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>
/// 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);
}
/// <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 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 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 TestFastQWhenParsingString()
{
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);
ISequenceParser parser = new FastQParser();
ISequence seq = parser.ParseOne(sr);
sr = new StringReader(str);
FastQParser fqParser = new FastQParser();
fqParser.AutoDetectFastQFormat = false;
fqParser.FastqType = FastQFormatType.Sanger;
IQualitativeSequence qualSeq = fqParser.ParseOne(sr);
}
public void TestDefaultFastQFormatType()
{
QualitativeSequence qualSeq = new QualitativeSequence(Alphabets.DNA);
Assert.AreEqual(qualSeq.Type, FastQFormatType.Illumina);
string str =
@"@Seq1
GGCGCACTTACACCCTACATCCATTG
+
ABCDEFGHIJKLMNOPQRSTUVWZYZ
";
StringReader sr = new StringReader(str);
FastQParser parser = new FastQParser();
IQualitativeSequence seq = parser.ParseOne(sr);
Assert.AreEqual(seq.Type, FastQFormatType.Illumina);
}
public void InvalidateFastQParseOneWithFastQFormat()
{
ISequenceParser parser = new FastQParser();
try
{
parser.ParseOne(
_utilityObj._xmlUtil.GetTextValue(
Constants.FastQInvalidFormatFileNode,
Constants.FilePathNode));
Assert.Fail();
}
catch (FormatException)
{
ApplicationLog.WriteLine(
"FastQ Parser P2 : Successfully validated the exception");
Console.WriteLine(
"FastQ Parser P2 : Successfully validated the exception");
}
finally
{
(parser as FastQParser).Dispose();
}
}
/// <summary>
/// General method to Invalidate FastQ Parser.
/// <param name="nodeName">xml node name.</param>
/// <param name="param">FastQ Formatter different parameters</param>
/// </summary>
void InValidateFastQFormatter(FastQFormatParameters param)
{
// Gets the expected sequence from the Xml
string filepath = _utilityObj._xmlUtil.GetTextValue(
Constants.MultiSeqSangerRnaProNode, Constants.FilePathNode);
FastQFormatType expectedFormatType = Utility.GetFastQFormatType(
_utilityObj._xmlUtil.GetTextValue(Constants.MultiSeqSangerRnaProNode,
Constants.FastQFormatType));
// Parse a FastQ file.
using (FastQParser fastQParser = new FastQParser())
{
fastQParser.AutoDetectFastQFormat = true;
fastQParser.FastqType = expectedFormatType;
IQualitativeSequence sequence = null;
sequence = fastQParser.ParseOne(filepath);
FastQFormatter fastQFormatter = new FastQFormatter();
TextWriter txtWriter = null;
switch (param)
{
case FastQFormatParameters.TextWriter:
try
{
fastQFormatter.Format(sequence, null as TextWriter);
Assert.Fail();
}
catch (Exception)
{
ApplicationLog.WriteLine(
"FastQ Parser P2 : Successfully validated the exception");
Console.WriteLine(
"FastQ Parser P2 : Successfully validated the exception");
}
break;
case FastQFormatParameters.Sequence:
try
{
fastQFormatter.Format(null as ISequence, txtWriter);
Assert.Fail();
}
catch (Exception)
{
ApplicationLog.WriteLine(
"FastQ Parser P2 : Successfully validated the exception");
Console.WriteLine(
"FastQ Parser P2 : Successfully validated the exception");
}
break;
case FastQFormatParameters.QualitativeSequence:
try
{
fastQFormatter.Format(null as IQualitativeSequence, txtWriter);
Assert.Fail();
}
catch (Exception)
{
ApplicationLog.WriteLine(
"FastQ Parser P2 : Successfully validated the exception");
Console.WriteLine(
"FastQ Parser P2 : Successfully validated the exception");
}
break;
default:
try
{
fastQFormatter.Format(sequence as QualitativeSequence, null as TextWriter);
Assert.Fail();
}
catch (Exception)
{
ApplicationLog.WriteLine(
"FastQ Parser P2 : Successfully validated the exception");
Console.WriteLine(
"FastQ Parser P2 : Successfully validated the exception");
}
break;
}
}
}
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 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);
}
}
