public void RunTraining(string rawDirectoryPath, string targetFilePath, string decoyFilePath, double hcdError = 30, double cidError = 500)
{
// Read target file
var targetReader = new LipidMapsDbReader <Lipid>();
var targets = targetReader.ReadFile(new FileInfo(targetFilePath));
// Read decoy file
var decoyReader = new LipidMapsDbReader <Lipid>();
var decoys = decoyReader.ReadFile(new FileInfo(decoyFilePath));
var files = Directory.GetFiles(rawDirectoryPath);
foreach (var rawFilePath in files.Where(file => file.EndsWith(".raw")))
{
// create output paths
var rawFileName = Path.GetFileName(rawFilePath);
var datasetPath = Path.GetDirectoryName(rawFilePath);
var datasetName = Path.GetFileNameWithoutExtension(rawFilePath);
var targetResultsPath = Path.Combine(datasetPath, string.Format("{0}_target.tsv", datasetName));
var decoyResultsPath = Path.Combine(datasetPath, string.Format("{0}_decoy.tsv", datasetName));
// Run liquid global workflow
var globalWorkflow = new GlobalWorkflow(rawFilePath);
var targetResults = globalWorkflow.RunGlobalWorkflow(targets, hcdError, cidError);
var decoyResults = globalWorkflow.RunGlobalWorkflow(decoys, hcdError, cidError);
// Output results
LipidGroupSearchResultWriter.OutputResults(targetResults, targetResultsPath, rawFileName);
LipidGroupSearchResultWriter.OutputResults(decoyResults, decoyResultsPath, rawFileName);
// Assure that the source data file is closed
globalWorkflow.LcMsRun.Close();
}
}
/// <summary>
/// Main functionality for running the LIQUID workflow and outputting the results
/// </summary>
/// <param name="targetsFilePath"></param>
/// <param name="outputFileName"></param>
/// <param name="datasetNamesList"></param>
private void RunWorkflowAndOutput(string targetsFilePath, string outputFileName, List <string> datasetNamesList)
{
var targetsFileInfo = new FileInfo(targetsFilePath);
var lipidReader = new LipidMapsDbReader <Lipid>();
var lipidList = lipidReader.ReadFile(targetsFileInfo);
var headerWritten = false;
foreach (var datasetName in datasetNamesList)
{
var rawFileName = datasetName + ".raw";
var rawFilePath = Path.Combine(@"D:\Data\Liquid\Original", rawFileName);
Console.WriteLine(DateTime.Now + ": Processing " + datasetName);
if (File.Exists(rawFilePath))
{
Console.WriteLine(DateTime.Now + ": Dataset already exists");
}
else
{
Console.WriteLine(DateTime.Now + ": Dataset does not exist locally, so we will go get it");
// Lookup in DMS via Mage
var dmsFolder = DmsDatasetFinder.FindLocationOfDataset(datasetName);
var dmsDirectoryInfo = new DirectoryInfo(dmsFolder);
var fullPathToDmsFile = Path.Combine(dmsDirectoryInfo.FullName, rawFileName);
// Copy Locally
// TODO: Handle files that are on MyEMSL
Console.WriteLine(DateTime.Now + ": Copying dataset from " + dmsDirectoryInfo.FullName);
File.Copy(fullPathToDmsFile, rawFilePath);
Console.WriteLine(DateTime.Now + ": Copy complete");
}
// Setup workflow
var globalWorkflow = new GlobalWorkflow(rawFilePath);
// Run workflow
var lipidGroupSearchResults = globalWorkflow.RunGlobalWorkflow(lipidList, 30, 500);
if (!headerWritten)
{
LipidGroupSearchResultWriter.OutputResults(lipidGroupSearchResults, outputFileName, rawFileName, null, true, true);
headerWritten = true;
}
else
{
LipidGroupSearchResultWriter.OutputResults(lipidGroupSearchResults, outputFileName, rawFileName, null, true, false);
}
// Assure that the source data file is closed
globalWorkflow.LcMsRun.Close();
}
}
public void TestMassCalibration()
{
var rawFileLocation = @"../../../testFiles/synaptosome_lipid_rafts_lipidomics_synlr_1_bottom__NEG_Polaroid_17Mar14_14-02-04.raw";
var globalWorkflow = new GlobalWorkflow(rawFileLocation);
var fileLocation = @"../../../testFiles/Global_LipidMaps_NEG_3.txt";
var fileInfo = new FileInfo(fileLocation);
var lipidReader = new LipidMapsDbReader <Lipid>();
var lipidList = lipidReader.ReadFile(fileInfo);
var massCalibrationResults = globalWorkflow.RunMassCalibration(lipidList, 50);
Console.WriteLine(massCalibrationResults.PpmError);
Console.WriteLine(massCalibrationResults.ErrorWidth);
}
public void TestGlobalWorkflowNegative()
{
var rawFileLocation = @"../../../testFiles/Dey_Lipids_Top_2_3_rerun_Neg_05Jul13_Gimli_12-07-05.raw";
var globalWorkflow = new GlobalWorkflow(rawFileLocation);
var fileLocation = @"../../../testFiles/Global_LipidMaps_Neg.txt";
var fileInfo = new FileInfo(fileLocation);
var lipidReader = new LipidMapsDbReader <Lipid>();
var lipidList = lipidReader.ReadFile(fileInfo);
globalWorkflow.RunGlobalWorkflow(lipidList, 30, 500);
// Assure that the source data file is closed
globalWorkflow.LcMsRun.Close();
}
public void TestGlobalWorkflowPositive()
{
var rawFileLocation = @"../../../testFiles/Dey_lipids_Bottom_2_1_pos_dil_Gimli_RZ-12-07-05.raw";
var globalWorkflow = new GlobalWorkflow(rawFileLocation);
var fileLocation = @"../../../testFiles/Global_LipidMaps_Pos.txt";
var fileInfo = new FileInfo(fileLocation);
var lipidReader = new LipidMapsDbReader <Lipid>();
var lipidList = lipidReader.ReadFile(fileInfo);
var lipidGroupSearchResults = globalWorkflow.RunGlobalWorkflow(lipidList, 30, 500);
var filteredLipidGroupSearchResults = new List <LipidGroupSearchResult>();
// Group results of same scan together
var resultsGroupedByScan = lipidGroupSearchResults.GroupBy(x => x.SpectrumSearchResult.HcdSpectrum.ScanNum);
// Grab the result(s) with the best score
foreach (var group in resultsGroupedByScan)
{
var groupOrdered = group.OrderByDescending(x => x.SpectrumSearchResult.Score).ToList();
for (var i = 0; i < 1 && i < groupOrdered.Count; i++)
{
var resultToAdd = groupOrdered[i];
if (resultToAdd.LipidTarget.LipidClass == LipidClass.PC && resultToAdd.LipidTarget.AcylChainList.Count(x => x.NumCarbons > 0) == 2 && resultToAdd.LipidTarget.AcylChainList.Count(x => x.AcylChainType == AcylChainType.Standard) == 2)
{
filteredLipidGroupSearchResults.Add(resultToAdd);
}
}
}
if (File.Exists("fragmentOutput.csv"))
{
File.Delete("fragmentOutput.csv");
}
TextWriter textWriter = new StreamWriter("fragmentOutput.csv");
LipidGroupSearchResultWriter.AddHeaderForScoring(filteredLipidGroupSearchResults[0], textWriter);
LipidGroupSearchResultWriter.WriteToCsvForScoring(filteredLipidGroupSearchResults, textWriter, "Dey_lipids_Bottom_2_1_pos_dil_Gimli_RZ-12-07-05");
// Assure that the source data file is closed
globalWorkflow.LcMsRun.Close();
textWriter.Close();
}
public void OnProcessAllTarget(double hcdError, double cidError, FragmentationMode fragmentationMode, int numResultsPerScanToInclude)
{
IProgress <int> progress = new Progress <int>(ReportGlobalWorkflowProgress);
// Make sure to only look at targets that match the fragmentation mode
var targetsToProcess = LipidTargetList.Where(x => x.LipidTarget.FragmentationMode == fragmentationMode);
// Run global analysis
LipidGroupSearchResultList = new List <LipidGroupSearchResult>();
IEnumerable <IGrouping <double, LipidGroupSearchResult> > resultsGrouped;
List <LipidGroupSearchResult> lipidGroupSearchResultList;
if (AverageSpec)
{
lipidGroupSearchResultList = GlobalWorkflow.RunGlobalWorkflowAvgSpec(targetsToProcess, LcMsRun, hcdError, cidError, ScoreModel, progress);
resultsGrouped = lipidGroupSearchResultList.GroupBy(x => x.SpectrumSearchResult.HcdSpectrum?.IsolationWindow.IsolationWindowTargetMz ?? x.SpectrumSearchResult.CidSpectrum.IsolationWindow.IsolationWindowTargetMz);
}
else
{
lipidGroupSearchResultList = GlobalWorkflow.RunGlobalWorkflow(targetsToProcess, LcMsRun, hcdError, cidError, ScoreModel, progress);
resultsGrouped = lipidGroupSearchResultList.GroupBy(x => x.SpectrumSearchResult.HcdSpectrum?.ScanNum ?? (double)x.SpectrumSearchResult.CidSpectrum.ScanNum);
}
// Group results of same scan together
// Grab the result(s) with the best score
foreach (var group in resultsGrouped)
{
var groupOrdered = group.OrderByDescending(x => x.Score).ToList();
for (var i = 0; i < numResultsPerScanToInclude && i < groupOrdered.Count; i++)
{
var resultToAdd = groupOrdered[i];
LipidGroupSearchResultList.Add(resultToAdd);
}
}
OnPropertyChanged("LipidGroupSearchResultList");
progress.Report(0);
}
public void TestCreateScoringOutput()
{
const string positiveTargetsFileLocation = @"../../../testFiles/Global_LipidMaps_POS_v3.txt";
var positiveTargetsFileInfo = new FileInfo(positiveTargetsFileLocation);
var lipidReader = new LipidMapsDbReader <Lipid>();
var lipidList = lipidReader.ReadFile(positiveTargetsFileInfo);
if (File.Exists("fragmentOutput.csv"))
{
File.Delete("fragmentOutput.csv");
}
TextWriter textWriter = new StreamWriter("fragmentOutput.csv");
var datasetNames = new List <string>
{
//datasetNames.Add("Dey_lipids_Top_1_1_pos_Gimli_RZ-12-07-05");
//datasetNames.Add("Dey_lipids_Top_1_2_pos_Gimli_RZ-12-07-05");
//datasetNames.Add("Dey_lipids_Top_1_3_pos_Gimli_RZ-12-07-05");
//datasetNames.Add("Dey_lipids_Bottom_1_1_pos_Gimli_RZ-12-07-05");
//datasetNames.Add("Dey_lipids_Bottom_1_2_pos_Gimli_RZ-12-07-05");
//datasetNames.Add("Dey_lipids_Bottom_1_3_pos_Gimli_RZ-12-07-05");
//datasetNames.Add("Dey_lipids_Top_2_1_pos_dil_Gimli_RZ-12-07-05");
//datasetNames.Add("Dey_lipids_Top_2_2_pos_Gimli_RZ-12-07-05");
//datasetNames.Add("Dey_lipids_Top_2_3_pos_Gimli_RZ-12-07-05");
//datasetNames.Add("Dey_lipids_Bottom_2_1_pos_dil_Gimli_RZ-12-07-05");
//datasetNames.Add("Dey_lipids_Bottom_2_2_pos_Gimli_RZ-12-07-05");
//datasetNames.Add("Dey_lipids_Bottom_2_3_pos_Gimli_RZ-12-07-05");
"XGA121_lipid_Calu3_1",
"XGA121_lipid_Calu3_2",
"XGA121_lipid_Calu3_3",
"XGA121_lipid_Skin_1",
"XGA121_lipid_Skin_2",
"XGA121_lipid_Skin_3",
"XGA121_lipid_plasma_1",
"XGA121_lipid_plasma_2",
"XGA121_lipid_plasma_3",
"Vero_01_CM_0d_4_Lipid_POS_Gimli_15Jan14_13-07-01",
"Vero_01_CM_0d_2_Lipid_POS_Gimli_15Jan14_13-07-01",
"Vero_01_CM_0d_3_Lipid_POS_Gimli_15Jan14_13-07-01",
"Vero_01_CM_0d_1_Lipid_POS_Gimli_15Jan14_13-07-01",
"Vero_01_MTBE_0d_4_Lipid_POS_Gimli_15Jan14_13-07-04",
"Vero_01_MTBE_0d_3_Lipid_POS_Gimli_15Jan14_13-07-01",
"Vero_01_MTBE_0d_2_Lipid_POS_Gimli_15Jan14_13-07-01",
"Vero_01_MTBE_0d_1_Lipid_POS_Gimli_15Jan14_13-07-01",
"LCA_Atta_B_gar2_b_Reruns_31May13_Gimli_12-07-01",
"LCA_Atta_T_gar1_a1_Reruns_31May13_Gimli_12-07-01",
"LCA_Atta_M_gar3_a_Reruns_31May13_Gimli_12-07-01",
"Da_12_1_POS_3K_Gimli_9Oct13_13-07-01",
"Da_24_1_POS_3K_Gimli_9Oct13_13-07-01",
//datasetNames.Add("Lipid_QC_1_14Jan_POS_Gimli_14Jan14_13-07-01");
//datasetNames.Add("Lipid_QC_1_14Jan_POS_Gimli_17JAN_13-07-01");
"Daphnia_gut_TLE_POS_Gimli_21Jan14_13-07-01",
"OMICS_HH_CDT_Lip_108_01_POS_Gimli_24Jan14_13-07-01",
"OMICS_HH_CDT_Lip_108_02_POS_Gimli_24Jan14_13-07-01",
"OMICS_HH_CDT_Lip_108_03_POS_Gimli_24Jan14_13-07-01",
"Oscar_28days_TLE__POS_04Feb14_13-07-01",
"Oscar_21days_TLE__POS_04Feb14_13-07-01",
"Oscar_21days_dark_TLE__POS_04Feb14_13-07-01",
"Oscar_14day_TLE__POS_04Feb14_13-07-01"
};
for (var datasetIndex = 0; datasetIndex < datasetNames.Count; datasetIndex++)
{
var datasetName = datasetNames[datasetIndex];
var rawFileName = datasetName + ".raw";
Console.WriteLine(DateTime.Now + ": Processing " + datasetName);
if (File.Exists(rawFileName))
{
Console.WriteLine(DateTime.Now + ": Dataset already exists");
}
else
{
Console.WriteLine(DateTime.Now + ": Dataset does not exist locally, so we will go get it");
// Lookup in DMS via Mage
var dmsFolder = DmsDatasetFinder.FindLocationOfDataset(datasetName);
var dmsDirectoryInfo = new DirectoryInfo(dmsFolder);
var fullPathToDmsFile = Path.Combine(dmsDirectoryInfo.FullName, rawFileName);
// Copy Locally
// TODO: Handle files that are on MyEMSL
Console.WriteLine(DateTime.Now + ": Copying dataset from " + dmsDirectoryInfo.FullName);
File.Copy(fullPathToDmsFile, rawFileName);
Console.WriteLine(DateTime.Now + ": Copy complete");
}
// Setup workflow
var globalWorkflow = new GlobalWorkflow(rawFileName);
// Run workflow
var lipidGroupSearchResults = globalWorkflow.RunGlobalWorkflow(lipidList, 30, 500);
var filteredLipidGroupSearchResults = new List <LipidGroupSearchResult>();
// Group results of same scan together
var resultsGroupedByScan = lipidGroupSearchResults.GroupBy(x => x.SpectrumSearchResult.HcdSpectrum.ScanNum);
// Grab the result(s) with the best score
foreach (var group in resultsGroupedByScan)
{
var groupOrdered = group.OrderByDescending(x => x.SpectrumSearchResult.Score).ToList();
for (var i = 0; i < 1 && i < groupOrdered.Count; i++)
{
var resultToAdd = groupOrdered[i];
if (resultToAdd.LipidTarget.LipidClass == LipidClass.PC &&
resultToAdd.LipidTarget.AcylChainList.Count(x => x.NumCarbons > 0) == 2 &&
resultToAdd.LipidTarget.AcylChainList.Count(x => x.AcylChainType == AcylChainType.Standard) == 2)
{
filteredLipidGroupSearchResults.Add(resultToAdd);
}
}
}
// Output results
if (datasetIndex == 0)
{
LipidGroupSearchResultWriter.AddHeaderForScoring(filteredLipidGroupSearchResults[0], textWriter);
}
LipidGroupSearchResultWriter.WriteToCsvForScoring(filteredLipidGroupSearchResults, textWriter, datasetName);
// Assure that the source data file is closed
globalWorkflow.LcMsRun.Close();
}
textWriter.Close();
}
public void RunTrainingOnFileList(
string fileListPath,
string posTargetFilePath,
string posDecoyFilePath,
string negTargetFilePath,
string negDecoyFilePath,
double hcdError = 30,
double cidError = 500)
{
// Read positive target file
var posTargetReader = new LipidMapsDbReader <Lipid>();
var posTargets = posTargetReader.ReadFile(new FileInfo(posTargetFilePath));
// Read positive decoy file
var posDecoyReader = new LipidMapsDbReader <Lipid>();
var posDecoys = posDecoyReader.ReadFile(new FileInfo(posDecoyFilePath));
// Read positive target file
var negTargetReader = new LipidMapsDbReader <Lipid>();
var negTargets = negTargetReader.ReadFile(new FileInfo(negTargetFilePath));
// Read positive decoy file
var negDecoyReader = new LipidMapsDbReader <Lipid>();
var negDecoys = negDecoyReader.ReadFile(new FileInfo(negDecoyFilePath));
var outputDirectory = Path.GetDirectoryName(fileListPath);
var errorFile = Path.Combine(outputDirectory, "failedDatasets.txt");
foreach (var datasetName in File.ReadLines(fileListPath))
{
if (datasetName.StartsWith("//"))
{
continue;
}
try
{
// create output paths
var rawFilePath = GetRawFilePath(outputDirectory, datasetName);
var rawFileName = Path.GetFileName(rawFilePath);
var targetResultsPath = Path.Combine(outputDirectory, string.Format("{0}_target.tsv", datasetName));
var decoyResultsPath = Path.Combine(outputDirectory, string.Format("{0}_decoy.tsv", datasetName));
IEnumerable <Lipid> targets;
IEnumerable <Lipid> decoys;
// Select targets and decoys
var lowerCaseName = datasetName.ToLower();
if (lowerCaseName.Contains("pos"))
{
targets = posTargets;
decoys = posDecoys;
}
else
{
targets = negTargets;
decoys = negDecoys;
}
// Run liquid global workflow
var globalWorkflow = new GlobalWorkflow(rawFilePath);
var targetResults = GetBestResultPerSpectrum(globalWorkflow.RunGlobalWorkflow(targets, hcdError, cidError));
var decoyResults = GetBestResultPerSpectrum(globalWorkflow.RunGlobalWorkflow(decoys, hcdError, cidError));
// Output results
LipidGroupSearchResultWriter.OutputResults(targetResults, targetResultsPath, rawFileName);
LipidGroupSearchResultWriter.OutputResults(decoyResults, decoyResultsPath, rawFileName);
// Assure that the source data file is closed
globalWorkflow.LcMsRun.Close();
}
catch (Exception)
{
Console.WriteLine("ERROR: Could not process dataset {0}.", datasetName);
using (var streamWriter = new StreamWriter(errorFile, true))
{
streamWriter.WriteLine(datasetName);
}
}
}
}
public ScoreModel CreateScoreModel(double hcdError, double cidError)
{
const int numTopHitsToConsider = 1;
var observationDictionary = new Dictionary <SpecificFragment, List <double> >();
foreach (var datasetLocation in DatasetLocations)
{
// Setup workflow
var globalWorkflow = new GlobalWorkflow(datasetLocation);
// Run workflow
var lipidGroupSearchResults = globalWorkflow.RunGlobalWorkflow(LipidList, 30, 500);
// Group results of same scan together
var resultsGroupedByScan = lipidGroupSearchResults.GroupBy(x => x.SpectrumSearchResult.HcdSpectrum.ScanNum);
// Grab the result(s) with the best score
foreach (var group in resultsGroupedByScan)
{
var groupOrdered = group.OrderByDescending(x => x.SpectrumSearchResult.Score).ToList();
for (var i = 0; i < numTopHitsToConsider && i < groupOrdered.Count; i++)
{
var resultToAdd = groupOrdered[i];
var lipidTarget = resultToAdd.LipidTarget;
var lipidClass = lipidTarget.LipidClass;
var lipidType = lipidTarget.LipidType;
var fragmentationMode = lipidTarget.FragmentationMode;
var spectrumSearchResult = resultToAdd.SpectrumSearchResult;
var cidResultList = spectrumSearchResult.CidSearchResultList;
var hcdResultList = spectrumSearchResult.HcdSearchResultList;
var cidMaxValue = spectrumSearchResult.CidSpectrum.Peaks.Any() ? spectrumSearchResult.CidSpectrum.Peaks.Max(x => x.Intensity) : 1;
var hcdMaxValue = spectrumSearchResult.HcdSpectrum.Peaks.Any() ? spectrumSearchResult.HcdSpectrum.Peaks.Max(x => x.Intensity) : 1;
// CID Results
foreach (var cidResult in cidResultList)
{
var fragment = cidResult.TheoreticalPeak.Description;
double intensity = 0;
if (cidResult.ObservedPeak != null)
{
intensity = Math.Log10(cidResult.ObservedPeak.Intensity) / Math.Log10(cidMaxValue);
}
var specificFragment = new SpecificFragment(lipidClass, lipidType, fragment, fragmentationMode, FragmentationType.CID);
// Either update the observation list or create a new one
List <double> observationList;
if (observationDictionary.TryGetValue(specificFragment, out observationList))
{
observationList.Add(intensity);
}
else
{
observationList = new List <double> {
intensity
};
observationDictionary.Add(specificFragment, observationList);
}
}
// HCD Results
foreach (var hcdResult in hcdResultList)
{
var fragment = hcdResult.TheoreticalPeak.Description;
double intensity = 0;
if (hcdResult.ObservedPeak != null)
{
intensity = Math.Log10(hcdResult.ObservedPeak.Intensity) / Math.Log10(hcdMaxValue);
}
var specificFragment = new SpecificFragment(lipidClass, lipidType, fragment, fragmentationMode, FragmentationType.HCD);
// Either update the observation list or create a new one
List <double> observationList;
if (observationDictionary.TryGetValue(specificFragment, out observationList))
{
observationList.Add(intensity);
}
else
{
observationList = new List <double> {
intensity
};
observationDictionary.Add(specificFragment, observationList);
}
}
}
}
// Assure that the source data file is closed
globalWorkflow.LcMsRun.Close();
}
var liquidScoreModelUnitList = PartitionIntoModelUnits(observationDictionary);
var liquidScoreModel = new ScoreModel(liquidScoreModelUnitList);
return(liquidScoreModel);
}
