public static string AutoDetermineBestInputFile(string inputDirectoryPath, List <string> datasetNames,
out PeptideHitResultTypes matchedResultType)
{
return(ReaderFactory.AutoDetermineBestInputFile(inputDirectoryPath, datasetNames, out matchedResultType));
}
public static void Main()
{
//const string synFileSequest = @"Seq201304121552_Auto934225\Firestone_Soil_07_18_05APR13_Frodo_12-12-04_syn.txt";
//const string synFileMSGFPlus = @"MSG201304261714_Auto938181\FSFA-299b_25Apr13_Methow_13-02-13_msgfplus_syn.txt";
const string resultsPathSequest = @"\\proto-7\VOrbi05\2013_2\Firestone_Soil_07_18_05APR13_Frodo_12-12-04\Seq201304121552_Auto934225";
// const string resultsPathMSGFPlus = "MSG201304261714_Auto938181"
// const string resultsPathMSGFPlus = "\\proto-7\VOrbiETD03\2015_1\proteogeomics_32_crude_heavy_peptides_200f_25Feb15_Tiger_15-01-26\MSG201503091410_Auto1169297"
const string resultsPathMSGFPlus = @"C:\DMS_WorkDir";
//const string resultsXTandem = @"\\proto-7\VOrbiETD01\2013_3\QC_Shew_13_04_pt1_1_2_27Jun13_Leopard_13-05-20\XTM201307011524_Auto958319"
//const string resultsMSAlign = @"\\proto-9\VOrbiETD02\2014_1\Synocho_D2_2\MSA201402281500_Auto1030272"
string synOrFhtFile;
var matchedResultType = PHRPReader.PeptideHitResultTypes.Unknown;
if (false)
{
Console.WriteLine();
synOrFhtFile = ReaderFactory.AutoDetermineBestInputFile(resultsPathSequest, out matchedResultType);
if (!string.IsNullOrEmpty(synOrFhtFile) && matchedResultType != PHRPReader.PeptideHitResultTypes.Unknown)
{
TestPHRPReader(synOrFhtFile, blnSkipDuplicates: true);
}
}
var msgfPlusDirectory = new DirectoryInfo(resultsPathMSGFPlus);
if (!msgfPlusDirectory.Exists)
{
Console.WriteLine("Warning, Folder not found: " + resultsPathMSGFPlus);
}
if (msgfPlusDirectory.Exists)
{
Console.WriteLine();
synOrFhtFile = ReaderFactory.AutoDetermineBestInputFile(resultsPathMSGFPlus, out matchedResultType);
if (!string.IsNullOrEmpty(synOrFhtFile) && matchedResultType != PHRPReader.PeptideHitResultTypes.Unknown)
{
TestPHRPReader(synOrFhtFile, blnSkipDuplicates: false);
}
}
if (msgfPlusDirectory.Exists)
{
Console.WriteLine();
synOrFhtFile = ReaderFactory.AutoDetermineBestInputFile(resultsPathMSGFPlus, out matchedResultType);
if (!string.IsNullOrEmpty(synOrFhtFile) && matchedResultType != PHRPReader.PeptideHitResultTypes.Unknown)
{
TestPHRPReader(synOrFhtFile, blnSkipDuplicates: true);
}
}
if (msgfPlusDirectory.Exists)
{
// Look for an MSGF+ parameter file to parse
var lstFiles = msgfPlusDirectory.GetFiles("MSGFDB*.txt");
if (lstFiles.Length > 0)
{
TestMSGFPlusParamFileParsing(lstFiles.First().FullName);
}
}
var sequestDirectory = new DirectoryInfo(resultsPathSequest);
if (!sequestDirectory.Exists)
{
Console.WriteLine("Warning, Folder not found: " + resultsPathSequest);
}
if (!sequestDirectory.Exists)
{
return;
}
var startTimeNoSkipDup = default(DateTime);
var endTimeNoSkipDup = default(DateTime);
var startTimeSkipDup = default(DateTime);
var endTimeSkipDup = default(DateTime);
Console.WriteLine();
synOrFhtFile = ReaderFactory.AutoDetermineBestInputFile(resultsPathSequest);
if (!string.IsNullOrEmpty(synOrFhtFile) && matchedResultType != PHRPReader.PeptideHitResultTypes.Unknown)
{
startTimeNoSkipDup = DateTime.UtcNow;
TestPHRPReader(synOrFhtFile, blnSkipDuplicates: false);
endTimeNoSkipDup = DateTime.UtcNow;
}
Console.WriteLine();
synOrFhtFile = ReaderFactory.AutoDetermineBestInputFile(resultsPathSequest, out matchedResultType);
if (!string.IsNullOrEmpty(synOrFhtFile) && matchedResultType != PHRPReader.PeptideHitResultTypes.Unknown)
{
startTimeSkipDup = DateTime.UtcNow;
TestPHRPReader(synOrFhtFile, blnSkipDuplicates: true);
endTimeSkipDup = DateTime.UtcNow;
}
Console.WriteLine();
Console.WriteLine("Elapsed time (Keep Duplicates): " + endTimeNoSkipDup.Subtract(startTimeNoSkipDup).TotalSeconds.ToString("0.0") + " seconds");
Console.WriteLine("Elapsed time (Skip Duplicates): " + endTimeSkipDup.Subtract(startTimeSkipDup).TotalSeconds.ToString("0.0") + " seconds");
Console.WriteLine();
}