public void HandleMultipleFastaFormatWithEmptyLines()
{
FastaReader fastaReader = new FastaReader(new StringReader(">DNA\nATCGGGCTAAT\nATCGGGCTAAT\n\n>Number2\nATCGGGCTAAT\nATCGGGCTAAT"));
Fasta fasta = fastaReader.Read();
Assert.AreEqual("DNA", fasta.Header);
Assert.AreEqual("ATCGGGCTAATATCGGGCTAAT", fasta.Dna);
fasta = fastaReader.Read();
Assert.AreEqual("Number2", fasta.Header);
Assert.AreEqual("ATCGGGCTAATATCGGGCTAAT", fasta.Dna);
}
public void PopulateATCGDnaFastaFormat()
{
FastaReader fastaReader = new FastaReader(new StringReader(">DNA\nATCG"));
Fasta fasta = fastaReader.Read();
Assert.AreEqual("ATCG", fasta.Dna);
}
public void PopulateMultiLineDnaFastaFormat()
{
FastaReader fastaReader = new FastaReader(new StringReader(">DNA\nATCGGGCTAAT\nATCGGGCTAAT\nATCGGGCTAAT\nATCGGGCTAAT"));
Fasta fasta = fastaReader.Read();
Assert.AreEqual("ATCGGGCTAATATCGGGCTAATATCGGGCTAATATCGGGCTAAT", fasta.Dna);
}
public void PopulateDEFHeaderFastaFormat()
{
FastaReader fastaReader = new FastaReader(new StringReader(">DEF"));
Fasta fasta = fastaReader.Read();
Assert.AreEqual("DEF", fasta.Header);
}
private Task Process()
{
Counter readerCounter = new Counter();
Counter searchCounter = new Counter();
readerCounter.progressChange += ReadProgressChanged;
searchCounter.progressChange += SearchProgressChanged;
// build pepeptides
Peptide.To.SetCysteine(ConfigureParameters.Access.Cysteine);
IProteinReader proteinReader = new FastaReader();
List <IProtein> proteins = proteinReader.Read(SearchingParameters.Access.FastaFile);
List <IProtein> decoyProteins = new List <IProtein>();
foreach (IProtein protein in proteins)
{
IProtein p = new BaseProtein();
p.SetSequence(MultiThreadingSearchHelper.Reverse(protein.Sequence()));
decoyProteins.Add(p);
}
List <string> peptides =
MultiThreadingSearchHelper.GeneratePeptides(proteins);
List <string> decoyPeptides =
MultiThreadingSearchHelper.GeneratePeptides(decoyProteins);
// build glycans
GlycanBuilder glycanBuilder = new GlycanBuilder(
SearchingParameters.Access.HexNAc,
SearchingParameters.Access.Hex,
SearchingParameters.Access.Fuc,
SearchingParameters.Access.NeuAc,
SearchingParameters.Access.NeuGc,
SearchingParameters.Access.ComplexInclude,
SearchingParameters.Access.HybridInclude,
SearchingParameters.Access.MannoseInclude);
glycanBuilder.Build();
int index = 1;
foreach (string file in SearchingParameters.Access.MSMSFiles)
{
ReadingCounter = 0;
ProgressCounter = 0;
UpdateProgress(100);
Readingprogress(100);
UpdateSignal($"Searching...({index++}/{SearchingParameters.Access.MSMSFiles.Count})");
MultiThreadingSearch search =
new MultiThreadingSearch(file, readerCounter, searchCounter,
peptides, decoyPeptides, glycanBuilder);
search.Run();
UpdateSignal("Analyzing...");
Analyze(file, search.Target(), search.Decoy(), glycanBuilder);
}
UpdateSignal("Done");
return(Task.CompletedTask);
}
public void test2()
{
string fasta = @"C:\Users\Rui Zhang\Downloads\haptoglobin.fasta";
// peptides
IProteinReader proteinReader = new FastaReader();
List <IProtein> proteins = proteinReader.Read(fasta);
List <Proteases> proteases = new List <Proteases>()
{
Proteases.Trypsin, Proteases.GluC
};
HashSet <string> peptides = new HashSet <string>();
ProteinDigest proteinDigest = new ProteinDigest(2, 5, proteases[0]);
foreach (IProtein protein in proteins)
{
peptides.UnionWith(proteinDigest.Sequences(protein.Sequence(),
ProteinPTM.ContainsNGlycanSite));
}
for (int i = 1; i < proteases.Count; i++)
{
proteinDigest.SetProtease(proteases[i]);
List <string> peptidesList = peptides.ToList();
foreach (string seq in peptidesList)
{
peptides.UnionWith(proteinDigest.Sequences(seq,
ProteinPTM.ContainsNGlycanSite));
}
}
HashSet <string> peptideModifieds = ProteinModification.DynamicModification(
peptides, ProteinPTM.ContainsNGlycanSite);
foreach (var s in peptideModifieds)
{
Console.WriteLine(s);
}
Console.WriteLine(peptides.Count);
Console.WriteLine(peptideModifieds.Count);
}
public void ReadReturnsFastaFormat()
{
FastaReader fastaReader = new FastaReader(new StringReader(""));
Fasta fasta = fastaReader.Read();
}
public void Test1()
{
string path = @"C:\Users\Rui Zhang\Downloads\ZC_20171218_C16_R1.raw";
string fasta = @"C:\Users\Rui Zhang\Downloads\haptoglobin.fasta";
// peptides
IProteinReader proteinReader = new FastaReader();
List <IProtein> proteins = proteinReader.Read(fasta);
List <IProtein> decoyProteins = new List <IProtein>();
foreach (IProtein protein in proteins)
{
IProtein p = new BaseProtein();
p.SetSequence(Reverse(protein.Sequence()));
decoyProteins.Add(p);
}
List <Proteases> proteases = new List <Proteases>()
{
Proteases.Trypsin, Proteases.GluC
};
HashSet <string> peptides = new HashSet <string>();
ProteinDigest proteinDigest = new ProteinDigest(2, 5, proteases[0]);
foreach (IProtein protein in decoyProteins)
{
peptides.UnionWith(proteinDigest.Sequences(protein.Sequence(),
ProteinPTM.ContainsNGlycanSite));
}
for (int i = 1; i < proteases.Count; i++)
{
proteinDigest.SetProtease(proteases[i]);
List <string> peptidesList = peptides.ToList();
foreach (string seq in peptidesList)
{
peptides.UnionWith(proteinDigest.Sequences(seq,
ProteinPTM.ContainsNGlycanSite));
}
}
Assert.True(peptides.Contains("KDNLTYVGDGETR"));
// build glycan
GlycanBuilder glycanBuilder = new GlycanBuilder();
glycanBuilder.Build();
// search
List <SearchResult> searchResults = new List <SearchResult>();
ThermoRawSpectrumReader reader = new ThermoRawSpectrumReader();
LocalMaximaPicking picking = new LocalMaximaPicking();
IProcess process = new LocalNeighborPicking();
reader.Init(path);
double searchRange = 2;
ISpectrum ms1 = null;
List <IPeak> majorPeaks = new List <IPeak>();
ISearch <string> oneSearcher = new BucketSearch <string>(ToleranceBy.PPM, 10);
PrecursorMatch precursorMatcher = new PrecursorMatch(oneSearcher);
precursorMatcher.Init(peptides.ToList(), glycanBuilder.GlycanMaps());
ISearch <string> moreSearcher = new BucketSearch <string>(ToleranceBy.Dalton, 0.01);
SequenceSearch sequenceSearcher = new SequenceSearch(moreSearcher);
ISearch <int> extraSearcher = new BucketSearch <int>(ToleranceBy.Dalton, 0.01);
GlycanSearch glycanSearcher = new GlycanSearch(extraSearcher, glycanBuilder.GlycanMaps());
SearchAnalyzer searchAnalyzer = new SearchAnalyzer();
for (int i = reader.GetFirstScan(); i < reader.GetLastScan(); i++)
{
if (reader.GetMSnOrder(i) < 2)
{
ms1 = reader.GetSpectrum(i);
majorPeaks = picking.Process(ms1.GetPeaks());
}
else
{
double mz = reader.GetPrecursorMass(i, reader.GetMSnOrder(i));
if (ms1.GetPeaks()
.Where(p => p.GetMZ() > mz - searchRange && p.GetMZ() < mz + searchRange)
.Count() == 0)
{
continue;
}
Patterson charger = new Patterson();
int charge = charger.Charge(ms1.GetPeaks(), mz - searchRange, mz + searchRange);
// find evelope cluster
EnvelopeProcess envelope = new EnvelopeProcess();
var cluster = envelope.Cluster(majorPeaks, mz, charge);
if (cluster.Count == 0)
{
continue;
}
// find monopeak
Averagine averagine = new Averagine(AveragineType.GlycoPeptide);
BrainCSharp braincs = new BrainCSharp();
MonoisotopicSearcher searcher = new MonoisotopicSearcher(averagine, braincs);
MonoisotopicScore result = searcher.Search(mz, charge, cluster);
double precursorMZ = result.GetMZ();
// search
ISpectrum ms2 = reader.GetSpectrum(i);
ms2 = process.Process(ms2);
//precursor match
var pre_results = precursorMatcher.Match(precursorMZ, charge);
if (pre_results.Count == 0)
{
continue;
}
// spectrum search
var peptide_results = sequenceSearcher.Search(ms2.GetPeaks(), charge, pre_results);
if (peptide_results.Count == 0)
{
continue;
}
var glycan_results = glycanSearcher.Search(ms2.GetPeaks(), charge, pre_results);
if (glycan_results.Count == 0)
{
continue;
}
var temp_results = searchAnalyzer.Analyze(i, ms2.GetPeaks(), peptide_results, glycan_results);
break;
}
}
}