public void ReadMzMLChromatogramsTestDelayedRandom(string inputFileRelativePath, int expectedChromatograms, bool immediateRandomAccess)
{
if (!TestPath.FindInputFile(inputFileRelativePath, out var sourceFile))
{
Console.WriteLine("File not found: " + inputFileRelativePath);
return;
}
using (var reader = new SimpleMzMLReader(sourceFile.FullName, immediateRandomAccess, true))
{
if (!immediateRandomAccess)
{
// For non-random access readers, the number of chromatograms (as reported by NumChromatograms)
// will not get populated until after all the spectra (if any) have been read
// Therefore, NumChromatograms should currently be zero since immediateRandomAccess was false
Assert.AreEqual(0, reader.NumChromatograms);
// You cannot use reader.TryMakeRandomAccessCapable() to make the chromatograms available
// Thus, exit this method
return;
}
Assert.AreEqual(expectedChromatograms, reader.NumChromatograms);
var stepSize = Math.Max(1, expectedChromatograms / 100);
var chromatogramNumber = 1;
while (chromatogramNumber <= expectedChromatograms)
{
var chrom = reader.ReadChromatogram(chromatogramNumber);
Console.WriteLine("Chromatogram {0,2}, NativeID {1,-35} has {2:N0} data points", chrom.Index, chrom.Id, chrom.Intensities.Length);
chromatogramNumber += stepSize;
}
}
}
//[TestCase(@"MzML\QC_Shew_16_01-15f_MPA_02redo_8Nov16_Tiger_16-02-14.mzML.gz", 9293)] // implemented, but decompresses first
public void ReadMzMLChromatogramsTestRandom(string inputFileRelativePath, int expectedChromatograms)
{
if (!TestPath.FindInputFile(inputFileRelativePath, out var sourceFile))
{
Console.WriteLine("File not found: " + inputFileRelativePath);
return;
}
using (var reader = new SimpleMzMLReader(sourceFile.FullName, true, true))
{
Assert.AreEqual(expectedChromatograms, reader.NumChromatograms);
var chromCount = 0;
foreach (var chrom in reader.ReadAllChromatograms(true))
{
if (chrom == null)
{
Console.WriteLine("ReadAllChromatograms returned null for chromatogram index {0}", chromCount);
}
else
{
Console.WriteLine("Chromatogram {0}, NativeID {1,-45} has {2:N0} data points", chrom.Index, chrom.Id, chrom.Intensities.Length);
}
chromCount++;
}
Assert.AreEqual(expectedChromatograms, chromCount);
}
}
public void ReadMzMLTest(string inputFileRelativePath, int expectedSpectra, bool includePeaks)
{
if (!TestPath.FindInputFile(inputFileRelativePath, out var sourceFile))
{
Console.WriteLine("File not found: " + inputFileRelativePath);
return;
}
using (var reader = new SimpleMzMLReader(sourceFile.FullName, false, true))
{
Assert.AreEqual(expectedSpectra, reader.NumSpectra);
var specCount = 0;
foreach (var spec in reader.ReadAllSpectra(includePeaks))
{
if (specCount < 100 || specCount >= expectedSpectra - 100)
{
Console.WriteLine("Spectrum {0,4}, NativeID {1,-45} has {2:N0} data points", spec.ScanNumber, spec.NativeId, spec.Peaks.Length);
}
else if (specCount == 100)
{
Console.WriteLine("...");
}
specCount++;
}
Assert.AreEqual(expectedSpectra, specCount);
}
}
public void ReadFileLowMem(string inputFileRelativePath, int expectedNativeIDs, int expectedResults, int expectedPeptides, int expectedProteinSeqs)
{
if (!TestPath.FindInputFile(inputFileRelativePath, out var sourceFile))
{
Console.WriteLine("File not found: " + inputFileRelativePath);
return;
}
var reader = new SimpleMZIdentMLReader();
var spectrumIDs = new SortedSet <string>();
var peptides = new SortedSet <string>();
var proteinSeqs = new SortedSet <string>();
var specResults = 0;
using (var results = reader.ReadLowMem(sourceFile.FullName))
{
var resultIdentifications = results.Identifications.ToList();
var resultCountTotal = resultIdentifications.Count;
foreach (var specItem in resultIdentifications)
{
specResults++;
if (!spectrumIDs.Contains(specItem.NativeId))
{
spectrumIDs.Add(specItem.NativeId);
}
foreach (var evidenceItem in specItem.PepEvidence)
{
if (!peptides.Contains(evidenceItem.SequenceWithNumericMods))
{
peptides.Add(evidenceItem.SequenceWithNumericMods);
}
if (!proteinSeqs.Contains(evidenceItem.DbSeq.Accession))
{
proteinSeqs.Add(evidenceItem.DbSeq.Accession);
}
}
if (specResults % 1000 == 0)
{
Console.WriteLine("{0,6:N0} / {1,6:N0}", specResults, resultCountTotal);
}
}
}
Console.WriteLine();
Console.WriteLine("Spectrum Identification Results: {0,6:N0}", specResults);
Console.WriteLine("Native IDs: {0,6:N0}", spectrumIDs.Count);
Console.WriteLine("Unique Peptides: {0,6:N0}", peptides.Count);
Console.WriteLine("Unique Protein Sequences: {0,6:N0}", proteinSeqs.Count);
Assert.AreEqual(expectedResults, specResults, "Spectrum Identification Results");
Assert.AreEqual(expectedNativeIDs, spectrumIDs.Count, "Native IDs");
Assert.AreEqual(expectedPeptides, peptides.Count, "Unique Peptides");
Assert.AreEqual(expectedProteinSeqs, proteinSeqs.Count, "Unique Protein Sequences");
}
public void MzIdentMLReadTest(string inputFileRelativePath, int expectedSpecResults, int expectedSpecItems, int expectedPeptides, int expectedSeqs)
{
if (!TestPath.FindInputFile(inputFileRelativePath, out var sourceFile))
{
Console.WriteLine("File not found: " + inputFileRelativePath);
return;
}
var identData = new IdentDataObj(MzIdentMlReaderWriter.Read(sourceFile.FullName));
var specResults = 0;
var specItems = 0;
foreach (var specList in identData.DataCollection.AnalysisData.SpectrumIdentificationList)
{
if (specList.SpectrumIdentificationResults == null)
{
continue;
}
specResults += specList.SpectrumIdentificationResults.Count;
foreach (var specResult in specList.SpectrumIdentificationResults)
{
specItems += specResult.SpectrumIdentificationItems.Count;
}
}
var observedPeptides = 0;
if (identData.SequenceCollection.Peptides != null)
{
observedPeptides = identData.SequenceCollection.Peptides.Count;
}
var observeProteins = 0;
if (identData.SequenceCollection.DBSequences != null)
{
observeProteins = identData.SequenceCollection.DBSequences.Count;
}
Console.WriteLine();
Console.WriteLine("Spectrum Identification Results: {0,6:N0}", specResults);
Console.WriteLine("Native IDs: {0,6:N0}", specItems);
Console.WriteLine("Unique Peptides: {0,6:N0}", observedPeptides);
Console.WriteLine("Unique Protein Sequences: {0,6:N0}", observeProteins);
Assert.AreEqual(expectedSpecResults, specResults, "Spectrum Identification Results");
Assert.AreEqual(expectedSpecItems, specItems, "Native IDs");
Assert.AreEqual(expectedPeptides, observedPeptides, "Unique Peptides");
Assert.AreEqual(expectedSeqs, observeProteins, "Unique Protein Sequences");
}
public void ReadMzMLChromatogramsTestNonRandom(string inputFileRelativePath, int expectedSpectra, int expectedChromatograms)
{
if (!TestPath.FindInputFile(inputFileRelativePath, out var sourceFile))
{
Console.WriteLine("File not found: " + inputFileRelativePath);
return;
}
using (var reader = new SimpleMzMLReader(sourceFile.FullName, false, true))
{
Assert.AreEqual(expectedSpectra, reader.NumSpectra);
if (expectedSpectra != 0)
{
Assert.AreEqual(0, reader.NumChromatograms);
}
var specCount = 0;
foreach (var spec in reader.ReadAllSpectra(true))
{
if (specCount < 100 || specCount >= expectedSpectra - 100)
{
Console.WriteLine("Spectrum {0,4}, NativeID {1,-45} has {2:N0} data points", spec.ScanNumber, spec.NativeId, spec.Peaks.Length);
}
else if (specCount == 100)
{
Console.WriteLine("...");
}
specCount++;
}
Assert.AreEqual(expectedSpectra, specCount);
Assert.AreEqual(expectedChromatograms, reader.NumChromatograms);
var chromCount = 0;
foreach (var chrom in reader.ReadAllChromatograms(false))
{
if (chrom == null)
{
Console.WriteLine("ReadAllChromatograms returned null for chromatogram index {0}", chromCount);
}
else
{
Console.WriteLine("Chromatogram {0}, NativeID {1,-45} has {2:N0} data points", chrom.Index, chrom.Id, chrom.Intensities.Length);
}
chromCount++;
}
Assert.AreEqual(expectedChromatograms, reader.NumChromatograms);
Assert.AreEqual(expectedChromatograms, chromCount);
}
}
public void MzMLIndexedReadTest(string inputFileRelativePath, int expectedSpectra)
{
if (!TestPath.FindInputFile(inputFileRelativePath, out var sourceFile))
{
Console.WriteLine("File not found: " + inputFileRelativePath);
return;
}
var reader = new MzMLReader(Path.Combine(TestPath.ExtTestDataDirectory, sourceFile.FullName));
//mzMLType mzMLData = reader.Read();
var mzMLData = new MSData(reader.Read());
Console.WriteLine("Spectrum count: " + mzMLData.Run.SpectrumList.Spectra.Count);
Assert.AreEqual(expectedSpectra, mzMLData.Run.SpectrumList.Spectra.Count, "Spectrum count");
}
public void ReadMzMLCompareScanNumbers(string inputFileRelativePath, string artificialScanNumberList, string expectedActualScanNumberList)
{
if (!TestPath.FindInputFile(inputFileRelativePath, out var sourceFile))
{
Console.WriteLine("File not found: " + inputFileRelativePath);
return;
}
var artificialScanNumbers = ParseOrderedIntegerList(artificialScanNumberList);
var expectedActualScanNumbers = ParseOrderedIntegerList(expectedActualScanNumberList);
// Run the test twice, first with randomAccess disabled, then with randomAccess enabled
for (var i = 0; i < 2; i++)
{
var randomAccess = i > 0;
using (var reader = new SimpleMzMLReader(sourceFile.FullName, randomAccess, true))
{
for (var j = 0; j < artificialScanNumbers.Count; j++)
{
var artificialScanNumber = artificialScanNumbers[j];
var expectedScanNumber = expectedActualScanNumbers[j];
var spectrum = reader.ReadMassSpectrum(artificialScanNumber, false);
if (expectedScanNumber <= 0)
{
Console.WriteLine("Spectrum {0,4} does not exist; this was expected", artificialScanNumber);
Assert.IsNull(spectrum);
continue;
}
Assert.IsNotNull(spectrum);
Console.WriteLine("Spectrum {0,4}, NativeID {1,-45}, scan {2,4}", spectrum.ScanNumber, spectrum.NativeId, spectrum.NativeIdScanNumber);
Assert.AreEqual(expectedScanNumber, spectrum.NativeIdScanNumber);
var comparisonSpectrum = reader.GetSpectrumForScan(spectrum.NativeIdScanNumber, false);
Assert.AreEqual(comparisonSpectrum.NativeId, spectrum.NativeId);
}
}
Console.WriteLine();
}
}
public void MzMLIndexedReadTest(string inputFileRelativePath, int expectedSpectra)
{
if (!TestPath.FindInputFile(inputFileRelativePath, out var sourceFile))
{
Console.WriteLine("File not found: " + inputFileRelativePath);
return;
}
var reader = new MzMLReader(sourceFile.FullName);
var mzMLData = reader.Read();
Console.WriteLine("Spectrum count: " + mzMLData.run.spectrumList.count);
Console.WriteLine("Array length: " + mzMLData.run.spectrumList.spectrum.Count);
Assert.AreEqual(expectedSpectra.ToString(), mzMLData.run.spectrumList.count, "Spectrum Count");
Assert.AreEqual(expectedSpectra, mzMLData.run.spectrumList.spectrum.Count, "Array length");
}
public void ReadMzMLTestRetrieveByScanNumber(string inputFileRelativePath, int expectedSpectra, bool includePeaks, string scanNumberList, string expectedMissingScanNumbers)
{
if (!TestPath.FindInputFile(inputFileRelativePath, out var sourceFile))
{
Console.WriteLine("File not found: " + inputFileRelativePath);
return;
}
var scanNumbers = ParseDelimitedIntegerList(scanNumberList);
var expectedMissingScans = ParseDelimitedIntegerList(expectedMissingScanNumbers);
using (var reader = new SimpleMzMLReader(sourceFile.FullName, true, true))
{
Assert.AreEqual(expectedSpectra, reader.NumSpectra);
foreach (var scanNumber in scanNumbers)
{
var spec = reader.GetSpectrumForScan(scanNumber, includePeaks);
if (spec == null)
{
if (expectedMissingScans.Contains(scanNumber))
{
Console.WriteLine("Scan {0} not found; this is expected", scanNumber);
continue;
}
Assert.Fail("GetSpectrumForScan returned null for scan {0}", scanNumber);
}
if (includePeaks)
{
Console.WriteLine("Spectrum {0,4}, NativeID {1,-45}, scan {2,4} has {3:N0} data points", spec.ScanNumber, spec.NativeId, spec.NativeIdScanNumber, spec.Peaks.Length);
}
else
{
Console.WriteLine("Spectrum {0,4}, NativeID {1,-45}, scan {2,4} (peaks not loaded)", spec.ScanNumber, spec.NativeId, spec.NativeIdScanNumber);
}
Assert.AreEqual(scanNumber, spec.NativeIdScanNumber);
}
}
}
public void ReadMzMLTestRandom(string inputFileRelativePath, int expectedSpectra, bool includePeaks, bool immediateRandomAccess)
{
if (!TestPath.FindInputFile(inputFileRelativePath, out var sourceFile))
{
Console.WriteLine("File not found: " + inputFileRelativePath);
return;
}
using (var reader = new SimpleMzMLReader(sourceFile.FullName, immediateRandomAccess, true))
{
if (!immediateRandomAccess)
{
reader.TryMakeRandomAccessCapable();
}
Assert.AreEqual(expectedSpectra, reader.NumSpectra);
var stepSize = Math.Max(1, expectedSpectra / 100);
// Note: calling .ReadMassSpectrum with scanNumber = 1 returns the first spectrum in the file, regardless of its actual scan number
var scanNumber = 1;
while (scanNumber <= expectedSpectra)
{
var spec = reader.ReadMassSpectrum(scanNumber, includePeaks);
if (includePeaks)
{
Console.WriteLine("Spectrum {0,4}, NativeID {1,-45}, scan {2,4} has {3:N0} data points", spec.ScanNumber, spec.NativeId, spec.NativeIdScanNumber, spec.Peaks.Length);
}
else
{
Console.WriteLine("Spectrum {0,4}, NativeID {1,-45}, scan {2,4} (peaks not loaded)", spec.ScanNumber, spec.NativeId, spec.NativeIdScanNumber);
}
scanNumber += stepSize;
}
}
}
public void TestGetParentScan(string inputFileRelativePath, int startScan, int endScan, params int[] expectedPrecursorScans)
{
if (!TestPath.FindInputFile(inputFileRelativePath, out var sourceFile))
{
Console.WriteLine("File not found: " + inputFileRelativePath);
return;
}
using (var reader = new SimpleMzMLReader(sourceFile.FullName, true, true))
{
for (var scanNumber = startScan; scanNumber <= endScan; scanNumber++)
{
var spectrum = reader.ReadMassSpectrum(scanNumber, false);
if (spectrum == null)
{
continue;
}
var targetIndex = scanNumber - startScan;
int expectedPrecursorScan;
if (targetIndex >= 0 && targetIndex < expectedPrecursorScans.Length)
{
expectedPrecursorScan = expectedPrecursorScans[targetIndex];
}
else
{
expectedPrecursorScan = 0;
}
if (spectrum.Precursors.Count == 0)
{
Console.WriteLine("Scan {0} is not a fragmentation scan", spectrum.ScanNumber);
if (expectedPrecursorScan > 0)
{
Assert.Fail("Scan {0} was supposed to have precursor scan {1}, but it has no precursors", spectrum.ScanNumber, expectedPrecursorScan);
}
continue;
}
var precursorSpectrumReference = spectrum.Precursors[0].PrecursorSpectrumRef;
// Parse out scan number from the precursor spectrum reference
// "controllerType=0 controllerNumber=1 scan=1"
if (!NativeIdConversion.TryGetScanNumberLong(precursorSpectrumReference, out var precursorScan))
{
Assert.Fail("Invalid spectrum reference: " + precursorSpectrumReference);
}
Console.WriteLine("Scan {0} has precursor {1:F2} m/z, precursor scan {2}",
spectrum.ScanNumber,
spectrum.Precursors[0].IsolationWindow.TargetMz,
precursorScan);
if (expectedPrecursorScan != 0)
{
Assert.AreEqual(expectedPrecursorScan, precursorScan,
"Precursor scan number does not match the expected value for scan {0}",
spectrum.ScanNumber);
}
}
}
}
