public void LoopbackTest()
{
var wigFixFile = new FileInfo(Resources.TopPath("mini.WigFix"));
var version = new DataSourceVersion("phylop", "0", DateTime.Now.Ticks, "unit test");
var phylopWriter = new PhylopWriter(wigFixFile.FullName, version, GenomeAssembly.Unknown, Path.GetTempPath(), 50);
using (phylopWriter)
{
phylopWriter.ExtractPhylopScores();
}
var phylopReader = new PhylopReader(FileUtilities.GetReadStream(Path.GetTempPath() + Path.DirectorySeparatorChar + "chr1.npd"));
using (phylopReader)
{
Assert.Equal(0.064, phylopReader.GetScore(100)); //first position of first block
Assert.Equal(0.058, phylopReader.GetScore(101)); // second position
Assert.Equal(0.064, phylopReader.GetScore(120)); // some internal position
Assert.Equal(0.058, phylopReader.GetScore(130)); //last position of first block
//moving on to the next block: should cause reloading from file
Assert.Equal(0.064, phylopReader.GetScore(175)); //first position of first block
Assert.Equal(-2.088, phylopReader.GetScore(182)); // some negative value
}
File.Delete(Path.GetTempPath() + Path.DirectorySeparatorChar + "chr1.npd");
}
public void AnnotationSourceConstructor()
{
var saPath = Resources.TopPath("DirectoryIntegrity");
var cacheStub = Resources.CacheGRCh37("ENST00000579787_chr1_Ensembl84");
var customAnnoPath = Resources.TopPath("DirectoryIntegrity");
var customIntervalsPath = Resources.TopPath("DirectoryIntegrity");
var conservationScoreReader = new PhylopReader(saPath);
var transcriptStream = ResourceUtilities.GetReadStream(cacheStub + ".ndb");
var siftStream = ResourceUtilities.GetReadStream(cacheStub + ".sift");
var polyPhenStream = ResourceUtilities.GetReadStream(cacheStub + ".polyphen");
var referenceStream = ResourceUtilities.GetReadStream(cacheStub + ".bases");
var streams = new AnnotationSourceStreams(transcriptStream, siftStream, polyPhenStream, referenceStream);
var customAnnotationProvider = new CustomAnnotationProvider(new[] { customAnnoPath });
var customIntervalProvider = new CustomIntervalProvider(new[] { customIntervalsPath });
var saProvider = new SupplementaryAnnotationProvider(saPath);
var annotationSource = new NirvanaAnnotationSource(streams, saProvider, conservationScoreReader,
customAnnotationProvider, customIntervalProvider, null);
Assert.NotNull(annotationSource);
}
public void WriteIntervalTest()
{
var randShorts = GetRandShorts();
var randomPath = Path.Combine(Path.GetTempPath(), Path.GetRandomFileName());
var writer = new ExtendedBinaryWriter(FileUtilities.GetCreateStream(randomPath));
var testInterval = new PhylopInterval(100, 0, 1);
var version = new DataSourceVersion("phylop", "0", DateTime.Now.Ticks, "unit test");
using (var phylopWriter = new PhylopWriter("chr1", version, GenomeAssembly.Unknown, randShorts, writer))
{
phylopWriter.WriteInterval(testInterval, writer);
}
using (var phylopReader = new PhylopReader(FileUtilities.GetReadStream(randomPath)))
{
var scoreCount = phylopReader.ReadIntervalScores(testInterval);
Assert.Equal(randShorts.Length, scoreCount);
var observedScores = phylopReader.GetAllScores();
for (var i = 0; i < randShorts.Length; i++)
{
Assert.Equal(randShorts[i], observedScores[i]);
}
}
File.Delete(randomPath);
}
public void ScoreToAndFromByteArray()
{
var randShorts = GetRandShorts();
var scoreBytes = new byte[PhylopCommon.MaxIntervalLength * 2];
var randomPath = Path.Combine(Path.GetTempPath(), Path.GetRandomFileName());
var writer = new ExtendedBinaryWriter(FileUtilities.GetCreateStream(randomPath));
var version = new DataSourceVersion("phylop", "0", DateTime.Now.Ticks, "unit test");
using (var phylopWriter = new PhylopWriter("chr1", version, GenomeAssembly.Unknown, randShorts, writer))
{
phylopWriter.ScoresToBytes(scoreBytes, randShorts, randShorts.Length);
}
var scores = new short[PhylopCommon.MaxIntervalLength];
using (var phylopReader = new PhylopReader(FileUtilities.GetReadStream(randomPath)))
{
phylopReader.BytesToScores(scoreBytes.Length, scoreBytes, scores);
}
for (var i = 0; i < randShorts.Length; i++)
{
Assert.Equal(randShorts[i], scores[i]);
}
File.Delete(randomPath);
}
public ConservationScoreProvider(IEnumerable <string> dirPaths)
{
Name = "Conservation score provider";
_phylopReader = new PhylopReader(dirPaths);
GenomeAssembly = _phylopReader.GenomeAssembly;
DataSourceVersions = _phylopReader.DataSourceVersions;
_currentUcscReferenceName = "";
}
public IAnnotationSource CreateAnnotationSource(IAnnotatorInfo annotatorInfo, IAnnotatorPaths annotatorPaths)
{
var conservationScoreReader = new PhylopReader(annotatorPaths.SupplementaryAnnotation);
var transcriptStream = FileUtilities.GetReadStream(CacheConstants.TranscriptPath(annotatorPaths.CachePrefix));
var siftStream = FileUtilities.GetReadStream(CacheConstants.SiftPath(annotatorPaths.CachePrefix));
var polyPhenStream = FileUtilities.GetReadStream(CacheConstants.PolyPhenPath(annotatorPaths.CachePrefix));
var referenceStream = FileUtilities.GetReadStream(annotatorPaths.CompressedReference);
var streams = new AnnotationSourceStreams(transcriptStream, siftStream, polyPhenStream, referenceStream);
var caProvider = annotatorPaths.CustomAnnotation.Any() ? new CustomAnnotationProvider(annotatorPaths.CustomAnnotation) : null;
var ciProvider = annotatorPaths.CustomIntervals.Any() ? new CustomIntervalProvider(annotatorPaths.CustomIntervals) : null;
var saProvider = annotatorPaths.SupplementaryAnnotation != null ? new SupplementaryAnnotationProvider(annotatorPaths.SupplementaryAnnotation) : null;
//adding the saPath because OMIM needs it
var annotationSource = new NirvanaAnnotationSource(streams, saProvider, conservationScoreReader, caProvider, ciProvider, annotatorPaths.SupplementaryAnnotation);
if (annotatorInfo.BooleanArguments.Contains(AnnotatorInfoCommon.ReferenceNoCall))
{
annotationSource.EnableReferenceNoCalls(annotatorInfo.BooleanArguments.Contains(AnnotatorInfoCommon.TranscriptOnlyRefNoCall));
}
if (annotatorInfo.BooleanArguments.Contains(AnnotatorInfoCommon.EnableMitochondrialAnnotation))
{
annotationSource.EnableMitochondrialAnnotation();
}
if (annotatorInfo.BooleanArguments.Contains(AnnotatorInfoCommon.ReportAllSvOverlappingTranscripts))
{
annotationSource.EnableReportAllSvOverlappingTranscripts();
}
if (annotatorInfo.BooleanArguments.Contains(AnnotatorInfoCommon.EnableLoftee))
{
annotationSource.AddPlugin(new Loftee());
}
return(annotationSource);
}
/// <summary>
/// constructor
/// </summary>
public MockConservationScoreReader(Stream stream)
{
_reader = new PhylopReader(stream);
IsInitialized = _reader != null;
}
//constructor
public PhylopGetScoreTests()
{
_npdReader = new PhylopReader(ResourceUtilities.GetReadStream(Resources.TopPath("chr1_10918_150000.npd")));
}
/// <summary>
/// constructor
/// </summary>
public PhylopGetScoreTests()
{
// TODO: Fix fragile constructor
_npdReader = new PhylopReader(ResourceUtilities.GetReadStream(Resources.TopPath("chr1_10918_150000.npd")));
}
