public static bool Run()
{
string outputPath = @"C:\_IRIC\DATA\Test\testMhc\Stats\";
vsCSVWriter writer = new vsCSVWriter(outputPath + "output.csv");
writer.AddLine("File,# MS1s,# MSMS,1 Charge,2 Charge,3 Charge,4 Charge,5 Charge,6 Charge,7 Charge,8 Charge,9 Charge,10 Charge,11 Charge,12 Charge,13 Charge,14 Charge");
DBOptions options = MhcSample.CreateOptions(outputPath);
string[] files = new string[] { @"N:\Thibault\-=Proteomics_Raw_Data=-\ELITE\JUL29_2013\Settepeptides_300713_10uL.raw",
@"N:\Thibault\-=Proteomics_Raw_Data=-\ELITE\JUL29_2013\Settepeptides_300713_10uL_MS60_MSMS15.raw",
@"N:\Thibault\-=Proteomics_Raw_Data=-\ELITE\JUL29_2013\Settepeptides_300713_10uL_MS60_MSMS30.raw",
@"N:\Thibault\-=Proteomics_Raw_Data=-\ELITE\JUL29_2013\Settepeptides_300713_10uL_MS60_MSMS60.raw",
@"N:\Thibault\-=Proteomics_Raw_Data=-\ELITE\JUL29_2013\Settepeptides_300713_10uL_MS120_MSMS15.raw",
@"N:\Thibault\-=Proteomics_Raw_Data=-\ELITE\JUL29_2013\Settepeptides_300713_10uL_MS120_MSMS30.raw",
@"N:\Thibault\-=Proteomics_Raw_Data=-\ELITE\JUL29_2013\Settepeptides_300713_10uL_MS120_MSMS60.raw" };
foreach (string file in files)
{
pwiz.CLI.msdata.MSDataFile msFile = new pwiz.CLI.msdata.MSDataFile(file);
Spectra spectra = Spectra.Load(msFile, options, file);
spectra.Sort(ProductSpectrum.AscendingPrecursorMassComparison);
Dictionary <Track, Precursor> DicOfComputedTracks = new Dictionary <Track, Precursor>();
int[] charges = new int[14];
foreach (Track track in spectra.tracks)
{
if (!DicOfComputedTracks.ContainsKey(track))
{
DicOfComputedTracks.Add(track, null);
int charge = 0;
foreach (Precursor precursor in Queries.GetIsotopes(track, options, spectra.tracks, null))
{
if (precursor.Charge > 0)
{
charge = precursor.Charge;
}
if (!DicOfComputedTracks.ContainsKey(precursor.Track))
{
DicOfComputedTracks.Add(precursor.Track, precursor);
}
}
charges[charge]++;
}
}
string line = file + "," + spectra.MS1s.Count + "," + spectra.Count;
for (int i = 0; i < charges.Length; i++)
{
line += "," + charges[i];
}
writer.AddLine(line);
}
writer.WriteToFile();
return(true);
}
public static bool Run()
{
//TODO test GPU instead
DBOptions dbOptions = MhcSample.CreateOptions("");
Dictionary <string, int> sequences = new Dictionary <string, int>();
List <Protein> proteins = Propheus.ReadProteomeFromFasta(Path.Combine(Path.GetDirectoryName(Environment.GetCommandLineArgs()[0]), "UnitTest", "proteins.fasta"), false, dbOptions);//ETLPAMCNVYYVNCMAPLTE
string sequence = proteins[0].BaseSequence;
double[] proteinMasses = new double[sequence.Length];
List <double> precursors = new List <double>();
for (int i = 0; i < sequence.Length; i++)
{
for (int j = i + dbOptions.MinimumPeptideLength - 1; j < sequence.Length; j++)
{
int size = j - i + 1;
if (size <= dbOptions.MaximumPeptideLength)
{
string subStr = sequence.Substring(i, j - i + 1);
if (!sequences.ContainsKey(subStr))
{
sequences.Add(subStr, 1);
}
else
{
sequences[subStr]++;
}
double mass = Constants.WATER_MONOISOTOPIC_MASS;
for (int k = 0; k < subStr.Length; k++)
{
mass += AminoAcidMasses.GetMonoisotopicMass(subStr[k]);
}
precursors.Add(mass);
}
}
proteinMasses[i] = AminoAcidMasses.GetMonoisotopicMass(sequence[i]);
}
precursors.Sort();
Queries queries = new Queries(dbOptions, precursors.ToArray());
Digestion ps = new Digestion(dbOptions);
List <Protein> lProt = new List <Protein>();
lProt.Add(proteins[0]);
//for each protein, build matrix of mass
//Trinity_Gpu.ProteinDigest pg = new Trinity_Gpu.ProteinDigest(precursors.ToArray(), sequence.Length);
//Test twice to test that precursor list stays in gpu memory
for (int iter = 0; iter < 2; iter++)
{
Dictionary <string, int> sequencesTmp = new Dictionary <string, int>(sequences);
foreach (Tuple <Peptide, int> item in ps.DigestProteomeOnTheFlyNoEnzyme(lProt, queries))
{
sequencesTmp[item.Item1.BaseSequence] -= 1;//TODO add modifications
}
/*
* foreach (Trinity_Gpu.ProteinPrecursorMatch match in pg.Execute(proteinMasses, 0.00005, 10000000))//TODO compute correct tolerance window
* {
* int size = match.proteinEndPos - match.proteinStartPos;
* string str = sequence.Substring(match.proteinStartPos, size);
* if (size >= dbOptions.MinimumPeptideLength)
* {
* sequencesTmp[str] -= 1;//TODO add modifications
* }
* }//*/
foreach (int val in sequencesTmp.Values)
{
if (val != 0)
{
return(false);//*/
}
}
}
//pg.Dispose();
return(true);
}
