[TestCase(@"032421_MALAT1Capture_5790_7045", 784.3348, 7045.937, 9)] // harmonic
public static void TestDeconvolutionDifferentCases(string dataFilePath, double mz, double monoMass, int z)
{
string filePath = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\DeconCases\" + dataFilePath + ".mzML");
var data = IO.MzML.Mzml.LoadAllStaticData(filePath);
var deconEngine = new DeconvolutionEngine(2000, 0.3, 6, 0.4, 3, 5, 2, 60, 3);
var scan = data.GetAllScansList().First();
Tolerance t = new AbsoluteTolerance(0.001);
var candidates = deconEngine.GetEnvelopeCandidates(scan.MassSpectrum, scan.ScanWindowRange);
deconEngine.CalculateSignalToNoise(scan.MassSpectrum, candidates);
var candidatesWithMz = candidates.Where(p => p.Peaks.Any(v => t.Within(v.ExperimentalMz, mz))).OrderByDescending(p => p.Score).ToList();
var parsimonyEnvelopes = deconEngine.RunEnvelopeParsimony(candidates, scan.MassSpectrum);
deconEngine.CalculateSignalToNoise(scan.MassSpectrum, parsimonyEnvelopes);
var parsimonyEnvsWithMz = parsimonyEnvelopes.Where(p => p.Peaks.Any(v => t.Within(v.ExperimentalMz, mz))).ToList();
//var envelopes = deconEngine.Deconvolute(data, filePath, 1).ToList();
//var finalEnvelopesWithMz = envelopes.Where(p => p.Peaks.Any(v => t.Within(v.ExperimentalMz, mz))).ToList();
//Assert.That(testedEnvelope.Count == 1);
//Assert.That(testedEnvelope[0].Charge == z);
//Assert.That(testedEnvelope[0].MonoisotopicMass == monoMass);
}
public static void TestDeconvolutionRealFile()
{
string filePath = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\mcf7_sliced\mcf7_sliced_td.raw");
var data = IO.ThermoRawFileReader.ThermoRawFileReader.LoadAllStaticData(filePath);
var deconEngine = new DeconvolutionEngine(2000, 0.4, 3, 0.4, 3, 5, 2, 60, 3);
var envelopes = deconEngine.Deconvolute(data, filePath, 1).ToList();
List <string> output = new List <string>()
{
DeconvolutedEnvelope.TabDelimitedHeader
};
foreach (var env in envelopes)
{
output.Add(env.ToOutputString());
}
string path = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestPfmExplorerDeconOutput_mcf7.tsv");
File.WriteAllLines(path, output);
var species = InputReaderParser.ReadSpeciesFromFile(path, out var errors);
Assert.That(!errors.Any());
Assert.That(species.Count > 0);
Assert.That(species.All(p => p.DeconvolutionFeature != null));
Assert.That(species.All(p => p.DeconvolutionFeature.AnnotatedEnvelopes != null && p.DeconvolutionFeature.AnnotatedEnvelopes.Count > 0));
Assert.That(species.All(p => p.DeconvolutionFeature.AnnotatedEnvelopes.All(v => v.PeakMzs.Count > 0)));
Assert.That(species.All(p => p.DeconvolutionFeature.SpectraFileNameWithoutExtension == Path.GetFileNameWithoutExtension(filePath)));
}
public static void TestDeconvolution()
{
UsefulProteomicsDatabases.Loaders.LoadElements();
// >sp|P49703|ARL4D_HUMAN ADP-ribosylation factor-like protein 4D OS=H**o sapiens OX=9606 GN=ARL4D PE=1 SV=2
string sequence = "MGNHLTEMAPTASSFLPHFQALHVVVIGLDSAGKTSLLYRLKFKEFVQSVPTKGFNTEKIRVPLGGSRGITFQ" +
"VWDVGGQEKLRPLWRSYTRRTDGLVFVVDAAEAERLEEAKVELHRISRASDNQGVPVLVLANKQDQPGALSAA" +
"EVEKRLAVRELAAATLTHVQGCSAVDGLGLQQGLERLYEMILKRKKAARGGKKRR";
int charge = 15;
double intensityMultiplier = 1e6;
Proteomics.AminoAcidPolymer.Peptide baseSequence = new Proteomics.AminoAcidPolymer.Peptide(sequence);
var formula = baseSequence.GetChemicalFormula();
var isotopicDistribution = IsotopicDistribution.GetDistribution(formula, 0.125, 1e-8);
double[] masses = isotopicDistribution.Masses.ToArray();
double[] abundances = isotopicDistribution.Intensities.ToArray();
double max = abundances.Max();
List <(double, double)> peaks = new List <(double, double)>();
for (int i = 0; i < masses.Length; i++)
{
abundances[i] /= max;
if (abundances[i] >= 0.05)
{
peaks.Add((masses[i].ToMz(charge), abundances[i] * intensityMultiplier));
}
}
Random r = new Random(1);
for (int i = 0; i < 1000; i++)
{
double mz = r.NextDouble() * 1200 + 400;
double intensity = r.NextDouble() * 30000 + 30000;
peaks.Add((mz, intensity));
}
peaks = peaks.OrderBy(p => p.Item1).ToList();
var spectrum = new MzSpectrum(peaks.Select(p => p.Item1).ToArray(), peaks.Select(p => p.Item2).ToArray(), true);
var engine = new DeconvolutionEngine(0, 0.4, 3, 0.4, 1.5, 5, 1, 60, 2);
var envs = engine.Deconvolute(spectrum, spectrum.Range).ToList();
List <string> output = new List <string> {
DeconvolutedEnvelope.TabDelimitedHeader
};
foreach (var env in envs)
{
env.SpectraFileName = "temp";
output.Add(env.ToOutputString());
}
string path = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestPfmExplorerDeconOutput.tsv");
File.WriteAllLines(path, output);
var species = InputReaderParser.ReadSpeciesFromFile(path, out var errors);
Assert.That(!errors.Any());
Assert.That(species.Count > 0);
Assert.That(species.All(p => p.DeconvolutionFeature != null));
Assert.That(species.All(p => p.DeconvolutionFeature.AnnotatedEnvelopes != null && p.DeconvolutionFeature.AnnotatedEnvelopes.Count > 0));
Assert.That(species.All(p => p.DeconvolutionFeature.AnnotatedEnvelopes.All(v => v.PeakMzs.Count > 0)));
//Assert.That(species.Count == 1);
}
