public ChromosomeRenamerTests()
{
var referenceMetadata = new List <ReferenceMetadata>
{
new ReferenceMetadata("chr1", "1", true),
new ReferenceMetadata("chrX", "X", true),
new ReferenceMetadata("chrM", "MT", true),
new ReferenceMetadata("chr1", "1", true),
new ReferenceMetadata(null, null, true),
new ReferenceMetadata("chrEBV", "EBV", false)
};
_renamer.AddReferenceMetadata(referenceMetadata);
}
public void AddReferenceNameEnsemblEmpty()
{
const string ucscReferenceName = "chr1";
var emptyChromosomeNamer = new ChromosomeRenamer();
var referenceMetadata = new List <ReferenceMetadata>
{
new ReferenceMetadata(null, ucscReferenceName, true)
};
emptyChromosomeNamer.AddReferenceMetadata(referenceMetadata);
var observedUcscReferenceName = emptyChromosomeNamer.GetUcscReferenceName(null);
var observedEnsemblReferenceName = emptyChromosomeNamer.GetEnsemblReferenceName(ucscReferenceName);
Assert.Equal(ucscReferenceName, observedEnsemblReferenceName);
Assert.Null(observedUcscReferenceName);
}
/// <summary>
/// converts the FASTA file to a compressed reference file
/// </summary>
public void Convert(string inputFastaPath, string inputCytogeneticBandpath, string inputChromosomeNamesPath,
string outputCompressedPath, GenomeAssembly genomeAssembly)
{
Console.Write("- getting reference metadata... ");
var referenceMetaDataList = GetReferenceMetadata(inputChromosomeNamesPath);
Console.WriteLine("{0} references found.", referenceMetaDataList.Count);
var renamer = new ChromosomeRenamer();
renamer.AddReferenceMetadata(referenceMetaDataList);
// pre-allocate the cytogenetic bands
Console.Write("- getting cytogenetic bands... ");
var cytogeneticBands = GetCytogeneticBands(inputCytogeneticBandpath, renamer);
Console.WriteLine("finished.\n");
// parse the reference
using (var fastaReader = new FastaReader(inputFastaPath))
{
using (var writer = new CompressedSequenceWriter(outputCompressedPath, referenceMetaDataList, cytogeneticBands, genomeAssembly))
{
Console.WriteLine("Converting the following reference sequences:");
while (true)
{
var referenceSequence = fastaReader.GetReferenceSequence();
if (referenceSequence == null)
{
break;
}
Console.WriteLine("- {0} ({1:n0} bytes)", referenceSequence.Name, referenceSequence.Bases.Length);
writer.Write(referenceSequence.Name, referenceSequence.Bases);
}
}
}
Console.WriteLine("\nFile size: {0}", new FileInfo(outputCompressedPath).Length);
}
