public void TestMSGFFilter()
{
const string workDir = @"F:\My Documents\Projects\JoshAldrich\AScore\AScore_DLL\TestCase";
var fht = Path.Combine(workDir, "GmaxP_itraq_NiNTA_15_29Apr10_Hawk_03-10-09p_fht.txt");
var param = Path.Combine(workDir, "AScore_CID_0.5Da_ETD_0.5Da_HCD_0.05Da_MSGF1E-12.xml");
var dta = Path.Combine(workDir, "GmaxP_itraq_NiNTA_15_29Apr10_Hawk_03-10-09p_dta.txt");
var resultsFile = Path.Combine(workDir, "GmaxP_itraq_NiNTA_15_29Apr10_Hawk_03-10-09p_fht_ascore.txt");
var peptideMassCalculator = GetDefaultPeptideMassCalculator();
PsmResultsManager dfht = new SequestFHT(fht);
var pfile = new ParameterFileManager(param);
var spectraCache = new SpectraManagerCache(peptideMassCalculator);
spectraCache.OpenFile(dta);
var sw = System.Diagnostics.Stopwatch.StartNew();
var ascoreEngine = new AScore_DLL.AScoreProcessor();
ascoreEngine.RunAScoreOnSingleFile(spectraCache, dfht, pfile, resultsFile);
sw.Stop();
Console.WriteLine("Time elapsed: {0:F1} seconds", sw.Elapsed.TotalSeconds);
Console.WriteLine("Results in " + resultsFile);
}
public void EcoliTest2()
{
var datasetname = new string[] {
@"C:\Documents and Settings\aldr699\My Documents2011\SisiTopDown\E_coli_BW_70_bottom_up_23Sep11_Draco_11-07-12_fht.txt"
};
var dtaname = new string[] {
@"C:\Documents and Settings\aldr699\My Documents2011\SisiTopDown\E_coli_BW_70_bottom_up_23Sep11_Draco_11-07-12_dta.txt"
};
var ascParam = new string[] {
@"C:\Documents and Settings\aldr699\My Documents2011\SisiTopDown\parameterFileForMus.xml"
};
var peptideMassCalculator = GetDefaultPeptideMassCalculator();
for (var i = 0; i < dtaname.Length; i++)
{
var outFile = datasetname[i].Substring(0, datasetname[i].Length - 8) + "_AScoreTry.txt";
PsmResultsManager datasetMan = new SequestFHT(datasetname[i]);
//DtaManager dtaManager = new DtaManager(dtaname[i]);
var spectraCache = new SpectraManagerCache(peptideMassCalculator);
spectraCache.OpenFile(dtaname[i]);
var paramFile = new ParameterFileManager(ascParam[i]);
var ascoreEngine = new AScore_DLL.AScoreProcessor();
//ascoreEngine.AlgorithmRun(dtaManager, datasetMan, paramFile, outFile);
ascoreEngine.RunAScoreOnSingleFile(spectraCache, datasetMan, paramFile, outFile);
}
}
public void FengTest2()
{
var datasetname = new string[] {
@"C:\Documents and Settings\aldr699\My Documents2011\FengTest\ETD\B_Mus_con_15Oct10_Hawk_03-10-10p_fht.txt"
};
var dtaname = new string[] {
@"C:\Documents and Settings\aldr699\My Documents2011\FengTest\ETD\B_Mus_con_15Oct10_Hawk_03-10-10p_dta.txt"
};
var ascParam = new string[] {
@"C:\Documents and Settings\aldr699\My Documents2011\FengTest\parameterFileForMusETD2.xml"
};
var peptideMassCalculator = GetDefaultPeptideMassCalculator();
for (var i = 0; i < dtaname.Length; i++)
{
var outFile = datasetname[i].Substring(0, datasetname[i].Length - 8) + "_AScoreTry.txt";
PsmResultsManager datasetMan = new SequestFHT(datasetname[i]);
//DtaManager dtaManager = new DtaManager(dtaname[i]);
var spectraCache = new SpectraManagerCache(peptideMassCalculator);
spectraCache.OpenFile(dtaname[i]);
var paramFile = new ParameterFileManager(ascParam[i]);
var ascoreEngine = new AScore_DLL.AScoreProcessor();
//ascoreEngine.AlgorithmRun(dtaManager, datasetMan, paramFile, outFile);
ascoreEngine.RunAScoreOnSingleFile(spectraCache, datasetMan, paramFile, outFile);
}
}
public void NewTest()
{
var ascore = new string[] { "SOSM_May_P1_R2_13Jun11_Hawk_11-04-02p_fht.txt" };
//"SOSM_May_G2_R2_13Jun11_Hawk_11-04-02p_fht.txt",
//"SOSM_May_M_R2_6Jun11_Hawk_11-04-02p_fht.txt",
//"SOSM_May_P1_R1_6Jun11_Hawk_11-04-02p_fht.txt",
//"SOSM_May_P1_R2_6Jun11_Hawk_11-04-02p_fht.txt"};
const string fhtPath = @"C:\Documents and Settings\aldr699\My Documents2011\SOSM\CID\ForAScore";
const string dtapath = @"C:\Documents and Settings\aldr699\My Documents2011\SOSM";
const string parFile = @"C:\Documents and Settings\aldr699\My Documents2011\SOSM\parameterFile.xml";
var peptideMassCalculator = GetDefaultPeptideMassCalculator();
foreach (var a in ascore)
{
var myFht = Path.Combine(fhtPath, a);
var myDta = Path.Combine(dtapath, a.Substring(0, a.Length - 8) + "_dta.txt");
var outFile = Path.Combine(fhtPath, a.Substring(0, a.Length - 8) + "_AScore.txt");
PsmResultsManager datasetMan = new SequestFHT(myFht);
//DtaManager dtaManager = new DtaManager(myDta);
var spectraCache = new SpectraManagerCache(peptideMassCalculator);
spectraCache.OpenFile(myDta);
var paramFile = new ParameterFileManager(parFile);
var ascoreEngine = new AScore_DLL.AScoreProcessor();
//ascoreEngine.AlgorithmRun(dtaManager, datasetMan, paramFile, outFile);
ascoreEngine.RunAScoreOnSingleFile(spectraCache, datasetMan, paramFile, outFile);
}
}
public void Sisi()
{
const string ascoreP = "parameterFile.xml";
const string direct = @"C:\Users\aldr699\Documents\2012\Sisi_ASCORE\Group2";
var fhtFiles = new List <string> {
"NMR_HetR_UG_01_20Jul11_Andromeda_11-06-19_fhtf.txt",
"NMR_HetR_UG_02_20Jul11_Andromeda_11-06-29_fhtf.txt",
"NMR_HetR_UG_03_20Jul11_Andromeda_11-06-19_fhtf.txt",
"NMR_HetR_LG_01_20Jul11_Andromeda_11-06-29_fhtf.txt",
"NMR_HetR_LG_02_20Jul11_Andromeda_11-06-29_fhtf.txt",
"NMR_HetR_LG_03_20Jul11_Andromeda_11-06-19_fhtf.txt",
"NMR_LaR80a_01_20Jul11_Andromeda_11-02-54_fhtf.txt",
"NMR_LaR80a_02_20Jul11_Andromeda_11-02-56_fhtf.txt",
"NMR_LaR80a_03_20Jul11_Andromeda_11-02-54_fhtf.txt"
};
var dtaFiles = new List <string> {
"NMR_HetR_UG_01_20Jul11_Andromeda_11-06-19_dta.txt",
"NMR_HetR_UG_02_20Jul11_Andromeda_11-06-29_dta.txt",
"NMR_HetR_UG_03_20Jul11_Andromeda_11-06-19_dta.txt",
"NMR_HetR_LG_01_20Jul11_Andromeda_11-06-29_dta.txt",
"NMR_HetR_LG_02_20Jul11_Andromeda_11-06-29_dta.txt",
"NMR_HetR_LG_03_20Jul11_Andromeda_11-06-19_dta.txt",
"NMR_LaR80a_01_20Jul11_Andromeda_11-02-54_dta.txt",
"NMR_LaR80a_02_20Jul11_Andromeda_11-02-56_dta.txt",
"NMR_LaR80a_03_20Jul11_Andromeda_11-02-54_dta.txt"
};
var peptideMassCalculator = GetDefaultPeptideMassCalculator();
for (var i = 0; i < fhtFiles.Count; i++)
{
var tempfht = Path.Combine(direct, fhtFiles[i]);
var tempdta = Path.Combine(direct, dtaFiles[i]);
var ascP = Path.Combine(direct, ascoreP);
var tempout = Path.Combine(direct, fhtFiles[i].Substring(0, fhtFiles[i].Length - 4) + "_AScore2.txt");
PsmResultsManager dsman = new SequestFHT(tempfht);
//DtaManager dtman = new DtaManager(tempdta);
var spectraCache = new SpectraManagerCache(peptideMassCalculator);
spectraCache.OpenFile(tempdta);
var pman = new ParameterFileManager(ascP);
var ascoreEngine = new AScore_DLL.AScoreProcessor();
//ascoreEngine.AlgorithmRun(dtman, dsman, pman, tempout);
ascoreEngine.RunAScoreOnSingleFile(spectraCache, dsman, pman, tempout);
}
}
/// <summary>
/// Configure and run the AScore algorithm
/// </summary>
/// <param name="ascoreOptions"></param>
/// <returns></returns>
public int RunAScore(AScoreOptions ascoreOptions)
{
var paramManager = new ParameterFileManager(ascoreOptions.AScoreParamFile);
RegisterEvents(paramManager);
Console.WriteLine();
if (paramManager.DynamicMods.Count > 0 || paramManager.StaticMods.Count > 0)
{
OnStatusEvent("Loaded modifications from: " + ascoreOptions.AScoreParamFile);
foreach (var mod in paramManager.StaticMods)
{
OnStatusEvent(Utilities.GetModDescription("Static, ", mod));
}
foreach (var mod in paramManager.DynamicMods)
{
OnStatusEvent(Utilities.GetModDescription("Dynamic, ", mod));
}
foreach (var mod in paramManager.TerminiMods)
{
OnStatusEvent(Utilities.GetModDescription("Terminus, ", mod));
}
Console.WriteLine();
}
PsmResultsManager psmResultsManager;
switch (ascoreOptions.SearchType)
{
case AScoreOptions.SearchMode.XTandem:
OnStatusEvent("Caching data in " + PathUtils.CompactPathString(ascoreOptions.DbSearchResultsFile, 80));
psmResultsManager = new XTandemFHT(ascoreOptions.DbSearchResultsFile);
break;
case AScoreOptions.SearchMode.Sequest:
OnStatusEvent("Caching data in " + PathUtils.CompactPathString(ascoreOptions.DbSearchResultsFile, 80));
psmResultsManager = new SequestFHT(ascoreOptions.DbSearchResultsFile);
break;
case AScoreOptions.SearchMode.Inspect:
OnStatusEvent("Caching data in " + PathUtils.CompactPathString(ascoreOptions.DbSearchResultsFile, 80));
psmResultsManager = new InspectFHT(ascoreOptions.DbSearchResultsFile);
break;
case AScoreOptions.SearchMode.Msgfdb:
case AScoreOptions.SearchMode.Msgfplus:
OnStatusEvent("Caching data in " + PathUtils.CompactPathString(ascoreOptions.DbSearchResultsFile, 80));
if (ascoreOptions.SearchResultsType == AScoreOptions.DbSearchResultsType.Mzid)
{
if (ascoreOptions.CreateUpdatedDbSearchResultsFile)
{
psmResultsManager = new MsgfMzidFull(ascoreOptions.DbSearchResultsFile);
}
else
{
psmResultsManager = new MsgfMzid(ascoreOptions.DbSearchResultsFile);
}
}
else
{
psmResultsManager = new MsgfdbFHT(ascoreOptions.DbSearchResultsFile);
}
break;
default:
OnErrorEvent(string.Format(
"Incorrect search type: {0} , supported values are {1}",
ascoreOptions.SearchType,
string.Join(", ", Enum.GetNames(typeof(AScoreOptions.SearchMode)))
));
return(-13);
}
var peptideMassCalculator = new PeptideMassCalculator();
var spectraManager = new SpectraManagerCache(peptideMassCalculator);
RegisterEvents(spectraManager);
OnStatusEvent("Output directory: " + ascoreOptions.OutputDirectoryInfo.FullName);
var ascoreEngine = new AScoreAlgorithm();
RegisterEvents(ascoreEngine);
// Initialize the options
FilterOnMSGFScore = ascoreOptions.FilterOnMSGFScore;
// Run the algorithm
if (ascoreOptions.MultiJobMode)
{
RunAScoreWithMappingFile(ascoreOptions, spectraManager, psmResultsManager, paramManager);
}
else
{
spectraManager.OpenFile(ascoreOptions.MassSpecFile, ascoreOptions.ModSummaryFile);
RunAScoreOnSingleFile(ascoreOptions, spectraManager, psmResultsManager, paramManager);
}
OnStatusEvent("AScore Complete");
if (ascoreOptions.CreateUpdatedDbSearchResultsFile)
{
if (ascoreOptions.SearchResultsType == AScoreOptions.DbSearchResultsType.Fht)
{
CreateUpdatedFirstHitsFile(ascoreOptions);
}
else if (psmResultsManager is MsgfMzidFull mzidFull)
{
mzidFull.WriteToMzidFile(ascoreOptions.UpdatedDbSearchResultsFileName);
OnStatusEvent("Results merged; new file: " + PathUtils.CompactPathString(ascoreOptions.UpdatedDbSearchResultsFileName, 80));
}
}
return(0);
}
public void Sisi_Kidneys()
{
const string ascoreP = "HCDPhos.xml";
const string directSeq = @"C:\Users\aldr699\Documents\2012\Sisi_Work\DarthVehDas\Sequest";
const string directMsg = @"C:\Users\aldr699\Documents\2012\Sisi_Work\DarthVehDas\MSGFDB";
var fhtFiles = new List <string> {
"Kidney_ACHN_Das_1_pTyr_HCD_8May12_Lynx_12-02-29_fht.txt",
"Kidney_ACHN_Veh_1_pTyr_HCD_10May12_Lynx_12-02-29_fht.txt",
"Kidney_ACHN_Veh_2_IMAC_HCD_10May12_Lynx_12-02-31_fht.txt",
"Kidney_ACHN_Das_2_IMAC_HCD_11May12_Lynx_12-02-31_fht.txt"
};
var msgfdbFile = new List <string> {
"Kidney_ACHN_Das_1_pTyr_HCD_8May12_Lynx_12-02-29_msgfdb_fht.txt",
"Kidney_ACHN_Veh_1_pTyr_HCD_10May12_Lynx_12-02-29_msgfdb_fht.txt",
"Kidney_ACHN_Veh_2_IMAC_HCD_10May12_Lynx_12-02-31_msgfdb_fht.txt",
"Kidney_ACHN_Das_2_IMAC_HCD_11May12_Lynx_12-02-31_msgfdb_fht.txt"
};
const string direct2 = @"C:\Users\aldr699\Documents\2012\Sisi_Work\DarthVehDas";
var dtaFiles = new List <string> {
"Kidney_ACHN_Das_1_pTyr_HCD_8May12_Lynx_12-02-29_dta.txt",
"Kidney_ACHN_Veh_1_pTyr_HCD_10May12_Lynx_12-02-29_dta.txt",
"Kidney_ACHN_Veh_2_IMAC_HCD_10May12_Lynx_12-02-31_dta.txt",
"Kidney_ACHN_Das_2_IMAC_HCD_11May12_Lynx_12-02-31_dta.txt"
};
var peptideMassCalculator = GetDefaultPeptideMassCalculator();
for (var j = 1; j < 2; j++)
{
for (var i = 0; i < 4; i++)
{
string fht;
string direct;
if (j == 0)
{
direct = directSeq;
fht = fhtFiles[i];
}
else
{
direct = directMsg;
fht = msgfdbFile[i];
}
var tempfht = Path.Combine(direct, fht);
var tempdta = Path.Combine(direct2, dtaFiles[i]);
var ascP = Path.Combine(direct2, ascoreP);
var tempout = Path.Combine(direct, fhtFiles[i].Substring(0, fhtFiles[i].Length - 4) + "_AScore.txt");
PsmResultsManager dsman;
if (j == 0)
{
dsman = new SequestFHT(tempfht);
}
else
{
dsman = new MsgfdbFHT(tempfht);
}
if (dsman == null)
{
Console.WriteLine("Failed to load fht");
}
//DtaManager dtman = new DtaManager(tempdta);
var spectraCache = new SpectraManagerCache(peptideMassCalculator);
spectraCache.OpenFile(tempdta);
var pman = new ParameterFileManager(ascP);
var ascoreEngine = new AScore_DLL.AScoreProcessor();
//ascoreEngine.AlgorithmRun(dtman, dsman, pman, tempout);
ascoreEngine.RunAScoreOnSingleFile(spectraCache, dsman, pman, tempout);
}
}
}
public void OsmaniRedux()
{
const string ascorePETD = "ETDPhos.xml";
const string ascorePCID = "CIDPhos.xml";
const string directETD = @"C:\Users\aldr699\Documents\2012\Osmani\ETD";
const string directCID = @"C:\Users\aldr699\Documents\2012\Osmani\CID";
var fhtFiles = new List <string> {
"SOSM_May_G2_RR1_26Jan12_Hawk_11-11-03p_fhtf.txt",
"SOSM_May_M_RR1_27Jan12_Hawk_11-11-03p_fhtf.txt",
"SOSM_May_G2_RR2_27Jan12_Hawk_11-11-03p_fhtf.txt",
"SOSM_May_M_RR2_29Jan12_Hawk_11-11-03p_fhtf.txt",
"SOSM_May_G_RR1_31Jan12_Hawk_11-11-03p_fhtf.txt",
"SOSM_May_P1_RR1_31Jan12_Hawk_11-11-03p_fhtf.txt"
};
const string direct2 = @"C:\Users\aldr699\Documents\2012\Osmani";
var dtaFiles = new List <string> {
"SOSM_May_G2_RR1_26Jan12_Hawk_11-11-03p_dta.txt",
"SOSM_May_M_RR1_27Jan12_Hawk_11-11-03p_dta.txt",
"SOSM_May_G2_RR2_27Jan12_Hawk_11-11-03p_dta.txt",
"SOSM_May_M_RR2_29Jan12_Hawk_11-11-03p_dta.txt",
"SOSM_May_G_RR1_31Jan12_Hawk_11-11-03p_dta.txt",
"SOSM_May_P1_RR1_31Jan12_Hawk_11-11-03p_dta.txt"
};
var peptideMassCalculator = GetDefaultPeptideMassCalculator();
for (var j = 0; j < 2; j++)
{
for (var i = 0; i < fhtFiles.Count; i++)
{
string direct;
string ascoreP;
if (j == 0)
{
direct = directETD;
ascoreP = ascorePETD;
}
else
{
direct = directCID;
ascoreP = ascorePCID;
}
var tempfht = Path.Combine(direct, fhtFiles[i]);
var tempdta = Path.Combine(direct2, dtaFiles[i]);
var ascP = Path.Combine(direct, ascoreP);
var tempout = Path.Combine(direct, fhtFiles[i].Substring(0, fhtFiles[i].Length - 4) + "_AScore.txt");
PsmResultsManager dsman = new SequestFHT(tempfht);
//DtaManager dtman = new DtaManager(tempdta);
var spectraCache = new SpectraManagerCache(peptideMassCalculator);
spectraCache.OpenFile(tempdta);
var pman = new ParameterFileManager(ascP);
var ascoreEngine = new AScore_DLL.AScoreProcessor();
//ascoreEngine.AlgorithmRun(dtman, dsman, pman, tempout);
ascoreEngine.RunAScoreOnSingleFile(spectraCache, dsman, pman, tempout);
}
}
}
