public void SnpParserPropertiesTest()
{
SimpleSnpParser snpParser = new SimpleSnpParser(Alphabets.DNA);
Assert.AreEqual("Basic SNP Parser that uses XSV format", snpParser.Description);
Assert.AreEqual("Basic SNP", snpParser.Name);
Assert.IsTrue(snpParser.ParseAlleleOne);
Assert.AreEqual(".tsv", snpParser.SupportedFileTypes);
}
public void SnpBvtParserProperties()
{
string filepath = utilityObj.xmlUtil.GetTextValue(Constants.SimpleSnpNodeName,
Constants.FilePathNode);
SimpleSnpParser snpParser = new SimpleSnpParser();
Assert.AreEqual(Constants.SnpDescription, snpParser.Description);
Assert.AreEqual(Constants.SnpFileTypes, snpParser.SupportedFileTypes);
Assert.AreEqual(Constants.SnpName, snpParser.Name);
Assert.IsTrue(snpParser.ParseAlleleOne);
Assert.AreEqual(Constants.SnpFileTypes, snpParser.SupportedFileTypes);
ApplicationLog.WriteLine
("Successfully validated all the properties of Snp Parser class.");
}
/// <summary>
/// Snp parser generic method called by all the test cases
/// to validate the test case based on the parameters passed.
/// </summary>
/// <param name="switchParam">Additional parameter
/// based on which the validation of test case is done.</param>
void SnpParserGeneralTestCases(string switchParam)
{
Assert.IsTrue(File.Exists(snpFileName));
IList<ISequence> seqList = null;
SparseSequence sparseSeq = null;
SimpleSnpParser parser = new SimpleSnpParser();
string expectedPosition = "45162,72434,145160,172534,245162,292534";
string[] expectedPositions = expectedPosition.Split(',');
string[] expectedCharacters = null;
switch (switchParam)
{
case "ParseAlleleTwo":
parser.ParseAlleleOne = false;
string expectedAlleleTwoSequence = "T,A,T,C,T,A";
expectedCharacters = expectedAlleleTwoSequence.Split(',');
break;
default:
string expectedSequence = "C,G,A,G,C,G";
expectedCharacters = expectedSequence.Split(',');
break;
}
seqList = parser.Parse(snpFileName).ToList();
sparseSeq = (SparseSequence)seqList[0];
if (null == sparseSeq)
{
Assert.IsNotNull(seqList);
Assert.AreEqual(1, seqList.Count);
}
for (int i = 0; i < expectedPositions.Length; i++)
{
byte item = sparseSeq[int.Parse(expectedPositions[i], null)];
char s = (char)item;
Assert.AreEqual(expectedCharacters[i], s.ToString());
}
Assert.IsNotNull(sparseSeq.Alphabet);
Assert.AreEqual(sparseSeq.Alphabet.Name.ToLower(), AmbiguousDnaAlphabet.Instance.Name.ToLower());
string expSequenceID = "Chr1";
Assert.AreEqual(expSequenceID, sparseSeq.ID);
}
/// <summary>
/// Snp parser generic method called by all the test cases
/// to validate the test case based on the parameters passed.
/// </summary>
/// <param name="nodename">Xml node Name.</param>
/// <param name="additionalParam">Additional parameter
/// based on which the validation of test case is done.</param>
void SnpParserGeneralTestCases(string nodename, AdditionalParameters additionalParam)
{
// Gets the expected sequence from the Xml
string filepath = utilityObj.xmlUtil.GetTextValue(nodename,
Constants.FilePathNode);
Assert.IsTrue(File.Exists(filepath));
// Logs information to the log file
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Snp Parser BVT: File Exists in the Path '{0}'.",
filepath));
IList<ISequence> seqList = null;
SparseSequence sparseSeq = null;
SimpleSnpParser parser = new SimpleSnpParser();
string expectedPosition = utilityObj.xmlUtil.GetTextValue(nodename,
Constants.ExpectedPositionNode);
string[] expectedPositions = expectedPosition.Split(',');
string[] expectedCharacters = null;
switch (additionalParam)
{
case AdditionalParameters.ParseAlleleTwo:
parser.ParseAlleleOne = false;
string expectedAlleleTwoSequence =
utilityObj.xmlUtil.GetTextValue(nodename,
Constants.ExpectedSequenceAllele2Node);
expectedCharacters = expectedAlleleTwoSequence.Split(',');
break;
default:
string expectedSequence = utilityObj.xmlUtil.GetTextValue(nodename,
Constants.ExpectedSequenceNode);
expectedCharacters = expectedSequence.Split(',');
break;
}
seqList = parser.Parse(filepath).ToList();
sparseSeq = (SparseSequence)seqList[0];
if (null == sparseSeq)
{
Assert.IsNotNull(seqList);
Assert.AreEqual(1, seqList.Count);
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Snp Parser BVT: Number of Sequences found are '{0}'.",
seqList.Count.ToString((IFormatProvider)null)));
}
for (int i = 0; i < expectedPositions.Length; i++)
{
byte item = sparseSeq[int.Parse(expectedPositions[i], (IFormatProvider)null)];
ASCIIEncoding enc = new ASCIIEncoding();
Assert.AreEqual(enc.GetBytes(expectedCharacters[i])[0].ToString((IFormatProvider)null),
item.ToString((IFormatProvider)null));
}
ApplicationLog.WriteLine(
"Snp Parser BVT: The Snp sequence with position is validated successfully with Parse() method.");
Assert.IsNotNull(sparseSeq.Alphabet);
Assert.IsTrue(sparseSeq.Alphabet.Name.ToLower(CultureInfo.CurrentCulture).Contains(utilityObj.xmlUtil.GetTextValue(nodename,
Constants.AlphabetNameNode).ToLower(CultureInfo.CurrentCulture)));
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Snp Parser BVT: The Sequence Alphabet is '{0}' and is as expected.",
sparseSeq.Alphabet.Name));
string expSequenceID = utilityObj.xmlUtil.GetTextValue(nodename,
Constants.SequenceIdNode);
Assert.AreEqual(expSequenceID, sparseSeq.ID);
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Snp Parser BVT: The Sequence ID is '{0}' and is as expected.", sparseSeq.ID));
}
/// <summary>
/// Snp parser generic method called by all the test cases to
/// validate the test case based on the parameters passed.
/// </summary>
/// <param name="nodename">Xml node Name.</param>
/// <param name="additionalParam">Additional parameter based on which
/// the validation of test case is done.</param>
void SnpParserGeneralTestCases(string nodename,
AdditionalParameters additionalParam)
{
// Gets the expected sequence from the Xml
string filePath = utilityObj.xmlUtil.GetTextValue(nodename,
Constants.FilePathNode);
Assert.IsTrue(File.Exists(filePath));
// Logs information to the log file
ApplicationLog.WriteLine(string.Format("Snp Parser P1: File Exists in the Path '{0}'.", filePath));
IList<ISequence> seqList = null;
SparseSequence sparseSeq = null;
SimpleSnpParser parser = new SimpleSnpParser();
switch (additionalParam)
{
case AdditionalParameters.ParseAlleleOne:
parser.ParseAlleleOne = true;
break;
default:
break;
}
string noOfChromos = utilityObj.xmlUtil.GetTextValue(nodename,
Constants.NumberOfChromosomesNode);
seqList = parser.Parse(filePath).ToList();
sparseSeq = (SparseSequence)seqList[0];
// Based on the number of chromosomes the validation is done reading from the xml
if (0 == string.Compare(noOfChromos, "1", true, CultureInfo.CurrentCulture))
{
string expectedPosition = utilityObj.xmlUtil.GetTextValue(nodename,
Constants.ExpectedPositionNode);
string[] expectedPositions = expectedPosition.Split(',');
string[] expectedCharacters = null;
string expectedSequence = utilityObj.xmlUtil.GetTextValue(nodename,
Constants.ExpectedSequenceNode);
expectedCharacters = expectedSequence.Split(',');
Assert.IsNotNull(seqList);
Assert.AreEqual(noOfChromos, seqList.Count.ToString((IFormatProvider)null));
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Snp Parser P1: Number of Sequences found are '{0}'.",
seqList.Count.ToString((IFormatProvider)null)));
// Validation of sequences with positions and xml is done in this section.
for (int i = 0; i < expectedPositions.Length; i++)
{
byte item = sparseSeq[int.Parse(expectedPositions[i], (IFormatProvider)null)];
Assert.AreEqual(encodingObj.GetBytes(expectedCharacters[i])[0].ToString((IFormatProvider)null),
item.ToString((IFormatProvider)null));
}
string expSequenceID = utilityObj.xmlUtil.GetTextValue(nodename,
Constants.SequenceIdNode);
Assert.AreEqual(expSequenceID, sparseSeq.ID);
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Snp Parser P1: The Sequence ID is '{0}' and is as expected.", sparseSeq.ID));
}
else
{
string[] expectedPositions = utilityObj.xmlUtil.GetTextValues(nodename,
Constants.ExpectedPositionsNode);
string[] expectedSequences = utilityObj.xmlUtil.GetTextValues(nodename,
Constants.ExpectedSequencesNode);
string[] expectedSequenceIds = utilityObj.xmlUtil.GetTextValues(nodename,
Constants.SequenceIdsNode);
// Validation of sequences with positions and xml is done in this section.
for (int i = 0; i < int.Parse(noOfChromos, (IFormatProvider)null); i++)
{
string[] expectedChromoPositions = expectedPositions[i].Split(',');
string[] expectedChromoSequences = expectedSequences[i].Split(',');
SparseSequence tempSparseSeq = (SparseSequence)seqList[i];
for (int j = 0; j < expectedChromoPositions.Length; j++)
{
byte item = tempSparseSeq[int.Parse(expectedChromoPositions[j], (IFormatProvider)null)];
Assert.AreEqual(encodingObj.GetBytes(expectedChromoSequences[j])[0].ToString((IFormatProvider)null),
item.ToString((IFormatProvider)null));
}
// Validation of Id are done in this section.
Assert.AreEqual(expectedSequenceIds[i], tempSparseSeq.ID);
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Snp Parser P1: The Sequence ID is '{0}' and is as expected.", tempSparseSeq.ID));
}
}
ApplicationLog.WriteLine(
"Snp Parser P1: The Snp sequence with position is validated successfully with Parse() method.");
Assert.IsNotNull(sparseSeq.Alphabet);
Assert.IsTrue(sparseSeq.Alphabet.Name.ToLower(CultureInfo.CurrentCulture).Contains(utilityObj.xmlUtil.GetTextValue(nodename,
Constants.AlphabetNameNode).ToLower(CultureInfo.CurrentCulture)));
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Snp Parser P1: The Sequence Alphabet is '{0}' and is as expected.",
sparseSeq.Alphabet.Name));
}
