public void BeforeInitialization()
{
var emptyChromosomeNamer = new ChromosomeRenamer();
Assert.Throws <InvalidOperationException>(() => emptyChromosomeNamer.GetUcscReferenceName("1"));
Assert.Throws <InvalidOperationException>(() => emptyChromosomeNamer.GetEnsemblReferenceName("chr1"));
}
public void Create()
{
string refName = null;
CustomIntervalWriter customIntervalWriter = null;
foreach (var interval in _intervalParser)
{
if (interval.ReferenceName != refName)
{
if (refName != null)
{
_observedRefSeq.Add(refName);
}
// need to close open file and open a new one
customIntervalWriter?.Dispose();
refName = interval.ReferenceName;
var ucscRefName = _renamer.GetUcscReferenceName(refName);
if (_observedRefSeq.Contains(refName))
{
throw new GeneralException("The input file does not seem to be sorted by reference names. Please sort it and retry.");
}
var intervalType = interval.Type;
customIntervalWriter = new CustomIntervalWriter(Path.Combine(_outputDirectory, ucscRefName + ".nci"), refName, intervalType, _dataVersion);
}
customIntervalWriter?.WriteInterval(interval);
}
customIntervalWriter?.Dispose();
}
public void GetUnknownDesiredReferenceName()
{
const string expectedChromosomeName = "O";
var observedUcscReferenceName = _renamer.GetUcscReferenceName(expectedChromosomeName);
Assert.Equal(expectedChromosomeName, observedUcscReferenceName);
var observedEnsemblReferenceName = _renamer.GetEnsemblReferenceName(expectedChromosomeName);
Assert.Equal(expectedChromosomeName, observedEnsemblReferenceName);
}
public SuppAnnotExtractor(string compressedRefFile, string inputSuppAnnotFile, int begin, int end,
string datasourceName = null, string outDirectory = null)
{
_renamer = ChromosomeRenamer.GetChromosomeRenamer(FileUtilities.GetReadStream(compressedRefFile));
long intervalsPosition;
var saHeader = SupplementaryAnnotationReader.GetHeader(inputSuppAnnotFile, out intervalsPosition);
_begin = begin;
_end = end;
string miniSuppAnnotFile;
if (datasourceName == null)
{
miniSuppAnnotFile = _renamer.GetUcscReferenceName(saHeader.ReferenceSequenceName)
+ '_' + begin.ToString(CultureInfo.InvariantCulture) + '_' +
end.ToString(CultureInfo.InvariantCulture) + ".nsa";
if (outDirectory != null)
{
miniSuppAnnotFile = Path.Combine(outDirectory, miniSuppAnnotFile);
}
}
else
{
miniSuppAnnotFile = _renamer.GetUcscReferenceName(saHeader.ReferenceSequenceName)
+ '_' + begin.ToString(CultureInfo.InvariantCulture) + '_' +
end.ToString(CultureInfo.InvariantCulture) + '_' + datasourceName + ".nsa";
if (outDirectory != null)
{
miniSuppAnnotFile = Path.Combine(outDirectory, miniSuppAnnotFile);
}
}
_writer = new SupplementaryAnnotationWriter(miniSuppAnnotFile, saHeader.ReferenceSequenceName, saHeader.DataSourceVersions);
Console.WriteLine("MiniSA output to: " + miniSuppAnnotFile);
}
public void AddReferenceNameEnsemblEmpty()
{
const string ucscReferenceName = "chr1";
var emptyChromosomeNamer = new ChromosomeRenamer();
var referenceMetadata = new List <ReferenceMetadata>
{
new ReferenceMetadata(null, ucscReferenceName, true)
};
emptyChromosomeNamer.AddReferenceMetadata(referenceMetadata);
var observedUcscReferenceName = emptyChromosomeNamer.GetUcscReferenceName(null);
var observedEnsemblReferenceName = emptyChromosomeNamer.GetEnsemblReferenceName(ucscReferenceName);
Assert.Equal(ucscReferenceName, observedEnsemblReferenceName);
Assert.Null(observedUcscReferenceName);
}
private void OpenNewSaWriter()
{
var currentEnsemblRefName = _renamer.GetEnsemblReferenceName(_currentRefName);
var currentUcscRefName = _renamer.GetUcscReferenceName(_currentRefName);
if (InputFileParserUtilities.ProcessedReferences.Contains(currentEnsemblRefName))
{
throw new Exception($"usorted file, for chromsome {_currentRefName}, SA will be rewritten");
}
InputFileParserUtilities.ProcessedReferences.Add(currentEnsemblRefName);
var saPath = Path.Combine(_nsdBaseFileName, currentUcscRefName + ".nsa");
_saWriter = new SupplementaryAnnotationWriter(saPath, _currentRefName, _dataSources, _compressedSequence.GenomeAssembly);
Console.WriteLine("Populating {0} data...", currentUcscRefName);
_creationBench.Reset();
_numSaWritten = 0;
}
public List <Tuple <string, string> > GetUcscKaryotypeOrder(string dirPath)
{
var vepDirectories = Directory.GetDirectories(dirPath);
var referenceDict = new SortedDictionary <ushort, Tuple <string, string> >();
foreach (var dir in vepDirectories)
{
string referenceName = Path.GetFileName(dir);
if (!_renamer.InReferenceAndVep(referenceName))
{
continue;
}
string ucscReferenceName = _renamer.GetUcscReferenceName(referenceName, false);
var refIndex = GetIndex(ucscReferenceName);
referenceDict[refIndex] = new Tuple <string, string>(ucscReferenceName, dir);
}
return(referenceDict.Values.ToList());
}
public void GetUcscReferenceName(string ensemblReferenceName, string expectedReferenceName)
{
var observedReferenceName = _renamer.GetUcscReferenceName(ensemblReferenceName);
Assert.Equal(expectedReferenceName, observedReferenceName);
}
