public static bool CheckIfValid(string fileName)
{
IFileHeader rawHeader = null;
// try to open the raw file header
try
{
rawHeader = FileHeaderReaderFactory.ReadFile(fileName);
}
catch (Exception)
{
Log.Information("{File} is not a valid raw file", fileName);
Console.WriteLine("{0} is not a valid raw file.", fileName);
return(false);
}
// is it a real raw file?
if (rawHeader.FileType == FileType.RawFile)
{
Log.Information("{File} is a valid raw file", fileName);
Log.Information("Creation date: {Date}", rawHeader.CreationDate);
Log.Information("File description: {Description}", rawHeader.FileDescription);
return(true);
}
else
{
Log.Information("{File} is not a valid raw file", fileName);
Console.WriteLine("{0} is not a valid raw file, continuing to next file.", fileName);
return(false);
}
}
public static bool CheckIfFilePresentInQcCollection(string fileName, QcDataCollection qcDataCollection)
{
IFileHeader rawHeader = FileHeaderReaderFactory.ReadFile(fileName);
if (qcDataCollection.QcData.Keys.Contains(rawHeader.CreationDate))
{
return(true);
}
else
{
return(false);
}
}
public static void DoQc(QcParameters qcParameters)
{
QcDataCollection qcDataCollection;
string dataDirectory = qcParameters.RawFileDirectory;
string qcDirectory = qcParameters.QcDirectory;
string qcSearchDataDirecotry = qcParameters.QcSearchDataDirectory;
SearchParameters searchParameters = qcParameters.searchParameters;
// our qc file
string qcFile = Path.Combine(qcDirectory, "QC.xml");
// see if the file exists
if (File.Exists(qcFile))
{
// if so, open it
try
{
qcDataCollection = XmlSerialization.ReadFromXmlFile <QcDataCollection>(qcFile);
Log.Information("QC data file loaded successfully");
}
catch (Exception e)
{
Log.Error(e, "Failed while loading QC data");
throw e;
}
}
else
{
// if not, check if the directory exists
if (!Directory.Exists(qcDirectory))
{
Directory.CreateDirectory(qcDirectory);
}
qcDataCollection = new QcDataCollection(dataDirectory, qcDirectory);
Log.Information("Appears to be a new QC directory. New QC data collection created.");
}
// get our list of new raw files. it is every raw file in the directory that is not listed in the qc data
var fileList = Directory.GetFiles(dataDirectory, "*.*", SearchOption.TopDirectoryOnly)
.Where(s => s.EndsWith(".raw", StringComparison.OrdinalIgnoreCase)).ToList();
if (fileList.Count() == 0)
{
Log.Error("No raw files found in {Directory}", dataDirectory);
Console.WriteLine("{0} contains no raw files!", dataDirectory);
Environment.Exit(1);
}
fileList.RemoveAll(s => qcDataCollection.ProcessedRawFiles.Contains(Path.GetFileName(s)));
Log.Information("Raw files in QC queue: {Files}", fileList);
if (fileList.Count() == 0)
{
Log.Information("No new files to QC");
Console.WriteLine("No new files in the directory to QC!");
Environment.Exit(0);
}
Console.WriteLine("{0} file(s) to process", fileList.Count());
foreach (string fileName in fileList)
{
Console.WriteLine("Processing {0}", fileName);
IFileHeader rawHeader;
// try to open the raw file header
try
{
rawHeader = FileHeaderReaderFactory.ReadFile(fileName);;
}
catch (Exception)
{
Log.Information("{File} is not a valid raw file", fileName);
Console.WriteLine("{0} is not a valid raw file, continuing to next file.", fileName);
continue;
}
// is it a real raw file?
if (rawHeader.FileType == FileType.RawFile)
{
Log.Information("{File} is a valid raw file", fileName);
Log.Information("Creation date: {Date}", rawHeader.CreationDate);
Log.Information("File description: {Description}", rawHeader.FileDescription);
}
else
{
Log.Information("{File} is not a valid raw file", fileName);
Console.WriteLine("{0} is not a valid raw file, continuing to next file.", 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 (qcDataCollection.QcData.Keys.Contains(rawHeader.CreationDate))
{
Log.Information("A file with the same creation date and time as {File} already exists in the QC data", fileName);
Console.WriteLine("{0} appears to already exist in the QC data with the name {1}. Skipping to next file.",
fileName, qcDataCollection.QcData[rawHeader.CreationDate].RawFile);
continue;
}
using (IRawDataPlus rawFile = RawFileReaderFactory.ReadFile(fileName))
{
rawFile.SelectInstrument(Device.MS, 1);
RawDataCollection rawData = new RawDataCollection(rawFile);
rawData.ExtractAll(rawFile);
/*
* if (idpyPars?.QuantMods != null)
* {
* rawData.quantData.Quantify(rawData, rawFile, )
* }
*/
QcDataContainer newQcData = ProcessQcData(Data: qcDataCollection, rawData: rawData, rawFile: rawFile, qcDirectory: qcDirectory);
if (searchParameters != null)
{
Search.WriteSearchMGF(qcParameters, rawData, rawFile, searchParameters.FixedScans);
Search.RunSearch(qcParameters, rawData, rawFile);
newQcData.ParseSearchResults(rawData, rawFile, qcParameters);
/*
* if (searchParameters.SearchAlgorithm == SearchAlgorithm.XTandem)
* {
* SearchQC.ParseXTandem(newQcData, qcParameters);
* newQcData.IdentipyParameters = String.Format("\"Algorithm: X!Tandem; fmods: {0}; nmod: {1}; kmod: {2}; xmod: {3}; fastaDB: {4}; xtandemDirectory: {5}\"",
* searchParameters.FixedMods, searchParameters.NMod, searchParameters.KMod, searchParameters.XMod, searchParameters.FastaDatabase, searchParameters.XTandemDirectory);
* }
* else
* {
* SearchQC.ParseIdentipy(newQcData, rawData, rawFile, qcParameters);
* newQcData.IdentipyParameters = String.Format("\"Algorithm: IdentiPy; fmods: {0}; nmod: {1}; kmod: {2}; xmod: {3}; fastaDB: {4}; pythonExecutable: {5}; identipyScript: {6}\"",
* searchParameters.FixedMods, searchParameters.NMod, searchParameters.KMod, searchParameters.XMod, searchParameters.FastaDatabase, searchParameters.PythonExecutable, searchParameters.IdentipyScript);
* }
*/
}
qcDataCollection.QcData.Add(rawFile.CreationDate, newQcData);
qcDataCollection.ProcessedRawFiles.Add(Path.GetFileName(rawData.rawFileName));
qcDataCollection.WriteQcToTable();
}
Log.Information("QC finished: {File}", fileName);
}
Log.Information("QC of all files completed");
Console.WriteLine("QC of all files completed!");
try
{
XmlSerialization.WriteToXmlFile <QcDataCollection>(qcFile, qcDataCollection);
Log.Information("QC file saved successfully");
Console.WriteLine("QC file saved successfully");
}
catch (Exception e)
{
Log.Error(e, "Failed during serialization of QC data");
throw e;
}
}
