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);
}
}
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 tempFileName1 = System.IO.Path.GetTempFileName();
string tempFileName2 = System.IO.Path.GetTempFileName();
// Parse a FastQ file using parseOne method.
using (FastQParser fastQParserObj = new FastQParser(filePath))
{
fastQParserObj.AutoDetectFastQFormat = false;
IEnumerable <ISequence> qualSequence = null;
qualSequence = fastQParserObj.Parse();
// New Sequence after formatting file.
IEnumerable <ISequence> newQualSeq = null;
FastQFormatter fastQFormatter = new FastQFormatter(tempFileName1);
FastQFormatter fastQFormatterFq = new FastQFormatter(tempFileName2);
string parsedValue = null;
string parsedID = null;
// Format Parsed Sequence to temp file with different extension.
switch (fileExtension)
{
case FastQFileParameters.FastQ:
fastQFormatter.Write(qualSequence.ElementAt(0));
fastQFormatter.Close();
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);
fastQParserObjTemp.Dispose();
break;
case FastQFileParameters.Fq:
fastQFormatterFq.Write(qualSequence.ElementAt(0));
fastQFormatterFq.Close();
FastQParser fastQParserObjTemp1 = new FastQParser(tempFileName2);
newQualSeq = fastQParserObjTemp1.Parse();
parsedValue = new string(newQualSeq.ElementAt(0).Select(a => (char)a).ToArray());
parsedID = newQualSeq.ElementAt(0).ID.ToString((IFormatProvider)null);
break;
default:
break;
}
// 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 NUnit 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;
fastQFormatter = null;
fastQFormatterFq = null;
GC.Collect();
GC.WaitForPendingFinalizers();
File.Delete(tempFileName1);
File.Delete(tempFileName2);
}
}
