private void AddDoubleISOFileForListView(RawFileInfo fileInfo)
{
if (fileInfo == null)
{
return;
}
if (dISOFileInfos.FirstOrDefault(f => f.ToString() == fileInfo.ToString()) == null)
{
dISOFileInfos.Add(fileInfo);
}
}
public static void TestFlashLFQ()
{
// get the raw file paths
RawFileInfo raw = new RawFileInfo(Path.Combine(TestContext.CurrentContext.TestDirectory, @"sliced-raw.raw"));
RawFileInfo mzml = new RawFileInfo(Path.Combine(TestContext.CurrentContext.TestDirectory, @"sliced-mzml.mzml"));
// create some PSMs
Identification id1 = new Identification(raw, "EGFQVADGPLYR", "EGFQVADGPLYR", 1350.65681, 94.12193, 2, new List <string> {
"MyProtein"
});
Identification id2 = new Identification(raw, "EGFQVADGPLYR", "EGFQVADGPLYR", 1350.65681, 94.05811, 2, new List <string> {
"MyProtein"
});
Identification id3 = new Identification(mzml, "EGFQVADGPLYR", "EGFQVADGPLYR", 1350.65681, 94.12193, 2, new List <string> {
"MyProtein"
});
Identification id4 = new Identification(mzml, "EGFQVADGPLYR", "EGFQVADGPLYR", 1350.65681, 94.05811, 2, new List <string> {
"MyProtein"
});
// create the FlashLFQ engine
FlashLFQEngine engine = new FlashLFQEngine(new List <Identification> {
id1, id2, id3, id4
});
// run the engine
var results = engine.Run();
// check raw results
Assert.That(results.peaks[raw].Count == 1);
Assert.That(results.peaks[raw].First().intensity > 0);
Assert.That(!results.peaks[raw].First().isMbrFeature);
Assert.That(results.peptideBaseSequences["EGFQVADGPLYR"].intensities[raw] > 0);
Assert.That(results.peptideModifiedSequences["EGFQVADGPLYR"].intensities[raw] > 0);
Assert.That(results.proteinGroups["MyProtein"].intensities[raw] > 0);
// check mzml results
Assert.That(results.peaks[mzml].Count == 1);
Assert.That(results.peaks[mzml].First().intensity > 0);
Assert.That(!results.peaks[mzml].First().isMbrFeature);
Assert.That(results.peptideBaseSequences["EGFQVADGPLYR"].intensities[mzml] > 0);
Assert.That(results.peptideModifiedSequences["EGFQVADGPLYR"].intensities[mzml] > 0);
Assert.That(results.proteinGroups["MyProtein"].intensities[mzml] > 0);
// test peak output
List <string> output = new List <string>()
{
FlashLFQ.ChromatographicPeak.TabSeparatedHeader
};
foreach (var peak in results.peaks.SelectMany(p => p.Value))
{
output.Add(peak.ToString());
}
Assert.That(output.Count == 3);
// test peptide base sequence output
output = new List <string>()
{
Peptide.TabSeparatedHeader
};
foreach (var pep in results.peptideBaseSequences)
{
output.Add(pep.Value.ToString());
}
Assert.That(output.Count == 2);
// test peptide mod sequence output
output = new List <string>()
{
Peptide.TabSeparatedHeader
};
foreach (var pep in results.peptideModifiedSequences)
{
output.Add(pep.Value.ToString());
}
Assert.That(output.Count == 2);
// test protein output
output = new List <string>()
{
ProteinGroup.TabSeparatedHeader
};
foreach (var protein in results.proteinGroups)
{
output.Add(protein.Value.ToString());
}
Assert.That(output.Count == 2);
}
static int Run(Dictionary <string, object> opts)
{
if ((bool)opts["ExampleCommands"] == true)
{
Examples.CommandLineUsage();
Environment.Exit(0);
}
if ((bool)opts["ExampleModifications"] == true)
{
Examples.ExampleMods();
Environment.Exit(0);
}
List <string> files = new List <string>();
QcDataCollection qcDataCollection = new QcDataCollection();
WorkflowParameters parameters = new WorkflowParameters(opts);
if (parameters.InputFiles != null) // did the user give us a list of files?
{
List <string> problems = new List <string>();
files = parameters.InputFiles.ToList();
// check if the list provided contains only .raw files
foreach (string file in files)
{
if (!file.EndsWith(".raw", StringComparison.OrdinalIgnoreCase))
{
problems.Add(file);
}
}
if (problems.Count() == 1)
{
Console.WriteLine("\nERROR: {0} does not appear to be a .raw file. Invoke '>RawTools --help' if you need help.", problems.ElementAt(0));
Log.Error("Invalid file provided: {0}", problems.ElementAt(0));
//Console.Write("Press any key to exit...");
//Console.ReadKey();
return(1);
}
if (problems.Count() > 1)
{
Console.WriteLine("\nERROR: The following {0} files do not appear to be .raw files. Invoke '>RawTools --help' if you need help." +
"\n\n{1}", problems.Count(), String.Join("\n", problems));
Log.Error("Invalid files provided: {0}", String.Join(" ", problems));
//Console.Write("Press any key to exit...");
//Console.ReadKey();
return(1);
}
files = RawFileInfo.RemoveInAcquistionFiles(files);
// if the file location(s) are relative, we need to get the absolute path to them
files.EnsureAbsolutePaths();
Log.Information("Files to be processed, provided as list: {0}", String.Join(" ", files));
}
else if (!String.IsNullOrEmpty(parameters.RawFileDirectory)) // did the user give us a directory?
{
// if QC is being done, use the QC method snf get the qc data collection at the same time
if (parameters.QcParams.QcDirectory != null)
{
(files, qcDataCollection) = QcWorkflow.GetFileListAndQcFile(parameters, parameters.IncludeSubdirectories);
}
// if not, the parse method
else if (Directory.Exists(parameters.RawFileDirectory))
{
files = Directory.GetFiles(parameters.RawFileDirectory, "*.*", SearchOption.TopDirectoryOnly)
.Where(s => s.EndsWith(".raw", StringComparison.OrdinalIgnoreCase)).ToList();
}
else
{
Console.WriteLine("ERROR: The provided directory does not appear to be valid.");
Log.Error("Invalid directory provided: {0}", parameters.RawFileDirectory);
//Console.Write("Press any key to exit...");
//Console.ReadKey();
return(1);
}
files = RawFileInfo.RemoveInAcquistionFiles(files);
// if the file location(s) are relative, we need to get the absolute path to them
files.EnsureAbsolutePaths();
Log.Information("Files to be processed, provided as directory: {0}", String.Join(" ", files));
}
else
{
Console.WriteLine("ERROR: At least one of the following arguments is required: -f, -d");
Log.Error("No raw files or directory specified.");
return(1);
}
if (parameters.ParseParams.Quant)
{
List <string> possible = new List <string>()
{
"TMT0", "TMT2", "TMT6", "TMT10", "TMT11", "iTRAQ4", "iTRAQ8"
};
if (!possible.Contains(parameters.ParseParams.LabelingReagents))
{
Console.WriteLine("ERROR: For quantification, the labeling reagent must be one of {TMT0, TMT2, TMT6, TMT10, TMT11, iTRAQ4, iTRAQ8}");
Log.Error("Invalid labeling reagent provided: {0}", parameters.ParseParams.LabelingReagents);
//Console.Write("Press any key to exit...");
//Console.ReadKey();
return(1);
}
}
if (parameters.ParseParams.Chromatogram != null)
{
List <string> possible = new List <string>()
{
"1", "2", "3", "T", "B"
};
foreach (var x in parameters.ParseParams.Chromatogram)
{
if (!possible.Contains(x.ToString()))
{
Console.WriteLine("ERROR: Incorrect format for -chro. See help.");
Log.Error("Invalid chromatogram argument provided: {Chro}", parameters.ParseParams.Chromatogram);
//Console.Write("Press any key to exit...");
//Console.ReadKey();
return(1);
}
}
}
System.Diagnostics.Stopwatch singleFileTime = new System.Diagnostics.Stopwatch();
System.Diagnostics.Stopwatch totalTime = new System.Diagnostics.Stopwatch();
totalTime.Start();
foreach (string file in files)
{
singleFileTime.Start();
Console.WriteLine("\nProcessing: {0}\n", file);
//using (IRawDataPlus rawFile = RawFileReaderFactory.ReadFile(fileName:file))
using (IRawFileThreadManager rawFile = RawFileReaderFactory.CreateThreadManager(file))
{
if (parameters.ParseParams.OutputDirectory == null)
{
parameters.ParseParams.OutputDirectory = Path.GetDirectoryName(file);
}
WorkFlowsDDA.UniversalDDA(rawFile, parameters, qcDataCollection);
}
singleFileTime.Stop();
Console.WriteLine("\nElapsed time: {0} s", Math.Round(Convert.ToDouble(singleFileTime.ElapsedMilliseconds) / 1000.0, 2));
singleFileTime.Reset();
}
if (parameters.LogDump)
{
Write.LogDump.WriteToDisk(parameters);
}
totalTime.Stop();
Console.WriteLine("\nTime to process all {0} files: {1}", files.Count(), totalTime.Elapsed);
//Console.Write("Press any key to exit...");
//Console.ReadKey();
return(0);
}
public RawFileInfoViewModel(RawFileInfo rawFileInfo)
{
_rawFileInfo = rawFileInfo;
}
public static void CalcRatioSignificanceProteinGroups(SilacType type, ICombinedData combinedData, RawFileInfo fileInfo)
{
if (type == SilacType.Doublets)
{
{
List <double> lNormRatio = new List <double>();
List <double> lRatio = new List <double>();
List <double> lIntensity = new List <double>();
List <int> indices = new List <int>();
for (int i = 0; i < combinedData.GetProteinGroupCount(); i++)
{
IIdentifiedProteinGroup group = combinedData.GetIProteinGroupAt(i);
double ratio;
double normalizedRatio;
int count;
double dev;
int nOutliers;
double pval;
group.GetRatio10(combinedData, out ratio, out normalizedRatio, out count, out dev, out nOutliers, out pval);
double intensity = group.GetIntensity0(combinedData) + group.GetIntensity1(combinedData);
if (normalizedRatio > 0 && !double.IsInfinity(normalizedRatio) && !double.IsNaN(normalizedRatio) && intensity > 0)
{
lNormRatio.Add(Math.Log(normalizedRatio));
lRatio.Add(Math.Log(ratio));
lIntensity.Add(Math.Log(intensity));
indices.Add(i);
}
}
double[] ratioSignificanceA = NumUtil.MovingBoxPlot(lNormRatio.ToArray(), lIntensity.ToArray(), 1);
double[] ratioSignificanceB = NumUtil.MovingBoxPlot(lNormRatio.ToArray(), lIntensity.ToArray(), -1);
for (int i = 0; i < indices.Count; i++)
{
IIdentifiedProteinGroup group = combinedData.GetIProteinGroupAt(indices[i]);
group.RatioSignificanceA10 = ratioSignificanceA[i];
group.RatioSignificanceB10 = ratioSignificanceB[i];
}
}
if (fileInfo.HasExperiment)
{
string[] exps = fileInfo.GetAllExperimentValues();
foreach (string exp in exps)
{
List <double> lratio = new List <double>();
List <double> lIntensity = new List <double>();
List <int> indices = new List <int>();
for (int i = 0; i < combinedData.GetProteinGroupCount(); i++)
{
IIdentifiedProteinGroup group = combinedData.GetIProteinGroupAt(i);
double ratio;
double normalizedRatio;
int count;
double dev;
int nOutliers;
double pval;
group.GetRatio10(combinedData, out ratio, out normalizedRatio, out count, out dev, out nOutliers,
fileInfo.GetRawFileIndicesFromExperiment(exp), out pval);
double intensity = group.GetIntensity0(combinedData) + group.GetIntensity1(combinedData);
if (normalizedRatio > 0 && !double.IsInfinity(normalizedRatio) && !double.IsNaN(normalizedRatio) && intensity > 0)
{
lratio.Add(Math.Log(normalizedRatio));
lIntensity.Add(Math.Log(intensity));
indices.Add(i);
}
}
double[] ratioSignificanceA = NumUtil.MovingBoxPlot(lratio.ToArray(), lIntensity.ToArray(), 1);
double[] ratioSignificanceB = NumUtil.MovingBoxPlot(lratio.ToArray(), lIntensity.ToArray(), -1);
for (int i = 0; i < indices.Count; i++)
{
IIdentifiedProteinGroup group = combinedData.GetIProteinGroupAt(indices[i]);
group.AddRatioSignificanceA10(exp, ratioSignificanceA[i]);
group.AddRatioSignificanceB10(exp, ratioSignificanceB[i]);
}
}
}
}
if (type == SilacType.Triplets)
{
{
List <double> lratio = new List <double>();
List <double> lIntensity = new List <double>();
List <int> indices = new List <int>();
for (int i = 0; i < combinedData.GetProteinGroupCount(); i++)
{
IIdentifiedProteinGroup group = combinedData.GetIProteinGroupAt(i);
double ratio;
double normalizedRatio;
int count;
double dev;
int nOutliers;
double pval;
group.GetRatio10(combinedData, out ratio, out normalizedRatio, out count, out dev, out nOutliers, out pval);
double intensity = group.GetIntensity0(combinedData) + group.GetIntensity1(combinedData) +
group.GetIntensity2(combinedData);
if (normalizedRatio > 0 && !double.IsInfinity(normalizedRatio) && !double.IsNaN(normalizedRatio) && intensity > 0)
{
lratio.Add(Math.Log(normalizedRatio));
lIntensity.Add(Math.Log(intensity));
indices.Add(i);
}
}
double[] ratioSignificanceA = NumUtil.MovingBoxPlot(lratio.ToArray(), lIntensity.ToArray(), 1);
double[] ratioSignificanceB = NumUtil.MovingBoxPlot(lratio.ToArray(), lIntensity.ToArray(), -1);
for (int i = 0; i < indices.Count; i++)
{
IIdentifiedProteinGroup group = combinedData.GetIProteinGroupAt(indices[i]);
group.RatioSignificanceA10 = ratioSignificanceA[i];
group.RatioSignificanceB10 = ratioSignificanceB[i];
}
}
if (fileInfo.HasExperiment)
{
string[] exps = fileInfo.GetAllExperimentValues();
foreach (string exp in exps)
{
List <double> lratio = new List <double>();
List <double> lIntensity = new List <double>();
List <int> indices = new List <int>();
for (int i = 0; i < combinedData.GetProteinGroupCount(); i++)
{
IIdentifiedProteinGroup group = combinedData.GetIProteinGroupAt(i);
double ratio;
double normalizedRatio;
int count;
double dev;
int nOutliers;
double pval;
group.GetRatio10(combinedData, out ratio, out normalizedRatio, out count, out dev, out nOutliers,
fileInfo.GetRawFileIndicesFromExperiment(exp), out pval);
double intensity = group.GetIntensity0(combinedData) + group.GetIntensity1(combinedData) +
group.GetIntensity2(combinedData);
if (normalizedRatio > 0 && !double.IsInfinity(normalizedRatio) && !double.IsNaN(normalizedRatio) && intensity > 0)
{
lratio.Add(Math.Log(normalizedRatio));
lIntensity.Add(Math.Log(intensity));
indices.Add(i);
}
}
double[] ratioSignificanceA = NumUtil.MovingBoxPlot(lratio.ToArray(), lIntensity.ToArray(), 1);
double[] ratioSignificanceB = NumUtil.MovingBoxPlot(lratio.ToArray(), lIntensity.ToArray(), -1);
for (int i = 0; i < indices.Count; i++)
{
IIdentifiedProteinGroup group = combinedData.GetIProteinGroupAt(indices[i]);
group.AddRatioSignificanceA10(exp, ratioSignificanceA[i]);
group.AddRatioSignificanceB10(exp, ratioSignificanceB[i]);
}
}
}
{
List <double> lratio = new List <double>();
List <double> lIntensity = new List <double>();
List <int> indices = new List <int>();
for (int i = 0; i < combinedData.GetProteinGroupCount(); i++)
{
IIdentifiedProteinGroup group = combinedData.GetIProteinGroupAt(i);
double ratio;
double normalizedRatio;
int count;
double dev;
int nOutliers;
double pval;
group.GetRatio20(combinedData, out ratio, out normalizedRatio, out count, out dev, out nOutliers, out pval);
double intensity = group.GetIntensity0(combinedData) + group.GetIntensity1(combinedData) +
group.GetIntensity2(combinedData);
if (normalizedRatio > 0 && !double.IsInfinity(normalizedRatio) && !double.IsNaN(normalizedRatio) && intensity > 0)
{
lratio.Add(Math.Log(normalizedRatio));
lIntensity.Add(Math.Log(intensity));
indices.Add(i);
}
}
double[] ratioSignificanceA = NumUtil.MovingBoxPlot(lratio.ToArray(), lIntensity.ToArray(), 1);
double[] ratioSignificanceB = NumUtil.MovingBoxPlot(lratio.ToArray(), lIntensity.ToArray(), -1);
for (int i = 0; i < indices.Count; i++)
{
IIdentifiedProteinGroup group = combinedData.GetIProteinGroupAt(indices[i]);
group.RatioSignificanceA20 = ratioSignificanceA[i];
group.RatioSignificanceB20 = ratioSignificanceB[i];
}
}
if (fileInfo.HasExperiment)
{
string[] exps = fileInfo.GetAllExperimentValues();
foreach (string exp in exps)
{
List <double> lratio = new List <double>();
List <double> lIntensity = new List <double>();
List <int> indices = new List <int>();
for (int i = 0; i < combinedData.GetProteinGroupCount(); i++)
{
IIdentifiedProteinGroup group = combinedData.GetIProteinGroupAt(i);
double ratio;
double normalizedRatio;
int count;
double dev;
int nOutliers;
double pval;
group.GetRatio20(combinedData, out ratio, out normalizedRatio, out count, out dev, out nOutliers,
fileInfo.GetRawFileIndicesFromExperiment(exp), out pval);
double intensity = group.GetIntensity0(combinedData) + group.GetIntensity1(combinedData) +
group.GetIntensity2(combinedData);
if (normalizedRatio > 0 && !double.IsInfinity(normalizedRatio) && !double.IsNaN(normalizedRatio) && intensity > 0)
{
lratio.Add(Math.Log(normalizedRatio));
lIntensity.Add(Math.Log(intensity));
indices.Add(i);
}
}
double[] ratioSignificanceA = NumUtil.MovingBoxPlot(lratio.ToArray(), lIntensity.ToArray(), 1);
double[] ratioSignificanceB = NumUtil.MovingBoxPlot(lratio.ToArray(), lIntensity.ToArray(), -1);
for (int i = 0; i < indices.Count; i++)
{
IIdentifiedProteinGroup group = combinedData.GetIProteinGroupAt(indices[i]);
group.AddRatioSignificanceA20(exp, ratioSignificanceA[i]);
group.AddRatioSignificanceB20(exp, ratioSignificanceB[i]);
}
}
}
{
List <double> lratio = new List <double>();
List <double> lIntensity = new List <double>();
List <int> indices = new List <int>();
for (int i = 0; i < combinedData.GetProteinGroupCount(); i++)
{
IIdentifiedProteinGroup group = combinedData.GetIProteinGroupAt(i);
double ratio;
double normalizedRatio;
int count;
double dev;
int nOutliers;
double pval;
group.GetRatio21(combinedData, out ratio, out normalizedRatio, out count, out dev, out nOutliers, out pval);
double intensity = group.GetIntensity0(combinedData) + group.GetIntensity1(combinedData) +
group.GetIntensity2(combinedData);
if (normalizedRatio > 0 && !double.IsInfinity(normalizedRatio) && !double.IsNaN(normalizedRatio) && intensity > 0)
{
lratio.Add(Math.Log(normalizedRatio));
lIntensity.Add(Math.Log(intensity));
indices.Add(i);
}
}
double[] ratioSignificanceA = NumUtil.MovingBoxPlot(lratio.ToArray(), lIntensity.ToArray(), 1);
double[] ratioSignificanceB = NumUtil.MovingBoxPlot(lratio.ToArray(), lIntensity.ToArray(), -1);
for (int i = 0; i < indices.Count; i++)
{
IIdentifiedProteinGroup group = combinedData.GetIProteinGroupAt(indices[i]);
group.RatioSignificanceA21 = ratioSignificanceA[i];
group.RatioSignificanceB21 = ratioSignificanceB[i];
}
}
if (fileInfo.HasExperiment)
{
string[] exps = fileInfo.GetAllExperimentValues();
foreach (string exp in exps)
{
List <double> lratio = new List <double>();
List <double> lIntensity = new List <double>();
List <int> indices = new List <int>();
for (int i = 0; i < combinedData.GetProteinGroupCount(); i++)
{
IIdentifiedProteinGroup group = combinedData.GetIProteinGroupAt(i);
double ratio;
double normalizedRatio;
int count;
double dev;
int nOutliers;
double pval;
group.GetRatio21(combinedData, out ratio, out normalizedRatio, out count, out dev, out nOutliers,
fileInfo.GetRawFileIndicesFromExperiment(exp), out pval);
double intensity = group.GetIntensity0(combinedData) + group.GetIntensity1(combinedData) +
group.GetIntensity2(combinedData);
if (normalizedRatio > 0 && !double.IsInfinity(normalizedRatio) && !double.IsNaN(normalizedRatio) && intensity > 0)
{
lratio.Add(Math.Log(normalizedRatio));
lIntensity.Add(Math.Log(intensity));
indices.Add(i);
}
}
double[] ratioSignificanceA = NumUtil.MovingBoxPlot(lratio.ToArray(), lIntensity.ToArray(), 1);
double[] ratioSignificanceB = NumUtil.MovingBoxPlot(lratio.ToArray(), lIntensity.ToArray(), -1);
for (int i = 0; i < indices.Count; i++)
{
IIdentifiedProteinGroup group = combinedData.GetIProteinGroupAt(indices[i]);
group.AddRatioSignificanceA21(exp, ratioSignificanceA[i]);
group.AddRatioSignificanceB21(exp, ratioSignificanceB[i]);
}
}
}
}
}
public static void DoQc(WorkflowParameters parameters)
{
//QcDataCollectionDDA qcDataCollection;
dynamic qcDataCollection;
string dataDirectory = parameters.RawFileDirectory;
string qcDirectory = parameters.QcParams.QcDirectory;
string qcSearchDataDirecotry = parameters.QcParams.QcSearchDataDirectory;
List <string> fileList = new List <string>();
string qcFile = Path.Combine(qcDirectory, "QC.xml");
(fileList, qcDataCollection) = GetFileListAndQcFile(parameters);
foreach (string fileName in fileList)
{
Console.WriteLine("\nProcessing {0}", fileName);
if (!RawFileInfo.CheckIfValid(fileName))
{
continue;
}
// okay, it is probably a real raw file, let's do the QC
// check if the raw file already exists in the QC data with a different name
if (CheckIfFilePresentInQcCollection(fileName, qcDataCollection))
{
Log.Information("A file with the same creation date and time as {File} already exists in the QC data", fileName);
Console.WriteLine("A file with the same creation date and time as {File} already exists in the QC data. Skipping to next file.",
fileName);
continue;
}
IRawFileThreadManager rawFileThreadManager = RawFileReaderFactory.CreateThreadManager(fileName);
if (parameters.ExpType == ExperimentType.DDA)
{
WorkFlowsDDA.QcDDA(rawFileThreadManager, parameters);
}
//else if (parameters.ExpType == ExperimentType.DIA)
//{
// WorkFlowsDIA.QcDIA(rawFileThreadManager, parameters);
//}
/*
* using (IRawDataPlus rawFile = RawFileReaderFactory.ReadFile(fileName))
* {
* rawFile.SelectInstrument(Device.MS, 1);
*
* if (parameters.ExpType == ExperimentType.DDA)
* {
* WorkFlowsDDA.QcDDA(rawFile, parameters);
* }
* else if (parameters.ExpType == ExperimentType.DIA)
* {
* WorkFlowsDIA.QcDIA(rawFile, parameters);
* }
* }*/
Log.Information("QC finished: {File}", fileName);
}
Log.Information("QC of all files completed");
Console.WriteLine("QC of all files completed!");
}
