public void TestPcaStep3DeletionInReferenceTwo()
{
Sequence r = new Sequence(DnaAlphabet.Instance, "CTACGATCGGGG");
// CTACGTGC // TGCGCA is deleted from reference
// GCATCG
// AGCATC
// GGGG
// CATCG
Sequence q = new Sequence(DnaAlphabet.Instance, "CTACGTGC");
Sequence q2 = new Sequence(DnaAlphabet.Instance, "GCATCG");
Sequence q3 = new Sequence(DnaAlphabet.Instance, "GGGG");
Sequence q4 = new Sequence(DnaAlphabet.Instance, "CATCG");
ComparativeGenomeAssembler asm = new ComparativeGenomeAssembler()
{
LengthOfMum = 3
};
var output = asm.Assemble(new List <ISequence> {
r
}, new List <ISequence> {
q, q2, q3, q4
});
string res = new string(output.ElementAt(0).Select(a => (char)a).ToArray());
Assert.AreEqual("CTACGTGCATCGGGG", res);
}
public void TestPcaStep2WithTwoReads()
{
ComparativeGenomeAssembler asm = new ComparativeGenomeAssembler()
{
LengthOfMum = 9, KmerLength = 9
};
Sequence q = new Sequence(DnaAlphabet.Instance, "AACCTTGGCC")
{
ID = ">read.F:TestPcaStep2WithTwoReads"
};
Sequence p = new Sequence(DnaAlphabet.Instance, "GGGGGGGGGG")
{
ID = ">read.R:TestPcaStep2WithTwoReads"
};
CloneLibrary.Instance.AddLibrary("TestPcaStep2WithTwoReads", (float)61, (float)1);
TestPcaAssemble(asm,
new List <Sequence> {
new Sequence(DnaAlphabet.Instance, "AACCTTGGCCCCCACGATCGCGCTAGATCGCATCGATCCCCAACCTTGGCCGGGGGGGGGG", false)
},
new List <ISequence> {
q, p
},
new List <string> {
"AACCTTGGCC",
"GGGGGGGGGG"
});
}
public void TestPcaStep3RepeatTest()
{
Sequence r = new Sequence(DnaAlphabet.Instance, "AACCTTGGCCCCCACGATCGCGCTAGATCGCATCGATCCCCAACCTTGGCCGGGGGGGGGG");
Sequence q = new Sequence(DnaAlphabet.Instance, "AACCTTGGCC");
q.ID = ">read.F:abc";
Sequence p = new Sequence(DnaAlphabet.Instance, "GGGGGGGGGG");
p.ID = ">read.R:abc";
CloneLibrary.Instance.AddLibrary("abc", (float)61, (float)1);
ComparativeGenomeAssembler asm = new ComparativeGenomeAssembler()
{
LengthOfMum = 9
};
var res = asm.Assemble(new List <ISequence> {
r
}, new List <ISequence> {
q, p
});
string[] expectedResult = new string[2];
expectedResult[0] = "AACCTTGGCC";
expectedResult[1] = "GGGGGGGGGG";
int i = 0;
foreach (var s in res)
{
string actual = new string(s.Select(a => (char)a).ToArray());
Assert.AreEqual(expectedResult[i], actual);
i++;
}
}
/// <summary>
/// Test Pca assemble.
/// </summary>
/// <param name="asm">Comparative Genome Assembler.</param>
/// <param name="reference">Reference sequence.</param>
/// <param name="query">Query sequence.</param>
/// <param name="expected">Expected strings.</param>
private static void TestPcaAssemble(ComparativeGenomeAssembler asm, IEnumerable <ISequence> reference, IEnumerable <ISequence> query, IList <string> expected)
{
IEnumerable <ISequence> result = asm.Assemble(reference, query);
Assert.IsTrue(result.Count() == expected.Count);
foreach (var act in result)
{
string actualStr = new string(act.Select(a => (char)a).ToArray());
Assert.IsTrue(expected.Contains(actualStr));
}
}
public void TestPcaStep4WithOverlappingReads()
{
ComparativeGenomeAssembler asm = new ComparativeGenomeAssembler()
{
LengthOfMum = 3
};
TestPcaAssemble(asm,
new List <Sequence> {
new Sequence(DnaAlphabet.Instance, "AGAAAAGTTTTCA", false)
},
new List <ISequence> {
new Sequence(DnaAlphabet.Instance, "AGAAAA", false),
new Sequence(DnaAlphabet.Instance, "AAAAGTTTT", false)
},
new List <string>
{
"AGAAAAGTTTT"
});
}
public void TestPcaStep3InsertionInReference()
{
Sequence r = new Sequence(DnaAlphabet.Instance, "AACCTTGGCCTAGTACGGATATTGCCCACGATCG");
// AACCTTGGCCTA CCCACGATCG
Sequence q = new Sequence(DnaAlphabet.Instance, "AACCTTGGCCTACCCACGATCG");
ComparativeGenomeAssembler asm = new ComparativeGenomeAssembler()
{
LengthOfMum = 9
};
var output = asm.Assemble(new List <ISequence> {
r
}, new List <ISequence> {
q
});
string res = new string(output.ElementAt(0).Select(a => (char)a).ToArray());
Assert.AreEqual("AACCTTGGCCTACCCACGATCG", res);
}
public void TestPcaStep3InsertionInReferenceThree()
{
Sequence refSeq = new Sequence(DnaAlphabet.Instance, "AAAACCCGGGGTTTTTTACGTGACTGCA");
Sequence q = new Sequence(DnaAlphabet.Instance, "AAAAGGGG");
Sequence r = new Sequence(DnaAlphabet.Instance, "ACGTTGCA");
ComparativeGenomeAssembler asm = new ComparativeGenomeAssembler()
{
LengthOfMum = 4
};
var output = asm.Assemble(new List <ISequence> {
refSeq
}, new List <ISequence> {
q, r
});
string res = new string(output.ElementAt(0).Select(a => (char)a).ToArray());
Assert.AreEqual("AAAAGGGG", res);
res = new string(output.ElementAt(1).Select(a => (char)a).ToArray());
Assert.AreEqual("ACGTTGCA", res);
}
/// <summary>
/// It assembles the sequences.
/// </summary>
public virtual void AssembleSequences()
{
if (this.FilePath.Length != 2)
{
Console.Error.WriteLine("\nError: A reference file and 1 query file are required.");
Environment.Exit(-1);
}
TimeSpan timeSpan = new TimeSpan();
Stopwatch runAlgorithm = new Stopwatch();
FileInfo inputFileinfo = new FileInfo(this.FilePath[0]);
long inputFileLength = inputFileinfo.Length;
inputFileinfo = null;
if (!string.IsNullOrEmpty(this.CloneLibraryName))
{
CloneLibrary.Instance.AddLibrary(this.CloneLibraryName, (float)this.MeanLengthOfInsert, (float)this.StandardDeviationOfInsert);
}
runAlgorithm.Restart();
// Parse input files
IEnumerable <ISequence> referenceSequences = new FastAParser(this.FilePath[0]).Parse();
runAlgorithm.Stop();
if (this.Verbose)
{
Console.Error.WriteLine();
Console.Error.WriteLine(" Processed reference file: {0}", Path.GetFullPath(this.FilePath[0]));
Console.Error.WriteLine(" Read/Processing time: {0}", runAlgorithm.Elapsed);
Console.Error.WriteLine(" File Size : {0}", inputFileLength);
}
inputFileinfo = new FileInfo(this.FilePath[1]);
inputFileLength = inputFileinfo.Length;
runAlgorithm.Restart();
FastASequencePositionParser queryParser = new FastASequencePositionParser(this.FilePath[1], true);
queryParser.CacheSequencesForRandomAccess();
IEnumerable <ISequence> reads = queryParser.Parse();
runAlgorithm.Stop();
if (this.Verbose)
{
Console.Error.WriteLine();
Console.Error.WriteLine(" Processed reads file: {0}", Path.GetFullPath(this.FilePath[1]));
Console.Error.WriteLine(" Read/Processing time: {0}", runAlgorithm.Elapsed);
Console.Error.WriteLine(" File Size : {0}", inputFileLength);
}
runAlgorithm.Restart();
ValidateAmbiguousReads(reads);
runAlgorithm.Stop();
if (this.Verbose)
{
Console.Error.WriteLine();
Console.Error.WriteLine(" Time taken for Validating reads: {0}", runAlgorithm.Elapsed);
}
runAlgorithm.Restart();
ComparativeGenomeAssembler assembler = new ComparativeGenomeAssembler();
assembler.StatusChanged += new EventHandler <StatusChangedEventArgs>(this.AssemblerStatusChanged);
assembler.ScaffoldingEnabled = this.Scaffold;
assembler.KmerLength = this.KmerLength;
assembler.LengthOfMum = this.MumLength;
IEnumerable <ISequence> assemblerResult = assembler.Assemble(referenceSequences, queryParser);
runAlgorithm.Stop();
timeSpan = timeSpan.Add(runAlgorithm.Elapsed);
runAlgorithm.Restart();
if (this.OutputFile == null)
{
// Write output to console.
this.WriteContigs(assemblerResult, Console.Out);
}
else
{
// Write output to the specified file.
this.WriteContigs(assemblerResult, null);
Console.WriteLine(Resources.OutPutWrittenToFileSpecified);
}
runAlgorithm.Stop();
if (this.Verbose)
{
Console.Error.WriteLine(" Assemble time: {0}", timeSpan);
Console.Error.WriteLine(" Write() time: {0}", runAlgorithm.Elapsed);
}
}
/// <summary>
/// It assembles the sequences.
/// </summary>
public virtual void AssembleSequences()
{
if (this.FilePath.Length != 2)
{
Output.WriteLine(OutputLevel.Error, "Error: A reference file and 1 query file are required.");
return;
}
TimeSpan timeSpan = new TimeSpan();
Stopwatch runAlgorithm = new Stopwatch();
FileInfo inputFileinfo = new FileInfo(this.FilePath[0]);
long inputFileLength = inputFileinfo.Length;
inputFileinfo = null;
if (!string.IsNullOrEmpty(this.CloneLibraryName))
{
CloneLibrary.Instance.AddLibrary(this.CloneLibraryName, (float)this.MeanLengthOfInsert, (float)this.StandardDeviationOfInsert);
}
runAlgorithm.Restart();
// Parse input files
IEnumerable <ISequence> referenceSequences = ParseFile(this.FilePath[0]);
runAlgorithm.Stop();
if (this.Verbose)
{
Output.WriteLine(OutputLevel.Verbose);
Output.WriteLine(OutputLevel.Verbose, "Processed reference file: {0}", Path.GetFullPath(this.FilePath[0]));
Output.WriteLine(OutputLevel.Verbose, " Read/Processing time : {0}", runAlgorithm.Elapsed);
Output.WriteLine(OutputLevel.Verbose, " File Size : {0}", inputFileLength);
}
inputFileinfo = new FileInfo(this.FilePath[1]);
inputFileLength = inputFileinfo.Length;
runAlgorithm.Restart();
FastASequencePositionParser queryParser = new FastASequencePositionParser(this.FilePath[1], true);
queryParser.CacheSequencesForRandomAccess();
IEnumerable <ISequence> reads = queryParser.Parse();
runAlgorithm.Stop();
if (this.Verbose)
{
Output.WriteLine(OutputLevel.Verbose);
Output.WriteLine(OutputLevel.Verbose, "Processed reads file : {0}", Path.GetFullPath(this.FilePath[1]));
Output.WriteLine(OutputLevel.Verbose, " Read/Processing time: {0}", runAlgorithm.Elapsed);
Output.WriteLine(OutputLevel.Verbose, " File Size : {0}", inputFileLength);
}
runAlgorithm.Restart();
ValidateAmbiguousReads(reads);
runAlgorithm.Stop();
if (this.Verbose)
{
Output.WriteLine(OutputLevel.Verbose);
Output.WriteLine(OutputLevel.Verbose, "Time taken for Validating reads: {0}", runAlgorithm.Elapsed);
Output.WriteLine(OutputLevel.Verbose);
}
runAlgorithm.Restart();
ComparativeGenomeAssembler assembler = new ComparativeGenomeAssembler();
assembler.StatusChanged += this.AssemblerStatusChanged;
assembler.ScaffoldingEnabled = this.Scaffold;
assembler.KmerLength = this.KmerLength;
assembler.LengthOfMum = this.MumLength;
IEnumerable <ISequence> assemblerResult = assembler.Assemble(referenceSequences, queryParser);
runAlgorithm.Stop();
timeSpan = timeSpan.Add(runAlgorithm.Elapsed);
runAlgorithm.Restart();
this.WriteContigs(assemblerResult);
runAlgorithm.Stop();
if (this.Verbose)
{
Output.WriteLine(OutputLevel.Verbose, "Assemble time: {0}", timeSpan);
Output.WriteLine(OutputLevel.Verbose, "Write time: {0}", runAlgorithm.Elapsed);
}
}