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 WriteSearchMGF(WorkflowParameters parameters, CentroidStreamCollection centroids, SegmentScanCollection segments, RetentionTimeCollection retentionTimes,
PrecursorMassCollection precursorMasses, PrecursorScanCollection precursorScans, TrailerExtraCollection trailerExtras, MethodDataContainer methodData,
ScanIndex index, string rawFileName, bool fixedScans = false)
{
var pars = parameters.QcParams.SearchParameters;
int[] scans = AdditionalMath.SelectRandomScans(scans: index.ScanEnumerators[MSOrderType.Ms2],
num: parameters.QcParams.NumberSpectra, fixedScans: parameters.QcParams.FixedScans);
string mgfFile = ReadWrite.GetPathToFile(parameters.QcParams.QcSearchDataDirectory, rawFileName, ".mgf");
MgfWriter.WriteMGF(rawFileName, centroids, segments, parameters, retentionTimes, precursorMasses, precursorScans,
trailerExtras, methodData, index, outputFile: mgfFile, scans: scans);
}
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]);
}