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();
}
}
public void TestReadLipidMaps()
{
var fileLocation = @"../../../testFiles/Global_LipidMaps_Pos.txt";
var fileInfo = new FileInfo(fileLocation);
var lipidReader = new LipidMapsDbReader <Lipid>();
var lipidList = lipidReader.ReadFile(fileInfo);
Console.WriteLine(lipidList.Count);
}
/// <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 TestReadLipidMapsNegativeAndCreateTargets()
{
var fileLocation = @"../../../testFiles/Global_LipidMaps_Neg.txt";
var fileInfo = new FileInfo(fileLocation);
var lipidReader = new LipidMapsDbReader <Lipid>();
var lipidList = lipidReader.ReadFile(fileInfo);
Console.WriteLine(lipidList.Count);
foreach (var lipid in lipidList)
{
var lipidTarget = lipid.LipidTarget;
}
}
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 LoadMoreLipidTargets(string fileLocation)
{
IProgress <int> progress = new Progress <int>(ReportLipidTargetLoadProgress);
var fileInfo = new FileInfo(fileLocation);
var lipidReader = new LipidMapsDbReader <Lipid>();
var lipidList = lipidReader.ReadFile(fileInfo, progress);
foreach (var lipid in lipidList)
{
LipidTargetList.Add(lipid);
}
OnPropertyChanged("LipidTargetList");
//// Reset and populate the list of lipid classes
//this.LipidClassList = new List<LipidClass>();
//var groupByLipidClass = this.LipidTargetList.GroupBy(x => x.LipidTarget.LipidClass);
//foreach (LipidClass lipidClass in groupByLipidClass.Select(@group => @group.Key))
//{
// this.LipidClassList.Add(lipidClass);
//}
//if (this.LipidClassList.Count > 0)
//{
// LipidClass lipidClass = this.LipidClassList[0];
// this.CurrentLipidClass = lipidClass;
// this.CurrentLipidTargetList = this.LipidTargetList.Where(x => x.LipidClass == lipidClass).ToList();
// OnPropertyChanged("CurrentLipidClass");
//}
//OnPropertyChanged("LipidClassList");
//OnPropertyChanged("CurrentLipidTargetList");
// Reset the progress bar back to 0
progress.Report(0);
}
public void CreateNewScoringModelNegative()
{
var datasetNames = new List <string>
{
"FECB_ATCC_29133_616_Dark_Lipid_NEG_150mm_20Mar15_Polaroid_14-12-16",
"FECB_ATCC_29133_616_Light_Lipid_NEG_150mm_20Mar15_Polaroid_14-12-16",
"FECB_ATCC_29133_819_Dark_Lipid_NEG_150mm_20Mar15_Polaroid_14-12-16",
"FECB_ATCC_29133_819_Light_Lipid_NEG_150mm_20Mar15_Polaroid_14-12-16",
"FSFA_Isolate_HL53_0700_lipid_NEG_150mm_24Aug15_Polaroid_HSST3-02",
"FSFA_Isolate_HL53_1000_lipid_NEG_150mm_24Aug15_Polaroid_HSST3-02",
"FSFA_Isolate_HL91_0050_1_lipid_NEG_150mm_24Aug15_Polaroid_HSST3-02",
"FSFA_Isolate_HL91_0050_2_lipid_NEG_150mm_24Aug15_Polaroid_HSST3-02",
"FSFA_Isolate_HL91_0050_3_lipid_NEG_150mm_24Aug15_Polaroid_HSST3-02",
"FSFA_Isolate_HL91_0200_1_lipid_NEG_150mm_24Aug15_Polaroid_HSST3-02",
"FSFA_Isolate_HL91_0200_2_lipid_NEG_150mm_24Aug15_Polaroid_HSST3-02",
"FSFA_Isolate_HL91_0200_3_lipid_NEG_150mm_24Aug15_Polaroid_HSST3-02",
"FSFA_Isolate_HL91_0400_1_lipid_NEG_150mm_24Aug15_Polaroid_HSST3-02",
"FSFA_Isolate_HL91_0400_2_lipid_NEG_150mm_24Aug15_Polaroid_HSST3-02",
"FSFA_Isolate_HL91_0400_3_lipid_NEG_150mm_24Aug15_Polaroid_HSST3-02",
"FSFA_Isolate_HL91_1000_1_lipid_NEG_150mm_24Aug15_Polaroid_HSST3-02",
"FSFA_Isolate_HL91_1000_2_lipid_NEG_150mm_24Aug15_Polaroid_HSST3-02",
"FSFA_Isolate_HL91_1000_3_lipid_NEG_150mm_24Aug15_Polaroid_HSST3-02",
"Kleb_11pt5Hr_Lipid_Neg_150mm_4Sept15_Polaroid_HSST3-02",
"Kleb_12Hr_Lipid_Neg_150mm_4Sept15_Polaroid_HSST3-02",
"Kleb_13Hr_Lipid_Neg_150mm_4Sept15_Polaroid_HSST3-02",
"Kleb_14Hr_Lipid_Neg_150mm_4Sept15_Polaroid_HSST3-02",
"Kleb_15Hr_Lipid_Neg_150mm_4Sept15_Polaroid_HSST3-02",
"Kleb_16Hr_Lipid_Neg_150mm_4Sept15_Polaroid_HSST3-02",
"Kleb_17Hr_Lipid_Neg_150mm_4Sept15_Polaroid_HSST3-02",
"Kleb_18Hr_Lipid_Neg_150mm_4Sept15_Polaroid_HSST3-02",
"Kleb_19Hr_Lipid_Neg_150mm_4Sept15_Polaroid_HSST3-02",
"Kleb_20Hr_Lipid_Neg_150mm_4Sept15_Polaroid_HSST3-02",
"LCA_Ariadna_B_lipid_NEG_150mm_2Apr15_Polaroid_14-12-16",
"LCA_Ariadna_M_lipid_NEG_150mm_2Apr15_Polaroid_14-12-16",
"LCA_Ariadna_T_lipid_NEG_150mm_2Apr15_Polaroid_14-12-16",
"LCA_Ariadna_T_lipid_NEG_150mm_31Mar15_Polaroid_14-12-16",
"LCA_Dora_B_lipid_NEG_150mm_2Apr15_Polaroid_14-12-16",
"LCA_Dora_B_lipid_NEG_150mm_31Mar15_Polaroid_14-12-16",
"LCA_Dora_M_lipid_NEG_150mm_2Apr15_Polaroid_14-12-16",
"LCA_Dora_M_lipid_NEG_150mm_31Mar15_Polaroid_14-12-16",
"LCA_Dora_T_lipid_NEG_150mm_2Apr15_Polaroid_14-12-16",
"LCA_Dora_T_lipid_NEG_150mm_31Mar15_Polaroid_14-12-16",
"LCA_Emma_B_lipid_NEG_150mm_2Apr15_Polaroid_14-12-16",
"LCA_Emma_B_lipid_NEG_150mm_31Mar15_Polaroid_14-12-16",
"LCA_Emma_M_lipid_NEG_150mm_2Apr15_Polaroid_14-12-16",
"LCA_Emma_T_lipid_NEG_150mm_2Apr15_Polaroid_14-12-16",
"LCA_leaf_lipid_NEG_150mm_2Apr15_Polaroid_14-12-16",
"MinT_Kans_Gly_A_Neg_rep1_10__lip_NEG_150mm_27May15_Polaroid_HSST3-02",
"MinT_Kans_Gly_A_Neg_rep2_11__lip_NEG_150mm_27May15_Polaroid_HSST3-02",
"MinT_Kans_Gly_A_Neg_rep3_12__lip_NEG_150mm_27May15_Polaroid_HSST3-02",
"MinT_Kans_Gly_A_Plus_rep1_01__lip_NEG_150mm_27May15_Polaroid_HSST3",
"MinT_Kans_Gly_A_Plus_rep2_02__lip_NEG_150mm_27May15_Polaroid_HSST3-02",
"MinT_Kans_Gly_A_Plus_rep3_03__lip_NEG_150mm_27May15_Polaroid_HSST3-02",
"mLM_CC_T2_002_lipid_19Dec14_Polaroid_14-12-16",
"mLM_CC_T2_010_lipid_19Dec14_Polaroid_14-12-16",
"mLM_CC_T2_011-014_Lipid_NEG_9Jan15_Polaroid_14-12-16",
"mLM_CC_T2_012-015_Lipid_NEG_9Jan15_Polaroid_14-12-16",
"mLM_CC_T2_013-016_Lipid_NEG_9Jan15_Polaroid_14-12-16",
"mLM_CC_T2_018-019_Lipid_NEG_9Jan15_Polaroid_14-12-16",
"mLM_CC_T2_020-023_P_Lipid_NEG_9Jan15_Polaroid_14-12-16",
"mLM_CC_T2_022-024_P_Lipid_NEG_9Jan15_Polaroid_14-12-16",
"mLM_Sub_Test_Mito_NEG_150mm_4Sept15_Polaroid_HSST3-02",
"OHSUblotter_PO6573_1__lipid_NEG_150mm_17Jun15_Polaroid_HSST3-02",
"OHSUblotter_PO6573_2__lipid_NEG_150mm_17Jun15_Polaroid_HSST3-02",
"OHSUblotter_PO6573_3__lipid_NEG_150mm_17Jun15_Polaroid_HSST3-02",
"OHSUblotter_PO6716_1__lipid_NEG_150mm_17Jun15_Polaroid_HSST3-02",
"OHSUblotter_PO6716_2__lipid_NEG_150mm_17Jun15_Polaroid_HSST3-02",
"OHSUblotter_PO6716_3__lipid_NEG_150mm_17Jun15_Polaroid_HSST3-02",
"OHSUblotter_PO6764_1__lipid_NEG_150mm_17Jun15_Polaroid_HSST3-02",
"OHSUblotter_PO6764_2__lipid_NEG_150mm_17Jun15_Polaroid_HSST3-02",
"OHSUblotter_PO6764_3__lipid_NEG_150mm_17Jun15_Polaroid_HSST3-02",
"OHSUblotter_PO6882_1__lipid_NEG_150mm_17Jun15_Polaroid_HSST3-02",
"OHSUblotter_PO6882_2__lipid_NEG_150mm_17Jun15_Polaroid_HSST3-02",
"OHSUblotter_PO6882_3__lipid_NEG_150mm_17Jun15_Polaroid_HSST3-02",
"OHSUblotter_PO6927_1__lipid_NEG_150mm_17Jun15_Polaroid_HSST3-02",
"OHSUblotter_PO6927_2__lipid_NEG_150mm_17Jun15_Polaroid_HSST3-02",
"OHSUblotter_PO6927_3__lipid_NEG_150mm_17Jun15_Polaroid_HSST3-02",
"OHSUblotter_PO6935_1__lipid_NEG_150mm_17Jun15_Polaroid_HSST3-02",
"OHSUblotter_PO6935_2__lipid_NEG_150mm_17Jun15_Polaroid_HSST3-02",
"OHSUblotter_PO6935_3__lipid_NEG_150mm_17Jun15_Polaroid_HSST3-02",
"OHSUblotter_PO6976_1__lipid_NEG_150mm_17Jun15_Polaroid_HSST3-02",
"OHSUblotter_PO6976_2__lipid_NEG_150mm_17Jun15_Polaroid_HSST3-02",
"OHSUblotter_PO6976_3__lipid_NEG_150mm_17Jun15_Polaroid_HSST3-02",
"OHSUblotter_PO7117_1__lipid_NEG_150mm_17Jun15_Polaroid_HSST3-02",
"OHSUblotter_PO7117_2__lipid_NEG_150mm_17Jun15_Polaroid_HSST3-02",
"OHSUblotter_PO7117_3__lipid_NEG_150mm_17Jun15_Polaroid_HSST3-02",
"OHSUblotter_PO7324_1__lipid_NEG_150mm_17Jun15_Polaroid_HSST3-02",
"OHSUblotter_PO7324_2__lipid_NEG_150mm_17Jun15_Polaroid_HSST3-02",
"OHSUblotter_PO7324_3__lipid_NEG_150mm_17Jun15_Polaroid_HSST3-02",
"OHSUblotter_PO7355_1__lipid_NEG_150mm_17Jun15_Polaroid_HSST3-02",
"OHSUblotter_PO7355_2__lipid_NEG_150mm_17Jun15_Polaroid_HSST3-02",
"OHSUblotter_PO7355_3__lipid_NEG_150mm_17Jun15_Polaroid_HSST3-02",
"OMICS_ICL102_691_0hr_Lipid_4_056_Neg_rr_28Jan15_Polaroid_14-12-16",
"OMICS_ICL102_691_0hr_Lipid_5_081_Neg_30Jan15_Polaroid_14-12-16",
"OMICS_ICL102_691_12hr_Lipid_4_053_Neg_rr_28Jan15_Polaroid_14-12-16",
"OMICS_ICL102_691_12hr_Lipid_5_079_NEG_15Jan15_Polaroid_14-12-16",
"OMICS_ICL102_691_18hr_Lipid_4_094_Neg_23Jan15_Polaroid_14-12-16",
"OMICS_ICL102_691_18hr_Lipid_5_097_Neg_rr_28Jan15_Polaroid_14-12-16",
"OMICS_ICL102_691_24hr_Lipid_4_114_NEG_19Jan15_Polaroid_14-12-16",
"OMICS_ICL102_691_24hr_Lipid_5_093_NEG_15Jan15_Polaroid_14-12-16",
"OMICS_ICL102_691_3hr_Lipid_4_044_Neg_23Jan15_Polaroid_14-12-16",
"OMICS_ICL102_691_3hr_Lipid_5_063_NEG_19Jan15_Polaroid_14-12-16",
"OMICS_ICL102_691_7hr_Lipid_4_057_Neg_30Jan15_Polaroid_14-12-16",
"OMICS_ICL102_691_7hr_Lipid_5_002_Neg_23Jan15_Polaroid_14-12-16",
"OMICS_ICL102_AH1_0hr_Lipid_4_088_NEG_19Jan15_Polaroid_14-12-16",
"OMICS_ICL102_AH1_0hr_Lipid_5_120_NEG_19Jan15_Polaroid_14-12-16",
"OMICS_ICL102_AH1_12hr_Lipid_4_065_Neg_30Jan15_Polaroid_14-12-16",
"OMICS_ICL102_AH1_12hr_Lipid_5_110_Neg_23Jan15_Polaroid_14-12-16",
"OMICS_ICL102_AH1_18hr_Lipid_4_030_Neg_23Jan15_Polaroid_14-12-16",
"OMICS_ICL102_AH1_18hr_Lipid_5_086_Neg_30Jan15_Polaroid_14-12-16",
"OMICS_ICL102_AH1_24hr_Lipid_4_078_Neg_30Jan15_Polaroid_14-12-16",
"OMICS_ICL102_AH1_24hr_Lipid_5_109_NEG_19Jan15_Polaroid_14-12-16",
"OMICS_ICL102_AH1_3hr_Lipid_4_117_NEG_19Jan15_Polaroid_14-12-16",
"OMICS_ICL102_AH1_3hr_Lipid_5_089_Neg_28Jan15_Polaroid_14-12-16",
"OMICS_ICL102_AH1_7hr_Lipid_4_047_Neg_30Jan15_Polaroid_14-12-16",
"OMICS_ICL102_AH1_7hr_Lipid_5_119_NEG_15Jan15_Polaroid_14-12-16",
"OMICS_ICL102_FM_0hr_Lipid_4_112_NEG_15Jan15_Polaroid_14-12-16",
"OMICS_ICL102_FM_0hr_Lipid_5_048_Neg_30Jan15_Polaroid_14-12-16",
"OMICS_ICL102_FM_12hr_Lipid_4_061_NEG_15Jan15_Polaroid_14-12-16",
"OMICS_ICL102_FM_12hr_Lipid_5_050_Neg_30Jan15_Polaroid_14-12-16",
"OMICS_ICL102_FM_18hr_Lipid_4_072_Neg_rr_28Jan15_Polaroid_14-12-16",
"OMICS_ICL102_FM_18hr_Lipid_5_113_NEG_15Jan15_Polaroid_14-12-16",
"OMICS_ICL102_FM_24hr_Lipid_4_046_NEG_15Jan15_Polaroid_14-12-16",
"OMICS_ICL102_FM_24hr_Lipid_5_008_NEG_15Jan15_Polaroid_14-12-16",
"OMICS_ICL102_FM_3hr_Lipid_4_020_Neg_30Jan15_Polaroid_14-12-16",
"OMICS_ICL102_FM_3hr_Lipid_5_060_Neg_30Jan15_Polaroid_14-12-16",
"OMICS_ICL102_FM_7hr_Lipid_4_115_NEG_19Jan15_Polaroid_14-12-16",
"OMICS_ICL102_FM_7hr_Lipid_5_038_Neg_30Jan15_Polaroid_14-12-16",
"OMICS_ICL102_Mock_0hr_Lipid_4_107_Neg_23Jan15_Polaroid_14-12-16",
"OMICS_ICL102_Mock_0hr_Lipid_5_034_NEG_15Jan15_Polaroid_14-12-16",
"OMICS_ICL102_Mock_12hr_Lipid_4_023_Neg_30Jan15_Polaroid_14-12-16",
"OMICS_ICL102_Mock_12hr_Lipid_5_052_NEG_19Jan15_Polaroid_14-12-16",
"OMICS_ICL102_Mock_18hr_Lipid_4_070_Neg_30Jan15_Polaroid_14-12-16",
"OMICS_ICL102_Mock_18hr_Lipid_5_102_Neg_23Jan15_Polaroid_14-12-16",
"OMICS_ICL102_Mock_24hr_Lipid_4_118_Neg_30Jan15_Polaroid_14-12-16",
"OMICS_ICL102_Mock_24hr_Lipid_5_064_Neg_rr_28Jan15_Polaroid_14-12-16",
"OMICS_ICL102_Mock_3hr_Lipid_4_091_NEG_19Jan15_Polaroid_14-12-16",
"OMICS_ICL102_Mock_3hr_Lipid_5_074_NEG_15Jan15_Polaroid_14-12-16",
"OMICS_ICL102_Mock_7hr_Lipid_4_111_NEG_15Jan15_Polaroid_14-12-16",
"OMICS_ICL102_Mock_7hr_Lipid_5_068_Neg_30Jan15_Polaroid_14-12-16",
"PVD_Test_lipid_1_PVD_test_lipids_NEG_150mm_22Mar15_Polaroid_14-12-16",
"PVD_Test_lipid_2_PVD_test_lipids_NEG_150mm_22Mar15_Polaroid_14-12-16",
"PVD_Test_lipid_3_PVD_test_lipids_NEG_150mm_22Mar15_Polaroid_14-12-16",
"PVD_Test_lipid_4_PVD_test_lipids_NEG_150mm_22Mar15_Polaroid_14-12-16",
"SOM_LIPIDS_1C_NEG_150mm_10Jun15_Polaroid_HSST3-02",
"SOM_LIPIDS_2C_NEG_150mm_10Jun15_Polaroid_HSST3-02",
"SOM_LIPIDS_Hol-1_NEG_150mm_10Jun15_Polaroid_HSST3-02",
"SOM_LIPIDS_Hol-3_NEG_150mm_10Jun15_Polaroid_HSST3-02",
"SOM_LIPIDS_Hol-4_NEG_150mm_10Jun15_Polaroid_HSST3-02",
"SOM_LIPIDS_SOF_NEG_150mm_10Jun15_Polaroid_HSST3-02",
"Sullivan_Cbaltica_5E6_test_NEG_150mm_28May15_Polaroid_HSST3-02",
"Sullivan_Cbaltica_5E7_test_NEG_150mm_28May15_Polaroid_HSST3-02"
};
var x = new Stopwatch();
x.Start();
const string negativeTargetsFileLocation = @"../../../testFiles/Global_LipidMaps_NEG_4.txt";
var negativeTargetsFileInfo = new FileInfo(negativeTargetsFileLocation);
var lipidReader = new LipidMapsDbReader <Lipid>();
var lipidList = lipidReader.ReadFile(negativeTargetsFileInfo);
var liquidScoreModelCreator = new ScoreModelCreator();
//liquidScoreModelCreator.AddDmsDatasets(new List<string> {datasetNames[0]});
liquidScoreModelCreator.AddDmsDatasets(datasetNames);
liquidScoreModelCreator.AddLipidTargets(lipidList);
var scoreModel = liquidScoreModelCreator.CreateScoreModel(30, 500);
//Console.WriteLine(scoreModel.ToString());
ScoreModelSerialization.Serialize(scoreModel, "scoringTestNegative_Grant.xml");
Console.WriteLine("Time Elapsed: " + x.Elapsed);
}
public void CreateNewScoringModelPositive()
{
var datasetNames = new List <string>
{
"BTL_MeOH_a_HF_POS_112414_150mm_12Dec14_Polaroid_14-06-12",
"BTL_MeOH_a_HF_POS_120514m_12Dec14_Polaroid_14-06-12",
"BTL_MeOH_a_HF_POS_120914m_12Dec14_Polaroid_14-06-12",
"BTL_MeOH_a_HF_POS_120914V2m_12Dec14_Polaroid_14-06-12",
"FECB_ATCC_29133_616_Dark_Lipid_POS_150mm_24Mar15_Polaroid_14-12-16",
"FECB_ATCC_29133_616_Light_Lipid_POS_150mm_24Mar15_Polaroid_14-12-16",
"FECB_ATCC_29133_819_Dark_Lipid_POS_150mm_24Mar15_Polaroid_14-12-16",
"FECB_ATCC_29133_819_Light_Lipid_POS_150mm_24Mar15_Polaroid_14-12-16",
"FSFA_Isolate_HL53_0700_lipid_POS_150mm_21Aug15_Polaroid_HSST3-02",
"FSFA_Isolate_HL53_1000_lipid_POS_150mm_21Aug15_Polaroid_HSST3-02",
"FSFA_Isolate_HL91_0050_1_lipid_POS_150mm_21Aug15_Polaroid_HSST3-02",
"FSFA_Isolate_HL91_0050_2_lipid_POS_150mm_21Aug15_Polaroid_HSST3-02",
"FSFA_Isolate_HL91_0050_3_lipid_POS_150mm_21Aug15_Polaroid_HSST3-02",
"FSFA_Isolate_HL91_0200_1_lipid_POS_150mm_21Aug15_Polaroid_HSST3-02",
"FSFA_Isolate_HL91_0200_2_lipid_POS_150mm_21Aug15_Polaroid_HSST3-02",
"FSFA_Isolate_HL91_0200_3_lipid_POS_150mm_21Aug15_Polaroid_HSST3-02",
"FSFA_Isolate_HL91_0400_1_lipid_POS_150mm_21Aug15_Polaroid_HSST3-02",
"FSFA_Isolate_HL91_0400_2_lipid_POS_150mm_21Aug15_Polaroid_HSST3-02",
"FSFA_Isolate_HL91_0400_3_lipid_POS_150mm_21Aug15_Polaroid_HSST3-02",
"FSFA_Isolate_HL91_1000_1_lipid_POS_150mm_21Aug15_Polaroid_HSST3-02",
"FSFA_Isolate_HL91_1000_2_lipid_POS_150mm_21Aug15_Polaroid_HSST3-02",
"FSFA_Isolate_HL91_1000_3_lipid_POS_150mm_21Aug15_Polaroid_HSST3-02",
"LCA_Ariadna_B_lipid_POS_150mm_25Mar15_Polaroid_14-12-16",
"LCA_Ariadna_M_lipid_POS_150mm_25Mar15_Polaroid_14-12-16",
"LCA_Ariadna_T_lipid_POS_150mm_25Mar15_Polaroid_14-12-16",
"LCA_conc_mix_lipid_POS_POS_150mm_25Mar15_Polaroid_14-12-16",
"LCA_Dora_B_lipid_POS_150mm_25Mar15_Polaroid_14-12-16",
"LCA_Dora_B_lipid_POS_rr_150mm_30Mar15_Polaroid_14-12-16",
"LCA_Dora_M_lipid_POS_150mm_25Mar15_Polaroid_14-12-16",
"LCA_Dora_M_lipid_POS_rr_150mm_30Mar15_Polaroid_14-12-16",
"LCA_Dora_T_lipid_POS_150mm_25Mar15_Polaroid_14-12-16",
"LCA_Dora_T_lipid_POS_rr_150mm_30Mar15_Polaroid_14-12-16",
"LCA_Emma_B_lipid_POS_150mm_25Mar15_Polaroid_14-12-16",
"LCA_Emma_B_lipid_POS_rr_150mm_30Mar15_Polaroid_14-12-16",
"LCA_Emma_M_lipid_POS_150mm_25Mar15_Polaroid_14-12-16",
"LCA_Emma_T_lipid_POS_150mm_25Mar15_Polaroid_14-12-16",
"LCA_leaf_lipid_POS_150mm_25Mar15_Polaroid_14-12-16",
"MinT_Kans_Gly_A_NEG_rep1_10__lip_POS_150mm_2Jun15_Polaroid_HSST3-02",
"MinT_Kans_Gly_A_NEG_rep2_11__lip_POS_150mm_2Jun15_Polaroid_HSST3-02",
"MinT_Kans_Gly_A_NEG_rep3_12__lip_POS_150mm_2Jun15_Polaroid_HSST3-02",
"MinT_Kans_Gly_A_Plus_rep1_01__lip_POS_150mm_2Jun15_Polaroid_HSST3",
"MinT_Kans_Gly_A_Plus_rep2_02__lip_POS_150mm_2Jun15_Polaroid_HSST3-02",
"MinT_Kans_Gly_A_Plus_rep3_03__lip_POS_150mm_2Jun15_Polaroid_HSST3-02",
"mLM_CC_T2_011-014_Lipid_POS_9Jan15_Polaroid_14-12-16",
"mLM_CC_T2_012-015_P_Lipid_POS_9Jan15_Polaroid_14-12-16",
"mLM_CC_T2_013-016_Lipid_POS_9Jan15_Polaroid_14-12-16",
"mLM_CC_T2_018-019_P_Lipid_POS_9Jan15_Polaroid_14-12-16",
"mLM_CC_T2_020-023_Lipid_POS_9Jan15_Polaroid_14-12-16",
"mLM_CC_T2_022-024_Lipid_POS_9Jan15_Polaroid_14-12-16",
"mLM_Sub_Test_Mito_POS_150mm_01Sept15_Polaroid_HSST3-02",
"OHSUblotter_PO6573_1__lipid_POS_150mm_12Jun15_Polaroid_HSST3-02",
"OHSUblotter_PO6573_2__lipid_POS_150mm_12Jun15_Polaroid_HSST3-02",
"OHSUblotter_PO6573_3__lipid_POS_150mm_12Jun15_Polaroid_HSST3-02",
"OHSUblotter_PO6716_1__lipid_POS_150mm_12Jun15_Polaroid_HSST3-02",
"OHSUblotter_PO6716_2__lipid_POS_150mm_12Jun15_Polaroid_HSST3-02",
"OHSUblotter_PO6716_3__lipid_POS_150mm_12Jun15_Polaroid_HSST3-02",
"OHSUblotter_PO6764_1__lipid_POS_150mm_12Jun15_Polaroid_HSST3-02",
"OHSUblotter_PO6764_2__lipid_POS_150mm_12Jun15_Polaroid_HSST3-02",
"OHSUblotter_PO6764_3__lipid_POS_150mm_12Jun15_Polaroid_HSST3-02",
"OHSUblotter_PO6882_1__lipid_POS_150mm_12Jun15_Polaroid_HSST3-02",
"OHSUblotter_PO6882_2__lipid_POS_150mm_12Jun15_Polaroid_HSST3-02",
"OHSUblotter_PO6882_3__lipid_POS_150mm_12Jun15_Polaroid_HSST3-02",
"OHSUblotter_PO6927_1__lipid_POS_150mm_12Jun15_Polaroid_HSST3-02",
"OHSUblotter_PO6927_2__lipid_POS_150mm_12Jun15_Polaroid_HSST3-02",
"OHSUblotter_PO6927_3__lipid_POS_150mm_12Jun15_Polaroid_HSST3-02",
"OHSUblotter_PO6935_1__lipid_POS_150mm_12Jun15_Polaroid_HSST3-02",
"OHSUblotter_PO6935_2__lipid_POS_150mm_12Jun15_Polaroid_HSST3-02",
"OHSUblotter_PO6935_3__lipid_POS_150mm_12Jun15_Polaroid_HSST3-02",
"OHSUblotter_PO6976_1__lipid_POS_150mm_12Jun15_Polaroid_HSST3-02",
"OHSUblotter_PO6976_2__lipid_POS_150mm_12Jun15_Polaroid_HSST3-02",
"OHSUblotter_PO6976_3__lipid_POS_150mm_12Jun15_Polaroid_HSST3-02",
"OHSUblotter_PO7117_1__lipid_POS_150mm_12Jun15_Polaroid_HSST3-02",
"OHSUblotter_PO7117_2__lipid_POS_150mm_12Jun15_Polaroid_HSST3-02",
"OHSUblotter_PO7117_3__lipid_POS_150mm_12Jun15_Polaroid_HSST3-02",
"OHSUblotter_PO7324_1__lipid_POS_150mm_12Jun15_Polaroid_HSST3-02",
"OHSUblotter_PO7324_2__lipid_POS_150mm_12Jun15_Polaroid_HSST3-02",
"OHSUblotter_PO7324_3__lipid_POS_150mm_12Jun15_Polaroid_HSST3-02",
"OHSUblotter_PO7355_1__lipid_POS_150mm_12Jun15_Polaroid_HSST3-02",
"OHSUblotter_PO7355_2__lipid_POS_150mm_12Jun15_Polaroid_HSST3-02",
"OHSUblotter_PO7355_3__lipid_POS_150mm_12Jun15_Polaroid_HSST3-02",
"OMICS_ICL102_691_0hr_Lipid_4_056_POS_22Dec14_Polaroid_14-12-16",
"OMICS_ICL102_691_0hr_Lipid_5_081_POS_6Jan15_Polaroid_14-12-16",
"OMICS_ICL102_691_12hr_Lipid_4_053_POS_22Dec14_Polaroid_14-12-16",
"OMICS_ICL102_691_12hr_Lipid_5_079_POS_17Dec14_Polaroid_14-12-16",
"OMICS_ICL102_691_18hr_Lipid_4_094_POS_27Dec14_Polaroid_14-12-16",
"OMICS_ICL102_691_18hr_Lipid_5_097_POS_22Dec14_Polaroid_14-12-16",
"OMICS_ICL102_691_24hr_Lipid_4_114_POS_22Dec14_Polaroid_14-12-16",
"OMICS_ICL102_691_24hr_Lipid_5_093_POS_17Dec14_Polaroid_14-12-16",
"OMICS_ICL102_691_3hr_Lipid_4_044_POS_27Dec14_Polaroid_14-12-16",
"OMICS_ICL102_691_3hr_Lipid_5_063_POS_22Dec14_Polaroid_14-12-16",
"OMICS_ICL102_691_7hr_Lipid_4_057_POS_6Jan15_Polaroid_14-12-16",
"OMICS_ICL102_691_7hr_Lipid_5_002_POS_27Dec14_Polaroid_14-12-16",
"OMICS_ICL102_AH1_0hr_Lipid_4_088_POS_22Dec14_Polaroid_14-12-16",
"OMICS_ICL102_AH1_0hr_Lipid_5_120_POS_22Dec14_Polaroid_14-12-16",
"OMICS_ICL102_AH1_12hr_Lipid_4_065_POS_6Jan15_Polaroid_14-12-16",
"OMICS_ICL102_AH1_12hr_Lipid_5_110_POS_27Dec14_Polaroid_14-12-16",
"OMICS_ICL102_AH1_18hr_Lipid_4_030_POS_27Dec14_Polaroid_14-12-16",
"OMICS_ICL102_AH1_18hr_Lipid_5_086_POS_6Jan15_Polaroid_14-12-16",
"OMICS_ICL102_AH1_24hr_Lipid_4_078_POS_6Jan15_Polaroid_14-12-16",
"OMICS_ICL102_AH1_24hr_Lipid_5_109_POS_22Dec14_Polaroid_14-12-16",
"OMICS_ICL102_AH1_3hr_Lipid_4_117_POS_22Dec14_Polaroid_14-12-16",
"OMICS_ICL102_AH1_3hr_Lipid_5_089_POS_27Dec14_Polaroid_14-12-16",
"OMICS_ICL102_AH1_7hr_Lipid_4_047_POS_6Jan15_Polaroid_14-12-16",
"OMICS_ICL102_AH1_7hr_Lipid_5_119_POS_17Dec14_Polaroid_14-12-16",
"OMICS_ICL102_FM_0hr_Lipid_4_112_POS_17Dec14_Polaroid_14-12-16",
"OMICS_ICL102_FM_0hr_Lipid_5_048_POS_6Jan15_Polaroid_14-12-16",
"OMICS_ICL102_FM_12hr_Lipid_4_061_POS_17Dec14_Polaroid_14-12-16",
"OMICS_ICL102_FM_12hr_Lipid_5_050_POS_6Jan15_Polaroid_14-12-16",
"OMICS_ICL102_FM_18hr_Lipid_4_072_POS_22Dec14_Polaroid_14-12-16",
"OMICS_ICL102_FM_18hr_Lipid_5_113_POS_17Dec14_Polaroid_14-12-16",
"OMICS_ICL102_FM_24hr_Lipid_4_046_POS_17Dec14_Polaroid_14-12-16",
"OMICS_ICL102_FM_24hr_Lipid_5_008_POS_17Dec14_Polaroid_14-12-16",
"OMICS_ICL102_FM_3hr_Lipid_4_020_POS_6Jan15_Polaroid_14-12-16",
"OMICS_ICL102_FM_3hr_Lipid_5_060_POS_6Jan15_Polaroid_14-12-16",
"OMICS_ICL102_FM_7hr_Lipid_4_115_POS_22Dec14_Polaroid_14-12-16",
"OMICS_ICL102_FM_7hr_Lipid_5_038_POS_6Jan15_Polaroid_14-12-16",
"OMICS_ICL102_Mock_0hr_Lipid_4_107_POS_27Dec14_Polaroid_14-12-16",
"OMICS_ICL102_Mock_0hr_Lipid_5_034_POS_17Dec14_Polaroid_14-12-16",
"OMICS_ICL102_Mock_12hr_Lipid_4_023_POS_6Jan15_Polaroid_14-12-16",
"OMICS_ICL102_Mock_12hr_Lipid_5_052_POS_22Dec14_Polaroid_14-12-16",
"OMICS_ICL102_Mock_18hr_Lipid_4_070_POS_6Jan15_Polaroid_14-12-16",
"OMICS_ICL102_Mock_18hr_Lipid_5_102_POS_27Dec14_Polaroid_14-12-16",
"OMICS_ICL102_Mock_24hr_Lipid_4_118_POS_6Jan15_Polaroid_14-12-16",
"OMICS_ICL102_Mock_24hr_Lipid_5_064_POS_22Dec14_Polaroid_14-12-16",
"OMICS_ICL102_Mock_3hr_Lipid_4_091_POS_22Dec14_Polaroid_14-12-16",
"OMICS_ICL102_Mock_3hr_Lipid_5_074_POS_17Dec14_Polaroid_14-12-16",
"OMICS_ICL102_Mock_7hr_Lipid_4_111_POS_17Dec14_Polaroid_14-12-16",
"OMICS_ICL102_Mock_7hr_Lipid_5_068_POS_6Jan15_Polaroid_14-12-16",
"PVD_Test_lipid_1_PVD_test_lipids_POS_150mm_23Mar15_Polaroid_14-12-16",
"PVD_Test_lipid_1_PVD_test_lipids_POS_150mm_24Mar15_Polaroid_14-12-16",
"PVD_Test_lipid_2_PVD_test_lipids_POS_150mm_23Mar15_Polaroid_14-12-16",
"PVD_Test_lipid_2_PVD_test_lipids_POS_150mm_24Mar15_Polaroid_14-12-16",
"PVD_Test_lipid_3_PVD_test_lipids_POS_150mm_23Mar15_Polaroid_14-12-16",
"PVD_Test_lipid_3_PVD_test_lipids_POS_150mm_24Mar15_Polaroid_14-12-16",
"PVD_Test_lipid_4_PVD_test_lipids_POS_150mm_23Mar15_Polaroid_14-12-16",
"PVD_Test_lipid_4_PVD_test_lipids_POS_150mm_24Mar15_Polaroid_14-12-16",
"SOM_LIPIDS_1C_POS_150mm_8Jun15_Polaroid_HSST3-02",
"SOM_LIPIDS_2C_POS_150mm_8Jun15_Polaroid_HSST3-02",
"SOM_LIPIDS_Hol-1_POS_150mm_8Jun15_Polaroid_HSST3-02",
"SOM_LIPIDS_Hol-3_POS_150mm_8Jun15_Polaroid_HSST3-02",
"SOM_LIPIDS_Hol-4_POS_150mm_8Jun15_Polaroid_HSST3-02",
"SOM_LIPIDS_SOF_POS_150mm_8Jun15_Polaroid_HSST3-02",
"Sullivan_Cbaltica_5E6_test_POS_150mm_2Jun15_Polaroid_HSST3-02",
"Sullivan_Cbaltica_5E7_test_POS_150mm_2Jun15_Polaroid_HSST3-02"
};
const string positiveTargetsFileLocation = @"../../../testFiles/Global_LipidMaps_POS_7b.txt";
var positiveTargetsFileInfo = new FileInfo(positiveTargetsFileLocation);
var lipidReader = new LipidMapsDbReader <Lipid>();
var lipidList = lipidReader.ReadFile(positiveTargetsFileInfo);
var liquidScoreModelCreator = new ScoreModelCreator();
//liquidScoreModelCreator.AddDmsDatasets(new List<string> {datasetNames[0]});
liquidScoreModelCreator.AddDmsDatasets(datasetNames);
liquidScoreModelCreator.AddLipidTargets(lipidList);
var scoreModel = liquidScoreModelCreator.CreateScoreModel(30, 500);
//Console.WriteLine(scoreModel.ToString());
ScoreModelSerialization.Serialize(scoreModel, "scoringTestPositive.xml");
}
public void TestCreatePositiveScoringModel()
{
var datasetNames = new List <string>
{
"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",
"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"
};
//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");
//datasetNames.Add("Lipid_QC_1_14Jan_POS_Gimli_14Jan14_13-07-01");
//datasetNames.Add("Lipid_QC_1_14Jan_POS_Gimli_17JAN_13-07-01");
const string positiveTargetsFileLocation = @"../../../testFiles/Global_LipidMaps_POS_5.txt";
var positiveTargetsFileInfo = new FileInfo(positiveTargetsFileLocation);
var lipidReader = new LipidMapsDbReader <Lipid>();
var lipidList = lipidReader.ReadFile(positiveTargetsFileInfo);
var liquidScoreModelCreator = new ScoreModelCreator();
//liquidScoreModelCreator.AddDmsDatasets(new List<string> {datasetNames[0]});
liquidScoreModelCreator.AddDmsDatasets(datasetNames);
liquidScoreModelCreator.AddLipidTargets(lipidList);
var scoreModel = liquidScoreModelCreator.CreateScoreModel(30, 500);
//Console.WriteLine(scoreModel.ToString());
ScoreModelSerialization.Serialize(scoreModel, "scoringTestPositive.xml");
//ScoreModel deserializedScoreModel = ScoreModelSerialization.Deserialize("scoringTestPositive.xml");
//Console.WriteLine(deserializedScoreModel);
//foreach (string datasetName in datasetNames)
//{
// // Setup workflow
// GlobalWorkflow globalWorkflow = new GlobalWorkflow(datasetName);
// // Run workflow
// List<LipidGroupSearchResult> lipidGroupSearchResults = globalWorkflow.RunGlobalWorkflow(lipidList, 30, 500);
// foreach (var lipidGroupSearchResult in lipidGroupSearchResults)
// {
// double score = scoreModel.ScoreLipid(lipidGroupSearchResult);
// //Console.WriteLine(score + "\t" + lipidGroupSearchResult.LipidTarget.StrippedDisplay);
// }
//}
}
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);
}
}
}
}
