private static HgncGene[] LoadHgncGenes(Stream stream, IDictionary <string, IChromosome> refNameToChromosome)
{
HgncGene[] genes;
using (var reader = new HgncReader(stream, refNameToChromosome)) genes = reader.GetGenes();
return(genes);
}
private static SymbolDataSource ParseHgncFile(string hgncPath,
Dictionary <string, UniqueString> entrezGeneIdToEnsemblId,
Dictionary <string, UniqueString> ensemblIdToEntrezGeneId)
{
Console.WriteLine();
Console.WriteLine("- loading HGNC file:");
var entrezGeneIdToSymbol = new Dictionary <string, UniqueString>();
var ensemblIdToSymbol = new Dictionary <string, UniqueString>();
var entrezGeneIdToHgncId = new Dictionary <string, UniqueInt>();
var ensemblIdToHgncId = new Dictionary <string, UniqueInt>();
int numEntries = 0;
using (var reader = new HgncReader(hgncPath))
{
while (true)
{
var geneinfo = reader.Next();
if (geneinfo == null)
{
break;
}
if (geneinfo.IsEmpty)
{
continue;
}
numEntries++;
bool hasEntrezGeneId = !string.IsNullOrEmpty(geneinfo.EntrezGeneId);
bool hasEnsemblId = !string.IsNullOrEmpty(geneinfo.EnsemblId);
bool hasSymbol = !string.IsNullOrEmpty(geneinfo.Symbol);
bool hasHgncId = geneinfo.HgncId != -1;
if (hasSymbol)
{
if (hasEntrezGeneId)
{
AddIdToUniqueString(entrezGeneIdToSymbol, geneinfo.EntrezGeneId, geneinfo.Symbol);
}
if (hasEnsemblId)
{
AddIdToUniqueString(ensemblIdToSymbol, geneinfo.EnsemblId, geneinfo.Symbol);
}
}
if (hasHgncId)
{
if (hasEntrezGeneId)
{
AddIdToHgncId(entrezGeneIdToHgncId, geneinfo.EntrezGeneId, geneinfo.HgncId);
}
if (hasEnsemblId)
{
AddIdToHgncId(ensemblIdToHgncId, geneinfo.EnsemblId, geneinfo.HgncId);
}
}
if (hasEnsemblId && hasEntrezGeneId)
{
AddIdToUniqueString(ensemblIdToEntrezGeneId, geneinfo.EnsemblId, geneinfo.EntrezGeneId);
AddIdToUniqueString(entrezGeneIdToEnsemblId, geneinfo.EntrezGeneId, geneinfo.EnsemblId);
}
}
}
Console.WriteLine($" - {numEntries} entries loaded.");
Console.WriteLine($" - Entrez Gene ID -> symbol: {entrezGeneIdToSymbol.Count} ({GetNonConflictCount(entrezGeneIdToSymbol)})");
Console.WriteLine($" - Ensembl ID -> symbol: {ensemblIdToSymbol.Count} ({GetNonConflictCount(ensemblIdToSymbol)})");
Console.WriteLine($" - Entrez Gene ID -> HGNC id: {entrezGeneIdToHgncId.Count} ({GetNonConflictCount(entrezGeneIdToHgncId)})");
Console.WriteLine($" - Ensembl ID -> HGNC id: {ensemblIdToHgncId.Count} ({GetNonConflictCount(ensemblIdToHgncId)})");
return(new SymbolDataSource(entrezGeneIdToSymbol, ensemblIdToSymbol, entrezGeneIdToHgncId, ensemblIdToHgncId));
}