public static void WriteSearchMGF(QcParameters qcParameters, RawDataCollection rawData, IRawDataPlus rawFile, bool fixedScans = false)
{
var pars = qcParameters.searchParameters;
int[] scans = AdditionalMath.SelectRandomScans(scans: rawData.scanIndex.ScanEnumerators[MSOrderType.Ms2], num: pars.NumSpectra, fixedScans: fixedScans);
MGF.WriteMGF(rawData, rawFile, qcParameters.QcSearchDataDirectory, pars.MgfMassCutoff, scans, pars.MgfIntensityCutoff);
}
public static void RunIdentipy(RawDataCollection rawData, IRawDataPlus rawFile, string QcDataDirectory, SearchParameters idpyPars, bool writeMGF = true)
{
int[] scans;
string pyExec, idpyScript, mgfFile;
// get the path to the python executable and identipy start script if they have not been specified
if (idpyPars.PythonExecutable == null & idpyPars.IdentipyScript == null)
{
string pyDir = GetPythonDir();
pyExec = GetPythonExec(pyDir);
idpyScript = GetIdentipyExec(pyDir);
Log.Information("Found python directory: {PyDir}", pyDir);
Log.Information("Found python executable: {PyExec}", pyExec);
Log.Information("Found identipy start script: {IdpyScript}", idpyScript);
}
else
{
pyExec = idpyPars.PythonExecutable;
idpyScript = idpyPars.IdentipyScript;
}
if (writeMGF)
{
// get a random subset of scans
scans = AdditionalMath.SelectRandomScans(scans: rawData.scanIndex.ScanEnumerators[MSOrderType.Ms2], num: idpyPars.NumSpectra);
// write them to a mgf file
MGF.WriteMGF(rawData, rawFile, QcDataDirectory, scans: scans, cutoff: idpyPars.MgfMassCutoff, intensityCutoff: idpyPars.MgfIntensityCutoff);
}
// recreate the path to the mgf
mgfFile = Path.Combine(QcDataDirectory, Path.GetFileName(rawData.rawFileName) + ".mgf");
// run identipy, supresseing RunTimeWarnings
//IdentipyExecute(idpyExec, idpyPars.FastaDatabase, idpyPars.FixedMods, idpyPars.VariableMods, mgfFile);
Console.WriteLine("Starting Identipy");
Log.Information("Starting Identipy");
IdentipyExecute(pyExec, idpyScript, mgfFile, idpyPars, rawData.methodData.MassAnalyzers[MSOrderType.Ms2]);
}
static int DoStuff(ArgumentParser.ParseOptions opts)
{
List <string> files = new List <string>();
if (opts.InputFiles.Count() > 0) // did the user give us a list of files?
{
List <string> problems = new List <string>();
files = opts.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));
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));
return(1);
}
Log.Information("Files to be processed, provided as list: {0}", String.Join(" ", files));
}
else // did the user give us a directory?
{
if (Directory.Exists(opts.InputDirectory))
{
files = Directory.GetFiles(opts.InputDirectory, "*.*", 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}", opts.InputDirectory);
return(1);
}
Log.Information("Files to be processed, provided as directory: {0}", String.Join(" ", files));
}
if (opts.Quant)
{
List <string> possible = new List <string>()
{
"TMT0", "TMT2", "TMT6", "TMT10", "TMT11", "iTRAQ4", "iTRAQ8"
};
if (!possible.Contains(opts.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}", opts.LabelingReagents);
return(1);
}
}
if (opts.Chromatogram != null)
{
List <string> possible = new List <string>()
{
"1T", "2T", "3T", "1B", "2B", "3B", "1TB", "2TB", "3TB", "1TB", "2TB", "3TB"
};
if (!possible.Contains(opts.Chromatogram))
{
Console.WriteLine("ERROR: Incorrect format for --chro. See help.");
Log.Error("Invalid chromatogram argument provided: {Chro}", opts.Chromatogram);
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))
{
rawFile.SelectInstrument(Device.MS, 1);
Log.Information("Now processing: {File} --- Instrument: {Instrument}", Path.GetFileName(file), rawFile.GetInstrumentData().Name);
RawDataCollection rawData = new RawDataCollection(rawFile: rawFile);
QuantDataCollection quantData = new QuantDataCollection();
bool isBoxCar = rawData.isBoxCar;
if (rawData.isBoxCar)
{
Console.WriteLine("\nRaw file appears to be a boxcar-type experiment. Precursor peak analysis won't be performed!\n");
}
if (opts.ParseData | opts.Metrics | opts.Quant)
{
rawData.ExtractAll(rawFile);
if (!isBoxCar)
{
rawData.CalcPeakRetTimesAndInts(rawFile: rawFile);
}
}
if (opts.Quant)
{
rawData.quantData.Quantify(rawData: rawData, rawFile: rawFile, labelingReagent: opts.LabelingReagents);
}
if (opts.UnlabeledQuant & !isBoxCar)
{
rawData.QuantifyPrecursorPeaks(rawFile);
}
if (opts.Metrics)
{
rawData.metaData.AggregateMetaData(rawData, rawFile);
}
if (opts.ParseData | opts.Quant)
{
if (opts.Quant)
{
Parse.WriteMatrix(rawData: rawData, rawFile: rawFile, metaData: rawData.metaData, quantData: rawData.quantData, outputDirectory: opts.OutputDirectory);
}
else
{
Parse.WriteMatrix(rawData: rawData, rawFile: rawFile, metaData: rawData.metaData, outputDirectory: opts.OutputDirectory);
}
}
if (opts.WriteMGF)
{
MGF.WriteMGF(rawData: rawData, rawFile: rawFile, outputDirectory: opts.OutputDirectory, cutoff: opts.MassCutOff,
intensityCutoff: opts.IntensityCutoff);
}
if (opts.Metrics)
{
MetricsData metricsData = new MetricsData();
if (opts.Quant)
{
metricsData.GetMetricsData(metaData: rawData.metaData, rawData: rawData, rawFile: rawFile, quantData: rawData.quantData);
}
else
{
metricsData.GetMetricsData(metaData: rawData.metaData, rawData: rawData, rawFile: rawFile);
}
metricsData.GetMetricsData(metaData: rawData.metaData, rawData: rawData, rawFile: rawFile);
Metrics.WriteMatrix(rawData, metricsData, opts.OutputDirectory);
}
if (opts.Chromatogram != null)
{
int order = Convert.ToInt32((opts.Chromatogram.ElementAt(0).ToString()));
if (order > (int)rawData.methodData.AnalysisOrder)
{
Log.Error("Specified MS order ({Order}) for chromatogram is higher than experiment order ({ExpOrder})",
(MSOrderType)order, rawData.methodData.AnalysisOrder);
Console.WriteLine("Specified MS order ({0}) for chromatogram is higher than experiment order ({1}). Chromatogram(s) won't be written.",
(MSOrderType)order, rawData.methodData.AnalysisOrder);
}
else
{
rawData.WriteChromatogram(rawFile, (MSOrderType)order, opts.Chromatogram.Contains("T"), opts.Chromatogram.Contains("B"), opts.OutputDirectory);
}
}
}
singleFileTime.Stop();
Console.WriteLine("\nElapsed time: {0} s", Math.Round(Convert.ToDouble(singleFileTime.ElapsedMilliseconds) / 1000.0, 2));
singleFileTime.Reset();
}
totalTime.Stop();
Console.WriteLine("\nTime to process all {0} files: {1}", files.Count(), totalTime.Elapsed);
return(0);
}