private static UgaGene[] UpdateGeneSymbols(this UgaGene[] genes, Dictionary <int, string> hgncIdToSymbol, Dictionary <string, string> entrezGeneIdToSymbol,
Dictionary <string, string> ensemblIdToSymbol, Dictionary <string, string> refseqGeneIdToSymbol)
{
var updater = new GeneSymbolUpdater(hgncIdToSymbol, entrezGeneIdToSymbol, ensemblIdToSymbol, refseqGeneIdToSymbol);
updater.Update(genes);
return(genes);
}
/// <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);
}
