/// <summary>
/// Creates a cache file
/// </summary>
/// <param name="rawPath"></param>
/// <param name="outPath"></param>
public void CreateSpectraSummaryFile(string rawPath, string outPath)
{
using (var readerY = RawLoaderFactory.CreateFileReader(rawPath))
{
readerY.AddDataFile(rawPath, 0);
var summary = readerY.GetScanData(0);
ScanSummaryCache.WriteCache(outPath, summary, rawPath);
}
}
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 = 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);
}
}
}
}
}