public void LoadCalibrationDataTest1()
{
var testFile =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\AlignmentInfo\LNA_A_Stat_Sample_SC_23_LNA_ExpA_Expo_Stat_SeattleBioMed_15Feb13_Cougar_12-12-35_MassAndGANETErrors_BeforeRefinement.txt";
var loader = new ViperMassCalibrationLoader(testFile);
var calibrationData = loader.ImportMassCalibrationData();
Console.WriteLine(calibrationData.MassError);
}
public void LoadAndApplyMassAlignmentFromViperDataTest1()
{
var testFile = @"\\protoapps\UserData\Slysz\DeconTools_TestFiles\QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18.RAW";
var run = new RunFactory().CreateRun(testFile);
var viperMassAlignmentFile =
@"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\AlignmentInfo\QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18_MassAndGANETErrors_BeforeRefinement.txt";
var loader = new ViperMassCalibrationLoader(viperMassAlignmentFile);
/*
* From unit test: targetedWorkflow_alignUsingDataFromFiles
* TargetID = 24702
* ChargeState = 3
* theor monomass= 2920.5319802
* theor m/z= 974.517936556667
* obs monomass= 2920.49120230408
* obs m/z= 974.504343924692
* ppmError before= 13.9597398284934
* ppmError after= 10.8899784905986
* calibrated mass= 2920.50017566955
* calibrated mass2= 2920.50017566955
* Database NET= 0.4197696
* Result NET= 0.42916464805603
* Result NET Error= -0.00934833288192749
* NumChromPeaksWithinTol= 3
*
*
*/
var calibrationData = loader.ImportMassCalibrationData();
var massAlignmentInfo = new MassAlignmentInfoLcmsWarp();
massAlignmentInfo.SetMassAlignmentData(calibrationData);
run.MassAlignmentInfo = massAlignmentInfo;
var testMZ = 974.504343924692;
var alignedMZ = run.GetAlignedMZ(testMZ);
var ppmDiff = (testMZ - alignedMZ) / testMZ * 1e6;
Console.WriteLine("input m/z= " + testMZ);
Console.WriteLine("aligned m/z= " + alignedMZ);
Console.WriteLine("ppmDiff= " + ppmDiff);
Assert.AreEqual(-3.6, (decimal)Math.Round(ppmDiff, 1));
}
public static bool AlignRunUsingAlignmentInfoInFiles(Run run, string alignmentDataFolder = "")
{
bool alignmentSuccessful;
string basePath;
if (string.IsNullOrEmpty(alignmentDataFolder))
{
basePath = run.DataSetPath;
}
else
{
if (Directory.Exists(alignmentDataFolder))
{
basePath = alignmentDataFolder;
}
else
{
throw new DirectoryNotFoundException(
"Cannot align dataset. Source alignment folder does not exist. Alignment folder = " +
alignmentDataFolder);
}
}
var expectedMZAlignmentFile = Path.Combine(basePath, run.DatasetName + "_MZAlignment.txt");
var expectedNETAlignmentFile = Path.Combine(basePath, run.DatasetName + "_NETAlignment.txt");
//first will try to load the multiAlign alignment info
if (File.Exists(expectedMZAlignmentFile))
{
var importer = new MassAlignmentInfoFromTextImporter(expectedMZAlignmentFile);
var massAlignmentData = importer.Import();
var massAlignmentInfo = new MassAlignmentInfoLcmsWarp();
massAlignmentInfo.SetMassAlignmentData(massAlignmentData);
run.MassAlignmentInfo = massAlignmentInfo;
}
if (File.Exists(expectedNETAlignmentFile))
{
var netAlignmentInfoImporter = new NETAlignmentFromTextImporter(expectedNETAlignmentFile);
var scanNETList = netAlignmentInfoImporter.Import();
NetAlignmentInfo netAlignmentInfo = new NetAlignmentInfoBasic(run.MinLCScan, run.MaxLCScan);
netAlignmentInfo.SetScanToNETAlignmentData(scanNETList);
run.NetAlignmentInfo = netAlignmentInfo;
}
//if still not aligned, try to get the NET alignment from UMCs file. (this is the older way to do it)
if (run.NETIsAligned)
{
alignmentSuccessful = true;
}
else
{
var alignmentDirInfo = new DirectoryInfo(basePath);
var umcFileInfo = alignmentDirInfo.GetFiles("*_umcs.txt");
var umcFileCount = umcFileInfo.Count();
if (umcFileCount == 1)
{
var targetUmcFileName = umcFileInfo.First().FullName;
var importer = new UMCFileImporter(targetUmcFileName, '\t');
var umcs = importer.Import();
var scannetPairs = umcs.GetScanNETLookupTable();
NetAlignmentInfo netAlignmentInfo = new NetAlignmentInfoBasic(run.MinLCScan, run.MaxLCScan);
netAlignmentInfo.SetScanToNETAlignmentData(scannetPairs);
run.NetAlignmentInfo = netAlignmentInfo;
Console.WriteLine(run.DatasetName + " aligned.");
alignmentSuccessful = true;
}
else if (umcFileCount > 1)
{
var expectedUMCName = Path.Combine(basePath, run.DatasetName + "_UMCs.txt");
if (File.Exists(expectedUMCName))
{
var importer = new UMCFileImporter(expectedUMCName, '\t');
var umcs = importer.Import();
var scannetPairs = umcs.GetScanNETLookupTable();
NetAlignmentInfo netAlignmentInfo = new NetAlignmentInfoBasic(run.MinLCScan, run.MaxLCScan);
netAlignmentInfo.SetScanToNETAlignmentData(scannetPairs);
run.NetAlignmentInfo = netAlignmentInfo;
Console.WriteLine(run.DatasetName + " NET aligned using UMC file: " + expectedUMCName);
alignmentSuccessful = true;
}
else
{
throw new FileNotFoundException("Trying to align dataset: " + run.DatasetName +
" but UMC file not found.");
}
}
else
{
Console.WriteLine(run.DatasetName + " is NOT NET aligned.");
alignmentSuccessful = false;
}
}
//mass is still not aligned... use data in viper output file: _MassAndGANETErrors_BeforeRefinement.txt
if (run.MassIsAligned == false)
{
var expectedViperMassAlignmentFile = Path.Combine(basePath, run.DatasetName + "_MassAndGANETErrors_BeforeRefinement.txt");
if (File.Exists(expectedViperMassAlignmentFile))
{
var importer = new ViperMassCalibrationLoader(expectedViperMassAlignmentFile);
var viperCalibrationData = importer.ImportMassCalibrationData();
var massAlignmentInfo = new MassAlignmentInfoLcmsWarp();
massAlignmentInfo.SetMassAlignmentData(viperCalibrationData);
run.MassAlignmentInfo = massAlignmentInfo;
Console.WriteLine(run.DatasetName + "- mass aligned using file: " + expectedViperMassAlignmentFile);
alignmentSuccessful = true;
}
else
{
Console.WriteLine(run.DatasetName + " is NOT mass aligned");
}
}
return(alignmentSuccessful);
}
