Exemplo n.º 1
0
        /// <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);
            }
        }
Exemplo n.º 2
0
        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();
                        }
                    }
                }
            }
        }
Exemplo n.º 3
0
        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);
                        }
                    }
                }
            }
        }