public void Flatten_ReturnSameGene_WhenListHasOneEntry()
{
var genes = new List <MutableGene>
{
new MutableGene(null, 100, 120, false, null, GeneSymbolSource.Unknown, "test", -1)
};
var flatGenes = GeneFlattener.FlattenWithSameId(genes);
Assert.Single(flatGenes);
Assert.Equal(genes[0].Start, flatGenes[0].Start);
Assert.Equal(genes[0].End, flatGenes[0].End);
}
public void Ensembl()
{
var genes = GetCdrt1EnsemblGenes();
var flattener = new GeneFlattener(genes, "test", false);
var flatGenes = flattener.Flatten();
Assert.Equal(1, flatGenes.Count);
var flatGene = flatGenes[0];
Assert.Equal(15468798, flatGene.Start);
Assert.Equal(15522826, flatGene.End);
}
public void Flatten_NoGenesShouldBeCombined()
{
var genes = new List <MutableGene>
{
new MutableGene(null, 100, 120, false, null, GeneSymbolSource.Unknown, "test", -1),
new MutableGene(null, 130, 140, false, null, GeneSymbolSource.Unknown, "test", -1),
new MutableGene(null, 150, 160, false, null, GeneSymbolSource.Unknown, "test", -1)
};
var flatGenes = GeneFlattener.FlattenWithSameId(genes);
Assert.Equal(3, flatGenes.Count);
for (int i = 0; i < flatGenes.Count; i++)
{
Assert.Equal(genes[i].Start, flatGenes[i].Start);
Assert.Equal(genes[i].End, flatGenes[i].End);
}
}
public void Flatten_AllGenesShouldBeCombined()
{
var genes = new List <MutableGene>
{
new MutableGene(null, 100, 120, false, null, GeneSymbolSource.Unknown, "test", -1),
new MutableGene(null, 110, 115, false, null, GeneSymbolSource.Unknown, "test", -1),
new MutableGene(null, 120, 130, false, null, GeneSymbolSource.Unknown, "test", -1)
};
var flatGenes = GeneFlattener.FlattenWithSameId(genes);
Assert.Single(flatGenes);
var flatGene = flatGenes[0];
Assert.Equal(100, flatGene.Start);
Assert.Equal(130, flatGene.End);
}
public void Flatten_ReturnNull_WhenInputNull()
{
var flatGenes = GeneFlattener.FlattenWithSameId(null as List <MutableGene>);
Assert.Null(flatGenes);
}
/// <summary>
/// constructor
/// </summary>
public GeneCombiner(string inputGenesPath, string inputGenes2Path, List <string> geneInfoPaths, string hgncPath,
string refSeqGff3Path)
{
_geneInfoSource = ParseGeneInfoFiles(geneInfoPaths);
var entrezGeneIdToEnsemblId = new Dictionary <string, UniqueString>();
var ensemblIdToEntrezGeneId = new Dictionary <string, UniqueString>();
_hgncSource = ParseHgncFile(hgncPath, entrezGeneIdToEnsemblId, ensemblIdToEntrezGeneId);
Console.WriteLine();
Console.WriteLine("- linking Ensembl and Entrez gene IDs: ");
var linkedEnsemblIds = LinkIds(entrezGeneIdToEnsemblId, ensemblIdToEntrezGeneId);
Console.WriteLine();
Console.WriteLine("- loading RefSeq GFF3: ");
_refSeqGff3GeneInfo = GetRefSeqGff3GeneInfo(refSeqGff3Path);
Console.WriteLine();
Console.WriteLine("- loading genes: ");
string descriptionA = Path.GetFileName(inputGenesPath);
string descriptionB = Path.GetFileName(inputGenes2Path);
var genesA = LoadGenes(inputGenesPath, descriptionA);
var genesB = LoadGenes(inputGenes2Path, descriptionB);
Console.WriteLine();
Console.WriteLine("- update gene symbols: ");
var updaterA = new GeneSymbolUpdater(genesA, descriptionA, _geneInfoSource, _hgncSource);
updaterA.Update();
var updaterB = new GeneSymbolUpdater(genesB, descriptionB, _geneInfoSource, _hgncSource);
updaterB.Update();
Console.WriteLine();
Console.WriteLine("- flattening genes: ");
var flattenerA = new GeneFlattener(genesA, descriptionA);
var flatGenesA = flattenerA.Flatten();
var flattenerB = new GeneFlattener(genesB, descriptionB);
var flatGenesB = flattenerB.Flatten();
Console.WriteLine();
Console.WriteLine("- merging Ensembl and RefSeq:");
var merger = new GeneMerger(flatGenesA, flatGenesB, linkedEnsemblIds);
_mergedGenes = merger.Merge();
Console.WriteLine();
Console.WriteLine("- update HGNC ids:");
UpdateHgncIds(_mergedGenes);
}
