public void OnekGenSvReader()
{
var inputFileInfo = new FileInfo(Resources.InputFiles("1000G_SVs.tsv"));
var svReader = new OneKGenSvReader(inputFileInfo, _renamer);
var svItemList = svReader.ToList();
var si = svItemList[0].GetSupplementaryInterval(_renamer);
Assert.Equal("esv3584976", si.StringValues["id"]);
Assert.Equal(668631, si.Start);
Assert.Equal(850204, si.End);
Assert.Equal(VariantType.copy_number_gain, si.VariantType);
Assert.Equal(0.02396, si.PopulationFrequencies["variantFreqAll"]);
Assert.Equal(2504, si.IntValues["sampleSize"]);
//checking out the next item that should be a copy number variant (both loss and gain)
si = svItemList[1].GetSupplementaryInterval(_renamer);
Assert.Equal("esv3584977;esv3584978", si.StringValues["id"]);
Assert.Equal(713045, si.Start);
Assert.Equal(755966, si.End);
Assert.Equal(VariantType.copy_number_variation, si.VariantType);
//next one is a del (copy_number_loss)
si = svItemList[2].GetSupplementaryInterval(_renamer);
Assert.Equal("esv3584979", si.StringValues["id"]);
Assert.Equal(738571, si.Start);
Assert.Equal(742020, si.End);
Assert.Equal(VariantType.copy_number_loss, si.VariantType);
}
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}".Replace(' ', '_');
using (var reader = GZipUtilities.GetAppropriateStreamReader(_inputFileName))
using (var oneKGenSvReader = new OneKGenSvReader(reader, referenceProvider.RefNameToChromosome))
using (var nsaStream = FileUtilities.GetCreateStream(Path.Combine(_outputDirectory, outFileName + SaCommon.IntervalFileSuffix)))
using (var nsiWriter = new NsiWriter(nsaStream, version, referenceProvider.Assembly,
SaCommon.OnekSvTag, ReportFor.StructuralVariants, SaCommon.SchemaVersion))
{
nsiWriter.Write(oneKGenSvReader.GetItems());
}
return(ExitCodes.Success);
}
public void OnekGenSvReader()
{
using (var reader = new StreamReader(GetOneKgSvStream()))
{
var svReader = new OneKGenSvReader(reader, _refChromDict);
var svItemList = svReader.GetItems().ToList();
Assert.Equal(4, svItemList.Count);
Assert.Equal("\"chromosome\":\"1\",\"begin\":668631,\"end\":850204,\"variantType\":\"copy_number_gain\",\"id\":\"esv3584976\",\"allAn\":5008,\"allAc\":64,\"allAf\":0.01278,\"afrAf\":0.0015,\"amrAf\":0,\"eurAf\":0.001,\"easAf\":0.0595,\"sasAf\":0.001", svItemList[0].GetJsonString());
Assert.Equal("\"chromosome\":\"1\",\"begin\":713045,\"end\":755966,\"variantType\":\"copy_number_variation\",\"id\":\"esv3584977;esv3584978\",\"allAn\":5008,\"allAc\":209,\"allAf\":0.041733,\"afrAf\":0.0303,\"amrAf\":0.0273,\"eurAf\":0.0427,\"easAf\":0.0625,\"sasAf\":0.045", svItemList[1].GetJsonString());
Assert.Equal("\"chromosome\":\"1\",\"begin\":738571,\"end\":742020,\"variantType\":\"copy_number_loss\",\"id\":\"esv3584979\",\"allAn\":5008,\"allAc\":1,\"allAf\":0.0002,\"afrAf\":0,\"amrAf\":0,\"eurAf\":0,\"easAf\":0.001,\"sasAf\":0", svItemList[2].GetJsonString());
Assert.Equal("\"chromosome\":\"1\",\"begin\":645711,\"end\":645932,\"variantType\":\"mobile_element_insertion\",\"id\":\"esv3584975\",\"allAn\":5008,\"allAc\":35,\"allAf\":0.006989,\"afrAf\":0,\"amrAf\":0.0072,\"eurAf\":0.0189,\"easAf\":0.0069,\"sasAf\":0.0041", svItemList[3].GetJsonString());
}
}
public void OnekGenSvReader()
{
using (var reader = new StreamReader(GetOneKgSvStream()))
{
var svReader = new OneKGenSvReader(reader, ChromosomeUtilities.RefNameToChromosome);
var svItemList = svReader.GetItems().ToList();
Assert.Equal(4, svItemList.Count);
Assert.Equal("\"chromosome\":\"1\",\"begin\":668631,\"end\":850204,\"variantType\":\"copy_number_gain\",\"id\":\"esv3584976\",\"allAn\":5008,\"allAc\":64,\"allAf\":0.01278,\"afrAf\":0.0015,\"amrAf\":0,\"eurAf\":0.001,\"easAf\":0.0595,\"sasAf\":0.001", svItemList[0].GetJsonString());
Assert.Equal("\"chromosome\":\"1\",\"begin\":713045,\"end\":755966,\"variantType\":\"copy_number_variation\",\"id\":\"esv3584977;esv3584978\",\"allAn\":5008,\"allAc\":209,\"allAf\":0.041733,\"afrAf\":0.0303,\"amrAf\":0.0273,\"eurAf\":0.0427,\"easAf\":0.0625,\"sasAf\":0.045", svItemList[1].GetJsonString());
Assert.Equal("\"chromosome\":\"1\",\"begin\":738571,\"end\":742020,\"variantType\":\"copy_number_loss\",\"id\":\"esv3584979\",\"allAn\":5008,\"allAc\":1,\"allAf\":0.0002,\"afrAf\":0,\"amrAf\":0,\"eurAf\":0,\"easAf\":0.001,\"sasAf\":0", svItemList[2].GetJsonString());
Assert.Equal("\"chromosome\":\"1\",\"begin\":2397656,\"end\":2401469,\"variantType\":\"copy_number_gain\",\"id\":\"esv3585028\",\"allAn\":5008,\"allAc\":96,\"allAf\":0.019169,\"afrAf\":0.0287,\"amrAf\":0.0216,\"eurAf\":0.0119,\"easAf\":0.0248,\"sasAf\":0.0061", svItemList[3].GetJsonString());
}
}
// 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>();
}
