public void TestFormatter()
{
string filePath = @"TestUtils\SAM\SeqAlignment1.sam";
string outputfilePath = "samtest.sam";
ISequenceAlignmentParser parser = new SAMParser();
IList<ISequenceAlignment> alignments = parser.Parse(filePath).ToList();
Assert.IsTrue(alignments != null);
Assert.AreEqual(alignments.Count, 1);
Assert.AreEqual(alignments[0].AlignedSequences.Count, 2);
try
{
SAMFormatter formatter = new SAMFormatter();
formatter.Format(alignments[0], outputfilePath);
alignments = parser.Parse(outputfilePath).ToList();
Assert.IsTrue(alignments != null);
Assert.AreEqual(alignments.Count, 1);
Assert.AreEqual(alignments[0].AlignedSequences.Count, 2);
}
finally
{
File.Delete(outputfilePath);
}
}
public void SAMProperties()
{
ISequenceAlignmentParser parser = new SAMParser();
Assert.AreEqual(parser.Name, Properties.Resource.SAM_NAME);
Assert.AreEqual(parser.Description, Properties.Resource.SAMPARSER_DESCRIPTION);
Assert.AreEqual(parser.SupportedFileTypes, Properties.Resource.SAM_FILEEXTENSION);
ISequenceAlignmentFormatter formatter = new SAMFormatter();
Assert.AreEqual(formatter.Name, Properties.Resource.SAM_NAME);
Assert.AreEqual(formatter.Description, Properties.Resource.SAMFORMATTER_DESCRIPTION);
Assert.AreEqual(formatter.SupportedFileTypes, Properties.Resource.SAM_FILEEXTENSION);
}
/// <summary>
/// General method to validate SAM Formatter method.
/// </summary>
/// <param name="nodeName">xml node name</param>
/// <param name="parseTypes">enum type to execute different overload</param>
void ValidateSAMFormatter(string nodeName)
{
// Gets the expected sequence from the Xml
string filePath = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.FilePathNode);
string expectedSequenceFile = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ExpectedSequence);
SAMParser parser = new SAMParser();
{
SequenceAlignmentMap alignments = (SequenceAlignmentMap) parser.ParseOne(filePath);
SAMFormatter formatter = new SAMFormatter();
using (var writer =
File.Create(Constants.SAMTempFileName))
{
formatter.Format(writer, alignments);
}
alignments = parser.ParseOne<SequenceAlignmentMap>(Constants.SAMTempFileName);
// Get expected sequences
FastAParser parserObj = new FastAParser();
{
IEnumerable<ISequence> expectedSequences =
parserObj.Parse(expectedSequenceFile);
IList<ISequence> expectedSequencesList = expectedSequences.ToList();
// Validate parsed output with expected output
for (int index = 0;
index < alignments.QuerySequences.Count;
index++)
{
for (int count = 0;
count < alignments.QuerySequences[index].Sequences.Count;
count++)
{
Assert.AreEqual(
new string(expectedSequencesList[index].Select(a => (char)a).ToArray()),
new string(alignments.QuerySequences[index].Sequences[count].Select(a => (char)a).ToArray()));
}
}
}
}
}
/// <summary>
/// Writes the SAM object to file in SAM/BAM format.
/// </summary>
private void PerformFormat()
{
if (_isSAM)
{
BAMFormatter format = new BAMFormatter();
try
{
format.Format(_sequenceAlignmentMap, OutputFilename);
}
catch (Exception ex)
{
throw new InvalidOperationException(Resources.WriteBAM + Environment.NewLine + ex.Message);
}
}
else
{
SAMFormatter format = new SAMFormatter();
try
{
format.Format(_sequenceAlignmentMap, OutputFilename);
}
catch (Exception ex)
{
throw new InvalidOperationException(Resources.WriteSAM + Environment.NewLine + ex.Message);
}
}
}
/// <summary>
/// Validate formatter all format method overloads with filePath\textwriter
/// </summary>
/// <param name="nodeName">xml node name</param>
/// <param name="formatTypes">enum type to execute different overload</param>
void ValidateSAMFormatter(string nodeName,
ParseOrFormatTypes formatTypes)
{
// Gets the expected sequence from the Xml
string filePath = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.FilePathNode);
string expectedSequenceFile = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ExpectedSequence);
ISequenceAlignmentParser parser = new SAMParser();
try
{
IList<ISequenceAlignment> alignments = parser.Parse(filePath).ToList();
SAMFormatter formatter = new SAMFormatter();
switch (formatTypes)
{
case ParseOrFormatTypes.ParseOrFormatText:
using (var writer = File.Create(Constants.SAMTempFileName))
{
formatter.Format(writer, alignments[0]);
}
break;
case ParseOrFormatTypes.ParseOrFormatFileName:
formatter.Format(alignments[0], Constants.SAMTempFileName);
break;
}
alignments = parser.Parse(Constants.SAMTempFileName).ToList();
// Get expected sequences
FastAParser parserObj = new FastAParser();
{
IEnumerable<ISequence> expectedSequences = parserObj.Parse(expectedSequenceFile);
IList<ISequence> expectedSequencesList = expectedSequences.ToList();
// Validate parsed output with expected output
int count = 0;
for (int index = 0; index < alignments.Count; index++)
{
for (int ialigned = 0; ialigned <
alignments[index].AlignedSequences.Count; ialigned++)
{
for (int iseq = 0; iseq <
alignments[index].AlignedSequences[ialigned].Sequences.Count; iseq++)
{
Assert.AreEqual(new string(expectedSequencesList[count].Select(a => (char)a).ToArray()),
new string(alignments[index].AlignedSequences[ialigned].Sequences[iseq].Select(a => (char)a).ToArray()));
count++;
}
}
}
}
}
finally
{
}
}
public void ValidateSAMFormatterFormatString()
{
string filePath = utilityObj.xmlUtil.GetTextValue(
Constants.SamFormatterFileNode,
Constants.FilePathNode);
ISequenceAlignmentParser parser = new SAMParser();
IList<ISequenceAlignment> alignment = parser.Parse(filePath).ToList();
SAMFormatter formatter = new SAMFormatter();
string writer = formatter.FormatString(alignment[0]);
Assert.AreEqual(writer, Constants.FormatterString.Replace("\r\n", Environment.NewLine));
}
public void ValidateSAMFormatterProperties()
{
SAMFormatter parser = new SAMFormatter();
Assert.AreEqual(Constants.SAMFormatterDescription, parser.Description);
Assert.AreEqual(Constants.SAMFileType, parser.SupportedFileTypes);
Assert.AreEqual(Constants.SAMName, parser.Name);
ApplicationLog.WriteLine("Successfully validated all the properties of SAM Parser class.");
}
public void ValidateSAMFormatterWithTextWriterAndAlignments()
{
// Gets the expected sequence from the Xml
string filePath = utilityObj.xmlUtil.GetTextValue(
Constants.SmallSAMFileNode, Constants.FilePathNode);
ISequenceAlignmentParser parser = new SAMParser();
IEnumerable<ISequenceAlignment> alignments = parser.Parse(filePath);
SAMFormatter formatter = new SAMFormatter();
try
{
using (var writer = File.Create(Constants.SAMTempFileName))
{
formatter.Format(writer, alignments);
}
Assert.Fail();
}
catch (NotSupportedException)
{
ApplicationLog.WriteLine("SAM Parser BVT : Validated the exception successfully");
}
}
public void ValidateSAMFormatterWithFileNameAndAlignments()
{
// Gets the expected sequence from the Xml
string filePath = utilityObj.xmlUtil.GetTextValue(
Constants.SmallSAMFileNode.Replace("\r\n", System.Environment.NewLine), Constants.FilePathNode);
ISequenceAlignmentParser parser = new SAMParser();
IEnumerable<ISequenceAlignment> alignments = parser.Parse(filePath);
SAMFormatter formatter = new SAMFormatter();
try
{
formatter.Format(alignments, Constants.SAMTempFileName);
Assert.Fail();
}
catch (NotSupportedException)
{
ApplicationLog.WriteLine("SAM Parser BVT : Validated the exception successfully");
}
}
public void ValidateBAMToSAMConversion()
{
// Get values from xml config file.
string expectedSamFilePath = this.utilityObj.xmlUtil.GetTextValue(Constants.BAMToSAMConversionNode,
Constants.FilePathNode1);
string bamFilePath = this.utilityObj.xmlUtil.GetTextValue(Constants.BAMToSAMConversionNode,
Constants.FilePathNode);
var samParserObj = new SAMParser();
SequenceAlignmentMap expextedSamAlignmentObj = samParserObj.ParseOne<SequenceAlignmentMap>(expectedSamFilePath);
var bamParserObj = new BAMParser();
SequenceAlignmentMap bamSeqAlignment = bamParserObj.ParseOne<SequenceAlignmentMap>(bamFilePath);
try
{
// Format BAM sequenceAlignment object to SAM file.
var samFormatterObj = new SAMFormatter();
samFormatterObj.Format(bamSeqAlignment, Constants.SAMTempFileName);
SequenceAlignmentMap samSeqAlignment = samParserObj.ParseOne<SequenceAlignmentMap>(Constants.SAMTempFileName);
Assert.IsTrue(CompareSequencedAlignmentHeader(samSeqAlignment, expextedSamAlignmentObj));
Assert.IsTrue(CompareAlignedSequences(samSeqAlignment, expextedSamAlignmentObj));
}
finally
{
// Delete temporary file.
File.Delete(Constants.SAMTempFileName);
}
}
/// <summary>
/// General method to validate BAM to SAM conversion.
/// </summary>
/// <param name="nodeName">Different nodeName used for different test cases.</param>
void ValidateBAMToSAMConversion(string nodeName)
{
// Get values from xml config file.
string expectedSamFilePath = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.FilePathNode1);
string BAMStoragePath = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.FilePathNode);
BAMParser bamParserObj = new BAMParser();
SAMParser samParserObj = new SAMParser();
SAMFormatter samFormatterObj = new SAMFormatter();
SequenceAlignmentMap samSeqAlignment = null;
SequenceAlignmentMap bamSeqAlignment = null;
// Parse expected SAM file.
SequenceAlignmentMap expectedSamAlignmentObj = samParserObj.ParseOne<SequenceAlignmentMap>(expectedSamFilePath);
// Parse a BAM file.
bamSeqAlignment = bamParserObj.ParseOne<SequenceAlignmentMap>(BAMStoragePath);
try
{
// Format BAM sequenceAlignment object to SAM file.
samFormatterObj.Format(bamSeqAlignment, Constants.SAMTempFileName);
// Parse a formatted SAM file.
samSeqAlignment = samParserObj.ParseOne<SequenceAlignmentMap>(Constants.SAMTempFileName);
// Validate converted SAM file with expected SAM file.
Assert.IsTrue(CompareSequencedAlignmentHeader(samSeqAlignment,
expectedSamAlignmentObj));
// Validate SAM file aligned sequences.
Assert.IsTrue(CompareAlignedSequences(samSeqAlignment,
expectedSamAlignmentObj));
// Log message to VSTest GUI.
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"BAM Parser P1 : Validated the BAM->SAM conversion successfully"));
}
finally
{
// Delete temporary file.
File.Delete(Constants.SAMTempFileName);
ApplicationLog.WriteLine("Deleted the temp file created.");
}
}
