/// <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 static void AddDmsDataset(string datasetName)
{
if (!File.Exists(datasetName))
{
// Lookup in DMS via Mage
var dmsFolder = DmsDatasetFinder.FindLocationOfDataset(datasetName.Replace(".raw", ""));
var dmsDirectoryInfo = new DirectoryInfo(dmsFolder);
var fullPathToDmsFile = Path.Combine(dmsDirectoryInfo.FullName, datasetName);
// Copy Locally
File.Copy(fullPathToDmsFile, datasetName);
}
}
public void AddDmsDataset(string datasetName)
{
var rawFileName = datasetName + ".raw";
if (!File.Exists(rawFileName))
{
// 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
File.Copy(fullPathToDmsFile, rawFileName);
}
AddDataset(rawFileName);
}
public string GetRawFilePath(string directory, string datasetName)
{
var rawFileName = datasetName + ".raw";
var rawFilePath = Path.Combine(directory, rawFileName);
Console.WriteLine(DateTime.Now + ": Processing " + datasetName);
if (File.Exists(rawFilePath))
{
Console.WriteLine(DateTime.Now + ": Dataset already exists");
}
else
{
try
{
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");
}
catch (Exception)
{
rawFilePath = string.Empty;
Console.WriteLine("Cannot get {0} from DMS", datasetName);
}
}
return(rawFilePath);
}
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();
}
