser.Parse().First();
Assert.IsNotNull(seq);
}
finally
{
parser.Dispose();
}
using (FastQParser fqParser = new FastQParser(filepath))
{
fqParser.AutoDetectFastQFormat = false;
fqParser.FormatType = FastQFormatType.Sanger;
fqParser.Alphabet = Alphabets.DNA;
QualitativeSequence qualSeq = fqParser.Parse().First();
Assert.IsNotNull(qualSeq);
}
}
/// <summary>
/// Returns parser which supports the specified file.
/// </summary>
/// <param name="fileName">File name for which the parser is required.</param>
/// <param name="parserName">Name of the parser to use.</param>
/// <returns>If found returns the open parser as ISequenceParser else returns null.</returns>
public static ISequenceParser FindParserByName(string fileName, string parserName)
{
ISequenceParser parser = null;
if (!string.IsNullOrEmpty(fileName) && !string.IsNullOrEmpty(parserName))
{
if (parserName == Properties.Resource.FastAName)
{
parser = new FastAParser(fileName);
}
else if (parserName == Properties.Resource.FastQName)
{
parser = new FastQParser(fileName);
}
else if (parserName == Properties.Resource.GENBANK_NAME)
{
parser = new GenBankParser(fileName);
}
else
{
// Do a search through the known parsers to pick up custom parsers added through add-in.
parser = All.FirstOrDefault(p => p.Name == parserName);
// If we found a match based on extension, then open the file - this
// matches the above behavior where a specific parser was created for
// the passed filename - the parser is opened automatically in the constructor.
if (parser != null)
{
parser.Open(fileName);
}
}
}
return(parser);
}
public void InvalidateFastQParseRange()
{
try
{
using (FastQParser fqParserObj = new FastQParser())
{
fqParserObj.ParseRange(-1, 0, new SequencePointer());
}
Assert.Fail();
}
catch (ArgumentOutOfRangeException)
{
ApplicationLog.WriteLine(
"FastQ Parser P2 : Successfully validated the exception");
Console.WriteLine(
"FastQ Parser P2 : Successfully validated the exception");
}
try
{
using (FastQParser fqParserObj = new FastQParser())
{
fqParserObj.ParseRange(0, -1, new SequencePointer());
}
Assert.Fail();
}
catch (ArgumentOutOfRangeException)
{
ApplicationLog.WriteLine(
"FastQ Parser P2 : Successfully validated the exception");
Console.WriteLine(
"FastQ Parser P2 : Successfully validated the exception");
}
}
/// <summary>
/// Returns parser which supports the specified file.
/// </summary>
/// <param name="fileName">File name for which the parser is required.</param>
/// <param name="parserName">Name of the parser to use.</param>
/// <returns>If found returns the parser as IParser else returns null.</returns>
public static ISequenceParser FindParserByName(string fileName, string parserName)
{
ISequenceParser parser = null;
if (!string.IsNullOrEmpty(fileName))
{
if (parserName == Properties.Resource.FastAName)
{
parser = new FastAParser(fileName);
}
else if (parserName == Properties.Resource.FastQName)
{
parser = new FastQParser(fileName);
}
else if (parserName == Properties.Resource.GENBANK_NAME)
{
parser = new GenBankParser(fileName);
}
else if (parserName == Properties.Resource.GFF_NAME)
{
parser = new GffParser(fileName);
}
else
{
parser = null;
}
}
return(parser);
}
/// <summary>
/// Finds a suitable parser that supports the specified file, opens the file and returns the parser.
/// </summary>
/// <param name="fileName">File name for which the parser is required.</param>
/// <returns>If found returns the parser as ISequenceParser else returns null.</returns>
public static ISequenceParser FindParserByFileName(string fileName)
{
ISequenceParser parser = null;
if (!string.IsNullOrEmpty(fileName))
{
if (IsFasta(fileName))
{
parser = new FastAParser(fileName);
}
else if (IsFastQ(fileName))
{
parser = new FastQParser(fileName);
}
else if (IsGenBank(fileName))
{
parser = new GenBankParser(fileName);
}
else if (fileName.EndsWith(Properties.Resource.GFF_FILEEXTENSION, StringComparison.InvariantCultureIgnoreCase))
{
parser = new GffParser(fileName);
}
else
{
parser = null;
}
}
return(parser);
}
/// <summary>
/// General method to validate FastQ Parser On Streams.
/// <param name="nodeName">xml node name.</param>
/// </summary>
private void ValidateFastQParserOnAStream(string nodeName)
{
// Gets the expected sequence from the Xml
string filePath = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.FilePathNode).TestDir();
string expectedQualitativeSequence = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ExpectedSequenceNode);
string expectedSequenceId = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.SequenceIdNode);
IList <IQualitativeSequence> qualSequenceList;
using (var reader = File.OpenRead(filePath))
{
// Parse a FastQ file.
var fastQParserObj = new FastQParser();
qualSequenceList = fastQParserObj.Parse(reader).ToList();
}
string actualQualitativeSequence = qualSequenceList[0].ConvertToString();
string actualId = qualSequenceList[0].ID;
// Validate qualitative Sequence upon parsing FastQ file.
Assert.AreEqual(expectedQualitativeSequence, actualQualitativeSequence);
Assert.AreEqual(actualId, expectedSequenceId);
ApplicationLog.WriteLine(string.Format("FastQ Parser BVT: The FASTQ sequence '{0}' validation after Parse(Stream) is found to be as expected.",
actualQualitativeSequence));
ApplicationLog.WriteLine(string.Format("FastQ Parser BVT: The FASTQ sequence ID '{0}' validation after Parse(Stream) is found to be as expected.",
actualId));
}
public void TestDefaultFastQFormatType()
{
using (FastQParser parser = new FastQParser())
{
Assert.AreEqual(parser.FormatType, FastQFormatType.Illumina);
}
}
public void FastQFormatter()
{
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
using (FastQFormatter formatter = new FastQFormatter(filepathTmp))
{
foreach (QualitativeSequence s in seqsOriginal)
{
formatter.Write(s);
}
}
}
// 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 FastQ Formatter on a Stream.
/// <param name="nodeName">xml node name.</param>
/// </summary>
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 = System.IO.Path.GetTempFileName();
string parsedValue = string.Empty;
string parsedID = string.Empty;
IEnumerable <QualitativeSequence> qualSequence = null;
// Parse a FastQ file using parseOne method.
using (FastQParser fastQParserObj = new FastQParser(filePath))
{
fastQParserObj.AutoDetectFastQFormat = false;
qualSequence = fastQParserObj.Parse();
// New Sequence after formatting file.
IEnumerable <QualitativeSequence> newQualSeq = null;
using (StreamWriter writer = new StreamWriter(tempFileName1))
{
using (FastQFormatter fastQFormatter = new FastQFormatter())
{
fastQFormatter.Open(writer);
fastQFormatter.Write(qualSequence.ElementAt(0));
}
}
using (FastQParser fastQParserObjTemp = new FastQParser(tempFileName1))
{
newQualSeq = fastQParserObjTemp.Parse();
parsedValue = new string(newQualSeq.ElementAt(0).Select(a => (char)a).ToArray());
parsedID = newQualSeq.ElementAt(0).ID.ToString((IFormatProvider)null);
}
// Validate qualitative parsing temporary file.
Assert.AreEqual(parsedValue, expectedQualitativeSequence);
Assert.AreEqual(parsedID, expectedSequenceId);
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"FastQ Formatter BVT: The FASTQ sequence '{0}' validation after Write() and Parse() is found to be as expected.",
parsedValue));
// Logs to the VSTest GUI (Console.Out) window
Console.WriteLine(string.Format((IFormatProvider)null,
"FastQ Formatter BVT: The FASTQ sequence '{0}' validation after Write() and Parse() is found to be as expected.",
parsedValue));
Console.WriteLine(string.Format((IFormatProvider)null,
"FastQ Formatter BVT: The FASTQ sequence '{0}' validation after Write() and Parse() is found to be as expected.",
parsedID));
qualSequence = null;
File.Delete(tempFileName1);
}
}
/// <summary>
/// General method to Invalidate FastQ Parser.
/// <param name="nodeName">xml node name.</param>
/// </summary>
private void InValidateFastQParser(string nodeName)
{
// Gets the expected sequence from the Xml
string filePath = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.FilePathNode);
// Create a FastQ Parser object.
var fastQParserObj = new FastQParser();
{
fastQParserObj.Parse(filePath).ToList();
}
}
void InValidateFastQFormatter(FastQFormatParameters param)
{
// Gets the expected sequence from the Xml
string filepath = utilityObj.xmlUtil.GetTextValue(
Constants.MultiSeqSangerRnaProNode, Constants.FilePathNode);
// Parse a FastQ file.
using (FastQParser fastQParser = new FastQParser(filepath))
{
fastQParser.AutoDetectFastQFormat = true;
IEnumerable <QualitativeSequence> sequence = null;
FastQFormatter fastQFormatter = null;
switch (param)
{
case FastQFormatParameters.Sequence:
try
{
fastQFormatter = new FastQFormatter(filepath);
fastQFormatter.Write(null as ISequence);
Assert.Fail();
}
catch (ArgumentNullException)
{
fastQFormatter.Close();
ApplicationLog.WriteLine(
"FastQ Parser P2 : Successfully validated the exception");
Console.WriteLine(
"FastQ Parser P2 : Successfully validated the exception");
}
break;
default:
try
{
sequence = fastQParser.Parse();
fastQFormatter = new FastQFormatter(Constants.FastQTempFileName);
fastQFormatter.Write(sequence as QualitativeSequence);
Assert.Fail();
}
catch (ArgumentNullException)
{
fastQFormatter.Close();
ApplicationLog.WriteLine(
"FastQ Parser P2 : Successfully validated the exception");
Console.WriteLine(
"FastQ Parser P2 : Successfully validated the exception");
}
break;
}
}
}
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 TestFastQWhenParsingOneOfMany()
{
// parse
ISequenceParser parser = new FastQParser();
string filepath = @"testdata\FASTQ\SRR002012_5.fastq";
ISequence seq = parser.ParseOne(filepath);
FastQParser fqParser = new FastQParser();
fqParser.AutoDetectFastQFormat = false;
fqParser.FastqType = FastQFormatType.Sanger;
IQualitativeSequence qualSeq = fqParser.ParseOne(filepath);
}
/// <summary>
/// Finds a suitable parser that supports the specified file, opens the file and returns the parser.
/// </summary>
/// <param name="fileName">File name for which the parser is required.</param>
/// <returns>If found returns the open parser as ISequenceParser else returns null.</returns>
public static ISequenceParser FindParserByFileName(string fileName)
{
ISequenceParser parser = null;
if (!string.IsNullOrEmpty(fileName))
{
if (Helper.IsZippedFasta(fileName))
{
parser = new FastAZippedParser(fileName);
}
else if (Helper.IsZippedFastQ(fileName))
{
parser = new FastQZippedParser(fileName);
}
else if (IsFasta(fileName))
{
parser = new FastAParser(fileName);
}
else if (IsFastQ(fileName))
{
parser = new FastQParser(fileName);
}
else if (Helper.IsBAM(fileName))
{
throw new NotImplementedException();
//parser = new BAMSequenceParser(fileName);
}
else if (IsGenBank(fileName))
{
parser = new GenBankParser(fileName);
}
else
{
// Do a search through the known parsers to pick up custom parsers added through add-in.
string fileExtension = Path.GetExtension(fileName);
if (!string.IsNullOrEmpty(fileExtension))
{
parser = All.FirstOrDefault(p => p.SupportedFileTypes.Contains(fileExtension));
// If we found a match based on extension, then open the file - this
// matches the above behavior where a specific parser was created for
// the passed filename - the parser is opened automatically in the constructor.
if (parser != null)
{
parser.Open(fileName);
}
}
}
}
return(parser);
}
public void FastQProperties()
{
FastQParser parser = new FastQParser();
Assert.AreEqual(parser.Name, Resource.FastQName);
Assert.AreEqual(parser.Description, Resource.FASTQPARSER_DESCRIPTION);
Assert.AreEqual(parser.SupportedFileTypes, Resource.FASTQ_FILEEXTENSION);
FastQFormatter formatter = new FastQFormatter();
Assert.AreEqual(formatter.Name, Resource.FastQName);
Assert.AreEqual(formatter.Description, Resource.FASTQFORMATTER_DESCRIPTION);
Assert.AreEqual(formatter.SupportedFileTypes, Resource.FASTQ_FILEEXTENSION);
}
public void FastQProperties()
{
ISequenceParser parser = new FastQParser();
Assert.AreEqual(parser.Name, Properties.Resource.FASTQ_NAME);
Assert.AreEqual(parser.Description, Properties.Resource.FASTQPARSER_DESCRIPTION);
Assert.AreEqual(parser.FileTypes, Properties.Resource.FASTQ_FILEEXTENSION);
ISequenceFormatter formatter = new FastQFormatter();
Assert.AreEqual(formatter.Name, Properties.Resource.FASTQ_NAME);
Assert.AreEqual(formatter.Description, Properties.Resource.FASTQFORMATTER_DESCRIPTION);
Assert.AreEqual(formatter.FileTypes, Properties.Resource.FASTQ_FILEEXTENSION);
}
/// <summary>
/// Gets the VirtualSequenceProvider
/// </summary>
/// <returns>Virtual Sequence Provider</returns>
static FileVirtualQualitativeSequenceProvider GetVirtualSequenceProvider()
{
string filePath = Utility._xmlUtil.GetTextValue(
Constants.SingleSequenceSangerFastQNode, Constants.FilePathNode);
FastQParser parserObj = new FastQParser();
parserObj.Parse(filePath);
FileVirtualQualitativeSequenceProvider provObj =
new FileVirtualQualitativeSequenceProvider(parserObj,
GetSequencePointer());
return(provObj);
}
GetVirtualQualitativeSequenceList(string nodeName)
{
// Gets the expected sequence from the Xml
string filePath = Utility._xmlUtil.GetTextValue(
nodeName,
Constants.FilePathNode);
FastQParser parserObj = new FastQParser();
parserObj.EnforceDataVirtualization = true;
VirtualQualitativeSequenceList seqList =
(VirtualQualitativeSequenceList)parserObj.Parse(filePath);
return(seqList);
}
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".TestDir();
Assert.IsTrue(File.Exists(FilepathOriginal));
string filepathTmp = Path.GetTempFileName();
IList <QualitativeSequence> seqsOriginal = new FastQParser()
.Parse(FilepathOriginal)
.Cast <QualitativeSequence>()
.ToList();
// 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
IList <QualitativeSequence> seqsNew = new FastQParser()
.Parse(filepathTmp)
.Cast <QualitativeSequence>()
.ToList();
// 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 = Encoding.ASCII.GetString(seqsOriginal[i].ToArray());
string newSeq = Encoding.ASCII.GetString(seqsNew[i].ToArray());
string orgscores = Encoding.ASCII.GetString(seqsOriginal[i].GetEncodedQualityScores());
string newscores = Encoding.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 Invalidate FastQ Parser.
/// <param name="nodeName">xml node name.</param>
/// <param name="IsParseOne">True for FastQParseOne validations, else false</param>
/// </summary>
void InValidateFastQParser(string nodeName, bool IsParseOne)
{
// Gets the expected sequence from the Xml
string filePath = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.FilePathNode);
FastQFormatType expectedFormatType = Utility.GetFastQFormatType(
_utilityObj._xmlUtil.GetTextValue(nodeName, Constants.FastQFormatType));
// Create a FastQ Parser object.
using (FastQParser fastQParserObj = new FastQParser())
{
fastQParserObj.AutoDetectFastQFormat = true;
fastQParserObj.FastqType = expectedFormatType;
if (IsParseOne)
{
try
{
fastQParserObj.ParseOne(filePath);
Assert.Fail();
}
catch (Exception)
{
ApplicationLog.WriteLine(
"FastQ Parser P2 : Successfully validated the exception");
Console.WriteLine(
"FastQ Parser P2 : Successfully validated the exception");
}
}
else
{
try
{
fastQParserObj.Parse(filePath);
Assert.Fail();
}
catch (Exception)
{
ApplicationLog.WriteLine(
"FastQ Parser P2 : Successfully validated the exception");
Console.WriteLine(
"FastQ Parser P2 : Successfully validated the exception");
}
}
}
}
public void TestFormatingString()
{
string str =
@"@SRR002012.1 Oct4:5:1:871:340 length=26
GGCGCACTTACACCCTACATCCATTG
+SRR002012.1 Oct4:5:1:871:340 length=26
IIIIG1?II;IIIII1IIII1%.I7I
";
StringReader sr = new StringReader(str);
FastQParser parser = new FastQParser();
IQualitativeSequence seq = parser.ParseOne(sr);
FastQFormatter formatter = new FastQFormatter();
string formatterStr = formatter.FormatString(seq);
Assert.AreEqual(str, formatterStr);
}
public static async void AssemblySequences(string fastqFileName)
{
var parser = new FastQParser();
List <IQualitativeSequence> sequences = new List <IQualitativeSequence>();
using (var fileStream = new FileStream(fastqFileName, FileMode.Open))
{
sequences = parser.Parse(fileStream).ToList();
}
OverlapDeNovoAssembler assembler = new OverlapDeNovoAssembler();
IDeNovoAssembly assembly = assembler.Assemble(sequences);
FastAFormatter outputFormatter = new FastAFormatter();
outputFormatter.Open("assembled_sequences.fasta");
outputFormatter.Format(assembly.AssembledSequences);
outputFormatter.Close();
}
public void InvalidateFastQParserGetSequenceId()
{
try
{
using (FastQParser fqParserObj = new FastQParser())
{
fqParserObj.GetSequenceID(null);
}
Assert.Fail();
}
catch (ArgumentNullException)
{
ApplicationLog.WriteLine(
"FastQ Parser P2 : Successfully validated the exception");
Console.WriteLine(
"FastQ Parser P2 : Successfully validated the exception");
}
}
public void InvalidateFastQParseNoFileName()
{
try
{
using (FastQParser fqParserObj = new FastQParser())
{
fqParserObj.Parse(null as string, true);
}
Assert.Fail();
}
catch (ArgumentNullException)
{
ApplicationLog.WriteLine(
"FastQ Parser P2 : Successfully validated the exception");
Console.WriteLine(
"FastQ Parser P2 : Successfully validated the exception");
}
}
/// <summary>
/// General method to validate FastQ Parser On Streams.
/// <param name="nodeName">xml node name.</param>
/// </summary>
void ValidateFastQParserOnAStream(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 actualQualitativeSequence = String.Empty;
string actualId = String.Empty;
IEnumerable <QualitativeSequence> qualSequence = null;
IList <QualitativeSequence> qualSequenceList = null;
using (StreamReader reader = new StreamReader(filePath))
{
// Parse a FastQ file.
using (FastQParser fastQParserObj = new FastQParser())
{
fastQParserObj.AutoDetectFastQFormat = false;
qualSequence = fastQParserObj.Parse(reader);
qualSequenceList = qualSequence.ToList();
}
}
actualQualitativeSequence = new string(qualSequenceList[0].Select(a => (char)a).ToArray());
actualId = qualSequenceList[0].ID.ToString((IFormatProvider)null);
// Validate qualitative Sequence upon parsing FastQ file.
Assert.AreEqual(expectedQualitativeSequence, actualQualitativeSequence);
Assert.AreEqual(actualId, expectedSequenceId);
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"FastQ Parser BVT: The FASTQ sequence '{0}' validation after Parse(Stream) is found to be as expected.",
actualQualitativeSequence));
// Logs to the VSTest GUI (Console.Out) window
Console.WriteLine(string.Format((IFormatProvider)null,
"FastQ Parser BVT: The FASTQ sequence ID '{0}' validation after Parse(Stream) is found to be as expected.",
actualQualitativeSequence));
Console.WriteLine(string.Format((IFormatProvider)null,
"FastQ Parser BVT: The FASTQ sequence ID '{0}' validation after Parse(Stream) is found to be as expected.",
actualId));
}
/// <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()
{
// parse
ISequenceParser parser = new FastQParser();
string filepath = @"TestUtils\FASTQ\SRR002012_5.fastq";
ISequence seq = parser.ParseOne(filepath);
Assert.IsNotNull(seq);
FastQParser fqParser = new FastQParser();
fqParser.AutoDetectFastQFormat = false;
fqParser.FastqType = FastQFormatType.Sanger;
IQualitativeSequence qualSeq = fqParser.ParseOne(filepath);
Assert.IsNotNull(qualSeq);
((FastQParser)parser).Dispose();
}
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 InvalidateFastQParseWithQualityScore()
{
try
{
ISequenceParser parser = new FastQParser();
parser.ParseOne(
Utility._xmlUtil.GetTextValue(
Constants.FastQInvalidQualScoreFileNode,
Constants.FilePathNode));
Assert.Fail();
}
catch (FormatException)
{
ApplicationLog.WriteLine(
"FastQ Parser P2 : Successfully validated the exception");
Console.WriteLine(
"FastQ Parser P2 : Successfully validated the exception");
}
}
public IEnumerable<ISequence> Parse(Stream stream)
{
FastQParser fqp = new FastQParser ();
foreach (var seq in fqp.Parse (stream)) {
var name = seq.ID;
var sp = name.Split ('/');
var movie = sp [0];
var hole = sp [1];
SAMAlignedSequence sam = new SAMAlignedSequence ();
sam.QuerySequence = seq;
sam.OptionalFields.Add (new SAMOptionalField () { Tag = "sn", Value = "f,0,0,0,0" });
sam.OptionalFields.Add (new SAMOptionalField () { Tag = "rs", Value = "f,0,0,0,0,0,0" });
sam.OptionalFields.Add (new SAMOptionalField () { Tag = "zs", Value = "f,0,0,0,0,0,0" });
PacBioCCSRead read = new PacBioCCSRead (sam) {
AvgZscore = Single.NaN,
HoleNumber = Convert.ToInt32 (hole),
Movie = movie
};
yield return read;
}
}
/// <summary>
/// General method to validate FastQ Parser On Streams.
/// <param name="nodeName">xml node name.</param>
/// </summary>
private void ValidateFastQParserOnAStream(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);
IList<IQualitativeSequence> qualSequenceList;
using (var reader = File.OpenRead(filePath))
{
// Parse a FastQ file.
var fastQParserObj = new FastQParser();
qualSequenceList = fastQParserObj.Parse(reader).ToList();
}
string actualQualitativeSequence = qualSequenceList[0].ConvertToString();
string actualId = qualSequenceList[0].ID;
// Validate qualitative Sequence upon parsing FastQ file.
Assert.AreEqual(expectedQualitativeSequence, actualQualitativeSequence);
Assert.AreEqual(actualId, expectedSequenceId);
ApplicationLog.WriteLine(string.Format("FastQ Parser BVT: The FASTQ sequence '{0}' validation after Parse(Stream) is found to be as expected.",
actualQualitativeSequence));
ApplicationLog.WriteLine(string.Format("FastQ Parser BVT: The FASTQ sequence ID '{0}' validation after Parse(Stream) is found to be as expected.",
actualId));
}
/// <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);
}
}
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 Invalidate FastQ Parser.
/// <param name="nodeName">xml node name.</param>
/// </summary>
private void InValidateFastQParser(string nodeName)
{
// Gets the expected sequence from the Xml
string filePath = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.FilePathNode);
// Create a FastQ Parser object.
var fastQParserObj = new FastQParser();
{
fastQParserObj.Parse(filePath).ToList();
}
}
public void InvalidateFastQParseNoFileName()
{
var fqParserObj = new FastQParser();
Assert.Throws<ArgumentNullException>( () => fqParserObj.Parse(null).ToList());
}
/// <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);
}
}
public void TestDefaultFastQFormatType()
{
FastQParser parser = new FastQParser();
Assert.AreEqual(parser.FormatType, FastQFormatType.Illumina_v1_8);
}
/// <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);
string expectedSeqCount = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.SeqsCount);
IAlphabet alphabet = Utility.GetAlphabet(utilityObj.xmlUtil.GetTextValue(nodeName, Constants.AlphabetNameNodeV2));
var fastQParserObj = new FastQParser();
{
// Validate qualitative Sequence upon parsing FastQ file.
IList<IQualitativeSequence> qualSequenceList = fastQParserObj.Parse<IQualitativeSequence>(filePath).ToList();
Assert.AreEqual(expectedSeqCount, qualSequenceList.Count.ToString((IFormatProvider) null));
Assert.AreEqual(expectedQualitativeSequence, qualSequenceList[0].ConvertToString());
Assert.AreEqual(expectedSequenceId, qualSequenceList[0].ID.ToString(null));
Assert.AreEqual(alphabet, qualSequenceList[0].Alphabet);
}
}
/// <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);
}
}
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 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));
}
}
public void FastQProperties()
{
FastQParser parser = new FastQParser();
Assert.AreEqual(parser.Name, Resource.FastQName);
Assert.AreEqual(parser.Description, Resource.FASTQPARSER_DESCRIPTION);
Assert.AreEqual(parser.SupportedFileTypes, Resource.FASTQ_FILEEXTENSION);
FastQFormatter formatter = new FastQFormatter();
Assert.AreEqual(formatter.Name, Resource.FastQName);
Assert.AreEqual(formatter.Description, Resource.FASTQFORMATTER_DESCRIPTION);
Assert.AreEqual(formatter.SupportedFileTypes, Resource.FASTQ_FILEEXTENSION);
}
/// <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 BasicSequence Parser.
/// <param name="nodeName">xml node name.</param>
/// </summary>
private void ValidateBasicSequenceParser(string nodeName)
{
// Gets the expected sequence from the Xml
string filepathOriginal = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.FilePathNode);
string expectedQualitativeSequence = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.ExpectedSequenceNode);
string expectedSequenceId = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.SequenceIdNode);
IAlphabet alphabet = Utility.GetAlphabet(utilityObj.xmlUtil.GetTextValue(nodeName, Constants.AlphabetNameNode));
Assert.IsTrue(File.Exists(filepathOriginal));
string tempPath = Path.GetTempFileName();
try
{
ISequenceParser fastQParserObj = SequenceParsers.FindParserByFileName("temp.fq");
// Read the original file
IEnumerable<ISequence> seqsOriginal = fastQParserObj.Parse(filepathOriginal);
Assert.IsNotNull(seqsOriginal);
// Use the formatter to write the original sequences to a temp file
var formatter = new FastQFormatter();
formatter.Format(seqsOriginal.ElementAt(0), tempPath);
// Read the new file, then compare the sequences
var fastQParserObjNew = new FastQParser();
IEnumerable<IQualitativeSequence> seqsNew = fastQParserObjNew.Parse(tempPath);
Assert.IsNotNull(seqsNew);
// Validate qualitative Sequence upon parsing FastQ file.
Assert.AreEqual(expectedQualitativeSequence,
new string(seqsOriginal.ElementAt(0).Select(a => (char) a).ToArray()));
Assert.AreEqual(
seqsOriginal.ElementAt(0).ID.ToString(null),
expectedSequenceId);
Assert.AreEqual(
seqsOriginal.ElementAt(0).Alphabet.Name,
alphabet.Name);
ApplicationLog.WriteLine(string.Format("FastQ Parser P1: The FASTQ sequence '{0}' validation after Parse() is found to be as expected.",
seqsOriginal.ElementAt(0)));
}
finally
{
File.Delete(tempPath);
}
}
