protected override IqTarget ConvertTextToIqTarget(List <string> processedRow)
{
var target = new IqTargetMsgfFirstHit();
target.ID = ParseIntField(processedRow, TargetIDHeaders, -1);
if (target.ID == -1)
{
target.ID = GetAutoIncrementForTargetID();
}
target.EmpiricalFormula = ParseStringField(processedRow, EmpiricalFormulaHeaders, string.Empty);
target.Code = ParseStringField(processedRow, CodeHeaders, "");
target.ElutionTimeTheor = ParseDoubleField(processedRow, NETHeaders, 0);
target.ScanLC = ParseIntField(processedRow, ScanHeaders, -1);
target.QualityScore = ParseDoubleField(processedRow, QualityScoreHeaders, -1);
target.ChargeState = ParseIntField(processedRow, ChargeStateHeaders, 0);
target.MassError = ParseDoubleField(processedRow, MassErrorHeaders, 0);
target.MZTheor = ParseDoubleField(processedRow, MzHeaders, 0);
target.MonoMassTheor = (target.MZTheor - DeconTools.Backend.Globals.PROTON_MASS) * target.ChargeState;
var targetUtilities = new IqTargetUtilities();
return(target);
}
public void ImportIqTargetsFromMsgfTest1()
{
var targetsFile = @"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\Unlabelled\Targets\Yellow_C13_070_23Mar10_Griffin_10-01-28_msgfplus.tsv";
var importer = new BasicIqTargetImporter(targetsFile);
var targets = importer.Import();
Assert.IsNotNull(targets);
Assert.IsTrue(targets.Any());
var utilities = new IqTargetUtilities();
foreach (var iqTarget in targets)
{
utilities.UpdateTargetMissingInfo(iqTarget, false);
}
Assert.IsTrue(targets.Count > 10);
foreach (var iqTarget in targets.Take(10))
{
Console.WriteLine(iqTarget.ToString() + "\t" + iqTarget.ScanLC + "\t" + iqTarget.QualityScore);
}
}
public void CreateTargetsFromEmpiricalFormulaOnlyLargePeptideTest1()
{
var util = new IqTargetUtilities();
var peptideSequence =
"PEPITIDEPEPITIDEPEPITIDEPEPITIDEPEPITIDEPEPITIDEPEPITIDEPEPITIDEPEPITIDEPEPITIDEPEPITIDEPEPITIDEPEPITIDEPEPITIDEPEPITIDEPEPITIDEPEPITIDEPEPITIDEPEPITIDEPEPITIDEPEPITIDEPEPITIDEPEPITIDEPEPITIDEPEPITIDE";
var peptideUtil = new PeptideUtils();
var empiricalFormula = peptideUtil.GetEmpiricalFormulaForPeptideSequence(peptideSequence);
var formulas = new string[] { empiricalFormula };
var targets = util.CreateTargets(formulas);
foreach (var parentTarget in targets)
{
Console.WriteLine(parentTarget.ID + "\t" + parentTarget.MonoMassTheor.ToString("0.00000") + "\tNumChildren= " + parentTarget.ChildTargets().Count());
if (parentTarget.HasChildren())
{
foreach (var childTarget in parentTarget.ChildTargets())
{
Console.WriteLine("\t\t\t" + childTarget.ID + "\t" + childTarget.MonoMassTheor.ToString("0.00000") + "\t" +
childTarget.MZTheor.ToString("0.00000") + "\t" + childTarget.ChargeState + "\t" + (1.00235d / childTarget.ChargeState).ToString("0.0000"));
}
}
}
}
public void ChromCorrelatorTest1()
{
var rawFilename = @"D:\Data\O16O18\Vlad_Mouse\mhp_plat_test_1_14April13_Frodo_12-12-04.raw";
var run = new RunFactory().CreateRun(rawFilename);
WorkflowExecutorBaseParameters executorBaseParameters = new BasicTargetedWorkflowExecutorParameters();
var executor = new IqExecutor(executorBaseParameters, run);
executor.LoadChromData(run);
var workflowAssigner = new IqWorkflowAssigner();
TargetedWorkflowParameters workflowParameters = new O16O18WorkflowParameters();
IqWorkflow workflow = new O16O18IqWorkflow(run, workflowParameters);
IqTarget iqTarget = new IqChargeStateTarget();
iqTarget.EmpiricalFormula = "C58H100N18O20";
iqTarget.Code = "GAAQNIIPASTGAAK";
iqTarget.ID = 1093;
iqTarget.ChargeState = 0;
var iqTargetList = new List <IqTarget>();
iqTargetList.Add(iqTarget);
var utilities = new IqTargetUtilities();
utilities.CreateChildTargets(iqTargetList);
workflowAssigner.AssignWorkflowToParent(workflow, iqTargetList);
workflowAssigner.AssignWorkflowToChildren(workflow, iqTargetList);
var theorFeatureGenerator = new JoshTheorFeatureGenerator();
foreach (var target in iqTarget.ChildTargets())
{
utilities.UpdateTargetMissingInfo(target);
target.TheorIsotopicProfile = theorFeatureGenerator.GenerateTheorProfile(target.EmpiricalFormula, target.ChargeState);
}
foreach (var childTarget in iqTarget.ChildTargets())
{
var result = childTarget.CreateResult();
var correlator = new O16O18ChromCorrelator(7, 0.1, 20, Globals.ToleranceUnit.PPM);
var corrData = correlator.CorrelateData(run, result, 5700, 6500);
var corrDataItem1 = corrData.CorrelationDataItems.First();
Console.WriteLine("z= \t" + childTarget.ChargeState + "\tCorrelationData (slope,intercept,rsquared)= \t" + corrDataItem1);
}
}
public void NodeLevelTest1()
{
var util = new IqTargetUtilities();
IqTarget iqTarget1 = new IqChargeStateTarget();
IqTarget iqTarget2 = new IqChargeStateTarget();
IqTarget iqTarget3_1 = new IqChargeStateTarget();
iqTarget3_1.ID = 3001;
IqTarget iqTarget3_2 = new IqChargeStateTarget();
iqTarget3_2.ID = 3002;
IqTarget iqTarget4 = new IqChargeStateTarget();
IqTarget iqTarget5 = new IqChargeStateTarget();
iqTarget4.AddTarget(iqTarget5);
iqTarget3_1.AddTarget(iqTarget4);
iqTarget2.AddTarget(iqTarget3_1);
iqTarget2.AddTarget(iqTarget3_2);
iqTarget1.AddTarget(iqTarget2);
var rootNode = iqTarget5.RootTarget;
Assert.AreEqual(rootNode, iqTarget1);
var nodeLevelCount = util.GetTotalNodelLevels(iqTarget1);
Assert.AreEqual(5, nodeLevelCount);
nodeLevelCount = util.GetTotalNodelLevels(iqTarget5);
Assert.AreEqual(5, nodeLevelCount);
var targetList = new List <IqTarget>();
targetList.Add(iqTarget1);
var level2Targets = util.GetTargetsFromNodelLevel(targetList, 2);
foreach (var level2Target in level2Targets)
{
Console.WriteLine(level2Target);
}
}
public void ExecutorCreatingTargetsTest1()
{
var util = new IqTargetUtilities();
var testFile = UnitTesting2.FileRefs.RawDataMSFiles.OrbitrapStdFile1;
var peaksTestFile = @"\\protoapps\UserData\Slysz\DeconTools_TestFiles\QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18_scans5500-6500_peaks.txt";
var targetsFile = @"\\protoapps\UserData\Slysz\Data\MassTags\QCShew_Formic_MassTags_Bin10_all.txt";
var resultsFolder = @"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\Unlabelled\Results";
var expectedResultsFilename = Path.Combine(resultsFolder, RunUtilities.GetDatasetName(testFile) + "_iqResults.txt");
if (File.Exists(expectedResultsFilename))
{
File.Delete(expectedResultsFilename);
}
WorkflowExecutorBaseParameters executorBaseParameters = new BasicTargetedWorkflowExecutorParameters();
executorBaseParameters.ChromGenSourceDataPeakBR = 3;
executorBaseParameters.ChromGenSourceDataSigNoise = 2;
executorBaseParameters.TargetsFilePath = targetsFile;
//create no more than two charge state targets per peptide
executorBaseParameters.MaxNumberOfChargeStateTargetsToCreate = 2;
var run = new RunFactory().CreateRun(testFile);
var executor = new IqExecutor(executorBaseParameters, run);
executor.ChromSourceDataFilePath = peaksTestFile;
executor.LoadAndInitializeTargets(targetsFile);
executor.Targets = (from n in executor.Targets where n.ElutionTimeTheor > 0.305 && n.ElutionTimeTheor < 0.325 select n).Take(10).ToList();
foreach (var iqTarget in executor.Targets)
{
var numChildTargets = iqTarget.GetChildCount();
Assert.IsTrue(numChildTargets <= 2); //MaxNumberOfChargeStateTargetsToCreate = 2;
Console.WriteLine(iqTarget + "\t" + numChildTargets);
}
}
public void CreateTargetsFromEmpiricalFormulaOnlyTest1()
{
var util = new IqTargetUtilities();
var formulas = new string[] { "C133H213N29O44", "C95H155N29O39", "C126H198N32O42", "C109H168N24O37", "C103H165N29O35" };
var targets = util.CreateTargets(formulas);
foreach (var parentTarget in targets)
{
Console.WriteLine(parentTarget.ID + "\t" + parentTarget.MonoMassTheor.ToString("0.00000") + "\tNumChildren= " + parentTarget.ChildTargets().Count());
if (parentTarget.HasChildren())
{
foreach (var childTarget in parentTarget.ChildTargets())
{
Console.WriteLine("\t\t\t" + childTarget.ID + "\t" + childTarget.MonoMassTheor.ToString("0.000") + "\t" +
childTarget.MZTheor.ToString("0.000") + "\t" + childTarget.ChargeState);
}
}
}
}
public void ExecuteMultipleTargetsTest1()
{
var util = new IqTargetUtilities();
var testFile = UnitTesting2.FileRefs.RawDataMSFiles.OrbitrapStdFile1;
var peaksTestFile = @"\\protoapps\UserData\Slysz\DeconTools_TestFiles\QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18_scans5500-6500_peaks.txt";
var targetsFile = @"\\protoapps\UserData\Slysz\Data\MassTags\QCShew_Formic_MassTags_Bin10_all.txt";
WorkflowExecutorBaseParameters executorBaseParameters = new BasicTargetedWorkflowExecutorParameters();
executorBaseParameters.ChromGenSourceDataPeakBR = 3;
executorBaseParameters.ChromGenSourceDataSigNoise = 2;
executorBaseParameters.TargetsFilePath = targetsFile;
executorBaseParameters.OutputFolderBase = @"\\protoapps\UserData\Slysz\Standard_Testing\Targeted_FeatureFinding\Unlabelled";
var expectedResultsFilename = Path.Combine(executorBaseParameters.OutputFolderBase,
"IqResults",
RunUtilities.GetDatasetName(testFile) + "_iqResults.txt");
if (File.Exists(expectedResultsFilename))
{
File.Delete(expectedResultsFilename);
}
var run = new RunFactory().CreateRun(testFile);
var executor = new IqExecutor(executorBaseParameters, run);
executor.ChromSourceDataFilePath = peaksTestFile;
executor.LoadAndInitializeTargets(targetsFile);
executor.Targets = (from n in executor.Targets where n.ElutionTimeTheor > 0.305 && n.ElutionTimeTheor < 0.325 select n).Take(10).ToList();
var targetedWorkflowParameters = new BasicTargetedWorkflowParameters();
targetedWorkflowParameters.ChromNETTolerance = 0.5;
//define workflows for parentTarget and childTargets
var parentWorkflow = new BasicIqWorkflow(run, targetedWorkflowParameters);
var childWorkflow = new BasicIqWorkflow(run, targetedWorkflowParameters);
var workflowAssigner = new IqWorkflowAssigner();
workflowAssigner.AssignWorkflowToParent(parentWorkflow, executor.Targets);
workflowAssigner.AssignWorkflowToChildren(childWorkflow, executor.Targets);
//Main line for executing IQ:
executor.Execute();
//Test the results...
Assert.IsTrue(File.Exists(expectedResultsFilename), "results file doesn't exist");
var numResultsInResultsFile = 0;
var outputToConsole = true;
using (var reader = new StreamReader(expectedResultsFilename))
{
while (reader.Peek() != -1)
{
var line = reader.ReadLine();
numResultsInResultsFile++;
if (outputToConsole)
{
Console.WriteLine(line);
}
}
}
Assert.IsTrue(numResultsInResultsFile > 1, "No results in output file");
//the Result Tree is flattened out in the results file.
Assert.IsTrue(numResultsInResultsFile == 11);
//the results in the Executor are in the a Result tree. So there should be just 10.
Assert.AreEqual(10, executor.Results.Count);
}
public void ExecutorTest1()
{
Console.WriteLine(Environment.CurrentDirectory);
var util = new IqTargetUtilities();
var testFile = @"\\proto-5\External_Waters_TOF_Xfer\MzML_Files\130716_iPRG14_004.mzML";
//string peaksTestFile =
//@"\\protoapps\UserData\Slysz\DeconTools_TestFiles\QC_Shew_08_04-pt5-2_11Jan09_Sphinx_08-11-18_scans5500-6500_peaks.txt";
var targetsFile = @"\\protoapps\UserData\Fujimoto\SangtaeBottomUp\msgfPlus\C~~data~iPRG 2014~130716_iPRG14_004.raw.-1_Filtered.tsv";
WorkflowExecutorBaseParameters executorBaseParameters = new BasicTargetedWorkflowExecutorParameters();
executorBaseParameters.ChromGenSourceDataPeakBR = 3;
executorBaseParameters.ChromGenSourceDataSigNoise = 2;
executorBaseParameters.TargetsFilePath = targetsFile;
executorBaseParameters.OutputFolderBase =
@"\\protoapps\UserData\Fujimoto\SangtaeBottomUp\Results";
var expectedResultsFilename = Path.Combine(executorBaseParameters.OutputFolderBase,
"IqResults",
RunUtilities.GetDatasetName(testFile) + "_iqResults.txt");
if (File.Exists(expectedResultsFilename))
{
File.Delete(expectedResultsFilename);
}
var run = new RunFactory().CreateRun(testFile);
var executor = new IqExecutor(executorBaseParameters, run);
//executor.ChromSourceDataFilePath = peaksTestFile;
executor.LoadAndInitializeTargets(targetsFile);
var targetedWorkflowParameters = new BasicTargetedWorkflowParameters();
targetedWorkflowParameters.ChromNETTolerance = 0.05;
//define workflows for parentTarget and childTargets
var parentWorkflow = new ChromPeakDeciderIqWorkflow(run, targetedWorkflowParameters);
var childWorkflow = new ChargeStateChildIqWorkflow(run, targetedWorkflowParameters);
var workflowAssigner = new IqWorkflowAssigner();
workflowAssigner.AssignWorkflowToParent(parentWorkflow, executor.Targets);
workflowAssigner.AssignWorkflowToChildren(childWorkflow, executor.Targets);
//SipperDataDump.DataDumpSetup(@"\\pnl\projects\MSSHARE\Merkley_Eric\For_Grant\IqResults\EXP6B_F1_CSCL_LIGHT_130520020056\EXP6B_F1_CSCL_LIGHT_FULLRESULTS.txt");
//Main line for executing IQ:
executor.Execute();
//Test the results...
var numResultsInResultsFile = 0;
var outputToConsole = true;
using (var reader = new StreamReader(expectedResultsFilename))
{
while (reader.Peek() != -1)
{
var line = reader.ReadLine();
numResultsInResultsFile++;
if (outputToConsole)
{
Console.WriteLine(line);
}
}
}
}