public void TwoStudyCosmicCoding()
{
var cosmicReader = new MergedCosmicReader(Resources.TopPath("cosm5428243.vcf"), Resources.TopPath("cosm5428243.tsv"), _renamer);
var enumerator = cosmicReader.GetEnumerator();
enumerator.MoveNext();
var cosmicItem = enumerator.Current;
foreach (var study in cosmicItem.Studies)
{
Assert.Equal("544", study.ID);
Assert.Equal("haematopoietic_and_lymphoid_tissue", study.PrimarySite);
Assert.Equal("haematopoietic_neoplasm", study.Histology);
}
enumerator.MoveNext();
cosmicItem = enumerator.Current;
foreach (var study in cosmicItem.Studies)
{
Assert.Equal("544", study.ID);
Assert.Equal("haematopoietic;lymphoid_tissue", study.PrimarySite);
Assert.Equal("haematopoietic_neoplasm", study.Histology);
}
enumerator.Dispose();
}
// 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>();
}
