private void MatchPeptides(AlignmentDataset datasetX,
AlignmentDataset datasetY,
Dictionary <int, ScanSummary> scanDataX,
Dictionary <int, ScanSummary> scanDataY,
IEnumerable <string> names,
SpectralOptions options)
{
// Read data for peptides
var reader = PeptideReaderFactory.CreateReader(SequenceFileType.MSGF);
var peptidesA = reader.Read(datasetX.PeptideFile);
var peptidesB = reader.Read(datasetY.PeptideFile);
peptidesA =
peptidesA.ToList().Where(x => PeptideUtility.PassesCutoff(x, options.IdScore, options.Fdr)).ToList();
peptidesB =
peptidesB.ToList().Where(x => PeptideUtility.PassesCutoff(x, options.IdScore, options.Fdr)).ToList();
var peptideMapX = PeptideUtility.MapWithBestScan(peptidesA);
var peptideMapY = PeptideUtility.MapWithBestScan(peptidesB);
// Determine the scan extrema
var maxX = scanDataX.Aggregate((l, r) => l.Value.Scan > r.Value.Scan ? l : r).Key;
var minX = scanDataX.Aggregate((l, r) => l.Value.Scan < r.Value.Scan ? l : r).Key;
var maxY = scanDataY.Aggregate((l, r) => l.Value.Scan > r.Value.Scan ? l : r).Key;
var minY = scanDataY.Aggregate((l, r) => l.Value.Scan < r.Value.Scan ? l : r).Key;
// Then map the peptide sequences to identify True Positive and False Positives
var count = (from scanx in peptideMapX.Keys
let peptideX = peptideMapX[scanx]
from scany in peptideMapY.Keys
let peptideY = peptideMapY[scany]
let netX = Convert.ToDouble(scanx - minX) / Convert.ToDouble(maxX - minX)
let netY = Convert.ToDouble(scany - minY) / Convert.ToDouble(maxY - minY)
let net = Convert.ToDouble(netX - netY)
where Math.Abs(net) < options.NetTolerance
where Math.Abs(peptideX.Mz - peptideY.Mz) < options.MzTolerance
where PeptideUtility.PassesCutoff(peptideX, options.IdScore, options.Fdr) &&
PeptideUtility.PassesCutoff(peptideY, options.IdScore, options.Fdr) &&
peptideX.Sequence.Equals(peptideY.Sequence)
select peptideX).Count();
Console.WriteLine();
foreach (var name in names)
{
Console.WriteLine(name);
}
Console.WriteLine(@"Matches - {0}", count);
}
protected static SpectralAnalysis MatchDatasets(SpectralComparison comparerType,
ISpectraProvider readerX,
ISpectraProvider readerY,
SpectralOptions options,
AlignmentDataset datasetX,
AlignmentDataset datasetY,
List <string> names)
{
var peptideReader = PeptideReaderFactory.CreateReader(SequenceFileType.MSGF);
var finder = new SpectralAnchorPointFinder();
var validator = new SpectralAnchorPointValidator();
var comparer = SpectralComparerFactory.CreateSpectraComparer(comparerType);
var filter = SpectrumFilterFactory.CreateFilter(SpectraFilters.TopPercent);
var matches = finder.FindAnchorPoints(readerX,
readerY,
comparer,
filter,
options);
var peptidesX = peptideReader.Read(datasetX.PeptideFile);
var peptidesY = peptideReader.Read(datasetY.PeptideFile);
validator.ValidateMatches(matches,
peptidesX,
peptidesY,
options);
var analysis = new SpectralAnalysis
{
DatasetNames = names,
Matches = matches,
Options = options
};
return(analysis);
}
public void GenerateFigure4_MetaMatches(string directory,
SpectralComparison comparerType,
double mzBinSize,
double mzTolerance,
double netTolerance,
double similarityScoreCutoff,
double peptideScore,
double peptideFdr,
double ionPercent,
int numberOfRequiredPeaks,
string name)
{
AlignmentAnalysisWriterFactory.BasePath = @"M:\doc\papers\paperAlignment\Data\figure4";
Console.WriteLine(@"Post-Pre Tests For {0}", directory);
var cacheFiles = Directory.GetFiles(directory, "*.mscache");
Console.WriteLine(@"Building data cache");
var data = cacheFiles.Select(path => new FigureBase.PathCache {
Cache = path
}).ToList();
// The options for the analysis
var options = new SpectralOptions
{
MzBinSize = mzBinSize,
MzTolerance = mzTolerance,
NetTolerance = netTolerance,
SimilarityCutoff = similarityScoreCutoff,
TopIonPercent = ionPercent,
IdScore = peptideScore,
ComparerType = comparerType,
Fdr = peptideFdr,
RequiredPeakCount = numberOfRequiredPeaks
};
var comparison = 0;
for (var i = 0; i < data.Count; i++)
{
var cachex = data[i];
// Get the raw path stored in the cache file...
// then get the dataset object
var rawPathX = ScanSummaryCache.ReadPath(cachex.Cache);
var datasetX = new AlignmentDataset(rawPathX, "", cachex.Msgf);
// create a raw file reader for the datasets
using (var readerX = new InformedProteomicsReader())
{
// wrap it in the cached object so we can load scan meta-data
var cacheReaderX = new RawLoaderCache(readerX);
var cacheDataX = ScanSummaryCache.ReadCache(cachex.Cache);
readerX.AddDataFile(rawPathX, 0);
cacheReaderX.AddCache(0, cacheDataX);
for (var j = i + 1; j < data.Count; j++)
{
var cachey = data[j];
// Get the raw path stored in the cache file...
// then get the dataset object
var rawPathY = ScanSummaryCache.ReadPath(cachey.Cache);
var datasetY = new AlignmentDataset(rawPathY, "", cachey.Msgf);
// create a raw file reader for the datasets
using (var readerY = new InformedProteomicsReader())
{
// Then the writer for creating a report
var writer =
AlignmentAnalysisWriterFactory.Create(AlignmentFigureType.Figure3, name + comparison);
comparison++;
// wrap it in the cached object so we can load scan meta-data
var cacheReaderY = new RawLoaderCache(readerY);
var cacheDataY = ScanSummaryCache.ReadCache(cachey.Cache);
cacheReaderY.AddCache(0, cacheDataY);
readerY.AddDataFile(rawPathY, 0);
var names = new List <string> {
data[i].Cache, data[j].Cache
};
var analysis = MatchDatasets(comparerType,
readerX,
readerY,
options,
datasetX,
datasetY,
names);
AlignMatches(analysis, writer);
writer.Close();
}
}
}
}
}
public void GenerateFigure3_Matches(string directory,
SpectralComparison comparerType,
double mzBinSize,
double mzTolerance,
double netTolerance,
double similarityScoreCutoff,
double peptideScore,
double peptideFdr,
double ionPercent,
int numberOfRequiredPeaks)
{
AlignmentAnalysisWriterFactory.BasePath = @"M:\doc\papers\paperAlignment\Data\figure4";
Console.WriteLine(@"Post-Pre Tests For {0}", directory);
var cacheFiles = Directory.GetFiles(directory, "*.mscache");
var msgfFiles = Directory.GetFiles(directory, "*_msgfdb_fht.txt");
Console.WriteLine(@"Building data cache");
var map = cacheFiles.ToDictionary<string, string, FigureBase.PathCache>(path => path.ToLower(), path => null);
var data = (from path in msgfFiles
let name = path.ToLower().Replace("_msgfdb_fht.txt", ".mscache")
let newName = Path.Combine(directory, name)
let features = Path.Combine(directory, name)
where map.ContainsKey(newName)
select new FigureBase.PathCache { Cache = newName, Msgf = path, Features = features }).ToList();
// The options for the analysis
var options = new SpectralOptions
{
MzBinSize = mzBinSize,
MzTolerance = mzTolerance,
NetTolerance = netTolerance,
SimilarityCutoff = similarityScoreCutoff,
TopIonPercent = ionPercent,
IdScore = peptideScore,
ComparerType = comparerType,
Fdr = peptideFdr,
RequiredPeakCount = numberOfRequiredPeaks
};
Console.WriteLine(@"{0}", data.Count);
var comparison = 0;
for (var i = 0; i < data.Count; i++)
{
var cachex = data[i];
// Get the raw path stored in the cache file...
// then get the dataset object
var rawPathX = ScanSummaryCache.ReadPath(cachex.Cache);
var datasetX = new AlignmentDataset(rawPathX, "", cachex.Msgf);
// create a raw file reader for the datasets
using (var readerX = RawLoaderFactory.CreateFileReader(datasetX.RawFile))
{
// wrap it in the cached object so we can load scan meta-data
var cacheReaderX = new RawLoaderCache(readerX);
var cacheDataX = ScanSummaryCache.ReadCache(cachex.Cache);
readerX.AddDataFile(rawPathX, 0);
cacheReaderX.AddCache(0, cacheDataX);
for (var j = i + 1; j < data.Count; j++)
{
// Then the writer for creating a report
var writer =
AlignmentAnalysisWriterFactory.Create(AlignmentFigureType.Figure3,
"results-figure3-largeScale" + comparison);
comparison++;
var cachey = data[j];
// Get the raw path stored in the cache file...
// then get the dataset object
var rawPathY = ScanSummaryCache.ReadPath(cachey.Cache);
var datasetY = new AlignmentDataset(rawPathY, "", cachey.Msgf);
// create a raw file reader for the datasets
using (var readerY = RawLoaderFactory.CreateFileReader(datasetY.RawFile))
{
// wrap it in the cached object so we can load scan meta-data
var cacheReaderY = new RawLoaderCache(readerY);
var cacheDataY = ScanSummaryCache.ReadCache(cachey.Cache);
cacheReaderY.AddCache(0, cacheDataY);
readerY.AddDataFile(rawPathY, 0);
var names = new List<string> { data[i].Cache, data[j].Cache };
// Write the results
var analysis = MatchDatasets(comparerType,
cacheReaderX,
cacheReaderY,
options,
datasetX,
datasetY,
names);
AlignMatches(analysis, writer);
}
}
}
}
}
protected static SpectralAnalysis MatchDatasets(SpectralComparison comparerType,
ISpectraProvider readerX,
ISpectraProvider readerY,
SpectralOptions options,
AlignmentDataset datasetX,
AlignmentDataset datasetY,
List<string> names)
{
var peptideReader = PeptideReaderFactory.CreateReader(SequenceFileType.MSGF);
var finder = new SpectralAnchorPointFinder();
var validator = new SpectralAnchorPointValidator();
var comparer = SpectralComparerFactory.CreateSpectraComparer(comparerType);
var filter = SpectrumFilterFactory.CreateFilter(SpectraFilters.TopPercent);
var matches = finder.FindAnchorPoints(readerX,
readerY,
comparer,
filter,
options);
var peptidesX = peptideReader.Read(datasetX.PeptideFile);
var peptidesY = peptideReader.Read(datasetY.PeptideFile);
validator.ValidateMatches(matches,
peptidesX,
peptidesY,
options);
var analysis = new SpectralAnalysis
{
DatasetNames = names,
Matches = matches,
Options = options
};
return analysis;
}
public void GenerateFigure3_Matches(string directory,
SpectralComparison comparerType,
double mzBinSize,
double mzTolerance,
double netTolerance,
double similarityScoreCutoff,
double peptideScore,
double peptideFdr,
double ionPercent,
int numberOfRequiredPeaks)
{
AlignmentAnalysisWriterFactory.BasePath = @"M:\doc\papers\paperAlignment\Data\figure4";
Console.WriteLine(@"Post-Pre Tests For {0}", directory);
var cacheFiles = Directory.GetFiles(directory, "*.mscache");
var msgfFiles = Directory.GetFiles(directory, "*_msgfdb_fht.txt");
Console.WriteLine(@"Building data cache");
var map = cacheFiles.ToDictionary <string, string, FigureBase.PathCache>(path => path.ToLower(), path => null);
var data = (from path in msgfFiles
let name = path.ToLower().Replace("_msgfdb_fht.txt", ".mscache")
let newName = Path.Combine(directory, name)
let features = Path.Combine(directory, name)
where map.ContainsKey(newName)
select new FigureBase.PathCache {
Cache = newName, Msgf = path, Features = features
}).ToList();
// The options for the analysis
var options = new SpectralOptions
{
MzBinSize = mzBinSize,
MzTolerance = mzTolerance,
NetTolerance = netTolerance,
SimilarityCutoff = similarityScoreCutoff,
TopIonPercent = ionPercent,
IdScore = peptideScore,
ComparerType = comparerType,
Fdr = peptideFdr,
RequiredPeakCount = numberOfRequiredPeaks
};
Console.WriteLine(@"{0}", data.Count);
var comparison = 0;
for (var i = 0; i < data.Count; i++)
{
var cachex = data[i];
// Get the raw path stored in the cache file...
// then get the dataset object
var rawPathX = ScanSummaryCache.ReadPath(cachex.Cache);
var datasetX = new AlignmentDataset(rawPathX, "", cachex.Msgf);
// create a raw file reader for the datasets
using (var readerX = new InformedProteomicsReader())
{
// wrap it in the cached object so we can load scan meta-data
var cacheReaderX = new RawLoaderCache(readerX);
var cacheDataX = ScanSummaryCache.ReadCache(cachex.Cache);
readerX.AddDataFile(rawPathX, 0);
cacheReaderX.AddCache(0, cacheDataX);
for (var j = i + 1; j < data.Count; j++)
{
// Then the writer for creating a report
var writer =
AlignmentAnalysisWriterFactory.Create(AlignmentFigureType.Figure3,
"results-figure3-largeScale" + comparison);
comparison++;
var cachey = data[j];
// Get the raw path stored in the cache file...
// then get the dataset object
var rawPathY = ScanSummaryCache.ReadPath(cachey.Cache);
var datasetY = new AlignmentDataset(rawPathY, "", cachey.Msgf);
// create a raw file reader for the datasets
using (var readerY = new InformedProteomicsReader())
{
// wrap it in the cached object so we can load scan meta-data
var cacheReaderY = new RawLoaderCache(readerY);
var cacheDataY = ScanSummaryCache.ReadCache(cachey.Cache);
cacheReaderY.AddCache(0, cacheDataY);
readerY.AddDataFile(rawPathY, 0);
var names = new List <string> {
data[i].Cache, data[j].Cache
};
// Write the results
var analysis = MatchDatasets(comparerType,
cacheReaderX,
cacheReaderY,
options,
datasetX,
datasetY,
names);
AlignMatches(analysis, writer);
}
}
}
}
}
public void GenerateFigure4_MetaMatches(string directory,
SpectralComparison comparerType,
double mzBinSize,
double mzTolerance,
double netTolerance,
double similarityScoreCutoff,
double peptideScore,
double peptideFdr,
double ionPercent,
int numberOfRequiredPeaks,
string name)
{
AlignmentAnalysisWriterFactory.BasePath = @"M:\doc\papers\paperAlignment\Data\figure4";
Console.WriteLine(@"Post-Pre Tests For {0}", directory);
var cacheFiles = Directory.GetFiles(directory, "*.mscache");
Console.WriteLine(@"Building data cache");
var data = cacheFiles.Select(path => new FigureBase.PathCache { Cache = path }).ToList();
// The options for the analysis
var options = new SpectralOptions
{
MzBinSize = mzBinSize,
MzTolerance = mzTolerance,
NetTolerance = netTolerance,
SimilarityCutoff = similarityScoreCutoff,
TopIonPercent = ionPercent,
IdScore = peptideScore,
ComparerType = comparerType,
Fdr = peptideFdr,
RequiredPeakCount = numberOfRequiredPeaks
};
var comparison = 0;
for (var i = 0; i < data.Count; i++)
{
var cachex = data[i];
// Get the raw path stored in the cache file...
// then get the dataset object
var rawPathX = ScanSummaryCache.ReadPath(cachex.Cache);
var datasetX = new AlignmentDataset(rawPathX, "", cachex.Msgf);
// create a raw file reader for the datasets
using (var readerX = RawLoaderFactory.CreateFileReader(datasetX.RawFile))
{
// wrap it in the cached object so we can load scan meta-data
var cacheReaderX = new RawLoaderCache(readerX);
var cacheDataX = ScanSummaryCache.ReadCache(cachex.Cache);
readerX.AddDataFile(rawPathX, 0);
cacheReaderX.AddCache(0, cacheDataX);
for (var j = i + 1; j < data.Count; j++)
{
var cachey = data[j];
// Get the raw path stored in the cache file...
// then get the dataset object
var rawPathY = ScanSummaryCache.ReadPath(cachey.Cache);
var datasetY = new AlignmentDataset(rawPathY, "", cachey.Msgf);
// create a raw file reader for the datasets
using (var readerY = RawLoaderFactory.CreateFileReader(datasetY.RawFile))
{
// Then the writer for creating a report
var writer =
AlignmentAnalysisWriterFactory.Create(AlignmentFigureType.Figure3, name + comparison);
comparison++;
// wrap it in the cached object so we can load scan meta-data
var cacheReaderY = new RawLoaderCache(readerY);
var cacheDataY = ScanSummaryCache.ReadCache(cachey.Cache);
cacheReaderY.AddCache(0, cacheDataY);
readerY.AddDataFile(rawPathY, 0);
var names = new List<string> { data[i].Cache, data[j].Cache };
var analysis = MatchDatasets(comparerType,
readerX,
readerY,
options,
datasetX,
datasetY,
names);
AlignMatches(analysis, writer);
writer.Close();
}
}
}
}
}
private void MatchPeptides(AlignmentDataset datasetX,
AlignmentDataset datasetY,
Dictionary<int, ScanSummary> scanDataX,
Dictionary<int, ScanSummary> scanDataY,
IEnumerable<string> names,
SpectralOptions options)
{
// Read data for peptides
var reader = PeptideReaderFactory.CreateReader(SequenceFileType.MSGF);
var peptidesA = reader.Read(datasetX.PeptideFile);
var peptidesB = reader.Read(datasetY.PeptideFile);
peptidesA =
peptidesA.ToList().Where(x => PeptideUtility.PassesCutoff(x, options.IdScore, options.Fdr)).ToList();
peptidesB =
peptidesB.ToList().Where(x => PeptideUtility.PassesCutoff(x, options.IdScore, options.Fdr)).ToList();
var peptideMapX = PeptideUtility.MapWithBestScan(peptidesA);
var peptideMapY = PeptideUtility.MapWithBestScan(peptidesB);
// Determine the scan extrema
var maxX = scanDataX.Aggregate((l, r) => l.Value.Scan > r.Value.Scan ? l : r).Key;
var minX = scanDataX.Aggregate((l, r) => l.Value.Scan < r.Value.Scan ? l : r).Key;
var maxY = scanDataY.Aggregate((l, r) => l.Value.Scan > r.Value.Scan ? l : r).Key;
var minY = scanDataY.Aggregate((l, r) => l.Value.Scan < r.Value.Scan ? l : r).Key;
// Then map the peptide sequences to identify True Positive and False Positives
var count = (from scanx in peptideMapX.Keys
let peptideX = peptideMapX[scanx]
from scany in peptideMapY.Keys
let peptideY = peptideMapY[scany]
let netX = Convert.ToDouble(scanx - minX)/Convert.ToDouble(maxX - minX)
let netY = Convert.ToDouble(scany - minY)/Convert.ToDouble(maxY - minY)
let net = Convert.ToDouble(netX - netY)
where Math.Abs(net) < options.NetTolerance
where Math.Abs(peptideX.Mz - peptideY.Mz) < options.MzTolerance
where PeptideUtility.PassesCutoff(peptideX, options.IdScore, options.Fdr)
&& PeptideUtility.PassesCutoff(peptideY, options.IdScore, options.Fdr)
&& peptideX.Sequence.Equals(peptideY.Sequence)
select peptideX).Count();
Console.WriteLine();
foreach (var name in names)
Console.WriteLine(name);
Console.WriteLine(@"Matches - {0}", count);
}
