public void FeatureFind(List<ProteinSpectrumMatch> prsms, LcMsRun run, string outTsvFilePath)
{
var featureFinder = new LcMsPeakMatrix(run, new LcMsFeatureLikelihood());
// write result files
var tsvWriter = new StreamWriter(outTsvFilePath);
tsvWriter.WriteLine(LcMsFeatureFinderLauncher.GetHeaderString(false));
var featureId = 1;
foreach (var match in prsms)
{
var minScan = run.GetPrevScanNum(match.ScanNum, 1);
var maxScan = run.GetNextScanNum(match.ScanNum, 1);
var feature = featureFinder.GetLcMsPeakCluster(match.Mass, match.Charge, minScan, maxScan);
if (feature == null) continue;
tsvWriter.WriteLine("{0}\t{1}", featureId, LcMsFeatureFinderLauncher.GetString(feature, false));
featureId++;
}
tsvWriter.Close();
}
public void TestLcMsFeatureXic()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const string rawFile = @"\\proto-11\MSXML_Cache\PBF_Gen_1_193\2015_1\CPTAC_Intact_rep2_15Jan15_Bane_C2-14-08-02RZ.pbf";
//const string rawFile = @"D:\MassSpecFiles\training\raw\QC_Shew_Intact_26Sep14_Bane_C2Column3.pbf";
if (!File.Exists(rawFile))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, rawFile);
}
var run = PbfLcMsRun.GetLcMsRun(rawFile);
var scorer = new LcMsFeatureLikelihood();
var featureFinder = new LcMsPeakMatrix(run, scorer);
var feature = featureFinder.GetLcMsPeakCluster(2388.278, 4, 3774, 3907);
//feature = featureFinder.GetLcMsPeakCluster(8151.3706, 7, 13, 4201, 4266);
//feature = featureFinder.GetLcMsPeakCluster(8151.41789, 7, 13, 2861, 2941);
var ms1ScanToIndex = run.GetMs1ScanNumToIndex();
var minCol = ms1ScanToIndex[feature.MinScanNum];
var maxCol = ms1ScanToIndex[feature.MaxScanNum];
//var minRow = feature.MinCharge - LcMsPeakMatrix.MinScanCharge;
//var maxRow = feature.MaxCharge - LcMsPeakMatrix.MinScanCharge;
Console.WriteLine("---------------------------------------------------------------");
for (var i = 0; i < feature.Envelopes.Length; i++)
{
for (var j = 0; j < feature.Envelopes[i].Length; j++)
{
Console.Write(feature.Envelopes[i][j] != null ? feature.Envelopes[i][j].PearsonCorrelation : 0);
Console.Write("\t");
}
Console.Write("\n");
}
Console.WriteLine("---------------------------------------------------------------");
for (var i = 0; i < feature.Envelopes.Length; i++)
{
for (var j = 0; j < feature.Envelopes[i].Length; j++)
{
Console.Write(feature.Envelopes[i][j] != null ? feature.Envelopes[i][j].BhattacharyyaDistance : 0);
Console.Write("\t");
}
Console.Write("\n");
}
Console.WriteLine("---------------------------------------------------------------");
for (var i = 0; i < feature.Envelopes.Length; i++)
{
for (var j = 0; j < feature.Envelopes[i].Length; j++)
{
Console.Write(feature.Envelopes[i][j] != null ? feature.Envelopes[i][j].Abundance : 0);
Console.Write("\t");
}
Console.Write("\n");
}
}
public void TestFeatureExampleForFigure()
{
var methodName = MethodBase.GetCurrentMethod().Name;
TestUtils.ShowStarting(methodName);
const string rawFile = @"\\proto-11\MSXML_Cache\PBF_Gen_1_193\2015_1\CPTAC_Intact_rep6_15Jan15_Bane_C2-14-08-02RZ.pbf";
//const string rawFile = @"D:\MassSpecFiles\training\raw\QC_Shew_Intact_26Sep14_Bane_C2Column3.pbf";
if (!File.Exists(rawFile))
{
Assert.Ignore(@"Skipping test {0} since file not found: {1}", methodName, rawFile);
}
var run = PbfLcMsRun.GetLcMsRun(rawFile);
var scorer = new LcMsFeatureLikelihood();
var featureFinder = new LcMsPeakMatrix(run, scorer);
var feature = featureFinder.GetLcMsPeakCluster(28061.6177, 20, 34, 7624, 7736);
var writer = new StreamWriter(@"D:\MassSpecFiles\CPTAC_rep10\example\peaks.txt");
var envelope = feature.TheoreticalEnvelope;
foreach (var e in envelope.Isotopes) Console.WriteLine(e.Ratio);
foreach (var env in feature.EnumerateEnvelopes())
{
var corr = env.PearsonCorrelation;
for(var i = 0; i < envelope.Size; i++)
{
var peak = env.Peaks[i];
if (peak == null) continue;
writer.Write("{0}\t{1}\t{2}\t{3}\t{4}\t{5}\t{6}\n", env.ScanNum, run.GetElutionTime(env.ScanNum), env.Charge, i, peak.Mz, peak.Intensity, corr);
}
}
writer.Close();
}
