private void TrainFace_Click(object sender, RoutedEventArgs e)
{
LoadFaces();
//Save all the current saved faces to file for quality check
for (int i = 0; i < _savedFaces.Count(); i++)
{
var success = MyFileManager.SaveImage(_savedFaces[i], i.ToString());
}
//Get data ready for training and train.
List <Face> faces = _dataClient.CallFaces("ALL_USERS");
byte[][] faceImages = new byte[faces.Count()][];
int[] faceLabels = new int[faces.Count()];
for (int i = 0; i < faces.Count(); i++)
{
faceImages[i] = (byte[])faces[i].Image.Clone();
faceLabels[i] = faces[i].UserId;
}
//Echo results to UI
if (_trainer.Train(faceImages, faceLabels))
{
ResultsString = "Training Successfull";
}
else
{
ResultsString = "Training Failed";
}
NotifyPropertyChanged("ResultsString");
}
public async Task Decrypt()
{
var keyQueueTask = Task.Run(() => KeepKeyQueueData());
while (
keyQueueTask.Status != TaskStatus.RanToCompletion ||
PendingKeysCount != 0)
{
for (int i = 0; i < tasks.Length; i++)
{
if (PendingKeysCount <= 0)
{
await Task.Delay(1);
break;
}
if (tasks[i] == null || tasks[i].Status == TaskStatus.RanToCompletion)
{
tasks[i] = Task.Run(() => ProccessNextKeyTask(i));
}
}
}
keyQueueTask.Wait();
MyFileManager.WriteBuilderToFile();
MyFileManagerSuccesses.WriteBuilderToFile();
MyFileManagerBad.WriteBuilderToFile();
}
public static void OxoniumIonAnalysis()
{
Assert.That(Glycan.AllOxoniumIons[4] == 13805550);
Assert.That(Glycan.AllOxoniumIons[5] == 14406607);
Assert.That(Glycan.AllOxoniumIons[9] == 20408720);
Assert.That(Glycan.AllOxoniumIons[10] == 27409268);
Assert.That(Glycan.AllOxoniumIons[12] == 29210324);
Assert.That(Glycan.AllOxoniumIons[14] == 36614002);
//Get Scan
CommonParameters commonParameters = new CommonParameters(dissociationType: DissociationType.EThcD, trimMsMsPeaks: false);
string spectraFile = Path.Combine(TestContext.CurrentContext.TestDirectory, @"GlycoTestData\2019_09_16_StcEmix_35trig_EThcD25_rep1_4565.mgf");
var file = new MyFileManager(true).LoadFile(spectraFile, commonParameters);
var scan = MetaMorpheusTask.GetMs2Scans(file, spectraFile, commonParameters).First();
var productSearchMode = new SinglePpmAroundZeroSearchMode(20);
var oxoniumIonIntensities = GlycoPeptides.ScanOxoniumIonFilter(scan, productSearchMode, DissociationType.EThcD);
//Get glycanBox
var glycanBox = OGlycanBoxes[19];
var satifyOxonium = GlycoPeptides.OxoniumIonsAnalysis(oxoniumIonIntensities, glycanBox);
Assert.That(satifyOxonium);
}
public MetaDraw()
{
UsefulProteomicsDatabases.Loaders.LoadElements();
InitializeComponent();
itemsControlSampleViewModel = new ItemsControlSampleViewModel();
DataContext = itemsControlSampleViewModel;
mainViewModel = new PsmAnnotationViewModel();
plotView.DataContext = mainViewModel;
allPsms = new ObservableCollection<PsmFromTsv>();
filteredListOfPsms = new ObservableCollection<PsmFromTsv>();
propertyView = new DataTable();
propertyView.Columns.Add("Name", typeof(string));
propertyView.Columns.Add("Value", typeof(string));
peptideSpectralMatchesView = CollectionViewSource.GetDefaultView(filteredListOfPsms);
dataGridScanNums.DataContext = peptideSpectralMatchesView;
dataGridProperties.DataContext = propertyView.DefaultView;
Title = "MetaDraw: version " + GlobalVariables.MetaMorpheusVersion;
spectraFileManager = new MyFileManager(true);
SetUpDictionaries();
modificationAnnotationColor = Brushes.Yellow;
metaDrawGraphicalSettings = new MetaDrawGraphicalSettings();
metaDrawFilterSettings = new MetaDrawFilterSettings();
base.Closing += this.OnClosing;
ParentChildScanView.Visibility = Visibility.Collapsed;
ParentScanView.Visibility = Visibility.Collapsed;
plotTypes = new ObservableCollection<string>();
SetUpPlots();
//plotsListBox.ItemsSource = plotTypes;
}
public static void ReplaceBadStdevTwo()
{
//here we are adding a really hydrophobic psm at the same time as a regular peptide so that there is a big difference in their computed hydrophobicities. The stdev of these hydrophobicities is out of whach the the collective and so it needs to get replaced by the global average
var variableModifications = new List <Modification>();
var fixedModifications = new List <Modification>();
var origDataFile = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\TaGe_SA_HeLa_04_subset_longestSeq.mzML");
MyFileManager myFileManager = new MyFileManager(true);
CommonParameters CommonParameters = new CommonParameters(digestionParams: new DigestionParams());
var myMsDataFile = myFileManager.LoadFile(origDataFile, CommonParameters);
var searchModes = new SinglePpmAroundZeroSearchMode(5);
List <Protein> proteinList = ProteinDbLoader.LoadProteinFasta(Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\hela_snip_for_unitTest.fasta"), true, DecoyType.Reverse, false, ProteinDbLoader.UniprotAccessionRegex, ProteinDbLoader.UniprotFullNameRegex, ProteinDbLoader.UniprotFullNameRegex, ProteinDbLoader.UniprotGeneNameRegex,
ProteinDbLoader.UniprotOrganismRegex, out var dbErrors, -1);
var listOfSortedms2Scans = MetaMorpheusTask.GetMs2Scans(myMsDataFile, @"TestData\TaGe_SA_HeLa_04_subset_longestSeq.mzML", CommonParameters).OrderBy(b => b.PrecursorMass).ToArray();
//adding a new scan that creates a psm at an isolated retention time. This will ultimately cause PEP to replace its retention time standard deviation "Z-score" with the global average.
Ms2ScanWithSpecificMass topMs2Scan = listOfSortedms2Scans[395];
int newOneBasedScanNumber = 1000;
MzRange range = new MzRange(topMs2Scan.TheScan.MassSpectrum.XArray.Min(), topMs2Scan.TheScan.MassSpectrum.XArray.Max());
MzSpectrum mzs = new MzSpectrum(topMs2Scan.TheScan.MassSpectrum.XArray, topMs2Scan.TheScan.MassSpectrum.YArray, true);
double newRetentionTime = topMs2Scan.TheScan.RetentionTime - 25;
MsDataScan msd = new MsDataScan(mzs, newOneBasedScanNumber, 2, topMs2Scan.TheScan.IsCentroid, Polarity.Positive, newRetentionTime, range, "", MZAnalyzerType.Orbitrap, topMs2Scan.TheScan.TotalIonCurrent, topMs2Scan.TheScan.InjectionTime, topMs2Scan.TheScan.NoiseData, "", topMs2Scan.TheScan.SelectedIonMZ, topMs2Scan.TheScan.SelectedIonChargeStateGuess, topMs2Scan.TheScan.SelectedIonIntensity, topMs2Scan.TheScan.IsolationMz, topMs2Scan.TheScan.IsolationWidth, DissociationType.HCD, topMs2Scan.TheScan.OneBasedPrecursorScanNumber, topMs2Scan.TheScan.SelectedIonMonoisotopicGuessMz);
Ms2ScanWithSpecificMass mwsm = new Ms2ScanWithSpecificMass(msd, topMs2Scan.PrecursorMonoisotopicPeakMz, topMs2Scan.PrecursorCharge, topMs2Scan.FullFilePath, new CommonParameters(), topMs2Scan.ExperimentalFragments);
Ms2ScanWithSpecificMass[] extendedArray = new Ms2ScanWithSpecificMass[listOfSortedms2Scans.Length + 1];
for (int i = 0; i < listOfSortedms2Scans.Length; i++)
{
extendedArray[i] = listOfSortedms2Scans[i];
}
extendedArray[listOfSortedms2Scans.Length] = mwsm;
extendedArray = extendedArray.OrderBy(b => b.PrecursorMass).ToArray();
PeptideSpectralMatch[] allPsmsArray = new PeptideSpectralMatch[extendedArray.Length];
new ClassicSearchEngine(allPsmsArray, extendedArray, variableModifications, fixedModifications, null, null, null, proteinList, searchModes, CommonParameters, new List <string>()).Run();
List <PeptideSpectralMatch> nonNullPsms = allPsmsArray.Where(p => p != null).ToList();
nonNullPsms = nonNullPsms.OrderByDescending(p => p.Score).ToList();
List <PeptideSpectralMatch> psmBloated = new List <PeptideSpectralMatch>();
psmBloated.AddRange(nonNullPsms);
int arrayMax = nonNullPsms.Count;
psmBloated.AddRange(nonNullPsms.GetRange(2, arrayMax - 2));
psmBloated.AddRange(nonNullPsms.GetRange(2, arrayMax - 2));
PeptideSpectralMatch pp = psmBloated.Where(p => p.ScanRetentionTime < (newRetentionTime + 1)).First();
PeptideWithSetModifications newPwsmTwo = new PeptideWithSetModifications(new Protein("WAGVLPWFPWAAVVWGFWF", "ACCESSION", "ORGANISM"), new DigestionParams(), 1, 2, CleavageSpecificity.Full, "", 0, new Dictionary <int, Modification>(), 0);
PeptideSpectralMatch newPsmTwo = new PeptideSpectralMatch(newPwsmTwo, pp.BestMatchingPeptides.First().Notch, pp.Score, pp.ScanIndex, mwsm, new DigestionParams(), pp.MatchedFragmentIons);
psmBloated.Add(newPsmTwo);
FdrAnalysisResults fdrResultsClassicDelta = (FdrAnalysisResults)(new FdrAnalysisEngine(psmBloated.Where(p => p != null).ToList(), 1, CommonParameters, new List <string>()).Run());
}
public static void GlyTest_GlyGetTheoreticalFragments()
{
Protein pep = new Protein("TKPREEQYNSTYR", "accession");
DigestionParams digestionParams = new DigestionParams(minPeptideLength: 7);
var aPeptideWithSetModifications = pep.Digest(digestionParams, new List <Modification>(), new List <Modification>());
string[] motifs = new string[] { "Nxs", "Nxt" };
var sites = GlycoSpectralMatch.GetPossibleModSites(aPeptideWithSetModifications.Last(), motifs);
Glycan glycan = Glycan.Struct2Glycan("(N(F)(N(H(H(N))(H(N)))))", 0);
//using (StreamWriter output = new StreamWriter(Path.Combine(TestContext.CurrentContext.TestDirectory, "GlycanFragmentions.txt")))
//{
// foreach (var product in fragmentIons)
// {
// foreach (var ion in product.Item2)
// {
// output.WriteLine(ion.Annotation + "\t" + ion.NeutralLoss.ToString() + "\t" + ion.NeutralMass.ToString());
// }
// }
//}
CommonParameters commonParameters = new CommonParameters(deconvolutionMassTolerance: new PpmTolerance(20), trimMsMsPeaks: false);
string filePath = Path.Combine(TestContext.CurrentContext.TestDirectory, @"GlycoTestData/Glyco_3383.mgf"); //"25170.mgf"
MyFileManager myFileManager = new MyFileManager(true);
var msDataFile = myFileManager.LoadFile(filePath, commonParameters);
var listOfSortedms2Scans = MetaMorpheusTask.GetMs2Scans(msDataFile, filePath, commonParameters).ToArray();
var glycanMod = Glycan.NGlycanToModification(glycan);
var glycopep = GlycoPeptides.GenerateGlycopeptide(sites[0], aPeptideWithSetModifications.Last(), glycan);
List <Product> fragmentIons = new List <Product>();
glycopep.Fragment(DissociationType.HCD, FragmentationTerminus.Both, fragmentIons);
var glycanYIons = GlycoPeptides.GetGlycanYIons(listOfSortedms2Scans[0].PrecursorMass, glycan);
var matchedGlycanYIons = MetaMorpheusEngine.MatchFragmentIons(listOfSortedms2Scans[0], glycanYIons, commonParameters);
Assert.AreEqual(matchedGlycanYIons.Count, 14);
//TO DO: The neutroloss is not annotated well.
var matchedFragmentIons = MetaMorpheusEngine.MatchFragmentIons(listOfSortedms2Scans[0], fragmentIons, commonParameters);
var coreIons = GlycoPeptides.ScanGetTrimannosylCore(matchedFragmentIons, glycan);
Assert.AreEqual(coreIons.Count, 6);
var filter = GlycoPeptides.ScanTrimannosylCoreFilter(matchedFragmentIons, glycan);
Assert.AreEqual(filter, true);
var NGlycans = GlycanDatabase.LoadGlycan(GlobalVariables.NGlycanLocations[0], true, false);
var bestGlycans = GlycoPeptides.MatchBestGlycan(listOfSortedms2Scans[0], NGlycans.ToArray(), commonParameters).Where(p => p != null && p.Item2 >= 2).OrderByDescending(p => p.Item2).Take(100).OrderBy(p => p.Item3).ToArray();;
}
public static void RemoveAmbiguousPeptides()
{
var variableModifications = new List <Modification>();
var fixedModifications = new List <Modification>();
var origDataFile = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\TaGe_SA_HeLa_04_subset_longestSeq.mzML");
MyFileManager myFileManager = new MyFileManager(true);
CommonParameters CommonParameters = new CommonParameters(digestionParams: new DigestionParams());
var myMsDataFile = myFileManager.LoadFile(origDataFile, CommonParameters);
var searchModes = new SinglePpmAroundZeroSearchMode(5);
List <Protein> proteinList = ProteinDbLoader.LoadProteinFasta(Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\hela_snip_for_unitTest.fasta"), true, DecoyType.Reverse, false, ProteinDbLoader.UniprotAccessionRegex, ProteinDbLoader.UniprotFullNameRegex, ProteinDbLoader.UniprotFullNameRegex, ProteinDbLoader.UniprotGeneNameRegex,
ProteinDbLoader.UniprotOrganismRegex, out var dbErrors, -1);
var listOfSortedms2Scans = MetaMorpheusTask.GetMs2Scans(myMsDataFile, @"TestData\TaGe_SA_HeLa_04_subset_longestSeq.mzML", CommonParameters).OrderBy(b => b.PrecursorMass).ToArray();
PeptideSpectralMatch[] allPsmsArray = new PeptideSpectralMatch[listOfSortedms2Scans.Length];
new ClassicSearchEngine(allPsmsArray, listOfSortedms2Scans, variableModifications, fixedModifications, null, null, null, proteinList, searchModes, CommonParameters, new List <string>()).Run();
var nonNullPsms = allPsmsArray.Where(p => p != null).ToList();
nonNullPsms.OrderByDescending(p => p.Score);
var maxScore = nonNullPsms.Select(n => n.Score).Max();
PeptideSpectralMatch maxScorePsm = nonNullPsms.Where(n => n.Score == maxScore).First();
Protein newProteinToRemove = new Protein("RREMVE", "BUBBA", isDecoy: false);
PeptideWithSetModifications pwsmToRemove = new PeptideWithSetModifications(newProteinToRemove, new DigestionParams(), 1, 6, CleavageSpecificity.Full, "peptideDescription", 2, new Dictionary <int, Modification>(), 1, "RREMVE");
maxScorePsm.AddOrReplace(pwsmToRemove, maxScore, 1, true, maxScorePsm.MatchedFragmentIons, maxScore);
maxScorePsm.ResolveAllAmbiguities();
List <PeptideSpectralMatch> psmBloated = new List <PeptideSpectralMatch>();
psmBloated.AddRange(nonNullPsms);
psmBloated.AddRange(nonNullPsms.GetRange(0, nonNullPsms.Count - 2));
foreach (PeptideSpectralMatch psm in nonNullPsms.GetRange(0, nonNullPsms.Count - 2))
{
Protein newDecoyProtein = new Protein(psm.BestMatchingPeptides.First().Peptide.BaseSequence + "K", "DECOY_" + psm.BestMatchingPeptides.First().Peptide.Protein.Accession, isDecoy: true);
PeptideWithSetModifications pwsmDecoy = new PeptideWithSetModifications(newDecoyProtein, new DigestionParams(), 1, psm.BestMatchingPeptides.First().Peptide.BaseSequence.Length + 1, CleavageSpecificity.Full, "peptideDescription", 2, new Dictionary <int, Modification>(), 1, psm.BestMatchingPeptides.First().Peptide.BaseSequence + "K");
PeptideSpectralMatch decoyPsm = new PeptideSpectralMatch(pwsmDecoy, 1, psm.Score, psm.ScanIndex, listOfSortedms2Scans[psm.ScanIndex], new DigestionParams(), psm.MatchedFragmentIons);
decoyPsm.ResolveAllAmbiguities();
psmBloated.Add(decoyPsm);
}
PeptideSpectralMatch oldBloatedMaxScorePsm = psmBloated.Where(n => n.Score == maxScore).First();
int countOfBestPeptidesBloatedMax = oldBloatedMaxScorePsm.BestMatchingPeptides.Count();
FdrAnalysisResults fdrResultsClassicDelta = (FdrAnalysisResults)(new FdrAnalysisEngine(psmBloated.Where(p => p != null).ToList(), 1, CommonParameters, new List <string>()).Run());
PeptideSpectralMatch newMaxScorePsm = psmBloated.Where(n => n.Score == maxScore).First();
Assert.AreEqual(countOfBestPeptidesBloatedMax - 1, newMaxScorePsm.BestMatchingPeptides.Count());
}
private void button1_Click(object sender, EventArgs e)
{
SqlConnection connection = MyDB.getConnection();
SqlCommand sqlCommand;
SqlDataReader dataReader;
string output_definition = "";
try
{
connection.Open();
sqlCommand = new SqlCommand("DECLARE @PKRepetida varchar(40), @longitud int = 0, @i int = 0, @Nombre_columna varchar (40), @anomalias int, @j int = 0, @Id_objeto int, @EstaVacio int SET @longitud = (select count(*) from ( select COlUMN_NAME, COUNT(COLUMN_NAME) as duplicados from ( select TABLE_NAME,COLUMN_NAME, CONSTRAINT_NAME, ORDINAL_POSITION from INFORMATION_SCHEMA.KEY_COLUMN_USAGE where TABLE_NAME NOT IN (select distinct TABLE_NAME from INFORMATION_SCHEMA.KEY_COLUMN_USAGE where ORDINAL_POSITION > 1 ) )T1 where CONSTRAINT_NAME LIKE 'PK%' or CONSTRAINT_NAME LIKE 'UPKCL%' group by COLUMN_NAME)T2) WHILE @i < @longitud BEGIN SET @i = @i + 1 IF ((select duplicados from ( select COUNT(COLUMN_NAME) as duplicados,ROW_NUMBER() OVER (ORDER BY (select 1)) AS a from ( select TABLE_NAME,COLUMN_NAME, CONSTRAINT_NAME, ORDINAL_POSITION from INFORMATION_SCHEMA.KEY_COLUMN_USAGE where TABLE_NAME NOT IN (select distinct TABLE_NAME from INFORMATION_SCHEMA.KEY_COLUMN_USAGE where ORDINAL_POSITION > 1 ) )T1 where CONSTRAINT_NAME LIKE 'PK%' or CONSTRAINT_NAME LIKE 'UPKCL%' group by COLUMN_NAME)T2 where a = @i)>1) Begin SET @Nombre_columna =(select COLUMN_NAME from ( select COUNT(COLUMN_NAME) as duplicados, COLUMN_NAME,ROW_NUMBER() OVER (ORDER BY (select 1)) AS a from ( select TABLE_NAME,COLUMN_NAME, CONSTRAINT_NAME, ORDINAL_POSITION from INFORMATION_SCHEMA.KEY_COLUMN_USAGE where TABLE_NAME NOT IN (select distinct TABLE_NAME from INFORMATION_SCHEMA.KEY_COLUMN_USAGE where ORDINAL_POSITION > 1 ) )T1 where CONSTRAINT_NAME LIKE 'PK%' or CONSTRAINT_NAME LIKE 'UPKCL%' group by COLUMN_NAME)T2 where a = @i) print @Nombre_columna SET @anomalias = (select count(*) from ( select ROW_NUMBER() OVER (ORDER BY (select 1)) AS a, object_id from ( select TABLE_NAME, CONSTRAINT_NAME from INFORMATION_SCHEMA.KEY_COLUMN_USAGE where COLUMN_NAME = @Nombre_columna)T1 join sys.objects so on (T1.TABLE_NAME = so.name) where CONSTRAINT_NAME LIKE 'PK%' or CONSTRAINT_NAME LIKE 'UPKCL%')T2) WHILE @j < @anomalias BEGIN SET @j = @j + 1 SET @Id_objeto = (select object_id from ( select ROW_NUMBER() OVER (ORDER BY (select 1)) AS a, object_id from ( select TABLE_NAME, CONSTRAINT_NAME from INFORMATION_SCHEMA.KEY_COLUMN_USAGE where COLUMN_NAME = @Nombre_columna) T1 join sys.objects so on (T1.TABLE_NAME = so.name) where CONSTRAINT_NAME LIKE 'PK%' or CONSTRAINT_NAME LIKE 'UPKCL%')T2 where a = @j) SET @EstaVacio = (select count(*) from sys.triggers st join sys.sql_modules ssm on (st.object_id = ssm.object_id ) where st.parent_id = @Id_objeto ) IF (@EstaVacio > 0) Begin select so.name as tabla,st.object_id, st.name , ssm.definition from sys.triggers st join sys.sql_modules ssm on (st.object_id = ssm.object_id ) join sys.objects so on (so.object_id = st.parent_id) where st.parent_id = @Id_objeto END END END END", connection);
dataReader = sqlCommand.ExecuteReader();
while (dataReader.Read())
{
// Console.WriteLine("LEYENDO " + dataReader.FieldCount);
int index = 0;
string tabla = dataReader.GetValue(index++).ToString();
long object_id = Int64.Parse(dataReader.GetValue(index++).ToString());
string name = dataReader.GetValue(index++).ToString();
string definition = dataReader.GetValue(index++).ToString();
output_definition += "Tabla: " + tabla + ", Object_id: " + object_id + ", nombre: " + name + "\nDefinition: " + definition + "\n\n";
}
this.richTextBox2.Text = output_definition;
MyFileManager.writeTXT(output_definition, "D://LOG_AUDITORIA_ANOMALIAS_DEFINICION.txt");
sqlCommand.Dispose();
dataReader.Close();
}
catch (Exception error)
{
Console.WriteLine("Error: " + error.Message);
}
finally
{
connection.Close();
}
}
public MetaDraw()
{
InitializeComponent();
mainViewModel = new PsmAnnotationViewModel();
plotView.DataContext = mainViewModel;
peptideSpectralMatches = new ObservableCollection <MetaDrawPsm>();
propertyView = new DataTable();
propertyView.Columns.Add("Name", typeof(string));
propertyView.Columns.Add("Value", typeof(string));
peptideSpectralMatchesView = CollectionViewSource.GetDefaultView(peptideSpectralMatches);
dataGridScanNums.DataContext = peptideSpectralMatchesView;
dataGridProperties.DataContext = propertyView.DefaultView;
Title = "MetaDraw: version " + GlobalVariables.MetaMorpheusVersion;
spectraFileManager = new MyFileManager(true);
}
// Use this for initialization
void Start()
{
createSingleton(); // Create a static reference to this object
activateRig(); // Adjust any settings at runtime
targetData = generateRandomTargets(10); // Generates randomized target data
fileManager = new MyFileManager(targetData, true); // Create a file manager using this target data
createTarget();
// Debug info
Debug.Log(Application.dataPath);
Debug.Log("Start Finished");
}
public MetaDraw()
{
UsefulProteomicsDatabases.Loaders.LoadElements();
InitializeComponent();
itemsControlSampleViewModel = new ItemsControlSampleViewModel();
DataContext = itemsControlSampleViewModel;
mainViewModel = new PsmAnnotationViewModel();
plotView.DataContext = mainViewModel;
allPsms = new ObservableCollection <PsmFromTsv>();
filteredListOfPsms = new ObservableCollection <PsmFromTsv>();
proteinTree = new ObservableCollection <ProteinForTreeView>();
filteredTree = new ObservableCollection <ProteinForTreeView>();
propertyView = new DataTable();
propertyView.Columns.Add("Name", typeof(string));
propertyView.Columns.Add("Value", typeof(string));
psmsWithMatch = new List <PsmFromTsv>();
proteinTreeView.DataContext = proteinTree;
dataGridProperties.DataContext = propertyView.DefaultView;
Title = "MetaDraw: version " + GlobalVariables.MetaMorpheusVersion;
spectraFileManager = new MyFileManager(true);
SetUpDictionaries();
variantCrossColor = Colors.Green;
modificationAnnotationColor = Brushes.Orange;
metaDrawGraphicalSettings = new MetaDrawGraphicalSettings();
metaDrawFilterSettings = new MetaDrawFilterSettings();
SearchModifications.Timer.Tick += new EventHandler(searchBox_TextChangedHandler);
base.Closing += this.OnClosing;
ParentChildScanView.Visibility = Visibility.Collapsed;
ParentScanView.Visibility = Visibility.Collapsed;
mapViewer.Visibility = Visibility.Collapsed;
legend.Visibility = Visibility.Collapsed;
plotTypes = new ObservableCollection <string>();
proteases = new string[1] {
"trypsin"
};
SetUpPlots();
//plotsListBox.ItemsSource = plotTypes;
ChangeMapScrollViewSize();
}
private void Page_Loaded(object sender, RoutedEventArgs e)
{
var Members = new List<Member>(MemberDao.getData());
myMembers = new BindingList<ListViewMember>();
foreach(var item in Members)
{
myMembers.Add(new ListViewMember { Info = MemberDao.ConvertString(item), Source = item.ImgSource });
}
MembersListView.ItemsSource = myMembers;
var Folder = AppDomain.CurrentDomain.BaseDirectory;
var path = $"{Folder}Resources/Data/AppInfo.txt";
MyFileManager.CheckFilePath(path);
var Data = File.ReadAllText(path);
AppInfo.Text = Data;
}
public static void TestCompressionDecompression()
{
string testInputFolder = Path.Combine(TestContext.CurrentContext.TestDirectory, @"CompressionTest");
DirectoryInfo testDirectory = new DirectoryInfo(testInputFolder);
MyFileManager.CompressDirectory(testDirectory);
foreach (FileInfo file in testDirectory.GetFiles())
{
Assert.AreEqual(".gz", file.Extension);
}
MyFileManager.DecompressDirectory(testDirectory);
foreach (FileInfo file in testDirectory.GetFiles())
{
Assert.AreNotEqual(".gz", file.Extension);
}
}
public static void AnotherSpectralLibrarySearchTestDecoy()
{
var testDir = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\SpectralLibrarySearch");
string myFile = Path.Combine(testDir, @"slicedMouse.raw");
MyFileManager myFileManager = new MyFileManager(true);
CommonParameters commonParameters = new CommonParameters(maxThreadsToUsePerFile: 1, scoreCutoff: 1);
MsDataFile myMsDataFile = myFileManager.LoadFile(myFile, commonParameters);
var variableModifications = new List <Modification>();
var fixedModifications = new List <Modification>();
var proteinList = new List <Protein> {
new Protein("QTATIAHVTTMLGEVIGFNDHIVK", "P16858")
};
string targetSpectralLibrary = Path.Combine(testDir, @"P16858_target.msp");
string decoySpectralLibrary = Path.Combine(testDir, @"P16858_decoy.msp");
List <string> specLibs = new List <string> {
targetSpectralLibrary, decoySpectralLibrary
};
SpectralLibrary sl = new SpectralLibrary(specLibs);
var searchModes = new SinglePpmAroundZeroSearchMode(5);
var listOfSortedms2Scans = MetaMorpheusTask.GetMs2Scans(myMsDataFile, null, new CommonParameters()).OrderBy(b => b.PrecursorMass).ToArray();
PeptideSpectralMatch[] allPsmsArray = new PeptideSpectralMatch[listOfSortedms2Scans.Length];
bool writeSpectralLibrary = false;
new ClassicSearchEngine(allPsmsArray, listOfSortedms2Scans, variableModifications, fixedModifications, null, null, null,
proteinList, searchModes, commonParameters, null, sl, new List <string>(), writeSpectralLibrary).Run();
// Single search mode
Assert.AreEqual(7, allPsmsArray.Length);
Assert.IsTrue(allPsmsArray[5].Score > 38);
Assert.AreEqual("VIHDNFGIVEGLMTTVHAITATQK", allPsmsArray[5].BaseSequence);
Assert.IsTrue(allPsmsArray[5].IsDecoy);
SpectralLibrarySearchFunction.CalculateSpectralAngles(sl, allPsmsArray, listOfSortedms2Scans, commonParameters);
Assert.That(allPsmsArray[5].SpectralAngle, Is.EqualTo(0.69).Within(0.01));
}
private void Window_Loaded(object sender, RoutedEventArgs e)
{
string Folder = AppDomain.CurrentDomain.BaseDirectory;
//Check file path
string newFolder = $"{Folder}Resources\\Data";
MyFileManager.CheckDictionary(newFolder);
newFolder = $"{Folder}Resources\\Images";
MyFileManager.CheckDictionary(newFolder);
newFolder = $"{Folder}Resources\\Icons";
MyFileManager.CheckDictionary(newFolder);
_list_menu = MenuDao.GetAll();
menuList.ItemsSource = _list_menu;
_content = new HomePage();
menuPage.Content = _content;
menuPage.Visibility = Visibility.Visible;
}
private void buttonDetectAnomalies_Click(object sender, EventArgs e)
{
List <Anomaly> anomalies_dbcc = AnomalyDetector.detectAnomaliesWithData();
List <Anomaly> anomalies_structure = AnomalyDetector.detectAnomaliesWithNoData();
string output_log = "";
output_log += "**********ANOMALY in DATA***********\n";
foreach (var item in anomalies_dbcc)
{
// string extra_summary = Trigger.getExtraSummary(item.object_id);
output_log += "\n***Anomalía del objeto " + item.object_id + ": \n" + item.summary; // + "\n" + extra_summary + "\n";
}
output_log += "\n\n**********ANOMALY STRUCTURE*************\n";
foreach (var item in anomalies_structure)
{
output_log += "\n***Anomalía structure in " + item.object_id + ": \n" + item.summary;
}
MyFileManager.writeTXT(output_log, "D://LOG_AUDITORIA_FULL_ANOMALIAS.txt");
if (anomalies_dbcc.Count + anomalies_structure.Count > 0)
{
output_log += "\n\nLOG GENERADO CON ANOMALÍAS en D://AUDITORIA_LOG_.txt";
}
else
{
output_log += "\n\nNO SE DETECTARON ANOMALÍAS";
}
this.richTextBox1.Text = output_log;
}
private void toolStripMenuItemFileCreateFolder_Click(object sender, EventArgs e)
{
newNameForm = new NewName();
newNameForm.LabelText = "Введите имя создаваемой папки";
newNameForm.TextBoxText = "Новая папка";
if (DialogResult.OK == newNameForm.ShowDialog() &&
newNameForm.TextBoxText != "")
{
string newPath = Path.Combine(fullPathSelected, newNameForm.TextBoxText);
try
{
MyFileManager.CreateDirectory(newPath);
}
catch (Exception ex)
{
MessageBox.Show(ex.Message,
"Создание папки " + newPath,
MessageBoxButtons.OK,
MessageBoxIcon.Error);
}
LoadList();
UpdateTreeNode(fullPathSelected);
}
}
public static void TestComputePEPValue()
{
var variableModifications = new List <Modification>();
var fixedModifications = new List <Modification>();
var origDataFile = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\TaGe_SA_HeLa_04_subset_longestSeq.mzML");
MyFileManager myFileManager = new MyFileManager(true);
CommonParameters CommonParameters = new CommonParameters(digestionParams: new DigestionParams());
var myMsDataFile = myFileManager.LoadFile(origDataFile, CommonParameters);
var searchModes = new SinglePpmAroundZeroSearchMode(5);
List <Protein> proteinList = ProteinDbLoader.LoadProteinFasta(Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\hela_snip_for_unitTest.fasta"), true, DecoyType.Reverse, false, ProteinDbLoader.UniprotAccessionRegex, ProteinDbLoader.UniprotFullNameRegex, ProteinDbLoader.UniprotFullNameRegex, ProteinDbLoader.UniprotGeneNameRegex,
ProteinDbLoader.UniprotOrganismRegex, out var dbErrors, -1);
var listOfSortedms2Scans = MetaMorpheusTask.GetMs2Scans(myMsDataFile, null, CommonParameters).OrderBy(b => b.PrecursorMass).ToArray();
PeptideSpectralMatch[] allPsmsArray = new PeptideSpectralMatch[listOfSortedms2Scans.Length];
new ClassicSearchEngine(allPsmsArray, listOfSortedms2Scans, variableModifications, fixedModifications, null, proteinList, searchModes, CommonParameters, new List <string>()).Run();
FdrAnalysisResults fdrResultsClassicDelta = (FdrAnalysisResults)(new FdrAnalysisEngine(allPsmsArray.Where(p => p != null).ToList(), 1, CommonParameters, new List <string>()).Run());
var nonNullPsms = allPsmsArray.Where(p => p != null).ToList();
var nonNullPsmsOriginalCopy = allPsmsArray.Where(p => p != null).ToList();
var accessionCounts = PEP_Analysis.GetAccessionCounts(nonNullPsms);
var maxScore = nonNullPsms.Select(n => n.Score).Max();
var maxScorePsm = nonNullPsms.Where(n => n.Score == maxScore).First();
Dictionary <string, int> sequenceToPsmCount = new Dictionary <string, int>();
List <string> sequences = new List <string>();
foreach (PeptideSpectralMatch psm in nonNullPsms)
{
var ss = psm.BestMatchingPeptides.Select(b => b.Peptide.FullSequence).ToList();
sequences.Add(String.Join("|", ss));
}
var s = sequences.GroupBy(i => i);
foreach (var grp in s)
{
sequenceToPsmCount.Add(grp.Key, grp.Count());
}
var maxPsmData = PEP_Analysis.CreateOnePsmDataFromPsm(maxScorePsm, accessionCounts, sequenceToPsmCount);
Assert.That(maxScorePsm.PeptidesToMatchingFragments.Count, Is.EqualTo(maxPsmData.Ambiguity));
Assert.That(maxScorePsm.DeltaScore, Is.EqualTo(maxPsmData.DeltaScore).Within(0.05));
Assert.That((float)(maxScorePsm.Score - (int)maxScorePsm.Score), Is.EqualTo(maxPsmData.Intensity).Within(0.05));
Assert.That(maxScorePsm.BestMatchingPeptides.Select(p => p.Peptide).First().MissedCleavages, Is.EqualTo(maxPsmData.MissedCleavagesCount));
Assert.That(maxScorePsm.BestMatchingPeptides.Select(p => p.Peptide).First().AllModsOneIsNterminus.Values.Count(), Is.EqualTo(maxPsmData.ModsCount));
Assert.That(maxScorePsm.Notch ?? 0, Is.EqualTo(maxPsmData.Notch));
Assert.That(maxScorePsm.PsmCount, Is.EqualTo(maxPsmData.PsmCount));
Assert.That(maxScorePsm.ScanPrecursorCharge, Is.EqualTo(maxPsmData.ScanPrecursorCharge));
PEP_Analysis.ComputePEPValuesForAllPSMsGeneric(nonNullPsms);
int trueCount = 0;
foreach (var item in allPsmsArray.Where(p => p != null))
{
var b = item.FdrInfo.PEP;
if (b >= 0.5)
{
trueCount++;
}
}
Assert.GreaterOrEqual(32, trueCount);
}
public static void OGlycoTest_Localization2()
{
//There may have a bug that MM cannot identify Peptide modified with (HexNAc), This is to test and find the bug.
//Get glycanBox
var glycanBox = OGlycanBoxes[0];
//Get unmodified peptide, products, allPossible modPos and all boxes.
Protein protein = new Protein("AATVGSLAGQPLQER", "P16150");
var peptide = protein.Digest(new DigestionParams(), new List <Modification>(), new List <Modification>()).First();
List <Product> products = new List <Product>();
peptide.Fragment(DissociationType.ETD, FragmentationTerminus.Both, products);
int[] modPos = GlycoSpectralMatch.GetPossibleModSites(peptide, new string[] { "S", "T" }).OrderBy(p => p).ToArray();
var boxes = GlycanBox.BuildChildOGlycanBoxes(glycanBox.NumberOfMods, glycanBox.ModIds).ToArray();
//Load scan.
CommonParameters commonParameters = new CommonParameters(dissociationType: DissociationType.ETD, trimMsMsPeaks: false);
string spectraFile = Path.Combine(TestContext.CurrentContext.TestDirectory, @"GlycoTestData\181217_Fusion_(LC2)_NewObj_Serum_deSA_Jacalin_HRM_4h_ETD_HCD_DDA_mz(400_1200)_21707.mgf");
var file = new MyFileManager(true).LoadFile(spectraFile, commonParameters);
var scans = MetaMorpheusTask.GetMs2Scans(file, spectraFile, commonParameters).ToArray();
//Known peptideWithMod match.
var peptideWithMod = GlycoPeptides.OGlyGetTheoreticalPeptide(new int[1] {
4
}, peptide, glycanBox);
Assert.That(peptideWithMod.FullSequence == "AAT[O-Glycosylation:N1 on X]VGSLAGQPLQER");
//List<Product> knownProducts = peptideWithMod.Fragment(DissociationType.EThcD, FragmentationTerminus.Both).ToList();
List <Product> knownProducts = GlycoPeptides.OGlyGetTheoreticalFragments(DissociationType.ETD, peptide, peptideWithMod);
var matchedKnownFragmentIons = MetaMorpheusEngine.MatchFragmentIons(scans.First(), knownProducts, commonParameters);
//Get hashset int
int obsPreviousFragmentCeilingMz = 0;
List <int> binsToSearch = new List <int>();
foreach (var envelope in scans.First().ExperimentalFragments)
{
// assume charge state 1 to calculate mass tolerance
double experimentalFragmentMass = envelope.MonoisotopicMass;
// get theoretical fragment bins within mass tolerance
int obsFragmentFloorMass = (int)Math.Floor((commonParameters.ProductMassTolerance.GetMinimumValue(experimentalFragmentMass)) * 1000);
int obsFragmentCeilingMass = (int)Math.Ceiling((commonParameters.ProductMassTolerance.GetMaximumValue(experimentalFragmentMass)) * 1000);
// prevents double-counting peaks close in m/z and lower-bound out of range exceptions
if (obsFragmentFloorMass < obsPreviousFragmentCeilingMz)
{
obsFragmentFloorMass = obsPreviousFragmentCeilingMz;
}
obsPreviousFragmentCeilingMz = obsFragmentCeilingMass + 1;
// search mass bins within a tolerance
for (int fragmentBin = obsFragmentFloorMass; fragmentBin <= obsFragmentCeilingMass; fragmentBin++)
{
binsToSearch.Add(fragmentBin);
}
}
HashSet <int> allPeaks = new HashSet <int>(binsToSearch);
//Graph Localization
LocalizationGraph localizationGraph = new LocalizationGraph(modPos, glycanBox, boxes, -1);
LocalizationGraph.LocalizeOGlycan(localizationGraph, scans.First(), commonParameters.ProductMassTolerance, products);
var allPaths = LocalizationGraph.GetAllHighestScorePaths(localizationGraph.array, localizationGraph.ChildModBoxes);
var knowPath = new int[2] {
1, 1
};
Assert.That(Enumerable.SequenceEqual(knowPath, allPaths[0]));
var local = LocalizationGraph.GetLocalizedPath(localizationGraph, allPaths.First());
Assert.That(Enumerable.SequenceEqual(local.Mods.Select(p => p.Item1), new List <int> {
4
}));
Assert.That(Enumerable.SequenceEqual(local.Mods.Select(p => p.Item2), new List <int> {
0
}));
}
public static void OGlycoTest_Localization()
{
//Get glycanBox
var glycanBox = OGlycanBoxes[19];
//Get unmodified peptide, products, allPossible modPos and all boxes.
Protein protein = new Protein("TTGSLEPSSGASGPQVSSVK", "P16150");
var peptide = protein.Digest(new DigestionParams(), new List <Modification>(), new List <Modification>()).First();
List <Product> products = new List <Product>();
peptide.Fragment(DissociationType.ETD, FragmentationTerminus.Both, products);
int[] modPos = GlycoSpectralMatch.GetPossibleModSites(peptide, new string[] { "S", "T" }).OrderBy(v => v).ToArray();
var boxes = GlycanBox.BuildChildOGlycanBoxes(3, glycanBox.ModIds).ToArray();
Assert.That(boxes.Count() == 6);
//Get Unlocal Fragment
var unlocalCost = GlycoPeptides.GetUnlocalFragment(products, modPos, glycanBox);
Assert.That(unlocalCost.Count == 4); //Basicly, the unlocal are c/z ions that don't localize glycosylation.
//Get scan
CommonParameters commonParameters = new CommonParameters(dissociationType: DissociationType.EThcD, trimMsMsPeaks: false);
string spectraFile = Path.Combine(TestContext.CurrentContext.TestDirectory, @"GlycoTestData\2019_09_16_StcEmix_35trig_EThcD25_rep1_4565.mgf");
var file = new MyFileManager(true).LoadFile(spectraFile, commonParameters);
var scans = MetaMorpheusTask.GetMs2Scans(file, spectraFile, commonParameters).ToArray();
//Known peptideWithMod match.
var peptideWithMod = GlycoPeptides.OGlyGetTheoreticalPeptide(new int[3] {
10, 2, 3
}, peptide, glycanBox);
Assert.That(peptideWithMod.FullSequence == "T[O-Glycosylation:H1N1 on X]T[O-Glycosylation:H1N1 on X]GSLEPSS[O-Glycosylation:N1 on X]GASGPQVSSVK");
List <Product> knownProducts = GlycoPeptides.OGlyGetTheoreticalFragments(DissociationType.EThcD, peptide, peptideWithMod);
var matchedKnownFragmentIons = MetaMorpheusEngine.MatchFragmentIons(scans.First(), knownProducts, commonParameters);
//Graph Localization
LocalizationGraph localizationGraph = new LocalizationGraph(modPos, glycanBox, boxes, -1);
LocalizationGraph.LocalizeOGlycan(localizationGraph, scans.First(), commonParameters.ProductMassTolerance, products);
var allPaths = LocalizationGraph.GetAllHighestScorePaths(localizationGraph.array, localizationGraph.ChildModBoxes);
var knowPath = new int[8] {
2, 4, 4, 4, 5, 5, 5, 5
};
Assert.That(Enumerable.SequenceEqual(knowPath, allPaths[0]));
//Get localized Route
var local = LocalizationGraph.GetLocalizedPath(localizationGraph, allPaths.First());
Assert.That(Enumerable.SequenceEqual(local.Mods.Select(v => v.Item1), new List <int> {
2, 3, 10
}));
Assert.That(Enumerable.SequenceEqual(local.Mods.Select(v => v.Item2), new List <int> {
1, 1, 0
}));
//Get all paths, calculate PScore and calculate position probability.
var p = scans.First().TheScan.MassSpectrum.Size *commonParameters.ProductMassTolerance.GetRange(1000).Width / scans.First().TheScan.MassSpectrum.Range.Width;
var n = knownProducts.Where(v => v.ProductType == ProductType.c || v.ProductType == ProductType.zDot).Count();
var allPathWithWeights = LocalizationGraph.GetAllPaths_CalP(localizationGraph, p, n);
Assert.That(allPathWithWeights.Count == 168);
//Calculate Site Specific Localization Probability
var y = LocalizationGraph.CalSiteSpecificLocalizationProbability(allPathWithWeights, localizationGraph.ModPos);
Assert.That(y.Count == 8);
Assert.That(y.First().Value[1].Item2 > 0.99);
}
private void button_get_integrity_metadata_Click(object sender, EventArgs e)
{
SqlConnection connection = MyDB.getConnection();
try
{
SqlCommand sqlCommand = new SqlCommand("SELECT LlaveForanea =o.name, Esquema =SCHEMA_NAME(t1.schema_id), Tabla =t1.name, Columna =c1.name, Esquema_Ref =SCHEMA_NAME(t2.schema_id), Tabla_Ref =t2.name, Columna_Ref =c2.name FROM sys.foreign_keys o INNER JOIN sys.foreign_key_columns fk ON o.object_id = fk.constraint_object_id INNER JOIN sys.tables t1 ON t1.object_id = fk.parent_object_id INNER JOIN sys.columns c1 ON c1.column_id = parent_column_id AND c1.object_id = t1.object_id INNER JOIN sys.tables t2 ON t2.object_id = fk.referenced_object_id INNER JOIN sys.columns c2 ON c2.column_id = referenced_column_id AND c2.object_id = t2.object_id", connection);
connection.Open();
// create data adapter
SqlDataAdapter dataAdapter = new SqlDataAdapter(sqlCommand);
DataTable dtRecord = new DataTable();
dataAdapter.Fill(dtRecord);
dataGridView1.DataSource = dtRecord;
sqlCommand = new SqlCommand("SELECT LlaveForanea =o.name, Esquema =SCHEMA_NAME(t1.schema_id), Tabla =t1.name, Columna =c1.name, Esquema_Ref =SCHEMA_NAME(t2.schema_id), Tabla_Ref =t2.name, Columna_Ref =c2.name FROM sys.foreign_keys o INNER JOIN sys.foreign_key_columns fk ON o.object_id = fk.constraint_object_id INNER JOIN sys.tables t1 ON t1.object_id = fk.parent_object_id INNER JOIN sys.columns c1 ON c1.column_id = parent_column_id AND c1.object_id = t1.object_id INNER JOIN sys.tables t2 ON t2.object_id = fk.referenced_object_id INNER JOIN sys.columns c2 ON c2.column_id = referenced_column_id AND c2.object_id = t2.object_id", connection);
SqlDataReader dataReader = sqlCommand.ExecuteReader();
string output_log = "LlaveForanea,Esquema,Tabla,Columna,Esquema_Ref,Tabla_Ref,Columna_Ref\n";
while (dataReader.Read())
{
// Console.WriteLine("LEYENDO " + dataReader.FieldCount);
int index = 0;
string LlaveForanea = dataReader.GetValue(index++).ToString();
string Esquema = dataReader.GetValue(index++).ToString();
string Tabla = dataReader.GetValue(index++).ToString();
string Columna = dataReader.GetValue(index++).ToString();
string Esquema_Ref = dataReader.GetValue(index++).ToString();
string Tabla_Ref = dataReader.GetValue(index++).ToString();
string Columna_Ref = dataReader.GetValue(index++).ToString();
output_log += LlaveForanea + "," + Esquema + "," + Tabla + "," + Columna + "," + Esquema_Ref + "," + Tabla_Ref + "," + Columna_Ref + "\n";
}
MyFileManager.writeTXT(output_log, "D://LOG_AUDITORIA_RELACIONES_INTEGRIDAD_REFERENCIAL.txt");
sqlCommand.Dispose();
dataReader.Close();
}
catch (Exception error)
{
Console.WriteLine("Error: " + error.Message);
}
finally
{
connection.Close();
}
/*
*
* string[][] sqls = new string[][] {
* //--->Esquemas
* //--Sys.schemas
* new string[]{"sys-schemas", "[name],[schema_id],[principal_id]", "SELECT [name],[schema_id],[principal_id] FROM [pubs].[sys].[schemas]"},
* //--->Información general de tablas:
* //--INFORMATION_SCHEMA.TABLES
* new string[]{ "INFORMATION_SCHEMA-TABLES", "[TABLE_CATALOG],[TABLE_SCHEMA],[TABLE_NAME]", "SELECT [TABLE_CATALOG],[TABLE_SCHEMA],[TABLE_NAME],[TABLE_TYPE] FROM[pubs].[INFORMATION_SCHEMA].[TABLES]"},
* //--->Información de claves primarias y foráneas
* //--INFORMATION_SCHEMA.REFERENTIAL_CONSTRAINTS
* new string[]{ "INFORMATION_SCHEMA-REFERENTIAL_CONSTRAINTS", "[CONSTRAINT_CATALOG],[CONSTRAINT_SCHEMA],[CONSTRAINT_NAME],[UNIQUE_CONSTRAINT_CATALOG],[UNIQUE_CONSTRAINT_SCHEMA],[UNIQUE_CONSTRAINT_NAME],[MATCH_OPTION],[UPDATE_RULE],[DELETE_RULE]", "SELECT [CONSTRAINT_CATALOG],[CONSTRAINT_SCHEMA],[CONSTRAINT_NAME],[UNIQUE_CONSTRAINT_CATALOG],[UNIQUE_CONSTRAINT_SCHEMA],[UNIQUE_CONSTRAINT_NAME],[MATCH_OPTION],[UPDATE_RULE],[DELETE_RULE] FROM [pubs].[INFORMATION_SCHEMA].[REFERENTIAL_CONSTRAINTS]"},
* //--INFORMATION_SCHEMA.TABLE_CONSTRAINTS
* new string[]{ "INFORMATION_SCHEMA-TABLE_CONSTRAINTS", "[CONSTRAINT_CATALOG],[CONSTRAINT_SCHEMA],[CONSTRAINT_NAME],[TABLE_CATALOG],[TABLE_SCHEMA],[TABLE_NAME],[CONSTRAINT_TYPE],[IS_DEFERRABLE],[INITIALLY_DEFERRED]", "SELECT [CONSTRAINT_CATALOG],[CONSTRAINT_SCHEMA],[CONSTRAINT_NAME],[TABLE_CATALOG],[TABLE_SCHEMA],[TABLE_NAME],[CONSTRAINT_TYPE],[IS_DEFERRABLE],[INITIALLY_DEFERRED] FROM [pubs].[INFORMATION_SCHEMA].[TABLE_CONSTRAINTS]"},
* //--Sys.key_constraints
* new string[]{ "sys-key_constraints", "[name], [object_id], [principal_id],[schema_id],[parent_object_id],[type],[type_desc],[create_date],[modify_date],[is_ms_shipped],[is_published],[is_schema_published],[unique_index_id],[is_system_named],[is_enforced]", "SELECT [name], [object_id], [principal_id],[schema_id],[parent_object_id],[type],[type_desc],[create_date],[modify_date],[is_ms_shipped],[is_published],[is_schema_published],[unique_index_id],[is_system_named],[is_enforced] FROM [pubs].[sys].[key_constraints]"},
* //--Sys.foreign_key_columns
* new string[]{ "sys-foreign_key_columns", "[constraint_object_id],[constraint_column_id],[parent_object_id],[parent_column_id],[referenced_object_id],[referenced_column_id]", "SELECT [constraint_object_id],[constraint_column_id],[parent_object_id],[parent_column_id],[referenced_object_id],[referenced_column_id] FROM [pubs].[sys].[foreign_key_columns]"},
* //--Sys.foreign_key
* new string[]{ "sys-foreign_key", "[name],[object_id],[principal_id],[schema_id],[parent_object_id],[type],[type_desc],[create_date],[modify_date],[is_ms_shipped],[is_published],[is_schema_published],[referenced_object_id],[key_index_id],[is_disabled],[is_not_for_replication],[is_not_trusted],[delete_referential_action],[delete_referential_action_desc],[update_referential_action],[update_referential_action_desc],[is_system_named]", "SELECT [name],[object_id],[principal_id],[schema_id],[parent_object_id],[type],[type_desc],[create_date],[modify_date],[is_ms_shipped],[is_published],[is_schema_published],[referenced_object_id],[key_index_id],[is_disabled],[is_not_for_replication],[is_not_trusted],[delete_referential_action],[delete_referential_action_desc],[update_referential_action],[update_referential_action_desc],[is_system_named] FROM [pubs].[sys].[foreign_keys]"},
* //--->Información general detallada de las tablas
* //--Sys.tables
* new string[]{ "sys-tables", "[name] ,[object_id] ,[principal_id] ,[schema_id] ,[parent_object_id] ,[type] ,[type_desc] ,[create_date] ,[modify_date] ,[is_ms_shipped] ,[is_published] ,[is_schema_published] ,[lob_data_space_id] ,[filestream_data_space_id] ,[max_column_id_used] ,[lock_on_bulk_load] ,[uses_ansi_nulls] ,[is_replicated] ,[has_replication_filter] ,[is_merge_published] ,[is_sync_tran_subscribed] ,[has_unchecked_assembly_data] ,[text_in_row_limit] ,[large_value_types_out_of_row] ,[is_tracked_by_cdc] ,[lock_escalation] ,[lock_escalation_desc] ,[is_filetable] ,[is_memory_optimized] ,[durability] ,[durability_desc] ,[temporal_type] ,[temporal_type_desc] ,[history_table_id] ,[is_remote_data_archive_enabled] ,[is_external] ,[history_retention_period] ,[history_retention_period_unit] ,[history_retention_period_unit_desc] ,[is_node] ,[is_edge]", "SELECT [name] ,[object_id] ,[principal_id] ,[schema_id] ,[parent_object_id] ,[type] ,[type_desc] ,[create_date] ,[modify_date] ,[is_ms_shipped] ,[is_published] ,[is_schema_published] ,[lob_data_space_id] ,[filestream_data_space_id] ,[max_column_id_used] ,[lock_on_bulk_load] ,[uses_ansi_nulls] ,[is_replicated] ,[has_replication_filter] ,[is_merge_published] ,[is_sync_tran_subscribed] ,[has_unchecked_assembly_data] ,[text_in_row_limit] ,[large_value_types_out_of_row] ,[is_tracked_by_cdc] ,[lock_escalation] ,[lock_escalation_desc] ,[is_filetable] ,[is_memory_optimized] ,[durability] ,[durability_desc] ,[temporal_type] ,[temporal_type_desc] ,[history_table_id] ,[is_remote_data_archive_enabled] ,[is_external] ,[history_retention_period] ,[history_retention_period_unit] ,[history_retention_period_unit_desc] ,[is_node] ,[is_edge] FROM [pubs].[sys].[tables]"},
* //--Sys.columns
* new string[]{ "sys-columns", "[object_id] ,[name] ,[column_id] ,[system_type_id] ,[user_type_id] ,[max_length] ,[precision] ,[scale] ,[collation_name] ,[is_nullable] ,[is_ansi_padded] ,[is_rowguidcol] ,[is_identity] ,[is_computed] ,[is_filestream] ,[is_replicated] ,[is_non_sql_subscribed] ,[is_merge_published] ,[is_dts_replicated] ,[is_xml_document] ,[xml_collection_id] ,[default_object_id] ,[rule_object_id] ,[is_sparse] ,[is_column_set] ,[generated_always_type] ,[generated_always_type_desc] ,[encryption_type] ,[encryption_type_desc] ,[encryption_algorithm_name] ,[column_encryption_key_id] ,[column_encryption_key_database_name] ,[is_hidden] ,[is_masked] ,[graph_type] ,[graph_type_desc]", "SELECT [object_id] ,[name] ,[column_id] ,[system_type_id] ,[user_type_id] ,[max_length] ,[precision] ,[scale] ,[collation_name] ,[is_nullable] ,[is_ansi_padded] ,[is_rowguidcol] ,[is_identity] ,[is_computed] ,[is_filestream] ,[is_replicated] ,[is_non_sql_subscribed] ,[is_merge_published] ,[is_dts_replicated] ,[is_xml_document] ,[xml_collection_id] ,[default_object_id] ,[rule_object_id] ,[is_sparse] ,[is_column_set] ,[generated_always_type] ,[generated_always_type_desc] ,[encryption_type] ,[encryption_type_desc] ,[encryption_algorithm_name] ,[column_encryption_key_id] ,[column_encryption_key_database_name] ,[is_hidden] ,[is_masked] ,[graph_type] ,[graph_type_desc] FROM [pubs].[sys].[columns]"},
* //--Sys.systypes
* new string[]{ "sys-systypes", "[name] ,[xtype] ,[status] ,[xusertype] ,[length] ,[xprec] ,[xscale] ,[tdefault] ,[domain] ,[uid] ,[reserved] ,[collationid] ,[usertype] ,[variable] ,[allownulls] ,[type] ,[printfmt] ,[prec] ,[scale] ,[collation]", "SELECT [name] ,[xtype] ,[status] ,[xusertype] ,[length] ,[xprec] ,[xscale] ,[tdefault] ,[domain] ,[uid] ,[reserved] ,[collationid] ,[usertype] ,[variable] ,[allownulls] ,[type] ,[printfmt] ,[prec] ,[scale] ,[collation] FROM [pubs].[sys].[systypes]"},
* //--Sys.default_constraints
* new string[]{ "sys-default_constraints", "[name] ,[object_id] ,[principal_id] ,[schema_id] ,[parent_object_id] ,[type] ,[type_desc] ,[create_date] ,[modify_date] ,[is_ms_shipped] ,[is_published] ,[is_schema_published] ,[parent_column_id] ,[definition] ,[is_system_named]", "SELECT [name] ,[object_id] ,[principal_id] ,[schema_id] ,[parent_object_id] ,[type] ,[type_desc] ,[create_date] ,[modify_date] ,[is_ms_shipped] ,[is_published] ,[is_schema_published] ,[parent_column_id] ,[definition] ,[is_system_named] FROM [pubs].[sys].[default_constraints]"},
* //--->Restricciones / Checks
* //--INFORMATION_SCHEMA.CHECK_CONSTRAINTS
* new string[]{ "INFORMATION_SCHEMA-CHECK_CONSTRAINTS", "[CONSTRAINT_CATALOG] ,[CONSTRAINT_SCHEMA] ,[CONSTRAINT_NAME] ,[CHECK_CLAUSE]", "SELECT [CONSTRAINT_CATALOG] ,[CONSTRAINT_SCHEMA] ,[CONSTRAINT_NAME] ,[CHECK_CLAUSE] FROM [pubs].[INFORMATION_SCHEMA].[CHECK_CONSTRAINTS]"},
* //--Sys.check_constraints
* new string[]{ "sys-check_constraints", "[name] ,[object_id] ,[principal_id] ,[schema_id] ,[parent_object_id] ,[type] ,[type_desc] ,[create_date] ,[modify_date] ,[is_ms_shipped] ,[is_published] ,[is_schema_published] ,[is_disabled] ,[is_not_for_replication] ,[is_not_trusted] ,[parent_column_id] ,[definition] ,[uses_database_collation] ,[is_system_named]", "SELECT [name] ,[object_id] ,[principal_id] ,[schema_id] ,[parent_object_id] ,[type] ,[type_desc] ,[create_date] ,[modify_date] ,[is_ms_shipped] ,[is_published] ,[is_schema_published] ,[is_disabled] ,[is_not_for_replication] ,[is_not_trusted] ,[parent_column_id] ,[definition] ,[uses_database_collation] ,[is_system_named] FROM [pubs].[sys].[check_constraints]"},
* //--Sys.triggers
* // new string[]{"sys-triggers", "[name] ,[object_id] ,[parent_class] ,[parent_class_desc] ,[parent_id] ,[type] ,[type_desc] ,[create_date] ,[modify_date] ,[is_ms_shipped] ,[is_disabled] ,[is_not_for_replication] ,[is_instead_of_trigger]", "SELECT [name] ,[object_id] ,[parent_class] ,[parent_class_desc] ,[parent_id] ,[type] ,[type_desc] ,[create_date] ,[modify_date] ,[is_ms_shipped] ,[is_disabled] ,[is_not_for_replication] ,[is_instead_of_trigger] FROM [pubs].[sys].[triggers]"},
*
* };
*
*
* for (int i = 0; i < sqls.Length; i++)
* {
* string filename = sqls[i][0], header = sqls[i][1], sql = sqls[i][2];
* MyDB.selectAllAndWrite(sql, "D://" + filename + ".txt", header);
* }
*
* MessageBox.Show("TXT generados con los metadatos en D://");
*/
}
public static void TestComputePEPValue()
{
var variableModifications = new List <Modification>();
var fixedModifications = new List <Modification>();
var origDataFile = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\TaGe_SA_HeLa_04_subset_longestSeq.mzML");
MyFileManager myFileManager = new MyFileManager(true);
CommonParameters CommonParameters = new CommonParameters(digestionParams: new DigestionParams());
var myMsDataFile = myFileManager.LoadFile(origDataFile, CommonParameters);
var searchModes = new SinglePpmAroundZeroSearchMode(5);
List <Protein> proteinList = ProteinDbLoader.LoadProteinFasta(Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\hela_snip_for_unitTest.fasta"), true, DecoyType.Reverse, false, ProteinDbLoader.UniprotAccessionRegex, ProteinDbLoader.UniprotFullNameRegex, ProteinDbLoader.UniprotFullNameRegex, ProteinDbLoader.UniprotGeneNameRegex,
ProteinDbLoader.UniprotOrganismRegex, out var dbErrors, -1);
var listOfSortedms2Scans = MetaMorpheusTask.GetMs2Scans(myMsDataFile, @"TestData\TaGe_SA_HeLa_04_subset_longestSeq.mzML", CommonParameters).OrderBy(b => b.PrecursorMass).ToArray();
PeptideSpectralMatch[] allPsmsArray = new PeptideSpectralMatch[listOfSortedms2Scans.Length];
new ClassicSearchEngine(allPsmsArray, listOfSortedms2Scans, variableModifications, fixedModifications, null, null, null, proteinList, searchModes, CommonParameters, new List <string>()).Run();
FdrAnalysisResults fdrResultsClassicDelta = (FdrAnalysisResults)(new FdrAnalysisEngine(allPsmsArray.Where(p => p != null).ToList(), 1, CommonParameters, new List <string>()).Run());
var nonNullPsms = allPsmsArray.Where(p => p != null).ToList();
var nonNullPsmsOriginalCopy = allPsmsArray.Where(p => p != null).ToList();
var maxScore = nonNullPsms.Select(n => n.Score).Max();
PeptideSpectralMatch maxScorePsm = nonNullPsms.Where(n => n.Score == maxScore).First();
Dictionary <string, int> sequenceToPsmCount = new Dictionary <string, int>();
List <string> sequences = new List <string>();
foreach (PeptideSpectralMatch psm in nonNullPsms)
{
var ss = psm.BestMatchingPeptides.Select(b => b.Peptide.FullSequence).ToList();
sequences.Add(String.Join("|", ss));
}
var s = sequences.GroupBy(i => i);
foreach (var grp in s)
{
sequenceToPsmCount.Add(grp.Key, grp.Count());
}
Dictionary <string, Dictionary <int, Tuple <double, double> > > fileSpecificRetTimeHI_behavior = new Dictionary <string, Dictionary <int, Tuple <double, double> > >();
Dictionary <string, Dictionary <int, Tuple <double, double> > > fileSpecificRetTemHI_behaviorModifiedPeptides = new Dictionary <string, Dictionary <int, Tuple <double, double> > >();
//average hydrophobicity, standard deviation hydrophobicity
Tuple <double, double> at = new Tuple <double, double>(33.0, 1.0);
Dictionary <int, Tuple <double, double> > HI_Time_avg_dev = new Dictionary <int, Tuple <double, double> >
{
{ 154, at }
};
fileSpecificRetTimeHI_behavior.Add(@"TestData\TaGe_SA_HeLa_04_subset_longestSeq.mzML", HI_Time_avg_dev);
string[] trainingVariables = new[] { "HydrophobicityZScore", "Intensity", "ScanPrecursorCharge", "DeltaScore", "Notch", "PsmCount", "ModsCount", "MissedCleavagesCount", "Ambiguity", "LongestFragmentIonSeries", "IsVariantPeptide" };
int chargeStateMode = 4;
var(notch, pwsm) = maxScorePsm.BestMatchingPeptides.First();
var maxPsmData = PEP_Analysis.CreateOnePsmDataEntry(maxScorePsm, sequenceToPsmCount, fileSpecificRetTimeHI_behavior, fileSpecificRetTemHI_behaviorModifiedPeptides, chargeStateMode, pwsm, trainingVariables, notch, !pwsm.Protein.IsDecoy);
Assert.That(maxScorePsm.PeptidesToMatchingFragments.Count - 1, Is.EqualTo(maxPsmData.Ambiguity));
Assert.That(maxScorePsm.DeltaScore, Is.EqualTo(maxPsmData.DeltaScore).Within(0.05));
Assert.That((float)(maxScorePsm.Score - (int)maxScorePsm.Score), Is.EqualTo(maxPsmData.Intensity).Within(0.05));
Assert.That(maxPsmData.HydrophobicityZScore, Is.EqualTo(5.170955).Within(0.05));
Assert.That(maxScorePsm.BestMatchingPeptides.Select(p => p.Peptide).First().MissedCleavages, Is.EqualTo(maxPsmData.MissedCleavagesCount));
Assert.That(maxScorePsm.BestMatchingPeptides.Select(p => p.Peptide).First().AllModsOneIsNterminus.Values.Count(), Is.EqualTo(maxPsmData.ModsCount));
Assert.That(maxScorePsm.Notch ?? 0, Is.EqualTo(maxPsmData.Notch));
Assert.That(maxScorePsm.PsmCount, Is.EqualTo(maxPsmData.PsmCount));
Assert.That(-Math.Abs(chargeStateMode - maxScorePsm.ScanPrecursorCharge), Is.EqualTo(maxPsmData.PrecursorChargeDiffToMode));
Assert.AreEqual((float)0, maxPsmData.IsVariantPeptide);
PEP_Analysis.ComputePEPValuesForAllPSMsGeneric(nonNullPsms);
int trueCount = 0;
foreach (var item in allPsmsArray.Where(p => p != null))
{
var b = item.FdrInfo.PEP;
if (b >= 0.5)
{
trueCount++;
}
}
List <PeptideSpectralMatch> moreNonNullPSMs = new List <PeptideSpectralMatch>();
for (int i = 0; i < 3; i++)
{
foreach (PeptideSpectralMatch psm in nonNullPsms)
{
moreNonNullPSMs.Add(psm);
}
}
string expectedMetrics = "************************************************************\r\n* Metrics for Determination of PEP Using Binary Classification \r\n" +
"*-----------------------------------------------------------\r\n* Accuracy: 1\r\n* Area Under Curve: 1\r\n* Area under Precision recall Curve: 1\r\n* F1Score: 1\r\n" +
"* LogLoss: 2.60551851621861E-10\r\n* LogLossReduction: 0.999999999599165\r\n* PositivePrecision: 1\r\n* PositiveRecall: 1\r\n* NegativePrecision: 1\r\n" +
"* NegativeRecall: 1\r\n* Count of Ambiguous Peptides Removed: 0\r\n************************************************************\r\n";
string metrics = PEP_Analysis.ComputePEPValuesForAllPSMsGeneric(moreNonNullPSMs);
Assert.AreEqual(expectedMetrics, metrics);
Assert.GreaterOrEqual(32, trueCount);
//Test Variant Peptide as Input is identified as such as part of PEP calculation input much of the next several lines simply necessry to create a psm.
var anMzSpectrum = new MzSpectrum(new double[] { 1, 1 }, new double[] { 2, 2 }, true);
Ms2ScanWithSpecificMass scan = new Ms2ScanWithSpecificMass(new MsDataScan(anMzSpectrum, 1, 1, true, Polarity.Negative, 2, null, "", MZAnalyzerType.Orbitrap, 2, null, null, null), 1, 1, "path", new CommonParameters());
Protein variantProtein = new Protein("MPEPPPTIDE", "protein3", sequenceVariations: new List <SequenceVariation> {
new SequenceVariation(4, 6, "PPP", "P", @"1\t50000000\t.\tA\tG\t.\tPASS\tANN=G||||||||||||||||\tGT:AD:DP\t1/1:30,30:30", null)
});
PeptideWithSetModifications varPep = variantProtein.GetVariantProteins().SelectMany(p => p.Digest(CommonParameters.DigestionParams, null, null)).FirstOrDefault();
PeptideSpectralMatch variantPSM = new PeptideSpectralMatch(varPep, 0, maxScorePsm.Score, maxScorePsm.ScanIndex, scan, new DigestionParams(), null);
sequenceToPsmCount = new Dictionary <string, int>();
sequences = new List <string>();
nonNullPsms.Add(variantPSM);
foreach (PeptideSpectralMatch psm in nonNullPsms)
{
var ss = psm.BestMatchingPeptides.Select(b => b.Peptide.FullSequence).ToList();
sequences.Add(String.Join("|", ss));
}
s = sequences.GroupBy(i => i);
foreach (var grp in s)
{
sequenceToPsmCount.Add(grp.Key, grp.Count());
}
var(vnotch, vpwsm) = variantPSM.BestMatchingPeptides.First();
PsmData variantPsmData = PEP_Analysis.CreateOnePsmDataEntry(variantPSM, sequenceToPsmCount, fileSpecificRetTimeHI_behavior, fileSpecificRetTemHI_behaviorModifiedPeptides, chargeStateMode, vpwsm, trainingVariables, vnotch, !maxScorePsm.IsDecoy);
Assert.AreEqual((float)1, variantPsmData.IsVariantPeptide);
}
private void ProcessAscii(DecryptedObject decryptedObject)
{
bool foundSomething = false;
string sDecryptOrig = decryptedObject.GetDecodedString(Encoding.UTF8);
var sDecyptPrintable = new StringBuilder(sDecryptOrig).RemoveAsciiControllChars().RemoveNewLines().RemoveChar(';').GetString();
if (new StringBuilder(sDecryptOrig).CountChar("[½|¿]") > 100)
{
string ln = $";{decryptedObject.GetBytesKeyHex()};;;;;;;;;;;;;{sDecyptPrintable}";
MyFileManagerBad.ConcatNewLine(ln);
return;
}
string sProcessed = new StringBuilder(sDecryptOrig).RemoveNoneAlphanumericChars().GetString();
int cDChars = new StringBuilder(sDecryptOrig).CountChars(); //Numero de Caracteres en String Decriptada
int cPChars = new StringBuilder(sProcessed).CountChars(); //Numero de Caracteres en String Procesada
int cCharDif = cDChars - cPChars; // Diferencia Numercia de Caracteres entre original y procesada
if (Regex.Match(sDecryptOrig, regex, RegexOptions.IgnoreCase).Success)
{
foundSomething = true;
}
//var sDecyptPrintable = new StringBuilder(sDecryptOrig).RemoveNewLines()
// .RemoveChar(';').RemoveChar('\n').RemoveChar('?').RemoveAsciiControllChars().GetString();
int cDIsAlpha = new StringBuilder(sDecryptOrig).CountAlphanumericChars(); //Numero de Caracteres Alphanumericos
int cDNoAlpha = new StringBuilder(sDecryptOrig).CountNoAlphanumericChars(); //Numero de Caracteres No Alphanumericos
int cDIsHex = new StringBuilder(sDecryptOrig).CountHexadecimalChars(); //Numero de Caracteres Hexadecimales
int cDNoHex = new StringBuilder(sDecryptOrig).CountNoHexadecimalChars(); //Numero de Caracteres No Hexadecimales
//int cPIsAlpha = new StringBuilder(sProcessed).CountAlphanumericChars(); //Numero de Caracteres Alphanumericos
int cPNoAlpha = new StringBuilder(sProcessed).CountNoAlphanumericChars(); //Numero de Caracteres No Alphanumericos
//int cPIsHex = new StringBuilder(sProcessed).CountHexadecimalChars(); //Numero de Caracteres Hexadecimales
int cPNoHex = new StringBuilder(sProcessed).CountNoHexadecimalChars(); //Numero de Caracteres No Hexadecimales
string line = $"{foundSomething}";
line += $";{decryptedObject.GetBytesKeyHex()}"; //Llave utilizada
line += $";{cDChars};{cPChars}"; //Numero de Caracteres en la String
line += $";{cCharDif}"; // Diferencia Numercia de Caracteres entre original y procesada
//cPIsAlpha
line += $";{cDIsAlpha};"; //Numero de Caracteres Alphanumericos original y procesada
line += $";{cDNoAlpha};{cPNoAlpha}"; //Numero de Caracteres No Alphanumericos original y procesada
//cPIsHex
line += $";{cDIsHex};"; //Numero de Caracteres Hexadecimales original y procesada
line += $";{cDNoHex};{cPNoHex}"; //Numero de Caracteres No Hexadecimales original y procesada
line += $";{sProcessed}"; // String Procesada
line += $";{sDecyptPrintable}"; // String original sin saltos de linea ni ';'
if (foundSomething == true)
{
MyFileManagerSuccesses.ConcatNewLine(line);
}
MyFileManager.ConcatNewLine(line);
}
public static void TestComputePEPValueTopDown()
{
//just making sure that topdown data goes through the pep calculator without crashing.
CommonParameters CommonParameters = new CommonParameters(
digestionParams: new DigestionParams(protease: "top-down"),
scoreCutoff: 1,
assumeOrphanPeaksAreZ1Fragments: false);
var variableModifications = new List <Modification>();
var fixedModifications = new List <Modification>();
List <Protein> proteinList = ProteinDbLoader.LoadProteinFasta(Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\HeLaFakeTopDown.fasta"), true, DecoyType.Reverse, false, ProteinDbLoader.UniprotAccessionRegex, ProteinDbLoader.UniprotFullNameRegex, ProteinDbLoader.UniprotFullNameRegex, ProteinDbLoader.UniprotGeneNameRegex,
ProteinDbLoader.UniprotOrganismRegex, out var dbErrors, -1);
var origDataFile = Path.Combine(TestContext.CurrentContext.TestDirectory, @"TestData\TaGe_SA_HeLa_04_subset_longestSeq.mzML");
MyFileManager myFileManager = new MyFileManager(true);
var myMsDataFile = myFileManager.LoadFile(origDataFile, CommonParameters);
var searchMode = new SinglePpmAroundZeroSearchMode(5);
Tolerance DeconvolutionMassTolerance = new PpmTolerance(5);
var listOfSortedms2Scans = MetaMorpheusTask.GetMs2Scans(myMsDataFile, null, new CommonParameters()).OrderBy(b => b.PrecursorMass).ToArray();
PeptideSpectralMatch[] allPsmsArray = new PeptideSpectralMatch[listOfSortedms2Scans.Length];
new ClassicSearchEngine(allPsmsArray, listOfSortedms2Scans, variableModifications, fixedModifications, null, null, null, proteinList, searchMode, CommonParameters, new List <string>()).Run();
var nonNullPsms = allPsmsArray.Where(p => p != null).ToList();
List <PeptideSpectralMatch> moreNonNullPSMs = new List <PeptideSpectralMatch>();
int reps = 3;
for (int i = 0; i < reps; i++)
{
foreach (PeptideSpectralMatch psm in nonNullPsms)
{
moreNonNullPSMs.Add(psm);
}
}
FdrAnalysisResults fdrResultsClassicDelta = (FdrAnalysisResults)(new FdrAnalysisEngine(moreNonNullPSMs.Where(p => p != null).ToList(), 1, CommonParameters, new List <string>()).Run());
var maxScore = nonNullPsms.Select(n => n.Score).Max();
PeptideSpectralMatch maxScorePsm = nonNullPsms.Where(n => n.Score == maxScore).First();
Dictionary <string, int> sequenceToPsmCount = new Dictionary <string, int>();
List <string> sequences = new List <string>();
foreach (PeptideSpectralMatch psm in nonNullPsms)
{
var ss = psm.BestMatchingPeptides.Select(b => b.Peptide.FullSequence).ToList();
sequences.Add(String.Join("|", ss));
}
var s = sequences.GroupBy(i => i);
foreach (var grp in s)
{
sequenceToPsmCount.Add(grp.Key, grp.Count());
}
Dictionary <string, Dictionary <int, Tuple <double, double> > > fileSpecificRetTimeHI_behavior = new Dictionary <string, Dictionary <int, Tuple <double, double> > >();
Dictionary <string, Dictionary <int, Tuple <double, double> > > fileSpecificRetTemHI_behaviorModifiedPeptides = new Dictionary <string, Dictionary <int, Tuple <double, double> > >();
string[] trainingVariables = PsmData.trainingInfos["topDown"];
int chargeStateMode = 4;
var(notch, pwsm) = maxScorePsm.BestMatchingPeptides.First();
var maxPsmData = PEP_Analysis.CreateOnePsmDataEntry(maxScorePsm, sequenceToPsmCount, fileSpecificRetTimeHI_behavior, fileSpecificRetTemHI_behaviorModifiedPeptides, chargeStateMode, pwsm, trainingVariables, notch, !pwsm.Protein.IsDecoy);
Assert.That(maxScorePsm.PeptidesToMatchingFragments.Count - 1, Is.EqualTo(maxPsmData.Ambiguity));
Assert.That(maxScorePsm.DeltaScore, Is.EqualTo(maxPsmData.DeltaScore).Within(0.05));
Assert.That((float)(maxScorePsm.Score - (int)maxScorePsm.Score), Is.EqualTo(maxPsmData.Intensity).Within(0.05));
Assert.AreEqual(maxPsmData.HydrophobicityZScore, float.NaN);
Assert.That(maxScorePsm.BestMatchingPeptides.Select(p => p.Peptide).First().MissedCleavages, Is.EqualTo(maxPsmData.MissedCleavagesCount));
Assert.That(maxScorePsm.BestMatchingPeptides.Select(p => p.Peptide).First().AllModsOneIsNterminus.Values.Count(), Is.EqualTo(maxPsmData.ModsCount));
Assert.That(maxScorePsm.Notch ?? 0, Is.EqualTo(maxPsmData.Notch));
Assert.That(maxScorePsm.PsmCount, Is.EqualTo(maxPsmData.PsmCount * reps));
Assert.That(-Math.Abs(chargeStateMode - maxScorePsm.ScanPrecursorCharge), Is.EqualTo(maxPsmData.PrecursorChargeDiffToMode));
Assert.AreEqual((float)0, maxPsmData.IsVariantPeptide);
}
private void toolStripMenuItemEditPaste_Click(object sender, EventArgs e)
{
if (fullPathForCopyList.Count > 0)
{
foreach (string source in fullPathForCopyList)
{
if (Path.GetExtension(source) != String.Empty)
{
string fileName = Path.GetFileName(source);
try
{
if (mustCutItems)
{
File.Move(source, Path.Combine(fullPathSelected, fileName));
this.toolStripStatusLabel1.Text = "Перемещение файла";
}
else
{
MyFileManager.CopyFile(source, Path.Combine(fullPathSelected, fileName));
this.toolStripStatusLabel1.Text = "Копирование файла";
}
}
catch (Exception ex)
{
MessageBox.Show(ex.Message,
"Ошибка при копировании файла " + source,
MessageBoxButtons.OK, MessageBoxIcon.Error);
}
}
else
{
string folderName = Path.GetFileName(source);
try
{
if (mustCutItems)
{
MyFileManager.MoveDirectory(source, Path.Combine(fullPathSelected, folderName));
this.toolStripStatusLabel1.Text = "Перемещение папки";
}
else
{
MyFileManager.CopyDirectory(source, Path.Combine(fullPathSelected, folderName));
this.toolStripStatusLabel1.Text = "Копирование папки";
}
}
catch (Exception ex)
{
MessageBox.Show(ex.Message,
"Ошибка при копировании папки " + source,
MessageBoxButtons.OK, MessageBoxIcon.Error);
}
}
}
LoadList();
UpdateTreeNode(Path.GetPathRoot(fullPathForCopyList[0]));
UpdateTreeNode(fullPathSelected);
fullPathForCopyList.Clear();
this.toolStripStatusLabel1.Text = "";
mustCutItems = false;
}
}
private void AddAFile(string draggedFilePath)
{
// this line is NOT used because .xml.gz (extensions with two dots) mess up with Path.GetExtension
//var theExtension = Path.GetExtension(draggedFilePath).ToLowerInvariant();
// we need to get the filename before parsing out the extension because if we assume that everything after the dot
// is the extension and there are dots in the file path (i.e. in a folder name), this will mess up
var filename = Path.GetFileName(draggedFilePath);
var theExtension = filename.Substring(filename.IndexOf(".")).ToLowerInvariant();
switch (theExtension)
{
case ".raw":
var versionCheckerResult = MyFileManager.ValidateThermoMsFileReaderVersion();
if (versionCheckerResult.Equals(MyFileManager.ThermoMsFileReaderVersionCheck.IncorrectVersion))
{
GuiWarnHandler(null, new StringEventArgs("Warning! Thermo MSFileReader is not version 3.0 SP2; a crash may result from searching this .raw file", null));
}
else if (versionCheckerResult.Equals(MyFileManager.ThermoMsFileReaderVersionCheck.DllsNotFound))
{
GuiWarnHandler(null, new StringEventArgs("Warning! Cannot find Thermo MSFileReader (v3.0 SP2 is preferred); a crash may result from searching this .raw file", null));
}
goto case ".mzml";
case ".mzml":
RawDataForDataGrid zz = new RawDataForDataGrid(draggedFilePath);
if (!ExistRaw(rawDataObservableCollection, zz))
{
rawDataObservableCollection.Add(zz);
}
UpdateFileSpecificParamsDisplayJustAdded(Path.ChangeExtension(draggedFilePath, ".toml"));
UpdateOutputFolderTextbox();
break;
case ".mzml.gz": // not implemented yet
case ".fasta.gz": // not implemented yet
GuiWarnHandler(null, new StringEventArgs("Cannot read, try uncompressing: " + draggedFilePath, null));
break;
case ".xml":
case ".xml.gz":
case ".fasta":
case ".fa":
ProteinDbForDataGrid uu = new ProteinDbForDataGrid(draggedFilePath);
if (!ExistDa(proteinDbObservableCollection, uu))
{
proteinDbObservableCollection.Add(uu);
if (theExtension.Equals(".xml") || theExtension.Equals(".xml.gz"))
{
try
{
GlobalVariables.AddMods(UsefulProteomicsDatabases.ProteinDbLoader.GetPtmListFromProteinXml(draggedFilePath).OfType <ModificationWithLocation>());
}
catch (Exception ee)
{
MessageBox.Show(ee.ToString());
GuiWarnHandler(null, new StringEventArgs("Cannot read: " + draggedFilePath, null));
proteinDbObservableCollection.Remove(uu);
}
}
}
break;
case ".toml":
var tomlFile = Toml.ReadFile(draggedFilePath, MetaMorpheusTask.tomlConfig);
if (tomlFile.Keys.Contains("PrecursorMassTolerance") && tomlFile.Keys.Contains("ProductMassTolerance") && tomlFile.Keys.Count == 2)
{
// do nothing; it's a ppm suggested tolerance toml from calibration, this gets read in elsewhere
}
else
{
try
{
switch (tomlFile.Get <string>("TaskType"))
{
case "Search":
var ye1 = Toml.ReadFile <SearchTask>(draggedFilePath, MetaMorpheusTask.tomlConfig);
AddTaskToCollection(ye1);
break;
case "Calibrate":
var ye2 = Toml.ReadFile <CalibrationTask>(draggedFilePath, MetaMorpheusTask.tomlConfig);
AddTaskToCollection(ye2);
break;
case "Gptmd":
var ye3 = Toml.ReadFile <GptmdTask>(draggedFilePath, MetaMorpheusTask.tomlConfig);
AddTaskToCollection(ye3);
break;
case "XLSearch":
var ye4 = Toml.ReadFile <XLSearchTask>(draggedFilePath, MetaMorpheusTask.tomlConfig);
AddTaskToCollection(ye4);
break;
case "Neo":
var ye5 = Toml.ReadFile <NeoSearchTask>(draggedFilePath, MetaMorpheusTask.tomlConfig);
foreach (MetaMorpheusTask task in NeoLoadTomls.LoadTomls(ye5))
{
AddTaskToCollection(task);
}
break;
}
}
catch (Exception e)
{
GuiWarnHandler(null, new StringEventArgs("Could not parse .toml: " + e.Message, null));
}
}
break;
default:
GuiWarnHandler(null, new StringEventArgs("Unrecognized file type: " + theExtension, null));
break;
}
}
