public void Execute(Run run)
{
Check.Require(run != null, "'Run' has not be defined");
Check.Require(run.Filename != null &&
run.Filename.Length > 0, "MS data file ('run') has not been initialized");
//Check.Require(run.ScanSetCollection != null && run.ScanSetCollection.ScanSetList.Count > 0, "ChromAligner failed. ScanSets have not been defined.");
if (m_targetUMCFileStoringAlignmentInfo == null)
{
var baseFileName = Path.Combine(run.DataSetPath, run.DatasetName);
m_targetUMCFileStoringAlignmentInfo = baseFileName + "_UMCs.txt";
}
Check.Require(File.Exists(m_targetUMCFileStoringAlignmentInfo), "ChromAligner failed. The UMC file from which alignment data is extracted does not exist.");
var umcs = new UMCCollection();
var importer = new UMCFileImporter(m_targetUMCFileStoringAlignmentInfo, '\t');
umcs = importer.Import();
var scannetPairs = umcs.GetScanNETLookupTable();
run.NetAlignmentInfo = new NetAlignmentInfoBasic(run.MinLCScan, run.MaxLCScan);
run.NetAlignmentInfo.SetScanToNETAlignmentData(scannetPairs);
}
public void importUMCsWithO16O18PairedDataTest1()
{
UMCCollection umcs = new UMCCollection();
UMCFileImporter importer = new UMCFileImporter(umcO16O18TestFile1, '\t');
importer.Import(umcs);
Assert.AreEqual(23073, umcs.UMCList.Count);
}
public void importUMCsTest1()
{
UMCCollection umcs = new UMCCollection();
UMCFileImporter importer = new UMCFileImporter(umcTestfile1, '\t');
importer.Import(umcs);
Assert.AreEqual(15381, umcs.UMCList.Count);
}
public void filterUMCsByMassTagsTest2()
{
UMCCollection umcs = new UMCCollection();
UMCFileImporter importer = new UMCFileImporter(umcO16O18TestFile1, '\t');
importer.Import(umcs);
UMCCollection filteredUMCs = new UMCCollection();
filteredUMCs.UMCList = umcs.FilterUMCsByMassTagMatch(new List <int> {
22807265, 22580887, 20791942, 20791939, 20750857, 20908613, 20842966, 22598396, 174124103
});
Assert.AreEqual(8, filteredUMCs.UMCList.Count);
filteredUMCs.DisplayUMCExpressionInfo();
}
public void filterOutPairedUMCsTest1()
{
UMCCollection umcs = new UMCCollection();
UMCFileImporter importer = new UMCFileImporter(umcO16O18TestFile1, '\t');
importer.Import(umcs);
UMCCollection filteredUMCs = new UMCCollection();
filteredUMCs.UMCList = umcs.FilterOutPairedData();
Assert.AreEqual(1734, filteredUMCs.UMCList.Count);
filteredUMCs.DisplayUMCExpressionInfo();
}
public void umcTest2()
{
UMCCollection umcs = new UMCCollection();
UMCFileImporter importer = new UMCFileImporter(umcTestfile1, '\t');
importer.Import(umcs);
Stopwatch sw = new Stopwatch();
sw.Start();
Dictionary <int, double> lookupTable = umcs.GetScanNETLookupTable();
sw.Stop();
double netVal = lookupTable[6005];
netVal = lookupTable[6004];
Console.Write(sw.ElapsedMilliseconds);
Assert.AreEqual(0.3216, netVal);
}
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);
}
