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 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);
}
/// <summary>
/// executes the program
/// </summary>
protected override void ProgramExecution()
{
Console.WriteLine("Reading file: {0}", ConfigurationSettings.InputWigFixFile);
var timer = new Benchmark();
var version = GetDataVersion();
using (var nirvanaPhylopDatabaseCreator = new PhylopWriter(ConfigurationSettings.InputWigFixFile, version, GenomeAssemblyUtilities.Convert(ConfigurationSettings.GenomeAssembly), ConfigurationSettings.OutputNirvanaDirectory))
{
nirvanaPhylopDatabaseCreator.ExtractPhylopScores();
}
Console.WriteLine("Time:{0}", timer.GetElapsedTime());
}
public void AddScoreTest()
{
var randShorts = GetRandShorts();
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");
var phylopWriter = new PhylopWriter("chr1", version, GenomeAssembly.Unknown, 100, writer);
foreach (short s in randShorts)
{
phylopWriter.AddScore(s); // artificially forcing the writer to flush at every 100 scores
}
// we should have 41 intervals but note that the last interval is not dumped by AddScore. Therefore, we have 40
Assert.Equal(40, phylopWriter.ChromosomeIntervals.Count);
writer.Dispose();
File.Delete(randomPath);
}
