private void CreateDbsnpGaTsv(string fileName) { if (fileName == null) { return; } var benchMark = new Benchmark(); var version = DataSourceVersionReader.GetSourceVersion(fileName); var dbsnpWriter = new SaTsvWriter(_outputDirectory, version, _genomeAssembly.ToString(), SaTsvCommon.DbSnpSchemaVersion, InterimSaCommon.DbsnpTag, null, true, new ReferenceSequenceProvider(FileUtilities.GetReadStream(_compressedReferencePath))); var globalAlleleWriter = new SaTsvWriter(_outputDirectory, version, _genomeAssembly.ToString(), SaTsvCommon.DbSnpSchemaVersion, InterimSaCommon.GlobalAlleleTag, "GMAF", false, new ReferenceSequenceProvider(FileUtilities.GetReadStream(_compressedReferencePath))); using (var tsvWriter = new DbsnpGaTsvWriter(dbsnpWriter, globalAlleleWriter)) { var dbSnpReader = new DbSnpReader(GZipUtilities.GetAppropriateReadStream(fileName), _refNamesDictionary); TsvWriterUtilities.WriteSortedItems(dbSnpReader.GetDbSnpItems(), tsvWriter); } var timeSpan = Benchmark.ToHumanReadable(benchMark.GetElapsedTime()); TsvWriterUtilities.WriteCompleteInfo("DbSNP", version.Version, timeSpan); }
private void CreateMitoMapVarTsv(IReadOnlyList <string> mitoMapFileNames) { if (mitoMapFileNames.Count == 0 || mitoMapFileNames.Any(string.IsNullOrEmpty)) { return; } var benchMark = new Benchmark(); var rootDirectory = new FileInfo(mitoMapFileNames[0]).Directory; var version = DataSourceVersionReader.GetSourceVersion(Path.Combine(rootDirectory.ToString(), "mitoMapVar")); var sequenceProvider = new ReferenceSequenceProvider(FileUtilities.GetReadStream(_compressedReferencePath)); sequenceProvider.LoadChromosome(new Chromosome("chrM", "MT", 24)); var mitoMapVarReaders = new List <MitoMapVariantReader>(); foreach (var mitoMapFileName in mitoMapFileNames) { mitoMapVarReaders.Add(new MitoMapVariantReader(new FileInfo(mitoMapFileName), sequenceProvider)); } var mergedMitoMapVarItems = MitoMapVariantReader.MergeAndSort(mitoMapVarReaders); const string outputFilePrefix = InterimSaCommon.MitoMapTag; using (var writer = new MitoMapVarTsvWriter(version, _outputDirectory, outputFilePrefix, sequenceProvider)) TsvWriterUtilities.WriteSortedItems(mergedMitoMapVarItems, writer); var timeSpan = Benchmark.ToHumanReadable(benchMark.GetElapsedTime()); TsvWriterUtilities.WriteCompleteInfo(InterimSaCommon.MitoMapTag, version.Version, timeSpan); }
public void CreateTsvs() { var benchMark = new Benchmark(); using (var writer = new TopMedTsvWriter(_version, _outputDirName, _refProvider.GenomeAssembly, _refProvider)) using (var reader = new TopMedReader(_streamReader, _refProvider.RefNameToChromosome)) { TsvWriterUtilities.WriteSortedItems(reader.GetGnomadItems(), writer); } var timeSpan = Benchmark.ToHumanReadable(benchMark.GetElapsedTime()); TsvWriterUtilities.WriteCompleteInfo("TOPMed", _version.Version, timeSpan); }
private void CreateOnekgTsv(string fileName) { if (fileName == null) { return; } var benchMark = new Benchmark(); var version = DataSourceVersionReader.GetSourceVersion(fileName); using (var tsvWriter = new OnekgTsvWriter(version, _outputDirectory, _genomeAssembly, new ReferenceSequenceProvider(FileUtilities.GetReadStream(_compressedReferencePath)))) { var onekgReader = new OneKGenReader(new FileInfo(fileName), _refNamesDictionary); TsvWriterUtilities.WriteSortedItems(onekgReader.GetOneKGenItems(), tsvWriter); } var timeSpan = Benchmark.ToHumanReadable(benchMark.GetElapsedTime()); TsvWriterUtilities.WriteCompleteInfo("OneKg", version.Version, timeSpan); }
private void CreateEvsTsv(string fileName) { if (string.IsNullOrEmpty(fileName)) { return; } var benchMark = new Benchmark(); var version = DataSourceVersionReader.GetSourceVersion(fileName); using (var writer = new EvsTsvWriter(version, _outputDirectory, _genomeAssembly, new ReferenceSequenceProvider(FileUtilities.GetReadStream(_compressedReferencePath)))) { var evsReader = new EvsReader(GZipUtilities.GetAppropriateStreamReader(fileName), _refNamesDictionary); TsvWriterUtilities.WriteSortedItems(evsReader.GetEvsItems(), writer); } var timeSpan = Benchmark.ToHumanReadable(benchMark.GetElapsedTime()); TsvWriterUtilities.WriteCompleteInfo("EVS", version.Version, timeSpan); }
private void CreateCutomAnnoTsv(string fileName) { if (string.IsNullOrEmpty(fileName)) { return; } Console.WriteLine($"Creating TSV from {fileName}"); var version = DataSourceVersionReader.GetSourceVersion(fileName); var customReader = new CustomAnnotationReader(new FileInfo(fileName), _refNamesDictionary); using (var writer = new CustomAnnoTsvWriter(version, _outputDirectory, _genomeAssembly, customReader.IsPositional, new ReferenceSequenceProvider(FileUtilities.GetReadStream(_compressedReferencePath)))) { TsvWriterUtilities.WriteSortedItems(customReader.GetCustomItems(), writer); } Console.WriteLine($"Finished {fileName}"); }
public void CreateTsvs() { var benchMark = new Benchmark(); using (var writer = new GnomadTsvWriter(_version, _outputDirectory, _refProvider.GenomeAssembly, _refProvider, _sequencingDataType)) { var count = 0; foreach (var fileStreamReader in _streamReaders) { var reader = new GnomadReader(fileStreamReader, _refProvider.RefNameToChromosome); TsvWriterUtilities.WriteSortedItems(reader.GetGnomadItems(), writer); Console.WriteLine($"ingested {count++} file in " + benchMark.GetElapsedTime()); } } var timeSpan = Benchmark.ToHumanReadable(benchMark.GetElapsedTime()); TsvWriterUtilities.WriteCompleteInfo("gnomAD", _version.Version, timeSpan); }
private void CreateClinvarTsv(string fileName) { if (fileName == null) { return; } var benchMark = new Benchmark(); var version = DataSourceVersionReader.GetSourceVersion(fileName); //clinvar items do not come in sorted order, hence we need to store them in an array, sort them and then flush them out using (var writer = new ClinvarTsvWriter(version, _outputDirectory, _genomeAssembly, new ReferenceSequenceProvider(FileUtilities.GetReadStream(_compressedReferencePath)))) { var clinvarReader = new ClinVarXmlReader(new FileInfo(fileName), new ReferenceSequenceProvider(FileUtilities.GetReadStream(_compressedReferencePath))); TsvWriterUtilities.WriteSortedItems(clinvarReader.GetItems(), writer); } var timeSpan = Benchmark.ToHumanReadable(benchMark.GetElapsedTime()); TsvWriterUtilities.WriteCompleteInfo("ClinVar", version.Version, timeSpan); }
private void CreateCosmicTsv(string vcfFile, string tsvFile) { if (string.IsNullOrEmpty(tsvFile) || string.IsNullOrEmpty(vcfFile)) { return; } var benchMark = new Benchmark(); var version = DataSourceVersionReader.GetSourceVersion(vcfFile); using (var writer = new CosmicTsvWriter(version, _outputDirectory, _genomeAssembly, new ReferenceSequenceProvider(FileUtilities.GetReadStream(_compressedReferencePath)))) { var tsvReader = GZipUtilities.GetAppropriateStreamReader(tsvFile); var vcfReader = GZipUtilities.GetAppropriateStreamReader(vcfFile); var reader = new MergedCosmicReader(vcfReader, tsvReader, _refNamesDictionary); TsvWriterUtilities.WriteSortedItems(reader.GetCosmicItems(), writer); } var timeSpan = Benchmark.ToHumanReadable(benchMark.GetElapsedTime()); TsvWriterUtilities.WriteCompleteInfo("COSMIC", version.Version, timeSpan); }