/// <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>
/// Parses a FastA file which has one or more sequences.
/// </summary>
/// <param name="filename">Path to the file to be parsed.</param>
/// <returns>ISequence objects</returns>
static IEnumerable <ISequence> ParseFastA(string filename)
{
// A new parser to import a file
FastAParser parser = new FastAParser(filename);
return(parser.Parse());
}
/// <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);
}
public void ValidateSequenceStatisticsToString()
{
ISequence seq = new Sequence(Alphabets.DNA, "ATCGATCG");
var seqStats = new SequenceStatistics(seq);
string actualString = seqStats.ToString();
string expectedString = "A - 2\r\nC - 2\r\nG - 2\r\nT - 2\r\n".Replace("\r\n", System.Environment.NewLine);
Assert.AreEqual(actualString, expectedString);
// Gets the expected sequence from the Xml
List <ISequence> seqsList;
IEnumerable <ISequence> sequences = null;
string filePath = this.utilityObj.xmlUtil.GetTextValue(Constants.SimpleFastaNodeName,
Constants.FilePathNode);
using (var reader = File.OpenRead(filePath))
{
var parser = new FastAParser();
{
parser.Alphabet = Alphabets.Protein;
sequences = parser.Parse(reader);
//Create a list of sequences.
seqsList = sequences.ToList();
}
}
foreach (ISequence Sequence in seqsList)
{
seqStats = new SequenceStatistics(Sequence);
string seqStatStr = seqStats.ToString();
Assert.IsTrue(seqStatStr.Contains(" - "));
}
}
public void testBug2()
{
//Test on DNA benchmark dataset
string filepath = @"TestUtils\122_raw.afa".TestDir();
FastAParser parser = new FastAParser();
IList <ISequence> orgSequences = parser.Parse(filepath).ToList();
List <ISequence> sequences = MsaUtils.UnAlign(orgSequences);
PAMSAMMultipleSequenceAligner.FasterVersion = false;
PAMSAMMultipleSequenceAligner.UseWeights = false;
PAMSAMMultipleSequenceAligner.UseStageB = false;
PAMSAMMultipleSequenceAligner.NumberOfCores = 2;
int gapOpenPenalty = -13;
int gapExtendPenalty = -5;
int kmerLength = 2;
int numberOfDegrees = 2; //Environment.ProcessorCount;
int numberOfPartitions = 16; // Environment.ProcessorCount * 2;
DistanceFunctionTypes distanceFunctionName = DistanceFunctionTypes.EuclideanDistance;
UpdateDistanceMethodsTypes hierarchicalClusteringMethodName = UpdateDistanceMethodsTypes.Average;
ProfileAlignerNames profileAlignerName = ProfileAlignerNames.NeedlemanWunschProfileAligner;
ProfileScoreFunctionNames profileProfileFunctionName = ProfileScoreFunctionNames.InnerProductFast;
SimilarityMatrix similarityMatrix = new SimilarityMatrix(SimilarityMatrix.StandardSimilarityMatrix.AmbiguousDna);
PAMSAMMultipleSequenceAligner msa = new PAMSAMMultipleSequenceAligner
(sequences, kmerLength, distanceFunctionName, hierarchicalClusteringMethodName,
profileAlignerName, profileProfileFunctionName, similarityMatrix, gapOpenPenalty, gapExtendPenalty,
numberOfPartitions, numberOfDegrees);
Assert.IsNotNull(msa.AlignedSequences);
}
public void ValidateNUCmerGetClusters()
{
// NOTE: Nigel ran this test with the same data through mmummer and mgaps and got the same result.
// Gets the reference sequence from the FastA file
string filePath = this.utilityObj.xmlUtil.GetTextValue(Constants.MediumSizeSequenceNodeName,
Constants.FilePathNode);
// Gets the query sequence from the FastA file
string queryFilePath = this.utilityObj.xmlUtil.GetTextValue(Constants.MediumSizeSequenceNodeName,
Constants.SearchSequenceFilePathNode);
FastAParser parser = new FastAParser();
IEnumerable <ISequence> seqs1 = parser.Parse(filePath);
IEnumerable <ISequence> seqs2 = parser.Parse(queryFilePath);
var nuc = new Bio.Algorithms.Alignment.NUCmer(seqs1.First())
{
LengthOfMUM = 5,
MinimumScore = 0,
};
var clusts = nuc.GetClusters(seqs2.First());
string clustCount1 = this.utilityObj.xmlUtil.GetTextValue(
Constants.MediumSizeSequenceNodeName, Constants.ClustCount1Node);
Assert.AreEqual(clustCount1, clusts.Count.ToString(CultureInfo.InvariantCulture));
}
/// <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 ValidateNUCmerGetClusters()
{
// Gets the reference sequence from the FastA file
string filePath = utilityObj.xmlUtil.GetTextValue(Constants.MediumSizeSequenceNodeName,
Constants.FilePathNode);
// Gets the query sequence from the FastA file
string queryFilePath = utilityObj.xmlUtil.GetTextValue(Constants.MediumSizeSequenceNodeName,
Constants.SearchSequenceFilePathNode);
using (FastAParser parser1 = new FastAParser(filePath))
{
using (FastAParser parser2 = new FastAParser(queryFilePath))
{
IEnumerable <ISequence> seqs1 = parser1.Parse();
IEnumerable <ISequence> seqs2 = parser2.Parse();
NUCmer nuc = new NUCmer((Sequence)seqs1.ElementAt(0));
nuc.LengthOfMUM = 5;
nuc.MinimumScore = 0;
nuc.BreakLength = 0;
IList <Cluster> clusts = nuc.GetClusters(seqs2.ElementAt(0), true);
string clustCount1 = utilityObj.xmlUtil.GetTextValue(Constants.MediumSizeSequenceNodeName,
Constants.ClustCount1Node);
Assert.AreEqual(clustCount1, clusts.Count.ToString((IFormatProvider)null));
}
}
}
public void FastAFormatterValidateWrite()
{
using (FastAFormatter formatter = new FastAFormatter(Constants.FastaTempFileName))
{
// Gets the actual sequence and the alphabet from the Xml
string actualSequence = utilityObj.xmlUtil.GetTextValue(Constants.SimpleFastaNodeName,
Constants.ExpectedSequenceNode);
string alpName = utilityObj.xmlUtil.GetTextValue(Constants.SimpleFastaNodeName,
Constants.AlphabetNameNode);
// Logs information to the log file
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"FastA Formatter BVT: Validating with Sequence '{0}' and Alphabet '{1}'.",
actualSequence, alpName));
Sequence seqOriginal = new Sequence(Utility.GetAlphabet(alpName),
actualSequence);
seqOriginal.ID = "";
Assert.IsNotNull(seqOriginal);
// Use the formatter to write the original sequences to a temp file
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"FastA Formatter BVT: Creating the Temp file '{0}'.", Constants.FastaTempFileName));
formatter.Write(seqOriginal);
formatter.Close();
IEnumerable <ISequence> seqsNew = null;
// Read the new file, then compare the sequences
using (FastAParser parser = new FastAParser(Constants.FastaTempFileName))
{
parser.Alphabet = Alphabets.Protein;
seqsNew = parser.Parse();
char[] seqString = seqsNew.ElementAt(0).Select(a => (char)a).ToArray();
string newSequence = new string(seqString);
Assert.IsNotNull(seqsNew);
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"FastA Formatter BVT: New Sequence is '{0}'.",
newSequence));
// Now compare the sequences.
int countNew = seqsNew.Count();
Assert.AreEqual(1, countNew);
ApplicationLog.WriteLine("The Number of sequences are matching.");
Assert.AreEqual(seqOriginal.ID, seqsNew.ElementAt(0).ID);
string orgSeq = new string(seqsNew.ElementAt(0).Select(a => (char)a).ToArray());
Assert.AreEqual(orgSeq, newSequence);
Console.WriteLine(string.Format((IFormatProvider)null,
"FastA Formatter BVT: The FASTA sequences '{0}' are matching with Format() method and is as expected.",
newSequence));
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"FastA Formatter BVT: The FASTA sequences '{0}' are matching with Format() method.",
newSequence));
}
// 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(Constants.FastaTempFileName);
ApplicationLog.WriteLine("Deleted the temp file created.");
}
}
/// <summary>
/// Parses the File.
/// </summary>
protected IEnumerable <ISequence> ParseFile()
{
// TODO: Add other parsers.
FastAParser parser = new FastAParser(this.Filename);
return(parser.Parse());
}
public void TranslateHardReverseStrand()
{
Genome genome = new Genome(Path.Combine(TestContext.CurrentContext.TestDirectory, "Homo_sapiens.GRCh38.dna.chromosome.14.fa"));
GeneModel geneModel = new GeneModel(genome, Path.Combine(TestContext.CurrentContext.TestDirectory, "HardReverseStrand", "reverse.gff3"));
List <Protein> proteins = geneModel.Translate(true).ToList();
ISequence codingSequence = new FastAParser().Parse(Path.Combine(TestContext.CurrentContext.TestDirectory, "HardReverseStrand", "codingSeq.fa")).First();
Assert.AreEqual(SequenceExtensions.ConvertToString(codingSequence),
SequenceExtensions.ConvertToString(geneModel.Genes[0].Transcripts[0].RetrieveCodingSequence()));
Assert.AreEqual("MNLQAQPKAQNKRKRCLFGGQEPAPKEQPPPLQPPQQSIRVKEEQYLGHEGPGGAVSTSQ" +
"PVELPPPSSLALLNSVVYGPERTSAAMLSQQVASVKWPNSVMAPGRGPERGGGGGVSDSS" +
"WQQQPGQPPPHSTWNCHSLSLYSATKGSPHPGVGVPTYYNHPEALKREKAGGPQLDRYVR" +
"PMMPQKVQLEVGRPQAPLNSFHAAKKPPNQSLPLQPFQLAFGHQVNRQVFRQGPPPPNPV" +
"AAFPPQKQQQQQQPQQQQQQQQAALPQMPLFENFYSMPQQPSQQPQDFGLQPAGPLGQSH" +
"LAHHSMAPYPFPPNPDMNPELRKALLQDSAPQPALPQVQIPFPRRSRRLSKEGILPPSAL" +
"DGAGTQPGQEATGNLFLHHWPLQQPPPGSLGQPHPEALGFPLELRESQLLPDGERLAPNG" +
"REREAPAMGSEEGMRAVSTGDCGQVLRGGVIQSTRRRRRASQEANLLTLAQKAVELASLQ" +
"NAKDGSGSEEKRKSVLASTTKCGVEFSEPSLATKRAREDSGMVPLIIPVSVPVRTVDPTE" +
"AAQAGGLDEDGKGPEQNPAEHKPSVIVTRRRSTRIPGTDAQAQAEDMNVKLEGEPSVRKP" +
"KQRPRPEPLIIPTKAGTFIAPPVYSNITPYQSHLRSPVRLADHPSERSFELPPYTPPPIL" +
"SPVREGSGLYFNAIISTSTIPAPPPITPKSAHRTLLRTNSAEVTPPVLSVMGEATPVSIE" +
"PRINVGSRFQAEIPLMRDRALAAADPHKADLVWQPWEDLESSREKQRQVEDLLTAACSSI" +
"FPGAGTNQELALHCLHESRGDILETLNKLLLKKPLRPHNHPLATYHYTGSDQWKMAERKL" +
"FNKGIAIYKKDFFLVQKLIQTKTVAQCVEFYYTYKKQVKIGRNGTLTFGDVDTSDEKSAQ" +
"EEVEVDIKTSQKFPRVPLPRRESPSEERLEPKREVKEPRKEGEEEVPEIQEKEEQEEGRE" +
"RSRRAAAVKATQTLQANESASDILILRSHESNAPGSAGGQASEKPREGTGKSRRALPFSE" +
"KKKKTETFSKTQNQENTFPCKKCGR",
proteins[0].BaseSequence);
}
public void TestFastaFor186972391()
{
string expectedSequence =
"IFYEPVEILGYDNKSSLVLVKRLITRMYQQKSLISSLNDSNQNEFWGHKNSFSSHFSSQMVSEGFGVILE" +
"IPFSSRLVSSLEEKRIPKSQNLRSIHSIFPFLEDKLSHLNYVSDLLIPHPIHLEILVQILQCWIKDVPSL" +
"HLLRLFFHEYHNLNSLITLNKSIYVFSKRKKRFFGFLHNSYVYECEYLFLFIRKKSSYLRSISSGVFLER" +
"THFYGKIKYLLVVCCNSFQRILWFLKDTFIHYVRYQGKAIMASKGTLILMKKWKFHLVNFWQSYFHFWFQ" +
"PYRINIKQLPNYSFSFLGYFSSVRKNPLVVRNQMLENSFLINTLTQKLDTIVPAISLIGSLSKAQFCTVL" +
"GHPISKPIWTDLSDSDILDRFCRICRNLCRYHSGSSKKQVLYRIKYIFRLSCARTLARKHKSTVRTFMRR" +
"LGSGFLEEFFLEEE";
// parse
string filepath = System.IO.Path.Combine("TestUtils", "Fasta", "186972391.fasta").TestDir();
Assert.IsTrue(File.Exists(filepath));
FastAParser parser = new FastAParser {
Alphabet = Alphabets.Protein
};
foreach (ISequence seq in parser.Parse(filepath))
{
Assert.IsNotNull(seq);
Assert.AreEqual(434, seq.Count);
string actual = seq.Aggregate("", (current, b) => current + (char)b);
Assert.AreEqual(expectedSequence, actual);
Assert.AreEqual(seq.Alphabet.Name, "Protein");
Assert.AreEqual("gi|186972391|gb|ACC99454.1| maturase K [Scaphosepalum rapax]", seq.ID);
}
}
public void ValidateDeltaAlignmentToString()
{
ISequence refSeq = new Sequence(Alphabets.DNA, "ATCGGGGGGGGAAAAAAATTTTCCCCGGGGG");
ISequence qrySeq = new Sequence(Alphabets.DNA, "GGGGG");
var delta = new DeltaAlignment(refSeq, qrySeq)
{
FirstSequenceEnd = 21, SecondSequenceEnd = 20
};
string actualString = delta.ToString();
string expectedString = this.utilityObj.xmlUtil.GetTextValue(Constants.ToStringNodeName, Constants.DeltaAlignmentExpectedNode);
Assert.AreEqual(expectedString, actualString);
// Gets the expected sequence from the Xml
List <ISequence> seqsList;
string filePath = this.utilityObj.xmlUtil.GetTextValue(Constants.SimpleFastaNodeName, Constants.FilePathNode);
using (var reader = File.OpenRead(filePath))
{
var parser = new FastAParser();
{
parser.Alphabet = Alphabets.Protein;
seqsList = parser.Parse(reader).ToList();
}
}
delta = new DeltaAlignment(seqsList[0], qrySeq)
{
FirstSequenceEnd = 21, SecondSequenceStart = 20, QueryDirection = Cluster.ReverseDirection
};
actualString = delta.ToString();
expectedString = this.utilityObj.xmlUtil.GetTextValue(Constants.ToStringNodeName, Constants.DeltaAlignmentExpected2Node);
Assert.AreEqual(expectedString, actualString);
}
public void ValidateSequenceConvertToString()
{
string seqLargeString = this.utilityObj.xmlUtil.GetTextValue(Constants.ToStringNodeName,
Constants.seqLargeStringNode);
ISequence seqLarge = new Sequence(Alphabets.DNA, seqLargeString);
string ActualLargeString = seqLarge.ToString();
string seqLargeExpected = this.utilityObj.xmlUtil.GetTextValue(Constants.ToStringNodeName,
Constants.seqLargeExpected2Node);
string expectedLargeString = string.Format(CultureInfo.CurrentCulture,
seqLargeExpected,
(seqLarge.Count - Helper.AlphabetsToShowInToString));
Assert.AreEqual(expectedLargeString, ActualLargeString);
List <ISequence> seqsList;
// Gets the expected sequence from the Xml
string filePath = this.utilityObj.xmlUtil.GetTextValue(Constants.SimpleFastaNodeName,
Constants.FilePathNode);
var parser = new FastAParser {
Alphabet = Alphabets.Protein
};
IEnumerable <ISequence> seq = parser.Parse(filePath);
//Create a list of sequences.
seqsList = seq.ToList();
var seqString = new string(seqsList[0].Select(a => (char)a).ToArray());
Assert.AreEqual(seqString.Substring(2, 5), ((Sequence)seqsList[0]).ConvertToString(2, 5));
}
public void TestFastaForMemoryMapFiles()
{
int sequenceCount = 300 * 1024 * 1024; // 300 MB of data
string filePath = CreateData(sequenceCount);
Assert.IsTrue(File.Exists(filePath));
FastAParser parser = null;
try
{
parser = new FastAParser(filePath);
parser.Alphabet = (IAlphabet)Alphabets.Protein;
foreach (ISequence seq in parser.Parse())
{
Assert.IsNotNull(seq);
Assert.AreEqual(sequenceCount, seq.Count);
Assert.AreEqual(seq.Alphabet.Name, "Protein");
}
}
finally
{
File.Delete(filePath);
parser.Dispose();
}
}
public void TestFastaWhenParsingOneOfMany()
{
// parse
string relativepath = @"\TestUtils\Fasta\5_sequences.fasta";
string assemblypath = System.IO.Path.GetDirectoryName(System.Reflection.Assembly.GetExecutingAssembly().GetName().CodeBase).Substring(6);
string filepath = assemblypath + relativepath;
using (FastAParser parser = new FastAParser(filepath))
{
parser.Alphabet = (IAlphabet)Alphabets.Protein;
int[] sequenceCountArray = new int[5];
sequenceCountArray[0] = 27;
sequenceCountArray[1] = 29;
sequenceCountArray[2] = 30;
sequenceCountArray[3] = 35;
sequenceCountArray[4] = 32;
int i = 0;
foreach (ISequence seq in parser.Parse())
{
Assert.IsNotNull(seq);
Assert.AreEqual(seq.Count, sequenceCountArray[i]);
i++;
}
}
}
public void TestLargeFasta()
{
if (Environment.Is64BitProcess)
{
int sequenceCount = 300 * 1024 * 1024; // 300 MB of data
string filePath = CreateData(sequenceCount);
Assert.IsTrue(File.Exists(filePath));
try
{
var parser = new FastAParser {
Alphabet = Alphabets.Protein
};
int count = 0;
foreach (ISequence seq in parser.Parse(filePath))
{
Assert.IsNotNull(seq);
Assert.AreEqual(sequenceCount, seq.Count);
Assert.AreEqual(seq.Alphabet.Name, "Protein");
count++;
}
Assert.AreEqual(1, count);
}
finally
{
File.Delete(filePath);
}
}
}
/// <summary>
/// Validates general Parse test cases with the xml node name specified.
/// </summary>
/// <param name="nodeName">xml node name.</param>
private void ValidateParseGeneralTestCases(string nodeName)
{
string filePath = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.FilePathNode).TestDir();
string alphabet = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.AlphabetNameNode);
Assert.IsTrue(File.Exists(filePath));
var parserObj = new FastAParser();
{
parserObj.Alphabet = Utility.GetAlphabet(alphabet);
IList <ISequence> seqs = parserObj.Parse(filePath).ToList();
Assert.AreEqual(1, seqs.Count);
// Gets the expected sequence from the Xml
string expectedSequence = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.ExpectedSequenceNode);
ISequence seq = seqs[0];
var newSequence = seq.ConvertToString();
Assert.AreEqual(expectedSequence, newSequence);
var tmpEncodedSeq = new byte[seq.Count];
seq.ToArray().CopyTo(tmpEncodedSeq, 0);
Assert.AreEqual(expectedSequence.Length, tmpEncodedSeq.Length);
Assert.IsNotNull(seq.Alphabet);
Assert.AreEqual(seq.Alphabet.Name.ToLower(CultureInfo.CurrentCulture), utilityObj.xmlUtil.GetTextValue(nodeName, Constants.AlphabetNameNode).ToLower(CultureInfo.CurrentCulture));
Assert.AreEqual(utilityObj.xmlUtil.GetTextValue(nodeName, Constants.SequenceIdNode), seq.ID);
}
}
/// <summary>
/// It parses the file.
/// </summary>
private IEnumerable <ISequence> ParseFile(string fileName)
{
// TODO: Add other parsers.
FastAParser parser = new FastAParser(fileName);
return(parser.Parse());
}
public void ValidateSeqParserProperties()
{
// Gets the expected sequence from the Xml
string fastaParserName = this.utilityObj.xmlUtil.GetTextValue(Constants.FastAFileParserNode,
Constants.ParserNameNode);
string genBankParserName = this.utilityObj.xmlUtil.GetTextValue(Constants.GenBankFileParserNode,
Constants.ParserNameNode);
string gffParserName = this.utilityObj.xmlUtil.GetTextValue(Constants.GffFileParserNode,
Constants.ParserNameNode);
string fastQParserName = this.utilityObj.xmlUtil.GetTextValue(Constants.FastQFileParserNode,
Constants.ParserNameNode);
// Get SequenceParser class properties.
FastAParser actualFastAParser = SequenceParsers.Fasta;
IReadOnlyList <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);
ApplicationLog.WriteLine("Type of the parser is validated successfully");
}
public void FastAParserValidateMoveNext()
{
string filePath = utilityObj.xmlUtil.GetTextValue(Constants.SimpleFastaNodeName,
Constants.FilePathNode);
Assert.IsTrue(File.Exists(filePath));
// Logs information to the log file
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"FastA Parser BVT: File Exists in the Path '{0}'.", filePath));
IEnumerable <ISequence> seqsList = null;
using (FastAParser parser = new FastAParser(filePath))
{
parser.Alphabet = Alphabets.Protein;
seqsList = parser.Parse();
Assert.IsNotNull(seqsList);
Assert.AreEqual(1, seqsList.Count());
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"FastA Parser BVT: Number of Sequences found are '{0}'.",
seqsList.Count()));
string expectedSequence = utilityObj.xmlUtil.GetTextValue(Constants.SimpleFastaNodeName,
Constants.ExpectedSequenceNode);
Assert.IsNotNull(seqsList.ElementAt(0));
Assert.AreEqual(expectedSequence, new string(seqsList.ElementAt(0).Select(a => (char)a).ToArray()));
}
}
/// <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);
SAMFormatter formatter = new SAMFormatter();
switch (formatTypes)
{
case ParseOrFormatTypes.ParseOrFormatText:
using (TextWriter writer =
new StreamWriter(Constants.SAMTempFileName))
{
formatter.Format(alignments[0], writer);
}
break;
case ParseOrFormatTypes.ParseOrFormatFileName:
formatter.Format(alignments[0], Constants.SAMTempFileName);
break;
}
alignments = parser.Parse(Constants.SAMTempFileName);
// Get expected sequences
using (FastAParser parserObj = new FastAParser(expectedSequenceFile))
{
IEnumerable <ISequence> expectedSequences = parserObj.Parse();
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
{
(parser as SAMParser).Dispose();
}
}
/// <summary>
/// Validates general FastA Parser test cases which are further Formatted
/// with the xml node name specified.
/// </summary>
/// <param name="nodeName">xml node name.</param>
private void ValidateParseFormatGeneralTestCases(string nodeName)
{
// Gets the expected sequence from the Xml
string filePath = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.FilePathNode);
string alphabet = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.AlphabetNameNode);
Assert.IsTrue(File.Exists(filePath));
string filepathTmp = Path.Combine(Path.GetTempPath(), "temp.fasta");
// Ensure output is deleted
if (File.Exists(filepathTmp))
{
File.Delete(filepathTmp);
}
List <ISequence> seqsOriginal;
using (var parserObj = new FastAParser(filePath))
{
// Read the original file
parserObj.Alphabet = Utility.GetAlphabet(alphabet);
seqsOriginal = parserObj.Parse().ToList();
Assert.IsFalse(seqsOriginal.Count == 0);
}
// Write to a new file
using (var formatter = new FastAFormatter(filepathTmp))
{
formatter.Write(seqsOriginal);
}
try
{
// Compare original with new file
using (var parserObjNew = new FastAParser(filepathTmp))
{
// Read the new file, then compare the sequences
parserObjNew.Alphabet = Utility.GetAlphabet(alphabet);
IEnumerable <ISequence> seqsNew = parserObjNew.Parse();
Assert.IsNotNull(seqsNew);
int count = 0;
foreach (ISequence newSequence in seqsNew)
{
string s1 = seqsOriginal[count].ConvertToString();
string s2 = newSequence.ConvertToString();
Assert.AreEqual(s1, s2);
count++;
}
Assert.AreEqual(count, seqsOriginal.Count, "Number of sequences is different.");
}
}
finally
{
// Delete new file
File.Delete(filepathTmp);
}
}
/// <summary>
/// Validate Submit Job and Fetch ResultSync() using multiple input sequences
/// </summary>
/// <param name="nodeName">xml node name</param>
void ValidateFetchResultSync(string nodeName)
{
// Read input from config file
string filepath = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.FilePathNode);
string emailId = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.EmailIDNode);
string clusterOption = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ClusterOptionNode);
string actionAlign = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ActionAlignNode);
// Initialize with parser and config params
ConfigParameters configparams = new ConfigParameters();
ClustalWParser clustalparser = new ClustalWParser();
configparams.UseBrowserProxy = true;
TestIClustalWServiceHandler handler =
new TestIClustalWServiceHandler(clustalparser, configparams);
ClustalWParameters parameters = new ClustalWParameters();
parameters.Values[ClustalWParameters.Email] = emailId;
parameters.Values[ClustalWParameters.ClusterOption] = clusterOption;
parameters.Values[ClustalWParameters.ActionAlign] = actionAlign;
IEnumerable <ISequence> sequence = null;
// Get the input sequences
using (FastAParser parser = new FastAParser(filepath))
{
sequence = parser.Parse();
// Submit job and validate it returned valid job id and control id
ServiceParameters svcparameters =
handler.SubmitRequest(sequence.ToList(), parameters);
Assert.IsFalse(string.IsNullOrEmpty(svcparameters.JobId));
ApplicationLog.WriteLine(string.Concat("JobId", svcparameters.JobId));
foreach (string key in svcparameters.Parameters.Keys)
{
Assert.IsFalse(string.IsNullOrEmpty(svcparameters.Parameters[key].ToString()));
ApplicationLog.WriteLine(string.Format((IFormatProvider)null, "{0}:{1}",
key, svcparameters.Parameters[key].ToString()));
}
// Get the results and validate it is not null.
ClustalWResult result = handler.FetchResultsSync(svcparameters);
Assert.IsNotNull(result);
Assert.IsNotNull(result.SequenceAlignment);
foreach (IAlignedSequence alignSeq in result.SequenceAlignment.AlignedSequences)
{
ApplicationLog.WriteLine("Aligned Sequence Sequences :");
foreach (ISequence seq in alignSeq.Sequences)
{
ApplicationLog.WriteLine(string.Concat("Sequence:", seq.ToString()));
}
}
}
ApplicationLog.WriteLine(@"ClustalWServiceHandler BVT : Submit job and Get Results is successfully completed using FetchResultSync()");
}
/// <summary>
/// Downloads sequence as fasta file from ncbi.
/// </summary>
/// <param name="fastaFileStream">
/// The fasta file stream.
/// </param>
/// <returns>
/// The <see cref="ISequence"/>.
/// </returns>
public static ISequence GetFastaSequence(Stream fastaFileStream)
{
var fastaParser = new FastAParser();
ISequence result = fastaParser.ParseOne(fastaFileStream);
fastaFileStream.Dispose();
return(result);
}
void ValidateParserGeneralTestCases(FastAParser parserObj)
{
IEnumerable <ISequence> seqs = null;
seqs = parserObj.Parse();
Assert.IsNotNull(seqs);
Assert.AreEqual(1, seqs.Count());
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"FastA Parser with Alphabet: Number of Sequences found are '{0}'.",
seqs.Count()));
// Gets the expected sequence from the Xml
string expectedSequence = utilityObj.xmlUtil.GetTextValue(
Constants.SimpleFastaDnaNodeName, Constants.ExpectedSequenceNode);
Sequence seq = (Sequence)seqs.ElementAt(0);
Assert.IsNotNull(seq);
char[] seqString = seqs.ElementAt(0).Select(a => (char)a).ToArray();
string newSequence = new string(seqString);
Assert.AreEqual(expectedSequence, newSequence);
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"FastA Parser with Alphabet: DNA Sequence is '{0}' and is as expected.",
newSequence));
// Logs to the NUnit GUI (Console.Out) window
Console.WriteLine(string.Format((IFormatProvider)null,
"FastA Parser with Alphabet: DNA Sequence is '{0}' and is as expected.",
newSequence));
byte[] tmpEncodedSeq = new byte[seq.Count];
(seq as IEnumerable <byte>).ToArray().CopyTo(tmpEncodedSeq, 0);
Assert.AreEqual(expectedSequence.Length, tmpEncodedSeq.Length);
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"FastA Parser with Alphabet: DNA Sequence Length is '{0}' and is as expected.",
expectedSequence.Length));
Assert.IsNotNull(seq.Alphabet);
Assert.AreEqual(seq.Alphabet.Name.ToLower(CultureInfo.CurrentCulture),
utilityObj.xmlUtil.GetTextValue(Constants.SimpleFastaDnaNodeName,
Constants.AlphabetNameNode).ToLower(CultureInfo.CurrentCulture));
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"FastA Parser with Alphabet: The Sequence Alphabet is '{0}' and is as expected.",
seq.Alphabet.Name));
Assert.AreEqual(utilityObj.xmlUtil.GetTextValue(
Constants.SimpleFastaDnaNodeName, Constants.SequenceIdNode), seq.ID);
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"FastA Parser with Alphabet: DNA Sequence ID is '{0}' and is as expected.",
seq.ID));
// Logs to the NUnit GUI (Console.Out) window
Console.WriteLine(string.Format((IFormatProvider)null,
"FastA Parser with Alphabet: DNA Sequence ID is '{0}' and is as expected.",
seq.ID));
}
public void ValidateFastaAFileSequence()
{
// Gets the expected sequence from the Xml
string expectedSequence = utilityObj.xmlUtil.GetTextValue(
Constants.SimpleFastaNodeName, Constants.ExpectedSequenceNode);
string fastAFilePath = utilityObj.xmlUtil.GetTextValue(
Constants.SimpleFastaNodeName, Constants.FilePathNode);
string alphabet = utilityObj.xmlUtil.GetTextValue(Constants.SimpleFastaNodeName,
Constants.AlphabetNameNode);
Assert.IsTrue(File.Exists(fastAFilePath));
// Logs information to the log file
ApplicationLog.WriteLine(string.Concat(
"Sequence BVT: The File exist in the Path ", fastAFilePath));
IEnumerable <ISequence> sequence = null;
using (FastAParser parser = new FastAParser(fastAFilePath))
{
// Parse a FastA file Using Parse method and convert the same to sequence.
parser.Alphabet = Utility.GetAlphabet(alphabet);
sequence = parser.Parse();
Assert.IsNotNull(sequence);
Sequence fastASequence = (Sequence)sequence.ElementAt(0);
Assert.IsNotNull(fastASequence);
char[] seqString = sequence.ElementAt(0).Select(a => (char)a).ToArray();
string newSequence = new string(seqString);
Assert.AreEqual(expectedSequence, newSequence);
ApplicationLog.WriteLine(string.Concat(
"Sequence BVT: The Sequence is as expected."));
byte[] tmpEncodedSeq = new byte[fastASequence.Count];
(fastASequence as IEnumerable <byte>).ToArray().CopyTo(tmpEncodedSeq, 0);
Assert.AreEqual(expectedSequence.Length, tmpEncodedSeq.Length);
ApplicationLog.WriteLine(string.Concat(
"Sequence BVT: Sequence Length is as expected."));
Assert.AreEqual(utilityObj.xmlUtil.GetTextValue(
Constants.SimpleProteinAlphabetNode, Constants.SequenceIdNode), fastASequence.ID);
ApplicationLog.WriteLine(string.Concat(
"Sequence BVT: SequenceID is as expected."));
Assert.AreEqual(fastASequence.Alphabet.Name,
utilityObj.xmlUtil.GetTextValue(Constants.SimpleFastaNodeName, Constants.AlphabetNameNode));
ApplicationLog.WriteLine(string.Concat(
"Sequence BVT: Sequence Alphabet is as expected."));
// Logs to Nunit GUI.
Console.WriteLine(
"Sequence BVT: Validation of FastaA file Sequence is completed successfully.");
}
}
private void ValidateMUMmerAlignGeneralTestCases(string nodeName)
{
// Gets the reference sequence from the configuration file
string filePath = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.FilePathNode).TestDir();
Assert.IsNotNull(filePath);
ApplicationLog.WriteLine(string.Format(null, "MUMmer P2 : Successfully validated the File Path '{0}'.", filePath));
var fastaParserObj = new FastAParser();
IEnumerable <ISequence> referenceSeqs = fastaParserObj.Parse(filePath);
ISequence referenceSeq = referenceSeqs.ElementAt(0);
// Gets the reference sequence from the configuration file
string queryFilePath = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.SearchSequenceFilePathNode).TestDir();
Assert.IsNotNull(queryFilePath);
ApplicationLog.WriteLine(string.Format(null, "MUMmer P2 : Successfully validated the Search File Path '{0}'.", queryFilePath));
var fastaParserObj1 = new FastAParser();
IEnumerable <ISequence> querySeqs = fastaParserObj1.Parse(queryFilePath);
string mumLength = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.MUMAlignLengthNode);
var mum = new MUMmerAligner
{
LengthOfMUM = long.Parse(mumLength, null),
StoreMUMs = true,
PairWiseAlgorithm = new NeedlemanWunschAligner(),
GapOpenCost = int.Parse(utilityObj.xmlUtil.GetTextValue(nodeName, Constants.GapOpenCostNode), null)
};
IList <IPairwiseSequenceAlignment> align = mum.Align(referenceSeq, querySeqs);
// Validate FinalMUMs and MUMs Properties.
Assert.IsNotNull(mum.MUMs);
string expectedScore = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.ScoreNodeName);
string[] expectedSequences = utilityObj.xmlUtil.GetTextValues(nodeName, Constants.ExpectedSequencesNode);
IList <IPairwiseSequenceAlignment> expectedOutput = new List <IPairwiseSequenceAlignment>();
IPairwiseSequenceAlignment seqAlign = new PairwiseSequenceAlignment();
var alignedSeq = new PairwiseAlignedSequence
{
FirstSequence = new Sequence(referenceSeq.Alphabet, expectedSequences[0]),
SecondSequence = new Sequence(referenceSeq.Alphabet, expectedSequences[1]),
Score = Convert.ToInt32(expectedScore, null),
FirstOffset = Int32.MinValue,
SecondOffset = Int32.MinValue,
};
seqAlign.PairwiseAlignedSequences.Add(alignedSeq);
expectedOutput.Add(seqAlign);
Assert.IsTrue(AlignmentHelpers.CompareAlignment(align, expectedOutput));
ApplicationLog.WriteLine("MUMmer P2 : Successfully validated the aligned sequences.");
}
public void FastAParserValidateParseWithStream()
{
List <ISequence> seqsList;
// Gets the expected sequence from the Xml
string filePath = utilityObj.xmlUtil.GetTextValue(Constants.SimpleFastaNodeName,
Constants.FilePathNode).TestDir();
Assert.IsTrue(File.Exists(filePath));
// Logs information to the log file
ApplicationLog.WriteLine(string.Format(null,
"FastA Parser BVT: File Exists in the Path '{0}'.", filePath));
using (var reader = File.OpenRead(filePath))
{
IEnumerable <ISequence> seq = null;
var parser = new FastAParser();
{
parser.Alphabet = Alphabets.Protein;
seq = parser.Parse(reader);
//Create a list of sequences.
seqsList = seq.ToList();
}
}
Assert.IsNotNull(seqsList);
string expectedSequence = utilityObj.xmlUtil.GetTextValue(Constants.SimpleFastaNodeName,
Constants.ExpectedSequenceNode);
var seqString = new string(seqsList[0].Select(a => (char)a).ToArray());
Assert.AreEqual(expectedSequence, seqString);
ApplicationLog.WriteLine(string.Format(null,
"FastA Parser BVT: The FASTA sequence '{0}' validation after Parse(Stream) is found to be as expected.",
seqString));
//Validate Alphabet type for a sequence.
Assert.IsNotNull(seqsList[0].Alphabet);
Assert.AreEqual(seqsList[0].Alphabet.Name.ToLower(CultureInfo.CurrentCulture),
utilityObj.xmlUtil.GetTextValue(Constants.SimpleFastaNodeName,
Constants.AlphabetNameNode)
.ToLower(CultureInfo.CurrentCulture));
ApplicationLog.WriteLine(string.Format(null,
"FastA Parser BVT: The Sequence Alphabet is '{0}' and is as expected.",
seqsList[0].Alphabet.Name));
//Validate ID for the sequence.
Assert.AreEqual(utilityObj.xmlUtil.GetTextValue(Constants.SimpleFastaNodeName,
Constants.SequenceIdNode), seqsList[0].ID);
ApplicationLog.WriteLine(string.Format(null,
"FastA Parser BVT: The Sequence ID is '{0}' and is as expected.",
seqsList[0].ID));
}
public void ValidateSequenceToString()
{
ISequence seqSmall = new Sequence(Alphabets.DNA, "ATCG");
string seqLargeString = utilityObj.xmlUtil.GetTextValue(Constants.ToStringNodeName,
Constants.seqLargeStringNode);
ISequence seqLarge = new Sequence(Alphabets.DNA, seqLargeString);
string ActualSmallString = seqSmall.ToString();
string ActualLargeString = seqLarge.ToString();
string ExpectedSmallString = "ATCG";
string seqLargeExpected = utilityObj.xmlUtil.GetTextValue(Constants.ToStringNodeName,
Constants.seqLargeExpected2Node);
string expectedLargeString = string.Format(CultureInfo.CurrentCulture,
seqLargeExpected,
(seqLarge.Count - Helper.AlphabetsToShowInToString));
Assert.AreEqual(ExpectedSmallString, ActualSmallString);
Assert.AreEqual(expectedLargeString, ActualLargeString);
//check with blank sequence
var seqBlank = new Sequence(Alphabets.DNA, "");
string blankString = seqBlank.ToString();
Assert.AreEqual(string.Empty, blankString);
//read sequence from file
List <ISequence> seqsList;
// Gets the expected sequence from the Xml
string filePath = utilityObj.xmlUtil.GetTextValue(Constants.SimpleFastaNodeName,
Constants.FilePathNode);
using (var reader = new StreamReader(filePath))
{
IEnumerable <ISequence> seq = null;
using (var parser = new FastAParser())
{
parser.Alphabet = Alphabets.Protein;
seq = parser.Parse(reader);
//Create a list of sequences.
seqsList = seq.ToList();
}
}
var seqString = new string(seqsList[0].Select(a => (char)a).ToArray());
if (seqString.Length > Helper.AlphabetsToShowInToString)
{
//check if the whole sequence string contains the string retrieved from ToString
Assert.IsTrue(seqString.Contains(seqsList[0].ToString().Substring(0, Helper.AlphabetsToShowInToString)));
Assert.IsTrue(seqsList[0].ToString().Contains("... +["));
}
else
{
Assert.AreEqual(seqString, seqsList[0].ToString());
}
}
