private void CreateSvTsv(string sourceName, string fileName) { if (string.IsNullOrEmpty(fileName)) { return; } var benchMark = new Benchmark(); //Console.WriteLine($"Creating TSV from {fileName}"); var dataSource = ""; var version = DataSourceVersionReader.GetSourceVersion(fileName); switch (sourceName) { case InterimSaCommon.DgvTag: dataSource = "DGV"; using (var writer = new IntervalTsvWriter(_outputDirectory, version, _genomeAssembly.ToString(), SaTsvCommon.DgvSchemaVersion, InterimSaCommon.DgvTag, ReportFor.StructuralVariants)) { var reader = new DgvReader(new FileInfo(fileName), _refNamesDictionary); CreateSvTsv(reader.GetDgvItems(), writer); } break; case InterimSaCommon.ClinGenTag: dataSource = "ClinGen"; using (var writer = new IntervalTsvWriter(_outputDirectory, version, _genomeAssembly.ToString(), SaTsvCommon.ClinGenSchemaVersion, InterimSaCommon.ClinGenTag, ReportFor.StructuralVariants)) { var reader = new ClinGenReader(new FileInfo(fileName), _refNamesDictionary); CreateSvTsv(reader.GetClinGenItems(), writer); } break; case InterimSaCommon.OnekSvTag: dataSource = "OnekSv"; using (var writer = new IntervalTsvWriter(_outputDirectory, version, _genomeAssembly.ToString(), SaTsvCommon.OneKgenSchemaVersion, InterimSaCommon.OnekSvTag, ReportFor.StructuralVariants)) { var reader = new OneKGenSvReader(new FileInfo(fileName), _refNamesDictionary); CreateSvTsv(reader.GetOneKGenSvItems(), writer); } break; default: Console.WriteLine("invalid source name"); break; } var timeSpan = Benchmark.ToHumanReadable(benchMark.GetElapsedTime()); TsvWriterUtilities.WriteCompleteInfo(dataSource, version.Version, timeSpan); }
public void GetItems() { using (var reader = new ClinGenReader(new StreamReader(GetStream()), ChromosomeUtilities.RefNameToChromosome)) { var items = reader.GetItems().ToList(); Assert.Equal(4, items.Count); Assert.Equal("\"chromosome\":\"1\",\"begin\":564405,\"end\":8597804,\"variantType\":\"copy_number_loss\",\"id\":\"nsv530705\",\"clinicalInterpretation\":\"pathogenic\",\"phenotypes\":[\"Developmental delay AND/OR other significant developmental or morphological phenotypes\"],\"observedLosses\":1", items[0].GetJsonString()); } }
public void ReadClingenItems() { var clingenReader = new ClinGenReader(new FileInfo(Resources.InputFiles("ClinGenMini.tsv")), _renamer); var clinGenList = clingenReader.ToList(); Assert.Equal("nsv530705", clinGenList[0].Id); Assert.Equal(564405, clinGenList[0].Start); Assert.Equal(8597804, clinGenList[0].End); Assert.Equal(new List <string> { "Developmental delay AND/OR other significant developmental or morphological phenotypes" }, clinGenList[0].Phenotypes); Assert.Equal(new HashSet <string>(), clinGenList[0].PhenotypeIds); Assert.Equal(ClinicalInterpretation.pathogenic, clinGenList[0].ClinicalInterpretation); }
private static ExitCodes ProgramExecution() { var referenceProvider = new ReferenceSequenceProvider(FileUtilities.GetReadStream(_compressedReference)); var version = DataSourceVersionReader.GetSourceVersion(_inputFileName + ".version"); string outFileName = $"{version.Name}_{version.Version}"; using (var clinGenReader = new ClinGenReader(GZipUtilities.GetAppropriateStreamReader(_inputFileName), referenceProvider.RefNameToChromosome)) using (var nsaStream = FileUtilities.GetCreateStream(Path.Combine(_outputDirectory, outFileName + SaCommon.SiFileSuffix))) using (var nsiWriter = new NsiWriter(new ExtendedBinaryWriter(nsaStream), version, referenceProvider.Assembly, SaCommon.ClinGenTag, ReportFor.StructuralVariants, SaCommon.SchemaVersion)) { nsiWriter.Write(clinGenReader.GetItems()); } return(ExitCodes.Success); }
public void TestClinGenUnifier() { ClinGenUnifier clinGenUnifier = new ClinGenUnifier(TestClinGenFile); clinGenUnifier.Unify(); string randomPath = Path.Combine(Path.GetTempPath(), Path.GetRandomFileName()); clinGenUnifier.Write(randomPath); var testUnifiedClinGenFile = new FileInfo(randomPath); ChromosomeRenamer renamer = null; // need to fix var clinGenReader = new ClinGenReader(testUnifiedClinGenFile, renamer); var expectedItems = CreateTruthClinGenItemSequence(); Assert.True(clinGenReader.SequenceEqual(expectedItems)); File.Delete(randomPath); }
public void GetInterval() { var clingenReader = new ClinGenReader(new FileInfo(Resources.InputFiles("ClinGenMini.tsv")), _renamer); var clinGenList = clingenReader.ToList(); var si = clinGenList[0].GetSupplementaryInterval(_renamer); Assert.Equal("nsv530705", si.StringValues["id"]); Assert.Equal(564405, si.Start); Assert.Equal(8597804, si.End); Assert.Equal(VariantType.copy_number_loss, si.VariantType); clinGenList[1].MergeItem(clinGenList[2]); si = clinGenList[1].GetSupplementaryInterval(_renamer); Assert.Equal("nsv530706", si.StringValues["id"]); Assert.Equal(564424, si.Start); Assert.Equal(3262790, si.End); Assert.Equal(new List <string> { "HP:0001252", "HP:0001263", "HP:0001627", "HP:0001999", "MedGen:CN001147", "MedGen:CN001157", "MedGen:CN001482", "MedGen:CN001810" }, si.StringLists["phenotypeIds"]); }
// constructor public CreateSupplementaryDatabase( string compressedReferencePath, string nsdBaseFileName, string dbSnpFileName = null, string cosmicVcfFile = null, string cosmicTsvFile = null, string clinVarFileName = null, string oneKGenomeAfFileName = null, string evsFileName = null, string exacFileName = null, List <string> customFiles = null, string dgvFileName = null, string oneKSvFileName = null, string clinGenFileName = null, string chrWhiteList = null) { _nsdBaseFileName = nsdBaseFileName; _dataSources = new List <DataSourceVersion>(); _iSupplementaryDataItemList = new List <IEnumerator <SupplementaryDataItem> >(); _supplementaryIntervalList = new List <SupplementaryInterval>(); Console.WriteLine("Creating supplementary annotation files... Data version: {0}, schema version: {1}", SupplementaryAnnotationCommon.DataVersion, SupplementaryAnnotationCommon.SchemaVersion); _compressedSequence = new CompressedSequence(); var compressedSequenceReader = new CompressedSequenceReader(FileUtilities.GetReadStream(compressedReferencePath), _compressedSequence); _renamer = _compressedSequence.Renamer; _dataFileManager = new DataFileManager(compressedSequenceReader, _compressedSequence); if (!string.IsNullOrEmpty(chrWhiteList)) { Console.WriteLine("Creating SA for the following chromosomes only:"); foreach (var refSeq in chrWhiteList.Split(',')) { InputFileParserUtilities.ChromosomeWhiteList.Add(_renamer.GetEnsemblReferenceName(refSeq)); Console.Write(refSeq + ","); } Console.WriteLine(); } else { InputFileParserUtilities.ChromosomeWhiteList = null; } if (dbSnpFileName != null) { AddSourceVersion(dbSnpFileName); var dbSnpReader = new DbSnpReader(new FileInfo(dbSnpFileName), _renamer); var dbSnpEnumerator = dbSnpReader.GetEnumerator(); _iSupplementaryDataItemList.Add(dbSnpEnumerator); } if (cosmicVcfFile != null && cosmicTsvFile != null) { AddSourceVersion(cosmicVcfFile); var cosmicReader = new MergedCosmicReader(cosmicVcfFile, cosmicTsvFile, _renamer); var cosmicEnumerator = cosmicReader.GetEnumerator(); _iSupplementaryDataItemList.Add(cosmicEnumerator); } if (oneKGenomeAfFileName != null) { AddSourceVersion(oneKGenomeAfFileName); var oneKGenReader = new OneKGenReader(new FileInfo(oneKGenomeAfFileName), _renamer); var oneKGenEnumerator = oneKGenReader.GetEnumerator(); _iSupplementaryDataItemList.Add(oneKGenEnumerator); } if (oneKSvFileName != null) { if (oneKGenomeAfFileName == null) { AddSourceVersion(oneKSvFileName); } var oneKGenSvReader = new OneKGenSvReader(new FileInfo(oneKSvFileName), _renamer); var oneKGenSvEnumerator = oneKGenSvReader.GetEnumerator(); _iSupplementaryDataItemList.Add(oneKGenSvEnumerator); } if (evsFileName != null) { AddSourceVersion(evsFileName); var evsReader = new EvsReader(new FileInfo(evsFileName), _renamer); var evsEnumerator = evsReader.GetEnumerator(); _iSupplementaryDataItemList.Add(evsEnumerator); } if (exacFileName != null) { AddSourceVersion(exacFileName); var exacReader = new ExacReader(new FileInfo(exacFileName), _renamer); var exacEnumerator = exacReader.GetEnumerator(); _iSupplementaryDataItemList.Add(exacEnumerator); } if (clinVarFileName != null) { AddSourceVersion(clinVarFileName); var clinVarReader = new ClinVarXmlReader(new FileInfo(clinVarFileName), compressedSequenceReader, _compressedSequence); var clinVarList = clinVarReader.ToList(); clinVarList.Sort(); Console.WriteLine($"{clinVarList.Count} clinvar items read form XML file"); IEnumerator <ClinVarItem> clinVarEnumerator = clinVarList.GetEnumerator(); _iSupplementaryDataItemList.Add(clinVarEnumerator); } if (dgvFileName != null) { AddSourceVersion(dgvFileName); var dgvReader = new DgvReader(new FileInfo(dgvFileName), _renamer); var dgvEnumerator = dgvReader.GetEnumerator(); _iSupplementaryDataItemList.Add(dgvEnumerator); } if (clinGenFileName != null) { AddSourceVersion(clinGenFileName); var clinGenReader = new ClinGenReader(new FileInfo(clinGenFileName), _renamer); var clinGenEnumerator = clinGenReader.GetEnumerator(); _iSupplementaryDataItemList.Add(clinGenEnumerator); } if (customFiles != null) { foreach (var customFile in customFiles) { AddSourceVersion(customFile); var customReader = new CustomAnnotationReader(new FileInfo(customFile), _renamer); var customEnumerator = customReader.GetEnumerator(); _iSupplementaryDataItemList.Add(customEnumerator); } } // initializing the IEnumerators in the list foreach (var iDataEnumerator in _iSupplementaryDataItemList) { if (!iDataEnumerator.MoveNext()) { _iSupplementaryDataItemList.Remove(iDataEnumerator); } } _additionalItemsList = new List <SupplementaryDataItem>(); }