/// <summary>
/// Builds a peak matcher object.
/// </summary>
public void BuildPeakMatcher(MultiAlignAnalysisOptions options)
{
var tolerances = new FeatureMatcherTolerances();
var stanleyMatcher = new STACAdapter <UMCClusterLight>
{
Options =
{
HistogramBinWidth = options.StacOptions.HistogramBinWidth,
HistogramMultiplier = options.StacOptions.HistogramMultiplier,
ShiftAmount = options.StacOptions.ShiftAmount,
ShouldCalculateHistogramFDR = options.StacOptions.ShouldCalculateHistogramFDR,
ShouldCalculateShiftFDR = options.StacOptions.ShouldCalculateShiftFDR,
ShouldCalculateSLiC = options.StacOptions.ShouldCalculateSLiC,
ShouldCalculateSTAC = options.StacOptions.ShouldCalculateSTAC,
UseDriftTime = options.StacOptions.UseDriftTime,
UseEllipsoid = options.StacOptions.UseEllipsoid,
UsePriors = options.StacOptions.UsePriors
}
};
tolerances.DriftTimeTolerance = Convert.ToSingle(options.StacOptions.DriftTimeTolerance);
tolerances.MassTolerancePPM = options.StacOptions.MassTolerancePPM;
tolerances.NETTolerance = options.StacOptions.NETTolerance;
tolerances.Refined = options.StacOptions.Refined;
stanleyMatcher.Options.UserTolerances = tolerances;
m_provider.PeakMatcher = stanleyMatcher;
}
/// <summary>
/// Builds a peak matcher object.
/// </summary>
public void BuildPeakMatcher(MultiAlignAnalysisOptions options)
{
var tolerances = new FeatureMatcherTolerances();
var stanleyMatcher = new STACAdapter<UMCClusterLight>
{
Options =
{
HistogramBinWidth = options.StacOptions.HistogramBinWidth,
HistogramMultiplier = options.StacOptions.HistogramMultiplier,
ShiftAmount = options.StacOptions.ShiftAmount,
ShouldCalculateHistogramFDR = options.StacOptions.ShouldCalculateHistogramFDR,
ShouldCalculateShiftFDR = options.StacOptions.ShouldCalculateShiftFDR,
ShouldCalculateSLiC = options.StacOptions.ShouldCalculateSLiC,
ShouldCalculateSTAC = options.StacOptions.ShouldCalculateSTAC,
UseDriftTime = options.StacOptions.UseDriftTime,
UseEllipsoid = options.StacOptions.UseEllipsoid,
UsePriors = options.StacOptions.UsePriors
}
};
tolerances.DriftTimeTolerance = Convert.ToSingle(options.StacOptions.DriftTimeTolerance);
tolerances.MassTolerancePPM = options.StacOptions.MassTolerancePPM;
tolerances.NETTolerance = options.StacOptions.NETTolerance;
tolerances.Refined = options.StacOptions.Refined;
stanleyMatcher.Options.UserTolerances = tolerances;
m_provider.PeakMatcher = stanleyMatcher;
}
public void TestLamarcheGridApp(string csvPath)
{
//Read a csv file, put the data into a new UMCLight for each one
var csvFileText = File.ReadAllLines(csvPath);
var csvDataList = new List <UMCLight> {
Capacity = csvFileText.Length
};
foreach (var line in csvFileText)
{
var parsedLine = line.Split(',');
var umcDataMember = new UMCLight();
//put the data from the parsed line into the umcDataMember in the appropriate fashion
csvDataList.Add(umcDataMember);
}
//Create clusters from the data read in from the file
UMCClusterLight cluster = null;
var filteredClusters = new List <UMCClusterLight>();
if (!Filter(cluster))
{
//Save the cluster
filteredClusters.Add(cluster);
}
//Read a mtdb file using MACore or sqliteDb
var databasePath = @"C:\UnitTestFolder\MSGFPlus\blah.db";
//Either read from console, or entered at program execution
// Console.ReadLine(databasePath) or databasePath = args[2]
var database = ReadDatabase(databasePath);
var stacAdapter = new STACAdapter <UMCClusterLight>();
var matchList = stacAdapter.PerformPeakMatching(filteredClusters, database);
string writePath = null;
// As with databasePath, could either be read from console, or entered at program execution
// Console.ReadLine(writePath) or, if(args.Length >= 4){ writePath = args[3]; }
// If writePath isn't entered, then it writes to a default file, defined inside the WriteData method
WriteData(matchList, writePath);
}
/// <summary>
/// Performs matching operation on the selected datasets.
/// </summary>
/// <param name="datasets">The datasets to perform AMT matching on.</param>
internal void PerformMatching(IEnumerable <DatasetInformationViewModel> datasets)
{
this.ShouldShowTotalProgress = true;
var progressData = new ProgressData(new Progress <ProgressData>(pd =>
{
// This is the progress percent after stepping by progressData
this.TotalProgress = pd.Percent;
}))
{
IsPartialRange = true, MaxPercentage = 95
};
var progress = new Progress <ProgressData>(pd => progressData.Report(pd.Percent));
// Get all possible charge states in data.
var chargeStates = this.analysis.DataProviders.FeatureCache.RetrieveChargeStates().ToList();
// Initialize STAC
var stac = new STACAdapter <UMCClusterLight>
{
Options = new FeatureMatcherParameters
{
UseEllipsoid = this.ShouldUseEllipsoid,
ShouldCalculateSLiC = this.ShouldCalculateSlic,
HistogramBinWidth = this.HistogramBinWidth,
HistogramMultiplier = this.HistogramMultiplier,
UserTolerances = new FeatureMatcherTolerances
{
MassTolerancePPM = this.DatabaseSelectionViewModel.MassTolerance,
NETTolerance = this.DatabaseSelectionViewModel.NetTolerance
},
ChargeStateList = chargeStates,
UsePriors = this.UsePriors,
ShouldCalculateSTAC = this.ShouldCalculateStac,
ShouldCalculateHistogramFDR = this.CalculateHistogramFdr,
ShouldCalculateShiftFDR = false,
},
};
// Initialize datasets
datasets.ForEach(ds => ds.DatasetState = DatasetInformationViewModel.DatasetStates.Matching);
// Get clusters and database
var clusters = this.analysis.DataProviders.ClusterCache.FindAll();
var clusterIdMap = clusters.ToDictionary(cluster => cluster.Id);
var database = this.analysis.MassTagDatabase;
// Run STAC
var matches = stac.PerformPeakMatching(clusters, database);
datasets.ForEach(ds => ds.DatasetState = DatasetInformationViewModel.DatasetStates.PersistingMatches);
// Persist matches
var clusterToMassTags = matches.Select(match => new ClusterToMassTagMap(match.Observed.Id, match.Target.Id)).ToList();
this.analysis.DataProviders.MassTagMatches.ClearAllMatches();
this.analysis.DataProviders.MassTagMatches.AddAllStateless(clusterToMassTags, progress);
try
{
// Write to file
this.WriteClusterData("crosstab.tsv", matches, clusterIdMap, progress);
}
catch (Exception ex)
{
var errMsg = "Error writing results to text file: " + ex.Message;
Logger.PrintMessage(errMsg);
// Todo: Add this: if (!GlobalSettings.AutomatedAnalysisMode)
MessageBox.Show(errMsg);
}
this.ShouldShowTotalProgress = false;
datasets.ForEach(ds => ds.DatasetState = DatasetInformationViewModel.DatasetStates.Matched);
}
public void TestLamarcheGridApp(string csvPath)
{
//Read a csv file, put the data into a new UMCLight for each one
var csvFileText = File.ReadAllLines(csvPath);
var csvDataList = new List<UMCLight> {Capacity = csvFileText.Length};
foreach (var line in csvFileText)
{
var parsedLine = line.Split(',');
var umcDataMember = new UMCLight();
//put the data from the parsed line into the umcDataMember in the appropriate fashion
csvDataList.Add(umcDataMember);
}
//Create clusters from the data read in from the file
UMCClusterLight cluster = null;
var filteredClusters = new List<UMCClusterLight>();
if (!Filter(cluster))
{
//Save the cluster
filteredClusters.Add(cluster);
}
//Read a mtdb file using MACore or sqliteDb
var databasePath = @"C:\UnitTestFolder\MSGFPlus\blah.db";
//Either read from console, or entered at program execution
// Console.ReadLine(databasePath) or databasePath = args[2]
var database = ReadDatabase(databasePath);
var stacAdapter = new STACAdapter<UMCClusterLight>();
var matchList = stacAdapter.PerformPeakMatching(filteredClusters, database);
string writePath = null;
// As with databasePath, could either be read from console, or entered at program execution
// Console.ReadLine(writePath) or, if(args.Length >= 4){ writePath = args[3]; }
// If writePath isn't entered, then it writes to a default file, defined inside the WriteData method
WriteData(matchList, writePath);
}
/// <summary>
/// The main entry point for the application.
/// </summary>
static int Main(string[] args)
{
var handle = System.Diagnostics.Process.GetCurrentProcess().MainWindowHandle;
SetConsoleMode(handle, ENABLE_EXTENDED_FLAGS);
var clusterIdMap = new Dictionary <int, UMCClusterLight>();
try
{
if (args.Length < 2)
{
Console.WriteLine("MultiAlignSTACRunner crosstabDirectory databasePath outputName");
Console.WriteLine("\tThe cross-tab file will be named similar to the database path");
return(1);
}
// Setup the analysis processing
Logger.PrintMessage("Find all datasets", true);
var directoryPath = args[0].Replace("\r", "").Replace("\n", "");
var databasePath = args[1].Replace("\r", "").Replace("\n", "");
var name = args[2].Replace("\r", "").Replace("\n", "");
var files = Directory.GetFiles(directoryPath, "*.csv");
Logger.PrintMessage("Creating Log File");
var loggerPath = AnalysisPathUtils.BuildLogPath(Path.GetDirectoryName(name), Path.GetFileNameWithoutExtension(name));
Logger.LogPath = loggerPath;
Logger.PrintMessage("Saving Log Data to: " + loggerPath);
Logger.PrintMessage(string.Format("Creating STAC"), true);
// Hardcode bad, but per discussions with OHSU
var stac = new STACAdapter <UMCClusterLight>
{
Options = new FeatureMatcherParameters
{
UserTolerances =
{
MassTolerancePPM = 25,
NETTolerance = .035,
DriftTimeTolerance = 3
},
UseDriftTime = true
}
};
var clusterFilteringOptions = new FilteringOptions();
WriteOptionsToLogFile(clusterFilteringOptions);
WriteOptionsToLogFile(stac.Options);
// Read the cluster data
var allClusters = new List <UMCClusterLight>();
var clusterId = 0;
foreach (var file in files)
{
var filename = Path.GetFileName(file);
Logger.PrintMessage(string.Format("Reading {0}", filename));
const string chargeString = "charge";
if (filename == null)
{
continue;
}
if (!filename.Contains(chargeString))
{
continue;
}
// Read each file.
var start = DateTime.Now;
var xname = filename.Replace("_", "");
// ReSharper disable once StringIndexOfIsCultureSpecific.1
var indexOfChargeString = xname.IndexOf(chargeString);
var charge = Convert.ToInt32(xname.Substring(indexOfChargeString + chargeString.Length, 1));
var clusters = ReadClusters(file, clusterFilteringOptions);
var end = DateTime.Now;
Logger.PrintMessage(string.Format("\tReading Took {0:.00} seconds", end.Subtract(start).TotalSeconds));
foreach (var cluster in clusters)
{
clusterIdMap.Add(clusterId, cluster);
cluster.Id = clusterId++;
cluster.ChargeState = charge;
}
allClusters.AddRange(clusters);
}
// Load the database
Logger.PrintMessage(string.Format("Loading Mass Tag Database: {0}", Path.GetFileNameWithoutExtension(databasePath)));
var options = new MassTagDatabaseOptions();
var databaseDefinition = new InputDatabase
{
DatabaseFormat = MassTagDatabaseFormat.Sqlite,
LocalPath = databasePath
};
var database = MtdbLoaderFactory.LoadMassTagDatabase(databaseDefinition, options);
// Run stac
try
{
Logger.PrintMessage("Matching clusters to peptides in mass tag database.");
var matches = stac.PerformPeakMatching(allClusters, database);
Logger.PrintMessage(string.Format("Writing Results To {0}", name));
var duplicateMatches = new Dictionary <int, Dictionary <int, FeatureMatchLight <UMCClusterLight, MassTagLight> > >();
foreach (var match in matches)
{
if (!duplicateMatches.ContainsKey(match.Observed.Id))
{
duplicateMatches.Add(match.Observed.Id, new Dictionary <int, FeatureMatchLight <UMCClusterLight, MassTagLight> >());
}
if (!duplicateMatches[match.Observed.Id].ContainsKey(match.Target.Id))
{
duplicateMatches[match.Observed.Id].Add(match.Target.Id, match);
}
}
WriteClusterData(name, duplicateMatches, clusterIdMap);
Logger.PrintMessage("ANALYSIS SUCCESS");
return(0);
}
catch (Exception ex)
{
Logger.PrintMessage("Unhandled Error: " + ex.Message);
var innerEx = ex.InnerException;
while (innerEx != null)
{
Logger.PrintMessage("Inner Exception: " + innerEx.Message);
innerEx = innerEx.InnerException;
}
Logger.PrintMessage("Stack: " + ex.StackTrace);
Logger.PrintMessage("");
Logger.PrintMessage("ANALYSIS FAILED");
return(1);
}
}
catch (Exception ex)
{
Logger.PrintMessage("Unhandled Error: " + ex.Message, true);
var innerEx = ex.InnerException;
while (innerEx != null)
{
Logger.PrintMessage("Inner Exception: " + innerEx.Message);
innerEx = innerEx.InnerException;
}
Logger.PrintMessage("Stack: " + ex.StackTrace, true);
Logger.PrintMessage("");
Logger.PrintMessage("ANALYSIS FAILED");
return(1);
}
}
public void CompareMs2IdsToMs1Ids(string liquidResultsPath, string isosFile, string rawFile)
{
// Read mass tags.
var massTagReader = new LiquidResultsFileLoader(liquidResultsPath);
var massTags = massTagReader.LoadDatabase();
// Get identifications - this rereads the liquid results file, but I'm leaving it that way
// for now because this is just a test.
var scansToIds = this.GetIds(liquidResultsPath);
// Read raw data file.
var spectraProviderCache = new SpectraProviderCache();
var spectraProvider = spectraProviderCache.GetSpectraProvider(rawFile);
// Read isos features
var isosReader = new MsFeatureLightFileReader();
isosReader.IsosFilteroptions = new DeconToolsIsosFilterOptions {
MaximumIsotopicFit = 0.15
};
var msFeatures = isosReader.ReadFile(isosFile).ToList();
// Get LCMS features
var msFeatureClusterer = new MsToLcmsFeatures(spectraProvider);
var lcmsFeatures = msFeatureClusterer.Convert(msFeatures);
lcmsFeatures.ForEach(feature => { feature.NetAligned = feature.Net; feature.MassMonoisotopicAligned = feature.MassMonoisotopic; });
// Create clusters - Since this is only working on a single dataset, there should be a 1:1 mapping
// between LCMS features and clusters.
var clusters = new List <UMCClusterLight> {
Capacity = lcmsFeatures.Count
};
foreach (var lcmsFeature in lcmsFeatures)
{
var cluster = new UMCClusterLight(lcmsFeature);
cluster.CalculateStatistics(ClusterCentroidRepresentation.Median);
clusters.Add(cluster);
}
// Do STAC AMT matching
var stacAdapter = new STACAdapter <UMCClusterLight>
{
Options = new FeatureMatcherParameters
{
ShouldCalculateShiftFDR = false,
UsePriors = true,
UseEllipsoid = true,
UseDriftTime = false,
ShouldCalculateSTAC = true,
}
};
var amtMatches = stacAdapter.PerformPeakMatching(clusters, massTags);
// Group AMT matches by cluster, convert MassTags to Protein objects (represents lipid ID,
// rather than Protein ID here) for simplicity in comparing them to the MS/MS IDs.
var ms1Matches = clusters.ToDictionary(cluster => cluster, cluster => new List <Protein>());
foreach (var amtMatch in amtMatches)
{
var cluster = amtMatch.Observed;
var massTag = amtMatch.Target;
ms1Matches[cluster].Add(new Protein
{
Name = massTag.ProteinName,
Sequence = massTag.PeptideSequence,
ChemicalFormula = massTag.PeptideSequence
});
}
// Now we need to backtrack MS/MS identifications -> clusters
var ms2Matches = new Dictionary <UMCClusterLight, List <Protein> >();
foreach (var cluster in clusters)
{
ms2Matches.Add(cluster, new List <Protein>());
foreach (var lcmsFeature in cluster.UmcList)
{
foreach (var msFeature in lcmsFeature.MsFeatures)
{
foreach (var msmsFeature in msFeature.MSnSpectra)
{
if (scansToIds.ContainsKey(msmsFeature.Scan))
{
ms2Matches[cluster].AddRange(scansToIds[msmsFeature.Scan]);
}
}
}
}
}
// How many clusters have IDs from MS/MS?
var clusterMs1IdCount = ms1Matches.Values.Count(value => value.Any());
var clusterMs2IdCount = ms2Matches.Values.Count(value => value.Any());
int overlapCount = 0; // Number of IDs that overlapped between MS1 and MS2 identifications.
// Finally compare the MS1 IDs to the MS2 IDs.
foreach (var cluster in clusters)
{
// For now only comparing by name
var ms1Ids = ms1Matches[cluster];
var ms1Lipids = ms1Ids.Select(id => id.Name);
var ms2Ids = ms2Matches[cluster];
var ms2Lipids = ms2Ids.Select(id => id.Name);
// Compare MS1 IDs for the cluster vs MS2 IDs for the cluster.
var ms1OnlyIds = ms1Lipids.Where(lipid => !ms2Lipids.Contains(lipid));
var ms2OnlyIds = ms2Lipids.Where(lipid => !ms1Lipids.Contains(lipid));
overlapCount += ms1OnlyIds.Intersect(ms2OnlyIds).Count();
// Write Results
if (ms1OnlyIds.Any() || ms2OnlyIds.Any())
{
Console.WriteLine("Cluster {0}:", cluster.Id);
if (ms1OnlyIds.Any())
{
Console.WriteLine("\tMs1 Only IDs:");
foreach (var id in ms1OnlyIds)
{
Console.WriteLine("\t\t{0}", id);
}
}
if (ms2OnlyIds.Any())
{
Console.WriteLine("\tMs2 Only IDs:");
foreach (var id in ms2OnlyIds)
{
Console.WriteLine("\t\t{0}", id);
}
}
}
}
Console.WriteLine("Overlap: {0}", overlapCount);
}
/// <summary>
/// The main entry point for the application.
/// </summary>
static int Main(string[] args)
{
var handle = System.Diagnostics.Process.GetCurrentProcess().MainWindowHandle;
SetConsoleMode(handle, ENABLE_EXTENDED_FLAGS);
var clusterIdMap = new Dictionary<int, UMCClusterLight>();
try
{
if (args.Length < 2)
{
Console.WriteLine("MultiAlignSTACRunner crosstabDirectory databasePath outputName");
Console.WriteLine("\tThe cross-tab file will be named similar to the database path");
return 1;
}
// Setup the analysis processing
Logger.PrintMessage("Find all datasets", true);
var directoryPath = args[0].Replace("\r","").Replace("\n","");
var databasePath = args[1].Replace("\r","").Replace("\n","");
var name = args[2].Replace("\r","").Replace("\n","");
var files = Directory.GetFiles(directoryPath, "*.csv");
Logger.PrintMessage("Creating Log File");
var loggerPath = AnalysisPathUtils.BuildLogPath(Path.GetDirectoryName(name), Path.GetFileNameWithoutExtension(name));
Logger.LogPath = loggerPath;
Logger.PrintMessage("Saving Log Data to: " + loggerPath);
Logger.PrintMessage(string.Format("Creating STAC"), true);
// Hardcode bad, but per discussions with OHSU
var stac = new STACAdapter<UMCClusterLight>
{
Options = new FeatureMatcherParameters
{
UserTolerances =
{
MassTolerancePPM = 25,
NETTolerance = .035,
DriftTimeTolerance = 3
},
UseDriftTime = true
}
};
var clusterFilteringOptions = new FilteringOptions();
WriteOptionsToLogFile(clusterFilteringOptions);
WriteOptionsToLogFile(stac.Options);
// Read the cluster data
var allClusters = new List<UMCClusterLight>();
var clusterId = 0;
foreach (var file in files)
{
var filename = Path.GetFileName(file);
Logger.PrintMessage(string.Format("Reading {0}", filename));
const string chargeString = "charge";
if (filename == null)
continue;
if (!filename.Contains(chargeString))
continue;
// Read each file.
var start = DateTime.Now;
var xname = filename.Replace("_", "");
// ReSharper disable once StringIndexOfIsCultureSpecific.1
var indexOfChargeString = xname.IndexOf(chargeString);
var charge = Convert.ToInt32(xname.Substring(indexOfChargeString + chargeString.Length, 1));
var clusters = ReadClusters(file, clusterFilteringOptions);
var end = DateTime.Now;
Logger.PrintMessage(string.Format("\tReading Took {0:.00} seconds", end.Subtract(start).TotalSeconds));
foreach (var cluster in clusters)
{
clusterIdMap.Add(clusterId, cluster);
cluster.Id = clusterId++;
cluster.ChargeState = charge;
}
allClusters.AddRange(clusters);
}
// Load the database
Logger.PrintMessage(string.Format("Loading Mass Tag Database: {0}", Path.GetFileNameWithoutExtension(databasePath)));
var options = new MassTagDatabaseOptions();
var databaseDefinition = new InputDatabase
{
DatabaseFormat = MassTagDatabaseFormat.Sqlite,
LocalPath = databasePath
};
var database = MtdbLoaderFactory.LoadMassTagDatabase(databaseDefinition, options);
// Run stac
try
{
Logger.PrintMessage("Matching clusters to peptides in mass tag database.");
var matches = stac.PerformPeakMatching(allClusters, database);
Logger.PrintMessage(string.Format("Writing Results To {0}", name));
var duplicateMatches = new Dictionary<int, Dictionary<int, FeatureMatchLight<UMCClusterLight, MassTagLight>>>();
foreach (var match in matches)
{
if (!duplicateMatches.ContainsKey(match.Observed.Id))
duplicateMatches.Add(match.Observed.Id, new Dictionary<int, FeatureMatchLight<UMCClusterLight, MassTagLight>>());
if (!duplicateMatches[match.Observed.Id].ContainsKey(match.Target.Id))
duplicateMatches[match.Observed.Id].Add(match.Target.Id, match);
}
WriteClusterData(name, duplicateMatches, clusterIdMap);
Logger.PrintMessage("ANALYSIS SUCCESS");
return 0;
}
catch (Exception ex)
{
Logger.PrintMessage("Unhandled Error: " + ex.Message);
var innerEx = ex.InnerException;
while (innerEx != null)
{
Logger.PrintMessage("Inner Exception: " + innerEx.Message);
innerEx = innerEx.InnerException;
}
Logger.PrintMessage("Stack: " + ex.StackTrace);
Logger.PrintMessage("");
Logger.PrintMessage("ANALYSIS FAILED");
return 1;
}
}
catch (Exception ex)
{
Logger.PrintMessage("Unhandled Error: " + ex.Message, true);
var innerEx = ex.InnerException;
while (innerEx != null)
{
Logger.PrintMessage("Inner Exception: " + innerEx.Message);
innerEx = innerEx.InnerException;
}
Logger.PrintMessage("Stack: " + ex.StackTrace, true);
Logger.PrintMessage("");
Logger.PrintMessage("ANALYSIS FAILED");
return 1;
}
}
