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 override void GetNextRow( out int scanNumber, out int scanCount, out int chargeState, out string peptideSeq, out double msgfScore, ref ParameterFileManager ascoreParams) { GetNextRow(out scanNumber, out scanCount, out chargeState, out peptideSeq, ref ascoreParams); double.TryParse((string)mDataTable.Rows[mCurrentRow]["MSGF_SpecProb"], out msgfScore); }
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); } }
/// <summary> /// コンストラクタ /// </summary> public MainWindowViewModel() { _kinectManager = new KinectManager(); _cameraOptions = new CameraOptions(); _jointsOption = new JointsOption(); _blenderOptions = new BlenderOptions(); _originPositionAutoSetter = new OriginPositionAutoSetter(_jointsOption); _kinectDataManager = new KinectDataManager(_cameraOptions, _blenderOptions, _jointsOption); _parameterFileManager = new ParameterFileManager(this); _statusBarMessage = ""; }
public override void GetNextRow(out int scanNumber, out int scanCount, out int chargeState, out string peptideSeq, ref ParameterFileManager ascoreParams) { if (mDataTable.Columns.Contains(RESULTS_COL_JOB)) { m_jobNum = (string)mDataTable.Rows[mCurrentRow][RESULTS_COL_JOB]; m_JobColumnDefined = true; } scanNumber = int.Parse((string)mDataTable.Rows[mCurrentRow]["Scan"]); scanCount = 1; chargeState = int.Parse((string)mDataTable.Rows[mCurrentRow]["Charge"]); peptideSeq = (string)mDataTable.Rows[mCurrentRow]["Peptide"]; }
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 override void GetNextRow( out int scanNumber, out int scanCount, out int chargeState, out string peptideSeq, out double msgfScore, ref ParameterFileManager ascoreParams) { this.GetNextRow(out scanNumber, out scanCount, out chargeState, out peptideSeq, ref ascoreParams); msgfScore = 0; if (this.MSGFSpecProbColumnPresent) { var msgfSpecProb = (string)mDataTable.Rows[mCurrentRow]["MSGF_SpecProb"]; if (!double.TryParse(msgfSpecProb, out msgfScore)) { msgfScore = 1; } } }
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 override void GetNextRow(out int scanNumber, out int scanCount, out int chargeState, out string peptideSeq, ref ParameterFileManager ascoreParams) { if (mDataTable.Columns.Contains(RESULTS_COL_JOB)) { m_jobNum = (string)mDataTable.Rows[mCurrentRow][RESULTS_COL_JOB]; m_JobColumnDefined = true; } scanNumber = int.Parse((string)mDataTable.Rows[mCurrentRow]["Scan"]); scanCount = 1; chargeState = int.Parse((string)mDataTable.Rows[mCurrentRow]["Charge"]); peptideSeq = (string)mDataTable.Rows[mCurrentRow]["Peptide"]; if (mDataTable.Columns.Contains("FragMethod")) { var fragType = ((string)mDataTable.Rows[mCurrentRow]["FragMethod"]).ToLower(); switch (fragType) { case "hcd": ascoreParams.FragmentType = FragmentType.HCD; break; case "etd": ascoreParams.FragmentType = FragmentType.ETD; break; case "cid": ascoreParams.FragmentType = FragmentType.CID; break; default: ascoreParams.FragmentType = FragmentType.Unspecified; break; } } else { ascoreParams.FragmentType = FragmentType.Unspecified; } }
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 abstract void GetNextRow(out int scanNumber, out int scanCount, out int chargeState, out string peptideSeq, out double msgfScore, ref ParameterFileManager ascoreParams);
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); } }
public override void GetNextRow(out int scanNumber, out int scanCount, out int chargeState, out string peptideSeq, out double msgfScore, ref ParameterFileManager ascoreParams) { GetNextRow(out scanNumber, out scanCount, out chargeState, out peptideSeq, ref ascoreParams); msgfScore = 0; if (mDataTable.Columns.Contains("MSGF_SpecProb")) { if (!double.TryParse((string)mDataTable.Rows[mCurrentRow]["MSGF_SpecProb"], out msgfScore)) { msgfScore = 0; } } else if (mDataTable.Columns.Contains("MSGFDB_SpecEValue")) { if (!double.TryParse((string)mDataTable.Rows[mCurrentRow]["MSGFDB_SpecEValue"], out msgfScore)) { msgfScore = 0; } } }
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 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); } } }