public void TestGetScanCountsByScanType(
string rawFileName,
int scanStart,
int scanEnd,
int expectedMS1,
int expectedMS2,
int expectedTotalScanCount)
{
// Keys in this Dictionary are filename, values are ScanCounts by collision mode, where the key is a Tuple of ScanType and FilterString
var expectedData = new Dictionary<string, Dictionary<Tuple<string, string>, int>>();
// Keys in this dictionary are scan type, values are a Dictionary of FilterString and the number of scans with that filter string
AddExpectedTupleAndCount(expectedData, "B5_50uM_MS_r1", "Q1MS", "+ c NSI Q1MS", 20);
AddExpectedTupleAndCount(expectedData, "MNSLTFKK_ms", "Q1MS", "+ p NSI Q1MS", 88);
AddExpectedTupleAndCount(expectedData, "QCShew200uL", "Q3MS", "+ c NSI Q3MS", 101);
AddExpectedTupleAndCount(expectedData, "Wrighton_MT2_SPE_200avg_240k_neg_330-380", "SIM ms", "FTMS - p NSI SIM ms", 200);
const string file5 = "1229_02blk1";
AddExpectedTupleAndCount(expectedData, file5, "MS", "ITMS + c NSI Full ms", 8);
AddExpectedTupleAndCount(expectedData, file5, "CID-MSn", "ITMS + c NSI d Full ms2 [email protected]", 24);
AddExpectedTupleAndCount(expectedData, file5, "SIM ms", "ITMS + p NSI SIM ms", 69);
const string file6 = "MCF7_histone_32_49B_400min_HCD_ETD_01172014_b";
AddExpectedTupleAndCount(expectedData, file6, "HMS", "FTMS + p NSI Full ms", 9);
AddExpectedTupleAndCount(expectedData, file6, "ETD-HMSn", "FTMS + p NSI d Full ms2 [email protected]", 46);
AddExpectedTupleAndCount(expectedData, file6, "HCD-HMSn", "FTMS + p NSI d Full ms2 [email protected]", 37);
AddExpectedTupleAndCount(expectedData, file6, "SIM ms", "FTMS + p NSI d SIM ms", 9);
const string file7 = "lowdose_IMAC_iTRAQ1_PQDMSA";
AddExpectedTupleAndCount(expectedData, file7, "HMS", "FTMS + p NSI Full ms", 16);
AddExpectedTupleAndCount(expectedData, file7, "CID-MSn", "ITMS + c NSI d Full ms2 [email protected]", 43);
AddExpectedTupleAndCount(expectedData, file7, "PQD-MSn", "ITMS + c NSI d Full ms2 [email protected]", 42);
const string file8 = "MZ20150721blank2";
AddExpectedTupleAndCount(expectedData, file8, "HMS", "FTMS + p NSI Full ms", 62);
AddExpectedTupleAndCount(expectedData, file8, "ETD-HMSn", "FTMS + p NSI d Full ms2 [email protected]", 186);
AddExpectedTupleAndCount(expectedData, file8, "ETD-HMSn", "FTMS + p NSI d Full ms2 [email protected]", 186);
const string file9 = "OG_CEPC_PU_22Oct13_Legolas_13-05-12";
AddExpectedTupleAndCount(expectedData, file9, "HMS", "FTMS + p NSI Full ms", 9);
AddExpectedTupleAndCount(expectedData, file9, "CID-MSn", "ITMS + c NSI d Full ms2 [email protected]", 46);
AddExpectedTupleAndCount(expectedData, file9, "ETD-MSn", "ITMS + c NSI d Full ms2 [email protected]", 1);
AddExpectedTupleAndCount(expectedData, file9, "ETD-MSn", "ITMS + c NSI d Full ms2 [email protected]", 1);
AddExpectedTupleAndCount(expectedData, file9, "ETD-MSn", "ITMS + c NSI d Full ms2 [email protected]", 8);
AddExpectedTupleAndCount(expectedData, file9, "ETD-MSn", "ITMS + c NSI d Full ms2 [email protected]", 8);
AddExpectedTupleAndCount(expectedData, file9, "ETD-MSn", "ITMS + c NSI d Full ms2 [email protected]", 56);
AddExpectedTupleAndCount(expectedData, file9, "SA_ETD-MSn", "ITMS + c NSI d sa Full ms2 [email protected]", 5);
AddExpectedTupleAndCount(expectedData, file9, "SA_ETD-MSn", "ITMS + c NSI d sa Full ms2 [email protected]", 1);
AddExpectedTupleAndCount(expectedData, file9, "SA_ETD-MSn", "ITMS + c NSI d sa Full ms2 [email protected]", 1);
AddExpectedTupleAndCount(expectedData, file9, "SA_ETD-MSn", "ITMS + c NSI d sa Full ms2 [email protected]", 14);
AddExpectedTupleAndCount(expectedData, file9, "SA_ETD-MSn", "ITMS + c NSI d sa Full ms2 [email protected]", 32);
AddExpectedTupleAndCount(expectedData, file9, "SA_ETD-MSn", "ITMS + c NSI d sa Full ms2 [email protected]", 260);
const string file10 = "blank_MeOH-3_18May16_Rainier_Thermo_10344958";
AddExpectedTupleAndCount(expectedData, file10, "HMS", "FTMS - p ESI Full ms", 190);
AddExpectedTupleAndCount(expectedData, file10, "CID-HMSn", "FTMS - c ESI d Full ms2 [email protected]", 207);
AddExpectedTupleAndCount(expectedData, file10, "CID-HMSn", "FTMS - c ESI d Full ms3 [email protected] [email protected]", 4);
const string file11 = "HCC-38_ETciD_EThcD_07Jan16_Pippin_15-08-53";
AddExpectedTupleAndCount(expectedData, file11, "HMS", "FTMS + p NSI Full ms", 20);
AddExpectedTupleAndCount(expectedData, file11, "CID-MSn", "ITMS + c NSI r d Full ms2 [email protected]", 231);
AddExpectedTupleAndCount(expectedData, file11, "ETciD-MSn", "ITMS + c NSI r d sa Full ms2 [email protected]@cid20.00", 46);
AddExpectedTupleAndCount(expectedData, file11, "ETciD-MSn", "ITMS + c NSI r d sa Full ms2 [email protected]@cid20.00", 4);
AddExpectedTupleAndCount(expectedData, file11, "ETD-MSn", "ITMS + c NSI r d Full ms2 [email protected]", 46);
AddExpectedTupleAndCount(expectedData, file11, "ETD-MSn", "ITMS + c NSI r d Full ms2 [email protected]", 4);
AddExpectedTupleAndCount(expectedData, file11, "EThcD-MSn", "ITMS + c NSI r d sa Full ms2 [email protected]@hcd20.00", 46);
AddExpectedTupleAndCount(expectedData, file11, "EThcD-MSn", "ITMS + c NSI r d sa Full ms2 [email protected]@hcd20.00", 4);
const string file12 = "MeOHBlank03POS_11May16_Legolas_HSS-T3_A925";
AddExpectedTupleAndCount(expectedData, file12, "HMS", "FTMS + p ESI Full ms", 8);
AddExpectedTupleAndCount(expectedData, file12, "CID-MSn", "ITMS + c ESI d Full ms2 [email protected]", 47);
AddExpectedTupleAndCount(expectedData, file12, "HCD-HMSn", "FTMS + c ESI d Full ms2 [email protected]", 38);
AddExpectedTupleAndCount(expectedData, file12, "HCD-HMSn", "FTMS + c ESI d Full ms2 [email protected]", 8);
AddExpectedTupleAndCount(expectedData, "IPA-blank-07_25Oct13_Gimli", "Zoom-MS", "ITMS + p NSI Z ms", 101);
var dataFile = GetRawDataFile(rawFileName);
using (var reader = new XRawFileIO(dataFile.FullName))
{
Console.WriteLine("Parsing scan headers for {0}", dataFile.Name);
var scanCount = reader.GetNumScans();
Console.WriteLine("Total scans: {0}", scanCount);
Assert.AreEqual(expectedTotalScanCount, scanCount, "Total scan count mismatch");
Console.WriteLine();
var scanCountMS1 = 0;
var scanCountMS2 = 0;
var scanTypeCountsActual = new Dictionary<Tuple<string, string>, int>();
for (var scanNumber = scanStart; scanNumber <= scanEnd; scanNumber++)
{
clsScanInfo scanInfo;
var success = reader.GetScanInfo(scanNumber, out scanInfo);
Assert.IsTrue(success, "GetScanInfo returned false for scan {0}", scanNumber);
var scanType = XRawFileIO.GetScanTypeNameFromFinniganScanFilterText(scanInfo.FilterText);
var genericScanFilter = XRawFileIO.MakeGenericFinniganScanFilter(scanInfo.FilterText);
var scanTypeKey = new Tuple<string, string>(scanType, genericScanFilter);
int observedScanCount;
if (scanTypeCountsActual.TryGetValue(scanTypeKey, out observedScanCount))
{
scanTypeCountsActual[scanTypeKey] = observedScanCount + 1;
}
else
{
scanTypeCountsActual.Add(scanTypeKey, 1);
}
if (scanInfo.MSLevel > 1)
scanCountMS2++;
else
scanCountMS1++;
}
Console.WriteLine("scanCountMS1={0}", scanCountMS1);
Console.WriteLine("scanCountMS2={0}", scanCountMS2);
Assert.AreEqual(expectedMS1, scanCountMS1, "MS1 scan count mismatch");
Assert.AreEqual(expectedMS2, scanCountMS2, "MS2 scan count mismatch");
Dictionary<Tuple<string, string>, int> expectedScanInfo;
if (!expectedData.TryGetValue(Path.GetFileNameWithoutExtension(dataFile.Name), out expectedScanInfo))
{
Assert.Fail("Dataset {0} not found in dictionary expectedData", dataFile.Name);
}
Console.WriteLine("{0,-5} {1,5} {2}", "Valid", "Count", "ScanType");
foreach (var scanType in (from item in scanTypeCountsActual orderby item.Key select item))
{
int expectedScanCount;
if (expectedScanInfo.TryGetValue(scanType.Key, out expectedScanCount))
{
var isValid = scanType.Value == expectedScanCount;
Console.WriteLine("{0,-5} {1,5} {2}", isValid, scanType.Value, scanType.Key);
Assert.AreEqual(expectedScanCount, scanType.Value, "Scan type count mismatch");
}
else
{
Console.WriteLine("Unexpected scan type found: {0}", scanType.Key);
Assert.Fail("Unexpected scan type found: {0}", scanType.Key);
}
}
}
}
public void TestCorruptDataHandling(
string rawFileName,
int scanStart,
int scanEnd,
int expectedMS1,
int expectedMS2,
int corruptScanStart,
int corruptScanEnd)
{
var dataFile = GetRawDataFile(rawFileName);
try
{
using (var reader = new XRawFileIO(dataFile.FullName))
{
var scanCount = reader.GetNumScans();
Console.WriteLine("Scan count for {0}: {1}", dataFile.Name, scanCount);
if (expectedMS1 + expectedMS2 == 0)
{
Assert.IsTrue(reader.FileInfo.CorruptFile, "CorruptFile is false while we expected it to be true");
Assert.IsTrue(scanCount == 0, "ScanCount is non-zero, while we expected it to be 0");
}
else
{
Assert.IsFalse(reader.FileInfo.CorruptFile, "CorruptFile is true while we expected it to be false");
Assert.IsTrue(scanCount > 0, "ScanCount is zero, while we expected it to be > 0");
}
var scanCountMS1 = 0;
var scanCountMS2 = 0;
for (var scanNumber = scanStart; scanNumber <= scanEnd; scanNumber++)
{
try
{
clsScanInfo scanInfo;
reader.GetScanInfo(scanNumber, out scanInfo);
if (reader.FileInfo.CorruptFile)
{
Assert.IsTrue(string.IsNullOrEmpty(scanInfo.FilterText), "FilterText is not empty but should be since corrupt file");
}
else
{
Assert.IsFalse(string.IsNullOrEmpty(scanInfo.FilterText), "FilterText is empty but should not be");
if (scanInfo.MSLevel > 1)
scanCountMS2++;
else
scanCountMS1++;
}
double[] mzList;
double[] intensityList;
// Note: this function call will fail randomly with file Corrupt_Scans6920-7021_AID_STM_013_101104_06_LTQ_16Nov04_Earth_0904-8.raw
// Furthermore, we are unable to catch the exception that occurs (or no exception is thrown) and adding
// [System.Runtime.ExceptionServices.HandleProcessCorruptedStateExceptions] to the function does not help
var dataPointCount = reader.GetScanData(scanNumber, out mzList, out intensityList);
if (reader.FileInfo.CorruptFile)
{
Assert.IsTrue(dataPointCount == 0, "GetScanData unexpectedly reported a non-zero data count for scan {0}", scanNumber);
Assert.IsTrue(mzList.Length == 0, "GetScanData unexpectedly returned m/z data for scan {0}", scanNumber);
Assert.IsTrue(intensityList.Length == 0, "GetScanData unexpectedly returned intensity data for scan {0}", scanNumber);
}
else
{
if (dataPointCount == 0)
{
Console.WriteLine("Corrupt scan encountered: {0}", scanNumber);
Assert.IsTrue(scanNumber >= corruptScanStart && scanNumber <= corruptScanEnd, "Unexpected corrupt scan found, scan {0}", scanNumber);
Assert.IsTrue(mzList.Length == 0, "GetScanData unexpectedly returned m/z data for scan {0}", scanNumber);
Assert.IsTrue(intensityList.Length == 0, "GetScanData unexpectedly returned intensity data for scan {0}", scanNumber);
}
else
{
Assert.IsTrue(dataPointCount > 0, "GetScanData reported a data point count of 0 for scan {0}", scanNumber);
Assert.IsTrue(mzList.Length > 0, "GetScanData unexpectedly returned no m/z data for scan {0}", scanNumber);
Assert.IsTrue(intensityList.Length > 0, "GetScanData unexpectedly returned no intensity data for scan {0}", scanNumber);
Assert.IsTrue(mzList.Length == intensityList.Length, "Array length mismatch for m/z and intensity data for scan {0}", scanNumber);
Assert.IsTrue(dataPointCount == mzList.Length, "Array length does not agree with dataPointCount for scan {0}", scanNumber);
}
}
}
catch (Exception ex)
{
Console.WriteLine("Exception reading scan {0}: {1}", scanNumber, ex.Message);
Assert.Fail("Exception reading scan {0}", scanNumber);
}
}
Console.WriteLine("scanCountMS1={0}", scanCountMS1);
Console.WriteLine("scanCountMS2={0}", scanCountMS2);
Assert.AreEqual(expectedMS1, scanCountMS1, "MS1 scan count mismatch");
Assert.AreEqual(expectedMS2, scanCountMS2, "MS2 scan count mismatch");
}
}
catch (Exception ex)
{
var msg = string.Format("Exception opening .raw file {0}:\n{1}", rawFileName, ex.Message);
Console.WriteLine(msg);
Assert.Fail(msg);
}
}
public void TestGetNumScans(string rawFileName, int expectedResult)
{
var dataFile = GetRawDataFile(rawFileName);
using (var reader = new XRawFileIO(dataFile.FullName))
{
var scanCount = reader.GetNumScans();
Console.WriteLine("Scan count for {0}: {1}", dataFile.Name, scanCount);
Assert.AreEqual(expectedResult, scanCount, "Scan count mismatch");
}
}
private static void TestReader(string rawFilePath, bool centroid = false, bool testSumming = false, int scanStart = 0, int scanEnd = 0)
{
try {
if (!File.Exists(rawFilePath)) {
Console.WriteLine("File not found, skipping: " + rawFilePath);
return;
}
using (var oReader = new XRawFileIO(rawFilePath))
{
foreach(var method in oReader.FileInfo.InstMethods) {
Console.WriteLine(method);
}
var iNumScans = oReader.GetNumScans();
var strCollisionEnergies = string.Empty;
ShowMethod(oReader);
var scanStep = 1;
if (scanStart < 1)
scanStart = 1;
if (scanEnd < 1) {
scanEnd = iNumScans;
scanStep = 21;
} else {
if (scanEnd < scanStart) {
scanEnd = scanStart;
}
}
for (var iScanNum = scanStart; iScanNum <= scanEnd; iScanNum += scanStep) {
clsScanInfo oScanInfo;
var bSuccess = oReader.GetScanInfo(iScanNum, out oScanInfo);
if (bSuccess) {
Console.Write("Scan " + iScanNum + " at " + oScanInfo.RetentionTime.ToString("0.00") + " minutes: " + oScanInfo.FilterText);
var lstCollisionEnergies = oReader.GetCollisionEnergy(iScanNum);
if (lstCollisionEnergies.Count == 0) {
strCollisionEnergies = string.Empty;
} else if (lstCollisionEnergies.Count >= 1) {
strCollisionEnergies = lstCollisionEnergies[0].ToString("0.0");
if (lstCollisionEnergies.Count > 1) {
for (var intIndex = 1; intIndex <= lstCollisionEnergies.Count - 1; intIndex++) {
strCollisionEnergies += ", " + lstCollisionEnergies[intIndex].ToString("0.0");
}
}
}
if (string.IsNullOrEmpty(strCollisionEnergies)) {
Console.WriteLine();
} else {
Console.WriteLine("; CE " + strCollisionEnergies);
}
string monoMZ;
string chargeState;
string isolationWidth;
if (oScanInfo.TryGetScanEvent("Monoisotopic M/Z:", out monoMZ, false)) {
Console.WriteLine("Monoisotopic M/Z: " + monoMZ);
}
if (oScanInfo.TryGetScanEvent("Charge State", out chargeState, true))
{
Console.WriteLine("Charge State: " + chargeState);
}
if (oScanInfo.TryGetScanEvent("MS2 Isolation Width", out isolationWidth, true))
{
Console.WriteLine("MS2 Isolation Width: " + isolationWidth);
}
if (iScanNum % 50 == 0 || scanEnd - scanStart <= 50) {
// Get the data for scan iScanNum
Console.WriteLine();
Console.WriteLine("Spectrum for scan " + iScanNum);
double[] dblMzList;
double[] dblIntensityList;
var intDataCount = oReader.GetScanData(iScanNum, out dblMzList, out dblIntensityList, 0, centroid);
var mzDisplayStepSize = 50;
if (centroid) {
mzDisplayStepSize = 1;
}
for (var iDataPoint = 0; iDataPoint <= dblMzList.Length - 1; iDataPoint += mzDisplayStepSize) {
Console.WriteLine(" " + dblMzList[iDataPoint].ToString("0.000") + " mz " + dblIntensityList[iDataPoint].ToString("0"));
}
Console.WriteLine();
const int scansToSum = 15;
if (iScanNum + scansToSum < iNumScans & testSumming) {
// Get the data for scan iScanNum through iScanNum + 15
double[,] dblMassIntensityPairs;
var dataCount = oReader.GetScanDataSumScans(iScanNum, iScanNum + scansToSum, out dblMassIntensityPairs, 0, centroid);
Console.WriteLine("Summed spectrum, scans " + iScanNum + " through " + (iScanNum + scansToSum));
for (var iDataPoint = 0; iDataPoint <= dblMassIntensityPairs.GetLength(1) - 1; iDataPoint += 50) {
Console.WriteLine(" " + dblMassIntensityPairs[0, iDataPoint].ToString("0.000") + " mz " + dblMassIntensityPairs[1, iDataPoint].ToString("0"));
}
Console.WriteLine();
}
if (oScanInfo.IsFTMS) {
udtFTLabelInfoType[] ftLabelData;
var dataCount = oReader.GetScanLabelData(iScanNum, out ftLabelData);
Console.WriteLine();
Console.WriteLine("{0,12}{1,12}{2,12}{3,12}{4,12}{5,12}", "Mass", "Intensity", "Resolution", "Baseline", "Noise", "Charge");
for (var iDataPoint = 0; iDataPoint <= dataCount - 1; iDataPoint += 50) {
Console.WriteLine("{0,12}{1,12}{2,12}{3,12}{4,12}{5,12}", ftLabelData[iDataPoint].Mass.ToString("0.000"), ftLabelData[iDataPoint].Intensity.ToString("0"), ftLabelData[iDataPoint].Resolution.ToString("0"), ftLabelData[iDataPoint].Baseline.ToString("0.0"), ftLabelData[iDataPoint].Noise.ToString("0"), ftLabelData[iDataPoint].Charge.ToString("0"));
}
udtMassPrecisionInfoType[] ftPrecisionData;
dataCount = oReader.GetScanPrecisionData(iScanNum, out ftPrecisionData);
Console.WriteLine();
Console.WriteLine("{0,12}{1,12}{2,12}{3,12}{4,12}", "Mass", "Intensity", "AccuracyMMU", "AccuracyPPM", "Resolution");
for (var iDataPoint = 0; iDataPoint <= dataCount - 1; iDataPoint += 50) {
Console.WriteLine("{0,12}{1,12}{2,12}{3,12}{4,12}", ftPrecisionData[iDataPoint].Mass.ToString("0.000"), ftPrecisionData[iDataPoint].Intensity.ToString("0"), ftPrecisionData[iDataPoint].AccuracyMMU.ToString("0.000"), ftPrecisionData[iDataPoint].AccuracyPPM.ToString("0.000"), ftPrecisionData[iDataPoint].Resolution.ToString("0"));
}
}
}
}
}
}
} catch (Exception ex) {
Console.WriteLine("Error in sub TestReader: " + ex.Message);
}
}
