public void TestDbSnpReader()
{
using (var dgvReader = new DgvReader(GZipUtilities.GetAppropriateStreamReader(TestDgvFile), ChromosomeUtilities.RefNameToChromosome))
{
Assert.True(dgvReader.GetItems().SequenceEqual(CreateTruthDgvItemSequence()));
}
}
public void ExtractDgvComplex()
{
const string dgvLine = "esv2421662 1 12841928 12971833 OTHER complex Altshuler_et_al_2010 20811451 SNP array essv5038349,essv5012238 M 1184 20 70 HNRNPCL1,LOC649330,PRAMEF1,PRAMEF10,PRAMEF11,PRAMEF2,PRAMEF4 NA10838,NA10847";
var dgvItem = DgvReader.ExtractDgvItem(dgvLine, ChromosomeUtilities.RefNameToChromosome);
var jsonString = dgvItem.GetJsonString();
Assert.Equal("\"chromosome\":\"1\",\"begin\":12841928,\"end\":12971833,\"variantType\":\"complex_structural_alteration\",\"id\":\"esv2421662\",\"sampleSize\":1184,\"observedGains\":20,\"observedLosses\":70,\"variantFreqAll\":0.07601", jsonString);
}
public void ExtractDgvCnv()
{
const string dgvLine = "nsv482937 1 1 2300000 CNV loss Iafrate_et_al_2004 15286789 BAC aCGH,FISH nssv2995976 M 39 0 1 ACAP3,AGRN,WASH7P ";
var dgvItem = DgvReader.ExtractDgvItem(dgvLine, ChromosomeUtilities.RefNameToChromosome);
var jsonString = dgvItem.GetJsonString();
Assert.Equal("\"chromosome\":\"1\",\"begin\":1,\"end\":2300000,\"variantType\":\"copy_number_loss\",\"id\":\"nsv482937\",\"sampleSize\":39,\"observedLosses\":1,\"variantFreqAll\":0.02564", jsonString);
}
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);
}
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 dgvReader = new DgvReader(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.DgvTag, ReportFor.StructuralVariants, SaCommon.SchemaVersion))
{
nsiWriter.Write(dgvReader.GetItems());
}
return(ExitCodes.Success);
}
public void EmptyObservedLossesAndGains()
{
const string dgvLine = "nsv161172 1 88190 89153 CNV deletion Mills_et_al_2006 16902084 Sequencing nssv179750 M 24 ";
var dgvItem = DgvReader.ExtractDgvItem(dgvLine, ChromosomeUtilities.RefNameToChromosome);
var jsonString = dgvItem.GetJsonString();
Assert.Equal("\"chromosome\":\"1\",\"begin\":88190,\"end\":89153,\"variantType\":\"copy_number_loss\",\"id\":\"nsv161172\",\"sampleSize\":24", jsonString);
//Assert.Equal("1", dgvInterval.Chromosome.EnsemblName);
//Assert.Equal(88190, dgvInterval.Start);
//Assert.Equal(89153, dgvInterval.End);
//Assert.Equal("copy_number_loss", dgvInterval.VariantType.ToString());
//Assert.Equal("dgv", dgvInterval.Source);
//Assert.Equal("nsv161172", dgvInterval.StringValues["id"]);
//Assert.Equal(24, dgvInterval.IntValues["sampleSize"]);
//Assert.False(dgvInterval.IntValues.ContainsKey("observedGains"));
//Assert.False(dgvInterval.IntValues.ContainsKey("observedLosses"));
//Assert.False(dgvInterval.PopulationFrequencies.ContainsKey("variantFreqAll"));
}
public void ExtractDgvComplex()
{
const string dgvLine = "esv2421662 1 12841928 12971833 OTHER complex Altshuler_et_al_2010 20811451 SNP array essv5038349,essv5012238 M 1184 20 70 HNRNPCL1,LOC649330,PRAMEF1,PRAMEF10,PRAMEF11,PRAMEF2,PRAMEF4 NA10838,NA10847";
var dgvItem = DgvReader.ExtractDgvItem(dgvLine, _renamer);
Assert.True(dgvItem.IsInterval);
var dgvInterval = dgvItem.GetSupplementaryInterval(_renamer);
Assert.Equal(12841928, dgvInterval.Start);
Assert.Equal(12971833, dgvInterval.End);
Assert.Equal("complex_structural_alteration", dgvInterval.VariantType.ToString());
Assert.Equal("DGV", dgvInterval.Source);
Assert.Equal("esv2421662", dgvInterval.StringValues["id"]);
Assert.Equal("0.07601", dgvInterval.PopulationFrequencies["variantFreqAll"].ToString("0.#####"));
Assert.Equal(1184, dgvInterval.IntValues["sampleSize"]);
Assert.Equal(70, dgvInterval.IntValues["observedLosses"]);
Assert.Equal(20, dgvInterval.IntValues["observedGains"]);
}
public void ExtractDgvCnv()
{
const string dgvLine = "nsv482937 1 1 2300000 CNV loss Iafrate_et_al_2004 15286789 BAC aCGH,FISH nssv2995976 M 39 0 1 ACAP3,AGRN,WASH7P ";
var dgvItem = DgvReader.ExtractDgvItem(dgvLine, _renamer);
Assert.True(dgvItem.IsInterval);
var dgvInterval = dgvItem.GetSupplementaryInterval(_renamer);
Assert.Equal(1, dgvInterval.Start);
Assert.Equal(2300000, dgvInterval.End);
Assert.Equal("copy_number_loss", dgvInterval.VariantType.ToString());
Assert.Equal("DGV", dgvInterval.Source);
Assert.Equal("nsv482937", dgvInterval.StringValues["id"]);
Assert.Equal("0.02564", dgvInterval.PopulationFrequencies["variantFreqAll"].ToString("0.#####"));
Assert.Equal(39, dgvInterval.IntValues["sampleSize"]);
Assert.Equal(1, dgvInterval.IntValues["observedLosses"]);
Assert.False(dgvInterval.IntValues.ContainsKey("observedGains"));
}
public void EmptyObservedLossesAndGains()
{
const string dgvLine = "nsv161172 1 88190 89153 CNV deletion Mills_et_al_2006 16902084 Sequencing nssv179750 M 24 ";
var dgvItem = DgvReader.ExtractDgvItem(dgvLine, _renamer);
Assert.True(dgvItem.IsInterval);
var dgvInterval = dgvItem.GetSupplementaryInterval(_renamer);
Assert.Equal("1", dgvInterval.ReferenceName);
Assert.Equal(88190, dgvInterval.Start);
Assert.Equal(89153, dgvInterval.End);
Assert.Equal("copy_number_loss", dgvInterval.VariantType.ToString());
Assert.Equal("DGV", dgvInterval.Source);
Assert.Equal("nsv161172", dgvInterval.StringValues["id"]);
Assert.Equal(24, dgvInterval.IntValues["sampleSize"]);
Assert.False(dgvInterval.IntValues.ContainsKey("observedGains"));
Assert.False(dgvInterval.IntValues.ContainsKey("observedLosses"));
Assert.False(dgvInterval.PopulationFrequencies.ContainsKey("variantFreqAll"));
}
public void TestDbSnpReader()
{
var dgvReader = new DgvReader(TestDgvFile, _renamer);
Assert.True(dgvReader.SequenceEqual(CreateTruthDgvItemSequence()));
}
public void TestDbSnpReader()
{
var dgvReader = new DgvReader(TestDgvFile, RefChromDict);
Assert.True(dgvReader.GetDgvItems().SequenceEqual(CreateTruthDgvItemSequence()));
}
// 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>();
}
