public static void TestSummedMsDataFile()
{
ThermoStaticData rawFile = ThermoStaticData.LoadAllStaticData(@"05-13-16_cali_MS_60K-res_MS.raw");
// 3 scans
SummedMsDataFile summed3 = new SummedMsDataFile(rawFile, 3, 10);
Assert.AreEqual(rawFile.NumSpectra - 2, summed3.NumSpectra);
var resultingTic = summed3.GetOneBasedScan(1).TotalIonCurrent;
var mySummedTic = rawFile.GetOneBasedScan(1).MassSpectrum.SumOfAllY + rawFile.GetOneBasedScan(2).MassSpectrum.SumOfAllY + rawFile.GetOneBasedScan(3).MassSpectrum.SumOfAllY;
var instrumentSummedTic = rawFile.GetOneBasedScan(1).TotalIonCurrent + rawFile.GetOneBasedScan(2).TotalIonCurrent + rawFile.GetOneBasedScan(3).TotalIonCurrent;
// Tics are approximately what they should be
Assert.IsTrue(Math.Abs(resultingTic - mySummedTic) / mySummedTic < 1e-4);
Assert.IsTrue(Math.Abs(resultingTic - instrumentSummedTic) / instrumentSummedTic < 1e-1);
// Equal to representative
Assert.AreEqual(summed3.GetOneBasedScan(1).RetentionTime, rawFile.GetOneBasedScan(2).RetentionTime);
Assert.IsTrue(summed3.GetOneBasedScan(1).MassSpectrum.Size <= rawFile.GetOneBasedScan(1).MassSpectrum.Size + rawFile.GetOneBasedScan(2).MassSpectrum.Size + rawFile.GetOneBasedScan(3).MassSpectrum.Size);
Assert.IsTrue(summed3.GetOneBasedScan(1).MassSpectrum.Size >= rawFile.GetOneBasedScan(1).MassSpectrum.Size);
Assert.IsTrue(summed3.GetOneBasedScan(1).MassSpectrum.Size >= rawFile.GetOneBasedScan(2).MassSpectrum.Size);
Assert.IsTrue(summed3.GetOneBasedScan(1).MassSpectrum.Size >= rawFile.GetOneBasedScan(3).MassSpectrum.Size);
Assert.IsTrue(summed3.GetOneBasedScan(1).MassSpectrum.YofPeakWithHighestY == rawFile.GetOneBasedScan(1).MassSpectrum.YofPeakWithHighestY + rawFile.GetOneBasedScan(2).MassSpectrum.YofPeakWithHighestY + rawFile.GetOneBasedScan(3).MassSpectrum.YofPeakWithHighestY);
// Interval of 893-899 mz
Assert.AreEqual(2, rawFile.GetOneBasedScan(1).MassSpectrum.NumPeaksWithinRange(893, 899));
Assert.AreEqual(2, rawFile.GetOneBasedScan(2).MassSpectrum.NumPeaksWithinRange(893, 899));
Assert.AreEqual(1, rawFile.GetOneBasedScan(3).MassSpectrum.NumPeaksWithinRange(893, 899));
// One peak persists across the three scans! So instead of 5 see three peaks in summed
Assert.AreEqual(3, summed3.GetOneBasedScan(1).MassSpectrum.NumPeaksWithinRange(893, 899));
Assert.AreEqual(summed3.GetOneBasedScan(1).MassSpectrum.FirstX, Math.Min(Math.Min(rawFile.GetOneBasedScan(1).MassSpectrum.FirstX.Value, rawFile.GetOneBasedScan(2).MassSpectrum.FirstX.Value), rawFile.GetOneBasedScan(3).MassSpectrum.FirstX.Value));
Assert.AreEqual(summed3.GetOneBasedScan(1).MassSpectrum.LastX, Math.Max(Math.Max(rawFile.GetOneBasedScan(1).MassSpectrum.LastX.Value, rawFile.GetOneBasedScan(2).MassSpectrum.LastX.Value), rawFile.GetOneBasedScan(3).MassSpectrum.LastX.Value));
// 5 scans
SummedMsDataFile summed5 = new SummedMsDataFile(rawFile, 5, 10);
Assert.AreEqual(rawFile.NumSpectra - 4, summed5.NumSpectra);
MzmlMethods.CreateAndWriteMyMzmlWithCalibratedSpectra(summed5, "testSummed.mzML", false);
var ok = Mzml.LoadAllStaticData("testSummed.mzML");
MzmlMethods.CreateAndWriteMyMzmlWithCalibratedSpectra(ok, "testSummed2.mzML", false);
Mzml.LoadAllStaticData("testSummed2.mzML");
}
private static void DoFileDecon(string[] args)
{
var p = new FluentCommandLineParser <ApplicationArguments>();
p.Setup(arg => arg.AggregationTolerancePpm)
.As("AggregationTolerancePpm");
p.Setup(arg => arg.DeconvolutionTolerancePpm)
.As("DeconvolutionTolerancePpm");
p.Setup(arg => arg.MinScan)
.As("MinScan");
p.Setup(arg => arg.MaxScan)
.As("MaxScan");
p.Setup(arg => arg.MinAssumedChargeState)
.As("MinAssumedChargeState");
p.Setup(arg => arg.MaxAssumedChargeState)
.As("MaxAssumedChargeState");
p.Setup(arg => arg.IntensityRatioLimit)
.As("IntensityRatioLimit");
p.Setup(arg => arg.AverageScans)
.As("AverageScans");
p.Setup(arg => arg.NumScansRequired)
.As("NumScansRequired");
p.Setup(arg => arg.FilePath)
.As("FilePath").
Required();
var result = p.Parse(args);
Console.WriteLine("Running deconvolution using the following parameters:");
Console.WriteLine(p.Object);
if (result.HasErrors == false)
{
MsDataFile myMsDataFile;
if (Path.GetExtension(p.Object.FilePath).Equals(".mzML", StringComparison.OrdinalIgnoreCase))
{
myMsDataFile = Mzml.LoadAllStaticData(p.Object.FilePath);
}
else
{
myMsDataFile = ThermoStaticData.LoadAllStaticData(p.Object.FilePath);
}
if (p.Object.AverageScans > 1)
{
myMsDataFile = new SummedMsDataFile(myMsDataFile, p.Object.AverageScans, p.Object.DeconvolutionTolerancePpm);
}
using (StreamWriter output = new StreamWriter(@"DeconvolutionOutput-" + DateTime.Now.ToString("yyyy-MM-dd-HH-mm-ss", CultureInfo.InvariantCulture) + ".tsv"))
{
output.WriteLine("Mass\tScore\tNumPeaks\tNumScans\tMinScan\tMaxScan\tElutionStart\tElutionEnd\tTotalNormalizedIntensity\tObservedCharges\tMostIntenseElutionTime\tMostIntenseCharge\tMostIntenseMz\tNumPeaksInMostIntenseEnvelope\tMostIntenseEnvelopeIntensity\tElutionOfMostIntenseCharge");
foreach (var nice in myMsDataFile.Deconvolute(p.Object.MinScan, p.Object.MaxScan, p.Object.MinAssumedChargeState, p.Object.MaxAssumedChargeState, p.Object.DeconvolutionTolerancePpm, p.Object.IntensityRatioLimit, p.Object.AggregationTolerancePpm, b => b.MsnOrder == 1).OrderByDescending(b => b.Score))
{
if ((nice.MaxScanIndex - nice.MinScanIndex + 1) >= p.Object.NumScansRequired)
{
output.WriteLine(nice.OneLineString());
}
}
}
}
else
{
Console.WriteLine("BAD PARAMETERS");
Console.WriteLine(result.ErrorText);
}
}
