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 TestMSGFPlusResults()
{
const string workDir = @"F:\My Documents\Projects\JoshAldrich\AScore\AScore_DLL\TestCase";
var fht = Path.Combine(workDir, "CPTAC_CompREF_00_iTRAQ_NiNTA_01b_22Mar12_Lynx_12-02-29_msgfdb_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, "CPTAC_CompREF_00_iTRAQ_NiNTA_01b_22Mar12_Lynx_12-02-29_dta.txt");
var resultsFile = Path.Combine(workDir, "CPTAC_CompREF_00_iTRAQ_NiNTA_01b_22Mar12_Lynx_12-02-29_msgfdb_fht_ascore.txt");
var peptideMassCalculator = GetDefaultPeptideMassCalculator();
PsmResultsManager dfht = new MsgfdbFHT(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);
}
}
public void SisiConfirm()
{
var dtaname = new string[] {
@"C:\Users\aldr699\Documents\2012\Sisi_Work\PhosphohistidineConfirmation\09302010_MG1655_phospho_S_08_B_100930113735_dta.txt",
@"C:\Users\aldr699\Documents\2012\Sisi_Work\PhosphohistidineConfirmation\10012010_MG1655_phospho_S_09_B_101001105913_dta.txt",
@"C:\Users\aldr699\Documents\2012\Sisi_Work\PhosphohistidineConfirmation\10012010_MG1655_phospho_s06_101002094806_dta.txt",
@"C:\Users\aldr699\Documents\2012\Sisi_Work\PhosphohistidineConfirmation\10012010_MG1655_phospho_s10_101001105913_dta.txt",
@"C:\Users\aldr699\Documents\2012\Sisi_Work\PhosphohistidineConfirmation\10022010_MG1655_phospho_S11_rerun_101005165350_dta.txt",
@"C:\Users\aldr699\Documents\2012\Sisi_Work\PhosphohistidineConfirmation\10022010_MG1655_phospho_s12_101002094806_dta.txt",
@"C:\Users\aldr699\Documents\2012\Sisi_Work\PhosphohistidineConfirmation\10022010_MG1655_phospho_s7_101002094806_dta.txt"
};
var datasetname = new string[] {
@"C:\Users\aldr699\Documents\2012\Sisi_Work\PhosphohistidineConfirmation\09302010_MG1655_phospho_S_08_B_100930113735_msgfdb_fht.txt",
@"C:\Users\aldr699\Documents\2012\Sisi_Work\PhosphohistidineConfirmation\10012010_MG1655_phospho_S_09_B_101001105913_msgfdb_fht.txt",
@"C:\Users\aldr699\Documents\2012\Sisi_Work\PhosphohistidineConfirmation\10012010_MG1655_phospho_s06_101002094806_msgfdb_fht.txt",
@"C:\Users\aldr699\Documents\2012\Sisi_Work\PhosphohistidineConfirmation\10012010_MG1655_phospho_s10_101001105913_msgfdb_fht.txt",
@"C:\Users\aldr699\Documents\2012\Sisi_Work\PhosphohistidineConfirmation\10022010_MG1655_phospho_S11_rerun_101005165350_msgfdb_fht.txt",
@"C:\Users\aldr699\Documents\2012\Sisi_Work\PhosphohistidineConfirmation\10022010_MG1655_phospho_s12_101002094806_msgfdb_fht.txt",
@"C:\Users\aldr699\Documents\2012\Sisi_Work\PhosphohistidineConfirmation\10022010_MG1655_phospho_s7_101002094806_msgfdb_fht.txt"
};
var ascParam = new string[] {
@"C:\Users\aldr699\Documents\2012\Sisi_Work\PhosphohistidineConfirmation\HistPhos.xml",
@"C:\Users\aldr699\Documents\2012\Sisi_Work\PhosphohistidineConfirmation\HistPhos.xml",
@"C:\Users\aldr699\Documents\2012\Sisi_Work\PhosphohistidineConfirmation\HistPhos.xml",
@"C:\Users\aldr699\Documents\2012\Sisi_Work\PhosphohistidineConfirmation\HistPhos.xml",
@"C:\Users\aldr699\Documents\2012\Sisi_Work\PhosphohistidineConfirmation\HistPhos.xml",
@"C:\Users\aldr699\Documents\2012\Sisi_Work\PhosphohistidineConfirmation\HistPhos.xml",
@"C:\Users\aldr699\Documents\2012\Sisi_Work\PhosphohistidineConfirmation\HistPhos.xml"
};
var peptideMassCalculator = GetDefaultPeptideMassCalculator();
for (var i = 0; i < dtaname.Length; i++)
{
var outFile = Path.Combine(
Path.GetDirectoryName(datasetname[i]),
Path.GetFileNameWithoutExtension(datasetname[i]) + "_AScore.txt");
PsmResultsManager datasetMan = new MsgfdbFHT(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 ForJohnJacobs()
{
const string myfht = @"C:\DMS_WorkDir\Step_1_ASCORE\U54_HPp1_LoBMI_NS_11_5Sep08_Draco_08-07-15_xt.txt";
const string mydta = @"C:\DMS_WorkDir\Step_1_ASCORE\dtas\U54_HPp1_LoBMI_NS_11_5Sep08_Draco_08-07-15_dta.txt";
const string mypar = @"C:\DMS_WorkDir\Step_1_ASCORE\DynMWPYOx_EmH20_QmNH3_cid.xml";
var peptideMassCalculator = GetDefaultPeptideMassCalculator();
PsmResultsManager dataman = new XTandemFHT(myfht);
//DtaManager dta = new DtaManager(mydta);
var spectraCache = new SpectraManagerCache(peptideMassCalculator);
spectraCache.OpenFile(mydta);
var par = new ParameterFileManager(mypar);
const string fileOutput = @"C:\DMS_WorkDir\Step_1_ASCORE\U54_HPp1_LoBMI_NS_11_5Sep08_Draco_08-07-15_xt_ascore.txt";
var ascoreEngine = new AScore_DLL.AScoreProcessor();
//ascoreEngine.AlgorithmRun(dta, dataman, par, fileOutput);
ascoreEngine.RunAScoreOnSingleFile(spectraCache, dataman, par, fileOutput);
}
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);
}
}
}
public void QuYi()
{
const string direct = @"C:\Documents and Settings\aldr699\My Documents2011\EColiPhos";
const string ascoreP = "parameterFile.xml";
var fhtFiles = new List <string> {
"775945_10012010_MG1655_phospho_s05_101002094806_msgfdb_fht.txt",
"775946_10012010_MG1655_phospho_s11_101002094806_msgfdb_fht.txt",
"775947_10022010_MG1655_phospho_s7_101002094806_msgfdb_fht.txt",
"775948_10012010_MG1655_phospho_s10_101001105913_msgfdb_fht.txt",
"775949_10012010_MG1655_phospho_s06_101002094806_msgfdb_fht.txt",
"775950_10022010_MG1655_phospho_s12_101002094806_msgfdb_fht.txt",
"775951_10022010_MG1655_phospho_S8FT_101005165350_msgfdb_fht.txt",
"775944_10012010_MG1655_phospho_S_09_B_101001105913_msgfdb_fht.txt",
"775942_09302010_MG1655_phospho_S_08_B_100930113735_msgfdb_fht.txt",
"775952_10022010_MG1655_phospho_S11_rerun_101005165350_msgfdb_fht.txt",
"775955_MG1655_phospho_S-01FT_5Nov10_Hawk_10-11-02p_msgfdb_fht.txt",
"775956_MG1655_phospho_S-02FT_5Nov10_Hawk_10-11-02p_msgfdb_fht.txt",
"775957_MG1655_phospho_S-03FT_8Nov10_Hawk_10-11-02p_msgfdb_fht.txt",
"775958_MG1655_phospho_S-06FT_8Nov10_Hawk_10-11-02p_msgfdb_fht.txt",
"775959_MG1655_phospho_S-09FT_12Nov10_Hawk_10-11-02p_msgfdb_fht.txt",
"775960_MG1655_phospho_S-10FT_12Nov10_Hawk_10-11-02p_msgfdb_fht.txt",
"775961_MG1655_phospho_S-12FT_15Nov10_Hawk_10-11-02p_msgfdb_fht.txt",
"775962_MG1655_phospho_S-01_15Nov10_Hawk_10-11-02p_msgfdb_fht.txt",
"775963_MG1655_phospho_S-02_17Nov10_Hawk_10-11-02p_msgfdb_fht.txt",
"775964_MG1655_phospho_S-03_17Nov10_Hawk_10-11-02p_msgfdb_fht.txt",
"775965_MG1655_phospho_S-04_17Nov10_Hawk_10-11-02p_msgfdb_fht.txt",
"775966_MG1655_phospho_S-07_17Nov10_Hawk_10-11-02p_msgfdb_fht.txt",
"775967_MG1655_phospho_S-12_19Nov10_Hawk_10-11-02p_msgfdb_fht.txt",
"775968_MG1655_phospho_S-10_19Nov10_Hawk_10-11-02p_msgfdb_fht.txt",
"775969_MG1655_phospho_S-09_19Nov10_Hawk_10-11-02p_msgfdb_fht.txt",
"775953_10022010_MG1655_phospho_S05_rerun_101005165350_msgfdb_fht.txt",
"775943_09302010_MG1655_phospho_S_04_B_100930113735_msgfdb_fht.txt",
"775954_10022010_MG1655_phospho_S06_rerun_101005165350_msgfdb_fht.txt"
};
var dtaFiles = new List <string> {
"10012010_MG1655_phospho_s05_101002094806_dta.txt",
"10012010_MG1655_phospho_s11_101002094806_dta.txt",
"10022010_MG1655_phospho_s7_101002094806_dta.txt",
"10012010_MG1655_phospho_s10_101001105913_dta.txt",
"10012010_MG1655_phospho_s06_101002094806_dta.txt",
"10022010_MG1655_phospho_s12_101002094806_dta.txt",
"10022010_MG1655_phospho_S8FT_101005165350_dta.txt",
"10012010_MG1655_phospho_S_09_B_101001105913_dta.txt",
"09302010_MG1655_phospho_S_08_B_100930113735_dta.txt",
"10022010_MG1655_phospho_S11_rerun_101005165350_dta.txt",
"MG1655_phospho_S-01FT_5Nov10_Hawk_10-11-02p_dta.txt",
"MG1655_phospho_S-02FT_5Nov10_Hawk_10-11-02p_dta.txt",
"MG1655_phospho_S-03FT_8Nov10_Hawk_10-11-02p_dta.txt",
"MG1655_phospho_S-06FT_8Nov10_Hawk_10-11-02p_dta.txt",
"MG1655_phospho_S-09FT_12Nov10_Hawk_10-11-02p_dta.txt",
"MG1655_phospho_S-10FT_12Nov10_Hawk_10-11-02p_dta.txt",
"MG1655_phospho_S-12FT_15Nov10_Hawk_10-11-02p_dta.txt",
"MG1655_phospho_S-01_15Nov10_Hawk_10-11-02p_dta.txt",
"MG1655_phospho_S-02_17Nov10_Hawk_10-11-02p_dta.txt",
"MG1655_phospho_S-03_17Nov10_Hawk_10-11-02p_dta.txt",
"MG1655_phospho_S-04_17Nov10_Hawk_10-11-02p_dta.txt",
"MG1655_phospho_S-07_17Nov10_Hawk_10-11-02p_dta.txt",
"MG1655_phospho_S-12_19Nov10_Hawk_10-11-02p_dta.txt",
"MG1655_phospho_S-10_19Nov10_Hawk_10-11-02p_dta.txt",
"MG1655_phospho_S-09_19Nov10_Hawk_10-11-02p_dta.txt",
"10022010_MG1655_phospho_S05_rerun_101005165350_dta.txt",
"09302010_MG1655_phospho_S_04_B_100930113735_dta.txt",
"10022010_MG1655_phospho_S06_rerun_101005165350_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) + "_AScore.txt");
PsmResultsManager dsman = new MsgfdbFHT(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);
}
}
