public void GenomeIOTest()
{
var gmdt1 = new GenomeMetadata();
var createdFile = Path.Combine(TestPaths.LocalScratchDirectory, "TestSavingGenome.xml");
var originalFile = Path.Combine(TestPaths.LocalScratchDirectory, "GenomeXml2.xml");
if (File.Exists(createdFile))
{
File.Delete(createdFile);
}
if (File.Exists(originalFile))
{
File.Delete(originalFile);
}
File.Copy(_genomeXML, originalFile);
gmdt1.Deserialize(originalFile);
TestGenomeMetadata(gmdt1);
gmdt1.Serialize(createdFile);
var gmdt2 = new GenomeMetadata();
gmdt2.Deserialize(createdFile);
TestGenomeMetadata(gmdt2);
}
protected override void ProgramExecution()
{
GenomeMetadata.CheckReferenceGenomeFolderState(_options.InputFastaFolder, false, false);
Console.WriteLine("Preparing GenomeSize.xml for folder {0}...", _options.OutputDirectory);
GenomeMetadata metadata = new GenomeMetadata();
metadata.ImportFromFastaFiles(_options.InputFastaFolder, _options.OutputDirectory);
metadata.Name = _options.SpeciesName;
string genomeSizePath = Path.Combine(_options.OutputDirectory, "GenomeSize.xml");
if (File.Exists(genomeSizePath))
{
throw new ArgumentException("GenomeSize.xml already exists on " + _options.OutputDirectory);
}
metadata.Serialize(genomeSizePath);
Console.WriteLine("GenomeSize.xml prepared at {0}", genomeSizePath);
}
public void HappyPath()
{
Assert.Equal(GenomeMetadata.GenomeFolderState.Ready, GenomeMetadata.CheckReferenceGenomeFolderState(_genomeFolder, false, false));
Assert.Equal(GenomeMetadata.GenomeFolderState.Ready, GenomeMetadata.CheckReferenceGenomeFolderState(_genomeFolder, true, false));
Assert.Equal(GenomeMetadata.GenomeFolderState.RequireWritableFolder, GenomeMetadata.CheckReferenceGenomeFolderState(_genomeFolder, false, true));
Assert.Equal(GenomeMetadata.GenomeFolderState.RequireWritableFolder, GenomeMetadata.CheckReferenceGenomeFolderState(_genomeFolder, true, true));
var firstGmdt = new GenomeMetadata();
firstGmdt.Deserialize(_genomeXML);
TestGenomeMetadata(firstGmdt);
firstGmdt.Serialize("temp.xml");
var secondGmdt = new GenomeMetadata();
secondGmdt.Deserialize("temp.xml");
TestGenomeMetadata(secondGmdt);
}
public void SequenceMetaDataTest()
{
var testFile = Path.Combine(AppDomain.CurrentDomain.BaseDirectory, "SequenceMetaDataTest.fa");
var gmdt = new GenomeMetadata();
gmdt.Deserialize(_genomeXML);
TestGenomeMetadata(gmdt);
gmdt.Serialize(testFile);
var seq1 = gmdt.Sequences[0];
Assert.True(seq1.CompareTo(seq1) == 0);
Assert.False(seq1.IsMito());
Assert.False(seq1.IsDecoyOrOther());
Assert.True(seq1.IsAutosome());
File.Delete(testFile);
}
