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");
}
/// <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());
}
