private void button1_Click(object sender, EventArgs e)
{
Convertor convertor = new Convertor();
convertor.Protease = Protease.Trypsin;
convertor.FastaDatabaseFile = @"C:\Users\Derek\Documents\Compass Tests\OmssaConvertor\CONCAT_Uniprot_yeast_canonicalIsoforms_20jan2013.fasta";
convertor.MissedClevages = 3;
convertor.FixedMods.Add(3);
ThermoRawFile rawFile = new ThermoRawFile(@"C:\Users\Derek\Documents\Compass Tests\OmssaConvertor\10sep2013_yeast_control_2.raw");
convertor.Convert(@"C:\Users\Derek\Documents\Compass Tests\OmssaConvertor\10sep2013_yeast_control_2_ITMS_HCD30.00.csv", rawFile);
}
public static void LoopOverEveryScan()
{
using (ThermoRawFile rawFile = new ThermoRawFile("Resources/ThermoRawFileMS1MS2.raw"))
{
rawFile.Open();
foreach (var scan in rawFile)
{
Console.WriteLine("{0,-4} {1,3} {2,-6:F4} {3,-5} {4,7} {5,-10} {6} {7}", scan.SpectrumNumber, scan.MsnOrder, scan.RetentionTime,
scan.Polarity, scan.MassSpectrum.Count, scan.MzAnalyzer, scan.MzRange, scan.MassSpectrum.IsHighResolution);
}
}
}
public static void RecalibrateThermoRawFile()
{
List<ISpectrum> spectra = new List<ISpectrum>();
using (ThermoRawFile rawFile = new ThermoRawFile("Resources/ThermoRawFileMS1MS2.raw"))
{
rawFile.Open();
for (int i = rawFile.FirstSpectrumNumber; i <= rawFile.LastSpectrumNumber; i++)
{
ThermoSpectrum spectrum = rawFile.GetLabeledSpectrum(i);
ThermoSpectrum correctedSpectrum = spectrum.CorrectMasses((mz) => mz - 5); // shift all masses 5 Th lower
spectra.Add(correctedSpectrum);
}
}
}
public static void Start(IProtease protease, int maxMissed = 3, int minLength = 5, int maxLength = 35)
{
Console.WriteLine("**Start Morpheus Search**");
Stopwatch watch = new Stopwatch();
watch.Start();
List<int> hashCodes = new List<int>();
// Generate peptide candidates
HashSet<Peptide> peptides = new HashSet<Peptide>();
using (FastaReader reader = new FastaReader("Resources/yeast_uniprot_120226.fasta"))
{
foreach (Protein protein in reader.ReadNextProtein())
{
foreach (Peptide peptide in protein.Digest(protease, maxMissed, minLength, maxLength))
{
peptides.Add(peptide);
}
}
}
MSSearchEngine engine = new MorpheusSearchEngine();
engine.PrecursorMassTolerance = Tolerance.FromPPM(100);
engine.ProductMassTolerance = Tolerance.FromPPM(10);
engine.LoadPeptides(peptides);
using (MSDataFile msDataFile = new ThermoRawFile("Resources/ThermoRawFileMS1MS2.raw"))
{
//SortedMaxSizedContainer<PeptideSpectralMatch> psms = engine.Search(msDataFile.Where(scan => scan.MsnOrder > 1));
//foreach (MSDataScan scan in msDataFile.Where(scan => scan.MsnOrder > 1))
//{
// List<PeptideSpectralMatch> psms = engine.Search(scan);
// Console.WriteLine("{0} {1}", scan.SpectrumNumber, psms.Count);
//}
}
watch.Stop();
Console.WriteLine("Time elapsed: {0}", watch.Elapsed);
Console.WriteLine("Memory used: {0:N0} MB", System.Environment.WorkingSet / (1024 * 1024));
Console.WriteLine("**End Morpheus Search**");
}
private void LoadRawFile(string filePath)
{
if (string.IsNullOrEmpty(filePath))
return;
_rawFile = new ThermoRawFile(filePath);
_rawFile.Open();
_scanNumbers.Clear();
_scanNumbers.RaiseListChangedEvents = false;
for (int i = _rawFile.FirstSpectrumNumber; i < _rawFile.LastSpectrumNumber; i++)
{
if (_rawFile.GetMsnOrder(i) > 1)
{
_scanNumbers.Add(i);
}
}
_scanNumbers.RaiseListChangedEvents = true;
_scanNumbers.ResetBindings();
textBox1.Text = filePath;
}
private void UpdatePsmInformation(IList<InputFile> csvFiles, string rawFolder, bool useMedian = true)
{
Log("Reading MS data...");
MSDataFile.CacheScans = false;
List<string> rawFileNames = Directory.EnumerateFiles(rawFolder, "*.raw", SearchOption.AllDirectories).ToList();
foreach (InputFile csvFile in csvFiles)
{
string rawFileName = csvFile.RawFileName;
if (string.IsNullOrEmpty(rawFileName))
{
throw new ArgumentException("Cannot parse the file name for: " + csvFile.FilePath);
}
csvFile.RawFilePath = "";
foreach (string file in rawFileNames)
{
string name = Path.GetFileNameWithoutExtension(file);
if (name != null && !rawFileName.Equals(name))
continue;
csvFile.RawFilePath = file;
break;
}
if (string.IsNullOrEmpty(csvFile.RawFilePath))
{
throw new ArgumentException("Cannot find the associated raw file for: " + csvFile.FilePath);
}
}
// update the precursor mass error
foreach (InputFile csvFile in csvFiles)
{
using (MSDataFile dataFile = new ThermoRawFile(csvFile.RawFilePath))
{
dataFile.Open();
csvFile.UpdatePsmInformation(dataFile, _is2DFDR, useMedian, _evalueThresholdPPMError);
}
if (_is2DFDR)
{
Log(string.Format("{0:F2} ppm {1} precursor mass error in {2}",
csvFile.SystematicPrecursorMassError, useMedian ? "median" : "average", csvFile.Name));
}
}
}
/// <summary>
///
/// </summary>
/// <param name="argFullPath"></param>
/// <param name="argFileType">ThermoRawFile</param>
public ThermoRawReader(string argFullPath)
{
_fullFilePath = argFullPath;
_raw = new CSMSL.IO.Thermo.ThermoRawFile(_fullFilePath);
_raw.Open();
}