public void ReadWriteCustomAnnotation()
{
var randomPath = GetRandomPath(true);
// create our expected data source versions
var dbSnpVersion = new DataSourceVersion("dbSNP", "142", DateTime.Parse("2015-01-02").Ticks);
var clinVarVersion = new DataSourceVersion("ClinVar", "13.5", DateTime.Parse("2015-01-19").Ticks);
var expectedDataSourceVersions = new List <DataSourceVersion> {
dbSnpVersion, clinVarVersion
};
var customFile = new FileInfo(Resources.TopPath("customCosmic.vcf"));
var customReader = new CustomAnnotationReader(customFile, _renamer);
// all items from this file should be of type cosmic.
var customItems = customReader.ToList();
var sa = new SupplementaryAnnotationPosition(69224);
var saCreator = new SupplementaryPositionCreator(sa);
foreach (var customItem in customItems)
{
// NOTE that the two custom items are for different position, but for the purpose of our test, this is not an issue.
customItem.SetSupplementaryAnnotations(saCreator);
}
// the above code was unit tested in MergeDbSnpClinVar()
using (var writer = new SupplementaryAnnotationWriter(randomPath, "chr1", expectedDataSourceVersions))
{
writer.Write(saCreator, sa.ReferencePosition);
}
// read the supplementary annotation file
using (var reader = new SupplementaryAnnotationReader(randomPath))
{
// extract the three annotations
var observedAnnotation1 = reader.GetAnnotation(69224);
Assert.NotNull(observedAnnotation1);
for (var i = 0; i < sa.CustomItems.Count; i++)
{
Assert.Equal(sa.CustomItems[i].Id, observedAnnotation1.CustomItems[i].Id);
Assert.Equal(sa.CustomItems[i].AnnotationType, observedAnnotation1.CustomItems[i].AnnotationType);
Assert.Equal(sa.CustomItems[i].IsAlleleSpecific, observedAnnotation1.CustomItems[i].IsAlleleSpecific);
Assert.True(sa.CustomItems[i].StringFields.SequenceEqual(observedAnnotation1.CustomItems[i].StringFields));
if (sa.CustomItems[i].BooleanFields.Count > 0)
{
Assert.True(sa.CustomItems[i].BooleanFields.SequenceEqual(observedAnnotation1.CustomItems[i].BooleanFields));
}
}
}
}
public void BasicReaderTest()
{
var customFile = new FileInfo(Resources.TopPath("customCosmic.vcf"));
var customReader = new CustomAnnotationReader(customFile, _refChromDict);
// all items from this file should be of type cosmic.
foreach (var customItem in customReader.GetCustomItems())
{
Assert.Equal("cosmic", customItem.AnnotationType);
}
}
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 StringFieldsTest()
{
var customFile = new FileInfo(Resources.TopPath("customCosmic.vcf"));
var customReader = new CustomAnnotationReader(customFile, _refChromDict);
// all items from this file should be of type cosmic.
var i = 0;
foreach (var customItem in customReader.GetCustomItems())
{
switch (i)
{
case 0: //checking the first item
Assert.Equal("COSM3677745", customItem.Id);
Assert.Equal("OR4F5", customItem.StringFields["gene"]);
Assert.Equal("+", customItem.StringFields["strand"]);
Assert.Equal("c.134A>C", customItem.StringFields["cds"]);
Assert.Equal("p.D45A", customItem.StringFields["aminoAcid"]);
Assert.Equal("1", customItem.StringFields["count"]);
break;
case 1:
Assert.Equal("COSM911918", customItem.Id);
Assert.Equal("OR4F5", customItem.StringFields["gene"]);
Assert.Equal("+", customItem.StringFields["strand"]);
Assert.Equal("c.255C>A", customItem.StringFields["cds"]);
Assert.Equal("p.I85I", customItem.StringFields["aminoAcid"]);
Assert.Equal("1", customItem.StringFields["count"]);
Assert.Equal("inExomeTarget", customItem.BooleanFields[0]);
break;
}
i++;
}
}
// 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>();
}