private static MutableGene GetFlattenedGene(MutableGene seedGene, List <MutableGene> genesWithSameGeneId,
int overlapStart, int overlapEnd)
{
var flattenedGene = MutableGene.Clone(seedGene);
bool useOverlap = overlapStart != -1 && overlapEnd != -1;
foreach (var gene in genesWithSameGeneId)
{
if (gene.Invalid || flattenedGene.OnReverseStrand != gene.OnReverseStrand ||
flattenedGene.ReferenceIndex != gene.ReferenceIndex)
{
continue;
}
if (useOverlap && !Overlap.Partial(overlapStart, overlapEnd, gene.Start, gene.End))
{
continue;
}
if (!useOverlap && !Overlap.Partial(flattenedGene.Start, flattenedGene.End, gene.Start, gene.End))
{
continue;
}
UpdateCoordinates(gene, flattenedGene);
gene.Invalid = true;
}
return(flattenedGene);
}
private void MergesGenesWithSameSymbol(MutableGene seedGene, List <MutableGene> genesWithSameSymbol)
{
int overlapStart, overlapEnd;
var validGenes = GetValidGenes(seedGene, genesWithSameSymbol, out overlapStart, out overlapEnd);
var ensemblGenes = GeneUtilities.GetGenesByDataSource(validGenes, TranscriptDataSource.Ensembl);
var refSeqGenes = GeneUtilities.GetGenesByDataSource(validGenes, TranscriptDataSource.RefSeq);
var ensemblFlattener = new GeneFlattener(ensemblGenes, "Ensembl", false);
var flatEnsemblGenes = ensemblFlattener.Flatten(overlapStart, overlapEnd);
var refSeqFlattener = new GeneFlattener(refSeqGenes, "RefSeq", false);
var flatRefSeqGenes = refSeqFlattener.Flatten(overlapStart, overlapEnd);
foreach (var ensemblGene in flatEnsemblGenes)
{
// add the unused Ensembl genes
string linkedEntrezId;
if (!_linkedEnsemblIds.TryGetValue(ensemblGene.EnsemblId.ToString(), out linkedEntrezId))
{
AddEnsemblOrphan(ensemblGene);
continue;
}
var refSeqGene = GeneUtilities.GetRefSeqGeneById(flatRefSeqGenes, linkedEntrezId);
if (refSeqGene == null)
{
AddEnsemblOrphan(ensemblGene);
continue;
}
// merge the Ensembl and RefSeq gene
var mergedGene = MutableGene.Clone(ensemblGene);
mergedGene.TranscriptDataSource = TranscriptDataSource.BothRefSeqAndEnsembl;
UpdateCoordinates(refSeqGene, mergedGene);
if (mergedGene.HgncId == -1 && refSeqGene.HgncId != -1)
{
mergedGene.HgncId = refSeqGene.HgncId;
}
mergedGene.EntrezGeneId = refSeqGene.EntrezGeneId;
_mergedGenes.Add(mergedGene);
refSeqGene.Invalid = true;
ensemblGene.Invalid = true;
_numMergedGenes++;
}
// add the unused RefSeq genes
foreach (var refSeqGene in flatRefSeqGenes)
{
if (refSeqGene.Invalid)
{
continue;
}
AddRefSeqOrphan(refSeqGene);
}
}
