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); }